Biochem Flashcards

Question

Lock and key hypothesis

Answer 1

Substrate and active site are perfectly complementary

Answer 2

Asserts tht the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme

Answer 3

1. Covalent modification 2. Proteolytic Cleavage 3. Association with other polypeptides 4. Allosteric Regulation

Answer 4

Proteins can have several different groups covalently attached to them and this can regulate their activity, lifespan in the cell, and/or cellular location Phosphorylation of these different sites on an enzyme can either activate or inactivate the enzyme

Answer 5

Many enzymes and other proteins are synthesized in inactive forms that are activated by cleavage of a protease (regulation of enzyme activity)

Answer 6

Some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory unit. Ex: Some proteins that demonstrate rapid continuous catalysis if their regulatory subunit is removed (constitutive activity) -Other proteins require association with another peptide in order to function

Answer 7

Modification of active-site activity through interactions of molecules with other specific sites on the enzyme. Binding of small molecules to particular sites on an enzyme that are distinct from the active site. allo-other steric-location in space Binding is noncovalent and reversible When bound the allosteric regulator can alter the conformation of the enzyme to increase or decrease catalysis even though it may be bound to the enzyme at a site distant from the active site or on a separate polypeptide

Answer 8

Stimulation of an enzyme by its substrate or by a molecule used in the synthesis of the substrate Ex; A might stimulate E3. This makes sense because when lots of A is around, we want the pathway for utilization of A to be active

Answer 9

Eventually there is so much substrate that the active sites of the enzymes are occupied much of the time, and adding more substrate doesn't increase the reaction rate as much, enzyme is saturated at Vmax

Answer 10

- Km is the substrate concentration at which the reaction velocity is half its maximum - Gives information on the affinity of the enzyme for its substrate - If an enzyme-substrate pair has a low Km, it means that not very much substrate is required to get the reaction rate to half the maximum rate; thus, the enzyme has a high affinity for this particular substrate

Answer 11

Binding of substrate to one subunit modulates the affinity of other subunits for substrate. Cooperative enzymes must have more than one active site. They are usually multisubunit complexes composed of more than one protein chain held together in a quaternary structure

Answer 12

Binding of a substrate to one subunit increases the affinity of the other subunits for substrate

Answer 13

Conformation of the enzyme prior to substrate binding with low substrate affinity (tense) and the conformation of enzyme with increased affinity (relaxed)

Answer 14

The binding of a substrate to one subunit reduces the affinity of the other subuits for substrate

Answer 15

Sigmoidal curve

Answer 16

Molecules that compete with substrate for binding at the active site. They resemble the substrate. Their inhibition can be overcome by adding more substrate. IF the substrate conc is high enough the substrate can outcompete the inhibitor. The Km of the reaction to which a competitive inhibitor has been added is increased compared to the Km of the uninhibited reaction. Vnax is not affected

Answer 17

Bind at an allosteric site not the active site. No matter how much substrate you add, the inhibitor will not be displaced from its site of action. Diminishes Vmax but does not change Km because the substrate can still bind to the active site but the inhibitor prevents the catalytic activity of the enzyme

Answer 18

an inhibitor is only able to bind to the enzyme-substrate complex (it cannot bind before the substrate has bound). They bind to allosteric sites which decreases Vmax by limiting the amount of available enzyme-substrate complex which can be converted to product. By sequestering enzyme bound to substrate, this increases the apparent affinity of the enzyme for the substrate as it cannot readily dissociate (decreasing Km)

Answer 19

Occurs when an inhibitor can bind to the unoccupied enzyme of the enzyme-substrate complex. If the enzyme has greater affinity for the inhibitor in its free form, the enzyme will have a lower affinity for the substrate similar to competitive inhibition (Km increases) If the enzyme substrate complex has greater affinity for the inhibitor the enzyme will have greater affinity for the substrate (Km decreases)

Answer 20

I/v = (Km/Vmax) (1/S) + 1/vmax Slope of the graph = Km/Vmax Y intercept = 1/Vmax X intercept = -1/Km

Answer 21

Moving hydrophobic residues to the interior of a protein increases entropy by allowing water molecules on the surface of the protein to have more possible positions and configurations. This positive Delta S makes Delta G < 0 stabilizing the protein

Answer 22

1. Lower the activation energy 2. Increase the rate of the reaction 3. Do not alter the equilibrium constant 4. Are not changed or consumed in the reaction (which means that they will appear in both the reactants and products) 5. Are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures 6. Do not overall the Delta G of the reaction 7. Are specific for a particular reaction or class of reactions

Answer 23

Catalyze oxidation-reduction reactions; the transfer of electrons between biological molecules. They often have a cofactor that acts as an electron carrier such as NAD+ or NADP+.

Answer 24

Catalyze the movement of a functional group from one molecule to another. Kinases also a member of the group which catalyze the transfer of a phosphate group, generally from ATP to another molecule

Answer 25

Catalyze the breaking of a compound into two molecules using the addition of water. Common ex: phosphatase which cleaves a phosphate group from another molecule

Answer 26

Catalyze the cleavage of a single molecule into two products. They do not require water as a substrate and do not act as oxidoreductases. Synthesis of two molecules into a single molecule may also be catalyzed by lyase

Answer 27

Catalyze rearrangement of bonds within a molecule

Answer 28

catalyze addition or synthesis reactions generally between large similar molecules and require ATP. nucleic acid synthesis

Answer 29

Nonprotein molecules that are small so they can bind to the active site of the enzyme and participate in the catalysis of the reaction usually by carrying charge through ionization, protonation, or deprotonation.

Answer 30

TIghtly bound cofactors or coenzymes that are necessary for enzyme function

Answer 31

inorganic molecules or metal ions and often ingested as dietary minerals

Answer 32

small organic groups the vast majority of which are vitamins or derivatives of vitamin such as NAD+ FAD and coenzyme A

Answer 33

``` Equation describes how the rate of the reaction, v, depends on the concentration of both the enzyme (E) and the substrate which forms product E + E = ES --> E + P v = vmax (S)/Km + (S) Vmax/2 = Vmax (S)/Km + (S) Vmax (Km + (S)) = 2(vmax (S)) Km + (S) = 2(S) Km = (S) ```

Answer 34

The substrate concentration at which half the enzyme's active sites are full (half the stress ball are in use). Often used to compare enzymes. Km is a measure of the affinity of the enzyme for its substrate. When comparing two enzymes, the one with the higher Km has the lower affinity for its substrate because it requires a higher substrate concentration to be half-saturated. Value cannot be changed by changing concentration of substrate or enzyme (intrinsic property)

Answer 35

Have many subunits and multiple binding sites. Subunits and enzymes exist in one of two states: a low affinity tense state and a high affinity relaxed state. Binding of the substrate encourages transition of other subunits from the T state to the R state which increases the likelihood of substrate binding by these other subunits. Loss of substrate can encourage the transition from the R state to the T state and promote dissociation of substrate from the remaining subunits.

Answer 36

A three dimensional web or scaffolding system for the cell. Composed of proteins that are anchored to the cell membrane by embedded protein complexes.

Answer 37

Characteristic trihelical fiber (three left-handed helices woven together to form a secondary right-handed helix) and makes up most of the extracellular matrix of connective tissue. Found throughout the body and is important in providing strength and flexibility

Answer 38

Another component of the extracellular matrix of connective tissue. Role is to stretch and recoil like a spring which restores the original shape of the tissue

Answer 39

Intermediate filament proteins found in epithelial cells. Contribute to the mechanical integrity of the cell and also function as regulatory proteins. Primary protein that makes up hair and nails

Answer 40

Protein that makes up microfilaments and the thin filaments in myofibrils. Have a positive and negative side. This polarity allows motor proteins to travel unidirectionally along an actin filament

Answer 41

Protein that makes up microtubules. Important for providing structure, chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein. Has polarity; the negative end of a microtubule is located adjacent to the nucleus, whereas the positive end is in the periphery of a cell.

Answer 42

Some structural proteins also have motor functions in the presence of motor proteins. These motor proteins display enzymatic activity, acting as ATPases that power the conformational change necessary for motor function

Answer 43

Motor proteins associated with microtubulues. They have two heads, at least one of which remains attached to tubulin at all times. Kinesins play roles in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis. Dyneins are involved in sliding movement of cilia and flagella. Both are important for vesicle transport but have opposite polarities. Kinesins bring vesicles toward the positive end of the microtubule and dyneins bring vesicles toward the negative end

Answer 44

Stabilizing functions that act by transporting or sequestering molecules by binding to them

Answer 45

Proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells.

Answer 46

Group of glycoproteins that mediate Calcium-dependent cell adhesion. They often hold similar cell types together such as epithelial cells. Different cells have type-specific cadherins

Answer 47

Group of proteins that all have two membrane-spanning chains called alpha and beta. These chains are important for binding to and communicating with the extracellular matrix. They play important role in cell signaling and can impact cell function by promoting cell divisions, apoptosis or other processes

Answer 48

Bind to carbohydrate molecules that project from other cell surfaces. These bonds are weakest formed by the CAMs. Expressed on WBC and endothelial cells that line blood vessels. They play an important role in host defense, including inflammation and WBC migration

Answer 49

Aka antibodies which are proteins produced by B cells that function to neutralize targets in the body such as toxins and bacteria and then recruit other cells to help eliminate the threat. Made of two identical heavy chains and two identical light chains which are held together by disulfide linkages and noncovalent interactions. Antibody has antigen binding region which has specific polypeptide sequences that will bind one specific antigenic sequence. The rest of the antibody molecule is the constant region which recruits and binds macrophages

Answer 50

1. Neutralizing the antigen, making the pathogen unable to exert effect on body 2. Marking pathogen for destruction by other WBC (opsonization) 3. Clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

Answer 51

Proteins that create specific pathways for charged molecules. Classified into three main groups that have different mechanisms of opening but that all permit facilitated diffusion of charged particles. It is used for molecules that are impermeable to the membrane (large, polar, or charged). Allows integral membrane proteins to serve as channels for these substrates to avoid the hydrophobic of the phospholipid bilayer.

Answer 52

Have no gates and are unregulated. Cells have ungated potassium channels that will result in a net efflux of potassium of ions unless potassium is at equilibrium

Answer 53

The gate is regulated by the membrane potential change near the channel. The channels are closed under resting conditions but membrane depolarization causes a protein conformation change that allows them to quickly open and close as the voltage increases

Answer 54

The binding of a specific substance or ligand to the channel causes it to open or close. Neurotransmitters act at ligand gated channels at the post synaptic membrane (GABA binds to a chloride channel and opens it)

Answer 55

Membrane receptors that demonstrate catalytic activity in response to ligand binding. They have three primary protein domains: a membrane spanning domain, a ligand binding domain, and a catalytic domain. This results in initiation of a second messenger cascade. Receptor tyrosine kinases are class examples

Answer 56

Anchors the receptor in the cell membrane

Answer 57

stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain

Answer 58

Composed of a monomer that dimerizes upon ligand binding. The dimer is the active form that phosphorylates additional cellular enzymes including the receptor itself.

Answer 59

Large family of integral membrane proteins involved in signal transduction. Characterized by their membrane spanning alpha helices. Receptors differ in specificity of the ligand binding area found on surface of the cell. To send signals to an effector in the cell, they utilize a heterotrimeric G protein. Binding of a ligand increases affinity of the receptor for the G protein and it represents a switch to the active state and affects the intracellular signaling pathway.

Answer 60

1. Gs stimulates adenylate cyclase which increases levels of cAMP in cell 2. Gi inhibits adenylate cyclase which decreases levels of cAMP in cell 3. Gq activates phospholipase C which cleaves a phospholipid from the membrane to form PIP2. PIP2 is then cleaved into DAG and IP3. IP3 can open calcium channels in the endoplasmic reticulum increasing Ca levels in cell

Answer 61

alpha, beta, and delta. The alpha subunit binds GDP and is in a complex with beta and delta subunits. When a ligand binds to the GPCR, the receptor becomes activated and turns on G protein. Once GDP is replaced with GTP, alpha subunit dissociates from delta and gamma subunits. The activated alpha subunit alters activity of adenylate cyclase. If the alpha subunit is as then the enzyme is activated if it is ai then it is inhibited. Once GTP on activated alpha subunit is dephosphorylated to GDP, alpha subunit will rebind to the beta and delta subunits making G protein inactive

Answer 62

Separating proteins. Negatively compounds will migrate toward the positively charged anode and positively charged compounds will migrate toward the negatively charged cathode. Migration velocity = Ez/f directly proportional to the electric field strength, E to the net charge on the molecule, z and inversely proportional to a frictional coefficient, f, which depends on the mass and shape of the migrating molecules

Answer 63

Standard medium for protein electrophoresis. Proteins travel through this matrix in relation to size and charge. Allowing smaller molecules to pass through easily while retaining large particles. A molecule will move faster through the medium if it is small highly charged or placed in a large electric field

Answer 64

Method for analyzing protein in their native states. Limited by the varying mass-to-charge and mass-to-size ratios of cellular proteins because multiple different proteins may experience the same level of migration. Functional native protein can be recovered after but only if it has not been stained. useful to compare the molecular size or charge known to be similar in size from other analytic methods

Answer 65

Separates proteins on the basis of mass alone. Starts with the premise of PAGE but adds SDS, a detergent that disrupts all noncovalent interactions. It binds to proteins and creates large chains with net negative charges neutralizing the protein's original charge and denaturing the protein. As the protein moves through the gel, the only variables affecting velocity are E, electric field strength, and f, frictional coefficient

Answer 66

Proteins can be separated based on pI. Exploits the acidic and basic properties of amino acids. Proteins placed in gel with a pH gradient (acidic gel at the positive anode basic gel at the negative cathode and neutral in the middle). Proteins that are positively charged will migrate toward the cathode and proteins negatively charged will migrate toward the anode. As the protein reaches the portion of gel where the pH is equal to the protein's pI the protein takes on a neutral charge and will stop moving

Answer 67

To determine the primary structure of a protein, sequential digestion of the protein with specific cleavage enzymes is used. Uses cleavage to sequence proteins of up to 50 to 70 amino acids. Removed the N-terminal amino acid of the protein which can be analyzed via mass spectroscopy. Larger proteins- digestion with chymotrypsin, trypsin, cyanogen bromide. This selectively cleaves proteins at specific amino acid residues creating smaller fragments that can be analyzed by electrophoresis or Edman degradation. Disulfide links and salt bridges are broken to primary structure positions cannot be determined.

Answer 68

Mixes a protein in solution with Coomassie Brilliant Blue Dye. In its protonated form, dye exists as a brown-green color. Dye gives up protons to the ionizable groups in the protein turning blue in the process. Noncovalent attractions between deprotonated dye and protein stabilize blue form of the dye. Increased protein concentrations correspond to a larger concentration of blue dye in solution. Samples of known protein concentrations are reacted withe the Bradford reagent and then absorbance is measured to create a standard curve. Unknown sample exposed to same conditions and concentration determined based on standard curve. Less accurate when more than one protein.

Answer 69

Monosaccharides that contain three carbon atoms

Answer 70

Carbohydrates that contain an aldehyde group as their most oxidized functional group

Answer 71

Carbohydrates with a ketone group as their most oxidized functional group

Answer 72

The most oxidized and has the (the carbonyl carbon) lowest possible number

Answer 73

Simplest Ketone sugar- dihydroxyacetone | The carbonyl carbon is C-2

Answer 74

Also called stereoisomers are compounds that have the same chemical formula. These molecules differ from one another in terms of the spatial arrangement of their component atoms

Answer 75

Special type of isomerism where stereoisomers are nonidentical nonsuperimposable mirror images of each other; have opposite configurations

Answer 76

Positive rotation

Answer 77

Negative rotation

Answer 78

Have the hydroxide of their highest numbered chiral center on the right

Answer 79

Have that hydroxide on the left

Answer 80

Two sugars that are in the same family (either ketoses or aldoses and have the same number of carbons) that are not identical and are not mirror images of each other

Answer 81

Subtype of diastereomers that differ in configuration at only one chiral center

Answer 82

Monosaccharides contain both a hydroxyl group which can serve as a nucleophile and a carbonyl group which is a common electrophile. They can undergo intramolecular reactions to form cyclic hemiacetals (from aldoses) and hemiketals (from ketoses)

Answer 83

Due to ring strain the only cyclic molecules that are stable in solution are six membered pyranose rings or five membered furanose rings. Sugars tend to exist in cyclic form

Answer 84

During cyclization of sugars, the carbonyl carbon becomes chiral

Answer 85

Exposing hemiacetal rings to water will cause them to spontaneously cycle between the open and closed form. Because the substituents on the single bond between C-1 and C-2 can rotate freely, either the alpha or beta anomer can be formed. Spontaneous change of conformation about C-1 is known as mutarotation and occurs more rapidly when the reaction is catalyzed with an acid or base. Results in a mixture that contains both a- and b- anomers at equilibrium concentrations

Answer 86

A-anomeric configuration is less favored because the hydroxyl group of the anomeric carbon is axial adding to the steric strain of the molecule

Answer 87

Any monosaccharide with a hemiacetal ring

Answer 88

Uses Ag(NH3)2+ as an oxidizing agent . In a positive Tollen's test aldehydes reduce Ag+ to metallic silver

Answer 89

The aldehyde group of an aldose is readily oxidized, indicated by a red precipitate of Cu2O. To test specifically for glucose, one may utilize the enzyme glucose oxidase which does not react with other reducing sugars

Answer 90

will oxidize both the aldehyde and the primary alcohol on C-6 to carboxylic acids

Answer 91

Also reducing sugars and give positive Tollen's and Benedict's tests. They cant be oxidized directly to carboxylic acids but they can tautomerize to form aldoses under basic conditions via keto-enol shifts. While in the aldose form , they can react with Tollen's or Benedict's reagents to form the carboxylic acid

Answer 92

Refers to the rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond. Ketone group picks up a hydrogen while the double bond is moved between the two adjacent carbons resulting in an enol: a compound with a double bond and an alcohol group

Answer 93

When the aldehyde group of an aldose is reduced to an alcohol

Answer 94

Contains a hydrogen that replaces a hydroxyl group on the sugar

Answer 95

Because carbohydrates have hydroxyl groups they are able to participate in reactions with carboxylic acid derivatives to form esters. p.116

Answer 96

Very similar to the phosphorylation of glucose in which a phosphate of ester is formed.

Answer 97

Important metabolic reaction of glycolysis in which a phosphate group is transferred from ATP to glucose, thus phosphorylating glucose while forming ADP Hexokinase or glucokinase in the liver and pancreatic b-islet cells catalyzes this reaction

Answer 98

Hemiacetals react with alcohols forming this. The anomeric hydroxyl group is transformed into an alkoxy group yielding a mixture of alpha and beta acetals (water as leaving group). Resulting carbon-oxygen bonds are called glycosidic bonds and the acetals formed are glycosides p.117 picture

Answer 99

Nonspecific in that the anomeric carbon of a cyclic sugar can react with an hydroxyl group on any other sugar molecule

Answer 100

Long chains of monosaccharides linked together b glycosidic bonds

Answer 101

Polysaccharide composed entirely of glucose or any other monosaccharide

Answer 102

Polymer made up of more than one type of monosaccharide

Answer 103

Happens when an internal monosaccharide in a polymer chain forms at least two glycosidic bonds, allowing branch formation

Answer 104

Main structural component of plants.

Answer 105

Polysaccharides that are more digestible by humans because they are linked alpha-D glucose monomers.

Answer 106

Polysaccharides that are more digestible by humans because they are linked alpha-D glucose monomers.

Answer 107

Amylose a linear glucose polymer linked via alpha-1,4 glycosidic bonds Amylopectin- another type of starch which starts off similar to amylose but also contains branches via alpha-1,6 glycosidic bonds Broken down by enzymes in the body and are used as a source of energy. Amylose degraded by alpha amylase and Beta amylase

Answer 108

cleaves amylose at the nonreducing end of the polymer (the end with the acetal) to yield maltose

Answer 109

cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose

Answer 110

Carbohydrate storing unit in animals. Similar to starch but it has more alpha 1,6 glycosidic bonds making it really branched. The branching optimizes the energy efficiency of glycogen and makes it more soluble in solution allowing more glucose to be stored in the body. Branching pattern allows enzymes that cleave glucose from glycogen such as glycogen phosphorylase to work on many sites within the molecule simultaneously

Answer 111

Functions by cleaving glucose from the nonreducing end of a glycogen branch and phosphorylating it, producing glucose 1-phosphate which plays an important role in metabolism

Answer 112

Form after the aldehyde group on a reducing sugar reduces another compound, becoming oxidized in the process

Answer 113

Characterized by insolubility in water and nonpolar organic solvents. Lipids diverge dramatically in their structural organization and biological functions, serving vital structural, signaling, and energy storage roles

Answer 114

It has both hydrophilic and hydrophobic regions (membrane) | Polar head is hydrophilic and the fatty acid tails are hydrophobic

Answer 115

Contain a phosphate and alcohol that comprise the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages

Answer 116

Will only have single bonds. Have greater van der Waals forces and a more stable overall structure. They form solids at room temperature

Answer 117

Includes one or more double bonds which introduce kinds into the fatty acid chain which makes it difficult for them to stack and solidify. Tend to be liquids at room temperature

Answer 118

Phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group.. named according to their head group.

Answer 119

Cell surface antigens involved in blood typing are examples Are sites of biological recognition at the cell surface and can be bonded to various head groups and fatty acids Have a sphingosine backbone. These molecules have longchain nonpolar fatty acid tails and polar head groups.Are also phospholipids because they contain a phosphodiester linkage. Others contain glycosidic linkages to sugars Four classes 1. Ceramide 2. Sphingomyelins 3. Glycosphingolipids 4. Gangliosides

Answer 120

Simplest sphingolipid which has a single hydrogen atom as its head group

Answer 121

Major class that are also phospholipids. These have either phosphatidycholine or phosphatidylethanolamine as head group and contain phosphodiester bond. Head groups have no net charge. Major component of plasma membrane producing myelin

Answer 122

Head groups composed of sugars bonded by glycosidic linkages are considered glycolipids or glycosphingolipids. These are not considered phospholipids because they do not have phosphodiester linkages. Found mainly on the surface of the plasma membrane and can be classified as cerebrosides or globosides. These molecules are referred to as neutral glycolipids because they have no net charge at physiological pH

Answer 123

Have a single sugar

Answer 124

Have two or more sugars

Answer 125

Glycolipids that have polar head groups composed of oligosaccharides with one or more N-acetylneuraminic acid molecules at the terminus and a negative charge. These molecules are also considered glycolipids because they have a glycosidic linkage and no phosphate group. They play a major role in cell interaction, recognition, and signal transduction

Answer 126

Esters of long chain fatty acids with long chain alcohols. They form pliable solids at room temperature. Biologically, they function as protection for both plants and animals. Plants; waxes secreted as a surface coating to prevent excessive evaporation and protect against parasites Animals: Waxes are secreted to prevent dehydration

Answer 127

Lipids serve as coenzymes in the electron transport chain and in glycosylation reactions. Also function as hormones that transmit signals over long distances and as intracellular messengers responding to extracellular signals

Answer 128

Odiferous chemicals are the metabolic precursors to steroids and other lipid signaling molecules. Class of lipids built from isoprene moieties (C5H8). Produced mainly by plants and also by some insects. Strongly scented.

Answer 129

Contain two isoprene units

Answer 130

Contain three isoprene units

Answer 131

Tetraterpenes and have eight isoprene units

Answer 132

Metabolic derivatives of terpenes and are characterized by having four cycloalkane rings fused together: three cyclohexane and one cyclopentane. Functionality is determined by the oxidation status of those rings as well as the functional groups they carry

Answer 133

Major component of the phospholipid bilayer and is important for mediating membrane fluidity. Amphipathic molecule. At low temperatures it keeps the cell membrane from solidifying and at high temperatures it holds the membrane intact and prevents it from becoming too permeable

Answer 134

- produced by almost all cells in the body - 20-Carbon molecules are unsaturated carboxylic acids derived from arachidonic acid and contain one five carbon ring - They act as paracrine or autocrine signaling molecules - Biological function is to regulate the synthesis of cAMP which is a ubiquitous intracellular messenger. cAMP mediates the actions of many other hormones - Downstream effects of prostaglandins include powerful effects on smooth muscle function, influence over the sleep wake cycle, and elevation of body temp with sickness

Answer 135

An essential nutrient that cannot be adequately synthesized by the body and thus must be consumed in the diet. Commonly divided into water-soluble and lipid-soluble categories. Can accumulate in stored fat whereas excess water soluble vitamins are excreted through the urine

Answer 136

Vitamins A, E, D, K

Answer 137

Or carotene is an unsaturated hydrocarbon that is important in vision, growth and development, and immune function. The most significant metabolite is retinal which is a component of the light sensing molecular system in the human eye

Answer 138

Storage form of vitamin A is also oxidized to retinoic acid, a hormone that regulates gene expression during epithelial development

Answer 139

Cholecalciferol, consumed or formed in a UV light driven reaction in the skin. In the liver and kidneys, vitamin D is converted to calcitriol which increases calcium and phosphate uptake in the intestines which promotes bone production.

Answer 140

Characterizes a group of closely related lipids called tocopherols and tocotrienols. Characterized by a substituted aromatic ring with a long isoprenoid side chain and are hydrophobic.

Answer 141

Biological antioxidants. The aromatic ring reacts with free radicals, destroying them. This in turn prevents oxidative damage, an important contributor to cancer and aging

Answer 142

- Group of compounds including phylloquinone (K1) and menaquinones (K2). ] - Vital to posttranslational modifications required to form prothrombin, an important clotting factor in the blood - Aromatic ring of vitamin K undergoes a cycle of oxidation and reduction during the formation of prothrombin - Required to introduce calcium binding sites on several calcium dependent proteins

Answer 143

1. Carbons of the fatty acids are more reduced than those of sugars which contain numerous alcohol groups. Oxidation of triacylglycerols yields twice the amount of energy as carbs 2. Hydrophobic: do not draw in water and do not require hydration for stability. This helps decrease their weight.

Answer 144

Composed of three fatty acids bonded by ester linkages to glycerol. These are nonpolar and hydrophobic. This contributes to their insolubility in water as the polar hydroxyl groups of the glycerol component and the polar carboxylates of fatty acids are bonded together decreasing their polarity. -Deposits can be observed in cells as oil droplets in the cytosol. These serve as depots of metabolic fuel that can be recruited when the cell needs additional energy to divide or survive when other fuel supplies are low Travel bidirectionally in the blood stream between liver and adipose tissue. Physical characteristics determined by saturation

Answer 145

Store large amounts of fat and are found under skin, around mamary glands and in abdominal caviy

Answer 146

Unesterified fatty acids with a free carboxylate group. These circulate in the blood bonded noncovalently to serum albumin

Answer 147

ester hydrolysis of triacylglycerols using a strong base. traditionally base is lye, common name for Na or K hydroxide. Result is the basic cleavage of fatty acid leaving the sodium salt of the fatty acid and glycerol. The fatty acid salt is known as soap

Answer 148

Soap | Lowers the surface tension at the surface of a liquid serving as a detergent or emulsifier.

Answer 149

Major cause of cirrhosis and liver failure. Causes ongoing damage and inflammation in the liver leading to scar tissue that replaces normal cells of the organ. This buildup makes liver unable to keep up with metabolic demands of the body and liver failure results. To fight this virus, infected hepatocytes release interferon, a peptide signal that interferes with viral replication. Because viruses must hijack the host cell's machinery to replicate, the body can limit spread of virus by shutting off processes of transcription and translation. Interferon not only curtails these processes but induces production of RNAse L, which cleaves RNA in cells to further reduce the ability of the virus to replicate. Interferon = efficient way to protect body from viral pathogens

Answer 150

Unit of DNA that encodes a specific protein or RNA molecule, and through transcription and translation, that gene can be expressed

Answer 151

Carries the information specifying the amino acid sequence of the protein to the ribosome. mRNA is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells. Then mRNA may undergo a host of posttranscriptional modifications prior to its release from nucleus. Only type of RNA that contains information and is translated into protein

Answer 152

Eukaryotes: monocistronic meaning that each RNA molecules translates into only one protein product Pro: Polycistronic so starting translation at different locations in the mRNA can result in different proteins

Answer 153

Responsible for converting language of nucleic acids to amino acids and peptides. Each tRNA molecules contains a folded strand of RNA that includes a three nucleotide anticodon which recognizes and pairs with the appropriate codon on an mRNA molecule while in the ribosome. Each type of amino acid is activated by a different aminoacyl-tRNA synthetase that requires two high energy bonds from ATP implying the attachment of the amino acid is an energy rich bond. The aminoacyl-tRNA synthetase transfers the activated amino acid to the 3' end of the correct tRNA. The bond will be used to supply the energy needed to create a peptide bond during translation

Answer 154

Synthesized in the nucleolus and functions as an important part of ribosomal machinery used during protein assembly in cytoplasm. Maany rRNA molecules function as ribozymes (enzymes made of RNA molecules instead of peptides). rRNA helps catalyze formation of peptide bonds and important for splicing out its own introns

Answer 155

Specific for one amino acid | Written in 5' -> 3'

Answer 156

-During translation, it recognizes the codon of the mRNA on a transfer RNA. It allows the tRNA to pair with the codon in the mRNA. Orientation of this interaction will be anti parallel (Add picture from page 220) -

Answer 157

Every preprocessed eukaryotic protein starts with methionine amino acid codon for methionine is AUG (start codon) for translation of the mRNA into protein

Answer 158

There are no charged tRNA molecules that recognize these codons which leads to release of protein from the ribosome Stop Codons are: UAG, UAA, and UGA

Answer 159

Genetic code is because more than one codon can specify a single amino acid.

Answer 160

The first two base are usually the same and the third is variable (wobble). Evolutionary development designed to protect against mutations in the coding regions of DNA. Mutations in the wobble position tend to be silent or degenerate which means there is no effect on the expression of the amino acid and no adverse effects on the polypeptide sequence

Answer 161

If a mutation occurs and it affects one of the nucleotides in a codon

Answer 162

Because these point mutations can affect the primary amino acid sequence of the protein (missense and nonsense)

Answer 163

A mutation where one amino acid substitutes for another

Answer 164

A mutation where the codon now encodes for a premature stop codon (truncation mutation)

Answer 165

Some number of nucleotides are added to or deleted from the mRNA sequence and shifts the reading frame

Answer 166

Although DNA contains the actual coding sequence for a protein, the machinery to generate protein is in cytoplasm. DNA cannot leave the nucleus because it will be degraded so it must use RNA to transmit genetic information. Creation of mRNA from a DNA template is known as transcription.

Answer 167

Involved in unwinding the double-stranded DNA and preventing formation of supercoils. This step is important in allowing the transcriptional machinery access to the DNA and the particular gene of interest

Answer 168

Transcription results in a single strand of mRNA synthesized from one of the two nucleotide strands of DNA aka the antisense strand. Newly synthesized strand is antiparallel and complementary to the DNA template strand

Answer 169

Synthesizes RNA;

Answer 170

Main player in transcribing mRNA and its binding site in the promoter region is known as the TATA box named for its high concentration of thymine and adenine bases

Answer 171

- RNA polymerase locates genes by searching for specialized DNA regions known as promoters. Transcription factors help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start. Unlike DNA polymerase 3, RNA polymerase does not require a primer to start generating a transcript - Travels along the template strand in the 3' -> 5' direction which allows for the construction of transcribed mRNA in the 5' -> 3' direction - RNA polymerase does not proofread its work

Answer 172

1. RNA Poly 1: located in nucleolus and synthesizes rRNA 2. RNA Poly 2: Located in the nucleus and synthesizes preprocessed mRNA and some small nuclear RNA 3. RNA Poly 3: Located in the nucleus and synthesizes tRNA and some rRNA

Answer 173

Transcription continues along the DNA coding region until RNA polymerase reaches termination signal. DNA double helix then reforms and primary transcript is termed hnRNA.mRNA is derived from hnRNA via posttranslational modification

Answer 174

- Maturation of the hnRNA includes splicing of the transcript to remove noncoding sequences (introns) and ligate coding sequences (exons) together. Splicing is accomplished by the spliceosome - In the spliceosome, small nuclear RNA molecules couple with proteins known as small nuclear ribonucleoproteins. This complex recognizes both the 5' and 3' splice sites of the introns - These sequences are excised in the form of a lariat and then degraded

Answer 175

Scientists hypothesize that they play an important role in the regulation of cellular gene expression levels and in maintaining the size of our genome`

Answer 176

A 7-methylguanylate triphosphate cap is added. The cap is added during transcription and is recognized by the ribosome as the binding site and protects the mRNA from degradation in the cytoplasm

Answer 177

A poladenosyl tail is added to the 3' end of the mRNA transcript and protects the message against rapid degradation. It is composed of adenine bases. As soon as the mRNA leaves the nucleus, it will start to get degraded from its 3' end. The longer the poly-A tail the more time the mRNA will be able to survive before being digested in the cytoplasm. Also assists with export of the mature mRNA from the nucleus

Answer 178

The A site (aminoacyl), P site (peptidyl), and E site (exit)

Answer 179

1. Small ribosomal subunit binds to the mRNA. In prokaryotes, small subunit binds to the Shine-Delgarno sequence in the 5' untranslated region of the mRNA. In eukaryotes, the small subunit binds to the 5' cap structure 2. Charged initiator binds to the AUG start codon through base pairing with anticodin within the P site of the ribosome 3. Initial amino acid is methionine 4. Large subunit then binds the small subunit forming the completed initiation complex. This is assisted by initiation factors that are not permanently associated with the ribosome

Answer 180

1. Repeated for each amino acid added to the protein after the initiator methionine 2. The ribosome moves in the 5' --> 3' direction along the mRNA synthesizing the protein from its amino (N-) to carboxyl (C-) terminus. Ribosome has 3 important binding sites a) The A site holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site b) P site holds the tRNA that carries the growing polypeptide chain. Where the first amino acid binds because it is starting the polypeptide chain. Peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires peptidyl transferase, an enzyme that is part of the large subunit. GTP is used for energy during the formation of the bond. c) E site is where the now inactivated tRNA pauses before exiting the ribosome. As the tRNA enters the E site it quickly unbinds from the mRNA and is ready to be recharged

Answer 181

Assist by locating and recruiting aminoacyl-tRNA along with GTP while helping to remove GDP once the energy has been used.

Answer 182

- When any of the three stop codons moves into the A site, a protein called release factor binds to termination codon, causing a water molecule to be added to the polypeptide chain. - Addition of the water molecule allows peptidyl transferase and termination factory to hydrolyze the completed polypeptide chain from the final tRNA - Polypeptide chain will be released from the tRNA in the P site and th two ribosomal subunits will dissociate

Answer 183

1. Proper folding: specialized class of proteins (Chaperones) assist int he protein folding process 2. Cleavage events: Example is insulin which needs to be cleaved from a larger, inactive peptide to achieve its active form. In peptides with signal sequences, signal sequence must be cleaved if the protein is to enter the organelle and accomplish the function

Answer 184

Addition of phosphates by protein kinases to activate or deactivate proteins

Answer 185

Addition of carboxylic acid groups usually to serve as calcium-binding sites

Answer 186

Addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination

Answer 187

Addition of lipid groups to certain membrane bound enzymes

Answer 188

Simplest example of an on-off switch that regulates gene expression levels in prokaryotes was discovered in E.coli. By sharing a single common promoter region on the DNA sequence, these genes are transcribed as a group. Operon is a cluster of genes transcribed as a single mRNA Two types: inducible and repressible

Answer 189

Used to describe the structure and function of operons. Operons contain structural genes, an operator site, a promoter site, and a regulator gene. Structural gene codes for the protein of interest. Upstream of the structural gene is the operator site, a nontranscribable region of DNA that is capable of binding a repressor protein. Further upstream is the promoter site which is similar in function to promoters in eukaryotes: it provides a place for RNA polymerase to bind. Furthest upstream is the regulator gene which codes for a protein known as the repressor

Answer 190

Repressor is bonded tightly to the operator systems and acts as a roadblock. RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way - Negative control mechanisms - To remove the block, an inducer must bind the repressor protein so that RNA polymerase can move down the gene - As the concentration of the inducer increases, it will pull more copies of the repressor off of the operator region, freeing up those genes for transcription. System is useful because it allows gene products to be produced only when they are needed

Answer 191

- Classic example of an inducible system - Contains the gene for lactase - Bacteria can digest lactose but it is more energetically expensive than digesting glucose. Therefore, bacteria only want to use this option if lactose is high and glucose is low - Lac operon induced by the presence of lactose - Assisted by binding of the catabolite activator protein (CAP)

Answer 192

transcriptional activator used by E. Coli when glucose levels are low to signal that alternative carbon sources should be used. Falling levels of glucose cause an increase in the signaling molecule cyclic AMP (cAMP) which binds to CAP. This induces a conformational change in CAP that allows it to bind to the promoter region of the operon increasing transcription of the lactate gene. (positive control mechanisms)

Answer 193

Allow constant production of a protein product. Repressor made by the regulator gene is inactive until it binds to a corepressor. This complex then binds the operator site to prevent further transcription. Tend to serve as negative feedback. The final structural product can serve as a corepressor. Thus, as its levels increase it can bind the repressor, and the complex will attach to the operator region to prevent further transcription of the same gene.

Answer 194

Operates as a negative repressible system - When tryptophan is high in the local environment, it acts as a corepressor - Binding of two molecules of tryptophan to the repressor causes the repressor to bind to the operator site and so the cell turns off its machinery to synthesize its own tryptophan which is an energetically expensive process because of its easy availability in the environment

Answer 195

Transcription activating proteins that search the DNA loooking for specific DNA-binding motifs

Answer 196

1. DNA binding domain | 2. Activation domain

Answer 197

binds to a specific nucleotide sequence in the promoter region or to a DNA response element (sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery

Answer 198

Response elements grouped together to control gene's expression by multiple signals. Enhancer regions in DNA can be up to 1000 base pairs away from gene they regulate and can be located in an intron or noncoding region of the gene. They differ from upstream promoter elements because upstream promoter elements must be 25 bp away from start of gene. BY using enhacer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels

Answer 199

Cells can increase expression of gene product by duplicating the relevant gene. Genes can be duplicated in series on the same chromosome yielding many copies in a row of the same genetic information. Genes can also be duplicated in parallel by opening the gene with helicases and permitting DNA replication of only that gene

Answer 200

IN eukaryotic cells, DNA is packaged in nucleus as chromatin which requires chromatin remodeling to allow transcription factors and transcriptional machinery access to DNA

Answer 201

Tightly coiled DNA that appears dark under microscope. Its tight coiling makes it inaccessible to the transcription machinery so these genes are inactive

Answer 202

Is looser and appears light under the microscope . Transcription machinery can access the genes of interest so these genes are active

Answer 203

Transcription factors that bind to the DNA can recuit other coactivators such as histone acetylases. These are involved in chromatin remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins. Acetylation of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA

Answer 204

Proteins that serve to remove acetyl groups from histones, which results in a closed chromatin conformation and overall decrease in gene expression levels in the cell

Answer 205

DNA methylases add methyl groups to cytosine and adenine nucleotides. Methylation is linked with the silencing of gene expression.

Answer 206

Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules. These rafts can serve roles in signaling. Both lipid rafts and proteins travel within the plane of the membrane but much more slowly

Answer 207

Responsible for movement of phospholipids between layers

Answer 208

Carboxylic acids that contain a hydrocarbon chain and terminal carboxyl group.

Answer 209

Storage lipids involved in human metabolic processes. They contain three fatty acid chains esterified to a glycerol molecule.

Answer 210

Regarded as healthier fats because they tend to have one or more double bonds and exist in liquid form at room temperature; in plasma membrane these characteristics impart fluidity to the membrane. Humans can only synthesize a few of these the rest come from essential fatty acids in the diet and are transported as triacylglycerols from the intestine inside chylomicrons

Answer 211

alpha-linolenic acid and linoleic acid

Answer 212

Found in processed foods and considered less healthy. They decrease the overall membrane fluidity

Answer 213

BY substituting one of the fatty acid chains with a phosphate group, a polar head group joins the nonpolar tails forming glyerophospholipid. Used for membrane synthesis and can produce a hydrophilic surface layer on lipoproteins such as very low density lipoprotein (VLDL) a lipid transporter. Can also serve as secondary messengers in signal transduction. Phosphate gorup provides attachment point for water soluble groups such as choline or inositol

Answer 214

Also important constituents of cell membranes. Do not contain glycerol but they are similar in structure to glyerophospholipids in that they contain a hydrophilic region and two fatty acid derived hdrophobic tails

Answer 215

Regulates membrane fluidity and also is necessary for synthesis of all steroids, which are derived from cholesterol. Structure contains both a hydrophilic and hydrophobic region. Cholesterol stabilizes adjacent phospholipids and occupies space between them. This prevents the formation of crystal structures in the membrane, increasing fluidity at lower temperatures. At higher temperatures, cholesterol limits movement of phospholipids within the bilayer decreasing fluidity and helps hold the membrane intact

Answer 216

Proteins that allow cells to recognize each other and contribute to proper cell differentiation and development that are part of cell-cell junctions

Answer 217

Provide direct pathways of communication between neighboring cells or between cells and the extracellular matrix

Answer 218

Allow for direct cell-cell communication and are often found in small bunches together. Also called connexons and are formed by alignment and interaction of pores composed of six molecules of connexins. They permit movement of water and some solutes directly between cells

Answer 219

Prevent solutes from leaking into the space between cells via paracellular route. Tight junctions are found in epithelial cells and function as a physician link between the cells as they form and a single layer of tissue. Can limit permeability enough to create a transepithelial voltage difference based on differing concentrations of ions on either side of the epithelium

Answer 220

Bind adjacent cells by anchoring to their cytoskeletons. Primarily found at the interface between two layers of epithelial tissue

Answer 221

Have a similar function, but their main function is to attach epithelial cells to underlying structures, especially the basement membrane

Answer 222

Substrates move down their concentration gradient directly across the membrane. Only particles that are freely permeable to the membrane are able to undergo this. Potential energy in a chemical gradient

Answer 223

Water will move from a region of lower solute concentration to one of higher solute concentration. From a region of higher water concentration down its gradient to a region of lower water concentration

Answer 224

If the concentration of solutes inside the cell is higher than the surrounding solution. Such a solution will cause a cell to swell as water rushes in sometimes to the point of burstin

Answer 225

A solution that is more concentrated than the cell and water will move out of the cell

Answer 226

Uses ATP or another energy molecule to directly power the transport of molecules across a membrane. Generally involves the use of a transmembrane ATPase

Answer 227

Also known as coupled transport, also uses energy to transport particles across the membrane however there is not direct coupling to ATP hydrolysis. Instead, this uses the energy released by one particle going down its electrochemical gradient to drive a different particle up its gradient

Answer 228

When both particles flow in the same direction across membrane

Answer 229

When particles flow in opposite direction

Answer 230

Highly permeable due to many large pores that allow for the passage of ions and small proteins

Answer 231

Has a much more restricted permeability compared to the outer membrane. Inner contains numerous infoldings, cristae, which increase the available surface area for the integral proteins associated with the membrane. Also encloses the mitochondrial matrix where the citric acid cycle produces high energy electron carriers used in the electron transport chain. Contains a very high level of cardiolipin and does not contain cholesterol

Answer 232

Composed of a five carbon sugar (pentose) bonded to a nitrogenous base and are formed by covalently linking the base to C-1' of the sugar

Answer 233

formed when one or more phosphate groups are attached to C-5 of a nucleoside. These are high energy compounds because of the energy associated with the repulsion between closely associated negative charges on the phosphate groups

Answer 234

Backbone of DNA is composed of alternating sugar and phosphate groups Determines the directionality of the DNA and is read from 5 to 3 It is formed as nucleotides are joined by 3 to 5 phosphodiester bonds which occurs when a phosphate group links the 3' carbon of one sugar to the 5' phosphate group of the next incoming sugar in the chain. Phosphates carry neg charge (DNA and RNA have an overall neg charge)

Answer 235

Contain two rings in their structure. Adenine and guanine

Answer 236

Contain only one ring in their structure (Cytosine, thymine, and uracil)

Answer 237

1. Compound is cyclic 2. Compound is planar 3. Compound is conjugated (alternating single and multiple bonds or lone pairs) 4. Compound has 4n+2

Answer 238

1. Two strands of DNA are antiparallel. One goes 5 to 3 down the page and one goes 3 to 5 up the page 2. Sugar phosphate backbone is on the outside but nitrogenous bases on the inside 3. Complementary base pairing. (A pairs with T via 2 hydrogen bonds and G always pairs with C via 3 hydrogen bonds) 4. The amount of A equals the amount of T and the amount of G equals the amount of C. Total purines will be equal to total pyrimidines (Chargaff's rules)

Answer 239

Double helix of most DNA is a right-handed helix. The helix makes a turn every 3.4 nm and contains about 10 bases within that span. Major and minor grooves can be identified between the interlocking strands and are often the site of protein binding

Answer 240

IT is a left handed helix that has a turn every 4.6 nm and contains 12 bases with each turn. A high GC content or a high salt concentration might contribute to this form of DNA. No biological research has been attributed because it is unstable and hard to research

Answer 241

DNA that makes up a chromosome is wound around a group of small basic proteins (histones) forming chromatin. Five histone proteins found in eukaryotic cells. two copies of each of the histone proteins (H2A, H2B, H3, and H4) form a histone core and about 200 base pairs of DNA are wrapped around this protein complex forming a nucleosome The last histone, H1, seals off the DNA as it enters and leaves the nucleosome adding stability to the structure -Are an example of nucleoproteins (proteins that associate with DNA)

Answer 242

DNA replication cannot extend all the way to the end of a chromosome. This will result in losing sequences and information with each round of replication. Solution is a simple repeating unit (TTAGGG) at the end of the DNA forming a telomere. High GC content creates exceptionally strong strand attractions at the end of chromosomes to prevent unraveling

Answer 243

some of the sequence is lost in each round of replication and is replaced by this enzyme -More highly expressed in rapidly dividing cells.

Answer 244

Are a region of DNA found in the center of chromosomes. Referred to as sites of constriction because they form noticeable indentations. This part is composed of heterochromatin which is composed of tandem repeat sequences that also contain high GC content. During cell division the two sister chromatids can remain connected at the centromere until microtubules separate the chromatids during anaphase

Answer 245

Set of specialized proteins that assist the DNA polymerases.

Answer 246

DNA unwinds here and creates replication forks on both sides of the origin.

Answer 247

Circular closed double stranded DNA molecule with a single origin of replication. There are two replication forks that move away from each other in opposite directions around the circle. The two replication forks eventually meet resulting in the production of two identical circular molecules of DNA

Answer 248

Contains one linear molecule of double stranded DNA having multiple origins of replication. As replication fork moves toward each other and sister chromatids are created, chromatids will remain connected at centromere

Answer 249

Enzyme responsible for unwinding the DNA, generating two single stranded template strands ahead of the polymerase. Once opened, the unpaired strands of DNA are very sticky. Free purines and pyrimidines seek out other molecules with which to hydrogen bond

Answer 250

Will bind to the unraveled strand, preventing both the reassociation of the DNA strands and the degradation of DNA by nucleases

Answer 251

Wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication. DNA topoisomerases relieve torsional stress and reduce risk of strand breakage by introducing negative supercoils. They do so by working ahead of helicase, nicking one or both strands, allowing relaxation of the torsional pressure and then resealing the cut strands

Answer 252

Responsible for reading the DNA template or parental strand and synthesizing the new daughter strand. It can read template in a 3 to 5 direction while synthesizing the complementary strand in the 5 to 3 direction. This will result in a new double helix of DNA that has the required antiparallel orientation

Answer 253

Is the strand that is copied in a continuous manner. Strand read in 3 to 5 and its complement will be synthesized in a 5 to 3 manner

Answer 254

Strand that is copied in a direction opposite to the direction of the replication fork. Parental strand has 5 to 3 polarity. DNA polymerase cannot read and synthesize on this strand. Because DNA polymerase can only synthesize in the 5 to 3 direction from a 3 to 5 template, small strands called Okazaki fragments are produced.

Answer 255

DNA replication first step is to lay down an RNA primer. Primase makes a short primer (10 nucleotides) in the 5 to 3 direction to start replication on each strand. These short RNA sequences are constantly being added to the lagging strand because each Okazaki fragment must start with a new primer

Answer 256

Will begin synthesizing the daughter strands of DNA in the 5 to 3 manner. As the new phosphodiester bond is made, a free pyrophosphate is released

Answer 257

The RNA must eventually be removed to maintain sanctity of the genome. Adds DNA nucleotides where the RNA primer has been

Answer 258

seals the ends of the DNA molecules together, creating one continuous strand of DNA

Answer 259

Work together to synthesize both the leading and lagging strands; DNA polymerase delta also fills the gaps left behind when RNA primers are removed

Answer 260

replicates mitochondrial DNA

Answer 261

important to the process of DNA repair

Answer 262

Assisted by the PCNA protein which assembles into a trimer to form the sliding clamp. The clamp helps to strengthen the interaction between these DNA polymerases and the template strand

Answer 263

Able to divide without stimulation from other cells and are no longer subject to the normal controls on cell proliferation. Are able to migrate by local invasion or metastasis, a migration to distant tissues by the bloodstream or lymphatic system

Answer 264

Mutated genes that cause cancer. Primarily encode cell cycle related proteins

Answer 265

Before oncogenes are mutated.

Answer 266

(names after sarcoma) The abnormal alleles encode proteins that are more active than normal proteins promoting a rapid cell cycle advancement.

Answer 267

It looks at the level of methylation: the template strand has existed in the cell for a long period of time, and therefore is more heavily methylated.

Answer 268

In lagging strand because DNA ligase which closes the gaps between Okazaki fragments lacks proofreading ability

Answer 269

Cells have machinery in the G2 phase of the cell cycle for mismatch repair. These enzymes are encoded by genes MSH2 and MLH1 which detect and remove errors introduced in replication that were missed during the S phase of the cell cycle. These enzymes are homologous of MutS and MutL in prokaryotes

Answer 270

UV light introduces formation of dimers between adjacent thymine residues in DNA. This interferes with DNA replication and normal gene expression and distorts the shape of the double helix. The dimers are eliminated from DNA by a nucleotide excision repair mechanism (cut and patch process). First, specific proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand. An excision endonuclease then makes nicks in the phosphodiester bond of the damaged strand on both sides of thymine dimer and removes defective olignonucleotide. DNA polymerase can fill gap by synthesizing DNA in the 5 to 3 direction using the undamaged strand as a template. DNA ligase seals nick in strand

Answer 271

Detection systems exist for small non-helix distorting mutations in other bases as well. First the affected base is recognized and removed by a glycosylase enzyme leaving behind an apurinic/apyrimidinic site also called an abasic site. The AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA. DNA polymerase and DNA ligase then fill the gap and seal the strand

Answer 272

Technology allows a DNA fragment from any source to be multiplied by either gene cloning or PCR. This provides a means of analyzing and altering genes and proteins. Useful for gene therapy and can provide a source of a specific protein

Answer 273

Technique that produces large amounts of a desired sequence. DNA to be cloned is present in a small quantity and is part of heterogeneous mixture containing other DNA sequences. Goal is to produce a large quantity of homogeneous DNA for other applications. DNA of interest must be ligated into a piece of nucleic acid referred to as vector forming a recombinant vector . Vectors are usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest. Bacteria then grown in colonies and a colony containing recombinant vector is isolated. Accomplished by ensuring the recombinant vector also includes a gene for the antibiotic resistance; antibiotics can then kill off all the colonies that do not contain the recombinant vector. Resulting colony grown in large quantities

Answer 274

Enzymes that recognize specific double stranded DNA sequences. They are palindromic meaning that the 5 to 3 sequences of one strand is equal to the 5 to 3 sequence of the other strand. Restriction enzymes isolated from bacteria where they act as part of a restriction and modification system that protects the bacteria from infection by DNA viruses. Once a specific sequence has been identified, restriction enzyme can cut through backbone of the double helix.

Answer 275

Some restriction enzymes produce offset cuts yielding stick ends on the fragments which are advantageous in facilitating the recombination of a restriction fragment with the vector DNA

Answer 276

Large collections of known DNA sequences. To make library, DNA fragments often digested randomly, are cloned into vectors and can be utilized for further study. Consist of either genomic DNA or cDNA

Answer 277

Contain large fragments of DNA and include both coding and noncoding regions of the genome

Answer 278

complementary DNA Constructed by reverse transcribing processed mRNA; lacks non-coding regions such as introns and only includes the genes that are expressed in the tissue from which the mRNA was isolated. Sometimes called expression libraries. Only cDNA libraries can be used reliably to sequence specific genes and identify disease causing mutations, produce recombinant proteins, or produce transgenic animals

Answer 279

The joining of complementary base pair sequences. Uses two single stranded sequences important for PCR and Southern blotting.

Answer 280

Can produce millions of copies of DNA sequence without amplifying the DNA in bacteria. Requires primers that are complementary to the DNA that flanks the region of interest, nucleotides, and DNA polymerase. Also needs heat to separate double helix. so it is denatured, replicated, and then reannealed

Answer 281

Southern blot is used to detect the presence and quantity of various DNA strands in a sample. DNA is cut by restriction enzymes and separated by gel electrophoresis. longer the dna the slower it will migrate in gel. Then DNA fragments transferred to another membrane retaining their separation. Membrane probed with many copies of a single stranded DNA sequence, The probe will then bind to its complementary sequence and form double stranded DNA

Answer 282

Intended for diseases in which a given gene is mutated or inactive giving rise to pathology. BY transferring a normal copy of the gene into the affected tissues, pathology should be fixed

Answer 283

Once DNA has been isolated it can be introduced into eukaryotic cells. Transgenic mice are altered at the germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells. The cloned gene that is introduced = transgene. If the transgene is a disease producing allele, the transgenic mice can be used to study the disease process from early development through adulthood.

Answer 284

Gene has been intentionally deleted

Answer 285

A cloned gene may be microinjected into the nucleus of a newly fertilized ovum. Rarely the gene may incorporate into the nuclear DNA of the zygote. The ovum is implanted into a surrogate mother and if successful, the resulting offspring will contain the transgene in all of their cells including germ line cells. Transgene will be passed to their offspring. Transgene coexists in the animals with their own copies of the gene which have not bee deleted. Approach is useful for studying dominant gene effects

Answer 286

Can also be used for developing transgenic mice. Advantages are that the cloned genes can be intro'd in cultures and that one can select for cells with the transgene successfully inserted. Altered stem cells are injected into developing blastocytes and implanted into surrogate mothers. Blastocyte is composed of two types of stem cells: ones containing transgene and original blastocyst cells that lack transgene. Resulting offspring is a chimera meaning that it has patches of cells including germ cells derived from each of the two lineages. This is evident if the two cell lineages come from mice with different coat colors

Answer 287

- Low affinity transporter in hepatocytes and pancreatic cells - After a meal, blood traveling through hepatic portal vein from the intestine is rich in glucose - GLUT2 captures excess glucose primarily for storage - Liver will pick up excess glucose and store it preferentially after a meal when blood glucose levels are high - In the B islet cells of the pancreas, GLUT2 along with the glycolytic enzyme glucokinase serves as the glucose sensor for insulin release - Km is high (15 mM)

Answer 288

- Is in adipose and musscle tissue and responds to the glucose concentration in peripheral blood. - The rate of glucose transport in these two tissues is increased by insulin which stimulates the movement of additional GLUT4 transporters to the membrane by a mechanism involving exocytosis - When a person has high blood sugar concentrations, these transporters will still permit only a constant rate of glucose influx because they will be saturated - Transport increases in adipose tissue and muscle when insulin levels rise - Muscle stores excess glucose as glycogen and adipose tissue requires glucose to form DHAP which is converted to glycerol phosphate to store incoming fatty acids such as triacylglyerols - Km around 5 mM so the transporters are saturated when blood glucose levels are just a bit higher than normal

Answer 289

- Cytoplasmic pathway that converts glucose into two pyruvate molecules, releasing a fairly modest amount of energy captured in two substrate level phosphorylations and one oxidation reaction - If a cell has mitochondria and oxygen, the energy carriers produced in glycolysis (NADH) can feed into the aerobic respiration pathway to generate energy for the cell - If mitochondria or oxygen are lacking glycolysis may occur anaerobically but some of the energy is lost - Also provides intermediates for other pathways

Answer 290

- First steps in glucose metabolism in any cell are transport across the membrane and phosphorylation by kinase enzymes inside the cell to prevent glucose from leaving via the transporter - Glucose enters cell by facilitated diffusion or active transport - Kinases convert glucose to glucose 6 phosphate so now it cannot leak out and is trapped inside cell because GLUT transporters are specific for glucose. Hexokinase is inhibited by glucose 6 phosphate. Glucokinase is found on in liver cells and pancreatic B-islet cells; in the liver glucokinase is induced by insulin - Hexokinase is present in most tissues but glucokinase is present in hepatocytes and pancreatic B-islet cells - Hexokinase has low Km and glucokinase has high Km (acts on glucose proportionally to its concentration)

Answer 291

- PFK-1 is the rate limiting enzyme and main control point in glycolysis. In this reaction fructose 6 phosphate is phosphorylated to fructose 1,6 bisphophate using ATP. - PFK-1 inhibited by ATP and citrate and activated by AMP because cell should turn off glycolysis when enough energy is there (high ATP) and turn on glycolysis when it needs energy (high AMP). Citrate is an intermediate of Citric acid cycle so high levels imply the cell is producing sufficient energy - Insulin stimulates PFK-2 which converts fructose 6 p to fructose 2 6-bis P activating PFK-1. - Glucagon inhibits PFK-2 lowering F2, 6-BP and inhibiting PFK-1 - By activating PFK-1, it allows these cells to override the inhibition caused by ATP so that glycolysis can continue even when the cell is energetically satisfied. Metabolites can be fed into production of glycogen and fatty acids instead of being burned to produce ATP

Answer 292

- Catalyzes an oxidation and addition of inorganic phosphate to its substrate, glyceraldehyde 3-phosphate - Results in production of high energy intermediate 1,3-biphosphoglycerate and the reduction of NAD+ to NADH - If glycolysis is aerobic, NADH can be oxidized by the electron transport chain providing energy for ATP synthesis by oxidative phosphorylation

Answer 293

Transfers the high energy phosphate from 1,3-bisphosphoglycerate to ADP forming ATP and 3-phosphoglycerate. Uses substrate level phosphorylation in which ADP is directly phosphorylated to ATP using a high energy intermediate

Answer 294

Catalyzes a substrate level phosphorylation of ADP using the high energy substrate phosphoenolpyruvate (PEP). Activated by fructose 1,6-bisphosphate from the PFK-1 reaction (referred to as feed forward activation)

Answer 295

Occurs in absence of oxygen. Key enzyme is lactate dehydrogenase, which oxidizes NADH to NAD+ replenishing the oxidized co-enzyme for glyceraldehyde-3-phosphate dehydrogenase

Answer 296

Conversion of pyruvate to ethanol (3C -> 2C) and carbon dioxide (one C). Result is replenishing NAD+

Answer 297

1. ) Dihydroxyacetone phosphate (DHAP) is used in hepatic and adipose tissue for triacylglycerol synthesis DHAP is formed from fructose 1,6-bisphosphate. Can be isomerized to glycerol 3-phosphate, which can be converted to glycerol the backbone of triacylglycerol 2. ) 1,3-Bisphosphoglycerate and phosphoenolpyruvate are high energy intermediates used to generate ATP by substrate level phosphorylation

Answer 298

1. Glucokinase and Hexokinase 2. PFK-1 3. Pyruvate kinase

Answer 299

- Anaerobic glycolysis only pathway for ATP production, yielding 2 ATP per glucose - RBC have bisphosphoglycerate mutase which produces 2,3-bisphosphoglycerate from 1,3-BPG in glycolysis. Phosphate is moved from the 1-position to the 2-position - 2,3-BPG binds allosterically to the B-chains of hemoglobin A and decreases its affinity for oxygen. - Although 2,3-BPG binds to HbA it does not bind well to fetal hemoglobin with the result that HbF has a higher affinity for oxygen than maternal HbA This allows transplacental passage of oxygen from mother to fetus

Answer 300

- Important source of galactose in diet is lactose (disaccharide) which is hydrolyzed to galactose and glucose by lactase which is a brush border enzyme of the duodenum - Galactose is phosphorylated by galactokinase trapping it in the cell - Galactose 1-phosphate is converted to glucose 1-phosphate by galactose 1-phosphate uridyltransferase and an epimerase

Answer 301

Enzymes that catalyze the conversion of one sugar epimer to another

Answer 302

Found in honey and fruit and as part of the disaccharide sucrose. Sucrose is hydrolyzed by the duodenal brush-border enzyme sucrase and the resulting monosaccharides glucose and fructose are absorbed into hepatic portal vein. Liver phosphorylates fructose using fructokinase to trap it in the cell. Resulting fructose-1-phosphate cleaved into glyceraldehyde and DHAP by aldolase B. Smaller amounts are metabolized in renal proximal tubule

Answer 303

Pyruvate from aerobic glycolysis enters mitochondria where it may be converted to acetyl-CoA for entry into the citric acid cycle if ATP is needed or for fatty acid synthesis if sufficient ATP is present. Pyruvate dehydrogenase complex (PDH) is irreversible and cannot be used to convert acetyl-CoA to pyruvate or to glucose. In the liver is activated by insulin whereas in nervous system enzyme is not responsive to hormones. PDH is a complex of enzymes carrying out multiple reactions in succession. -large complex requires multiple cofactors and coenzymes -Inhibited by its product acetyl-CoA -Buildup of acetyl-CoA which happens during Beta-oxidation causes a shift in metabolism: pyruvate is no longer converted into acetyl-CoA ( to enter CAC), but rather into oxaloacetate to enter gluconeogenesis

Answer 304

1. Conversion to acetyl CoA by PDH 2. Conversion to lactate by lactate dehydrogenase 3. Conversion to oxaloacetate by pyruvate carboxylase

Answer 305

Branched polymer of glucose represents a storage form of glucose Glycogen synthesis and breakdown occur primarily in liver and skeletal muscle although other tissues store smaller quantities. Glycogen stored in cytoplasm as granules. Each granule has a central protein core with polyglucose chains radiating out to form a sphere. Glycogen granules with linear chains have higher density near core. If chains are branched density highest at periphery allowing more rapid release. Glycogen stored in the liver is a source of glucose that is mobilized between meals to prevent low blood sugar whereas muscle glycogen is stored as an energy reserve for muscle contraction

Answer 306

Synthesis of glycogen granules and begins with core protein called glycogenin. -Glucose addition to granule begins with glucose-6-phosphate which is converted to glucose -1 phoshpate which is then activated by coupling to a molecule of uridine diphosphate which permits its integration into the glycogen chain by glycogen synthase.

Answer 307

Rate limiting enzyme of glycogen synthesis and forms the alpha 1,4 glycosidic bond found in the linear glucose chains of the granule. It is stimulated by epinephrine and glucagon through a protein kinase cascade that phosphorylates and inactivates the enzyme

Answer 308

Responsible for introducing alpha 1,6 linked branches into the granule as it grows. Branching enzyme: 1. Hydrolyzes one of the alpha 1,4 bonds to release a block of oligoglucose which is then moved and added in a slightly different location 2. Forms an alpha-1,6 bond to create a branch

Answer 309

- Rate limiting enzyme, the process of breaking down glycogen is glycogen phosphorylase - Phosphorylase breaks bonds using an inorganic phosphate instead of water - Glucose 1 phosphate is converted to glucose 6 phosphate by the same mutase in glycogen synthesis

Answer 310

-Breaks alpha 1,4 glycosidic bonds releasing glucose 1 phosphate from the periphery of the granule. It cannot break 1.6 bonds. It is activated by glucagon in the liver so tht glucose can be provided for rest of the body. In skeletal muscle, it is activated by AMP and epinephrine and inhibited by ATP

Answer 311

two enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase 1. Breaks an alpha 1,4 bond adjacent to the branch point and moves the small oligoglucose chain that is released to the exposed end of the other chain 2. Forms new alpha 1.4 bond 3. Hydrolyzes the alpha 1,6 bond, releasing the single residue at the branch point as free glucose (only free glucose produced directly in glycogenolysis)

Answer 312

Liver maintain glucose levels in blood during fasting this way. These pathways are promoted by glucagon and epinephrine which raise blood sugar levels and are inhibited by insulin. During fasting glycogen drops in first 12 hours and then after 24 hours it represents sole source of energy

Answer 313

1. Glycerol 3 phosphate 2. Lactate 3. Glucogenic amino acids

Answer 314

all except leucine and lysine can be converted into intermediates that feed into gluconeogenesis while ketogenic amino acids can be converted into ketone bodies which can be used as an alternative fuel esp during prolonged starvation

Answer 315

Mitochondrial enzyme that is activated b acetyl-CoA from beta oxidation. Product oxaloacetate is a citric acid cycle intermediate and cannot leave the mitochondrion. Rather it is reduced to malate which can leave the mitochondrion via the malate-aspartate shuttle. Once in the cytoplasm, malate oxidized to OAA. Aetyl-CoA inhibits pyruvate dehydrogenase because ahigh level of acetyl-CoA implies that the cell is energetically satisfied and need not run the CAC in forward direction so cell should stop burning glucose. Pyruvate will be shunted through pyruvate carboxylase to help make more glucose. Source of acetyl-CoA is from fatty acids. Thus to produce glucose in the liver during gluconeogenesis fatty acids must be burned to provide this energy

Answer 316

In the cytoplasm is induced by glucagon and cortisol which generally act to raise blood sugar levels. It converts OAA to PEP in a reaction that requires GTP. PEP continues in the pathway to fructose 1,6 bisphosphate. Combination of pyruvate carboxylase and PEPCK are used to circumvent action of pyruvate kinase by converting pyruvate back into PEP

Answer 317

In cytoplasm is a key control point of gluconeogenesis and represents rate limiting step of process. Reverses action of PFK-1 by removing phosphate from fructose 1,6-bisphosphate to produce fructose 6 phosphate. Fructose 1, 6-bisphosphatase activated by ATP and inhibited by AMP and fructose 2,6 bisphosphate which controls both gluconeogenesis and glcolysis in the liver

Answer 318

Found only in the lumen of the ER in liver cells. Is transported into the ER and free glucose is transported back into the cytoplasm from where it can diffuse out of the cell using GLUT transporters. The absence of G-6-P in skeletal muscle means that muscle glycogen cannot serve as a source of blood glucose and rather is for use only within the muscle. Glucose 6 phophatase is used to to circumvent glucokinase and hexokinase which convert glucose to g-6-p

Answer 319

Occurs in the cytoplasm of all cells; production of NADH and serving as a source of ribose 5-phosphate for nucleotide synthesis. First part of reaction begins with G-6-P ends with ribulose 5-phosphate and is irreversible. This part produces NADPH and involves rate limiting enzyme G6PD which is induced by insulin because the abundance of sugar entering the cell under insulin stimulation will be shunted into both fuel utilization pathways as well as fuel storage pathways Shunt is also inhibited by its product NADPH and is activated by one of its reactants NADP+. Second part of pathway begins with ribulose 5-phosphate represents a series of reversible reactions that produce equilibrated pool of sugars for biosynthesis including ribose 5-phosphate for nucleotide synthesis. Because F6P and glyceraldehyde 3 phosphate are among sugars produced intermediates can feed back into glycolysis pentoses can then also be made from glycolytic intermediates without going through the G6PD reaction accomplished by transketolase and transaldolase

Answer 320

NAD+ acts as a high energy electron acceptor and is an oxidizing agent. NADH produced from this reduction of NAD+ can then feed into ETC to produce ATP. NADPH acts as an electron donor and is a reducing agent because it helps other molecules be reduced. Cells require NADPH for 1 biosynthesis of fatty acids and cholesterol 2. assisiting in cellular bleach production in certain WBC 3. maintaining supply of reduced glutathione to protect against reactive oxygen species acting as body antioxidant 4. Protecting cells from free radical oxidative damage caused by peroxides. Free radicals can attack lipids when oxidized these lipids lose their function and weaken the membrane causing cell lysis.

Answer 321

is a reducing agent that can help reverse radical formation before dmange is done to the cell

Answer 322

Occurs in the mitochondria. Main function is the oxidation of acetyl-CoA to CO2 and H2O. Cycle produces FADH2 and NADH. Acetyl CoA can be obtained from metabolism of carbs, fatty acids, and amino acids

Answer 323

After glucose undergoes glcolysis its product, pyruvate enters mitochondria via active transport and is oxidized and decarboxylated. Reactions catalyzed by pyruvate dehydrogenase complex which is located in the mitochondrial matrix. Exergonic reaction

Answer 324

CoA is a thiol and contains an SH group. When acetyl-CoA forms, it does so via covalent attachment of the acetyl group to the SH group resulting in the formation of a thioester which contains sulfur instead of the typical oxygen ester. Thioester is high energy and when is undergoes a reaction like hydrolysis a significant amount of energy will be released. This can be enough to drive other reactions forward like CAC

Answer 325

1. Pyruvate dehydrogenase (PDH): oxidized yielding CO2 while the remaining two carbon molecule binds covalently to TPP (coenzyme held by noncovalent interactions to PDH) Mg2+ also require

Answer 326

two carbon molecule bonded to TPP is oxidized and transferred to lipoic acid (coenzyme that covalently bonded to enzyme). Lipoic's acid disulfide group acts as an oxidizing agent, creating acetyl group. Acetyl group bonded to lipoic acid via thioester linkage. After, dihydrolipoyl transacetylase catalyzes CoA-SH interaction with new thioester link causing transfer of acetyl group to form acetyl CoA

Answer 327

FAD is used as a coenzyme in order to reoxidize lipoic acid allowing lipoic acid to facilitate acetyl CoA formation in future reactions in future reactions. As lipoic acid is reoxidized FAD reduced to FADH2

Answer 328

In the cytosol, a process (activation) causes a thioester bond to form between carboxyl groups of fatty acids and COA-SH. Activated fatty acyl-CoA is then transported to intermembrane space of mitochondrion. Because fatt acyl-CoA cannot cross inner mitochondrial membrane, fatty acyl group transferred to carnitine via a transesterification reaction. Carnitine can cross membrane. Once it does it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification reaction. Once acyl-CoA formed B-oxidation can occur which removes two carbon fragments from the carboxyl end

Answer 329

Certain amino acids can be used to form acetyl-CoA. They must lose their amino group via transamination; their carbon skeletons can then form ketone bodies.

Answer 330

Although acetyl-CoA is used to produce ketones when pyruvate dehydrogenase complex is inhibited, reverse reaction can occur as well

Answer 331

When alcohol consumed in moderate amounts, enzymes alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA. Reaction accompanied by NADH buildup which inhibits KREB cycle. Acetyl-CoA mainly used to make fatty acids

Answer 332

Mitochondrial matrix

Answer 333

Because NADH and FADH2 will accumulate if oxygen is not available for the electron transport chain and will inhibit the cycle

Answer 334

Enzymes that form new covalent bonds without needing significant energy

Answer 335

- Phosphorylation of PDH is done by pyruvate dehydrogenase kinase (phosphorylating PDH inhibits acetyl-CoA production - PDH reactivated by pyruvate dehydrogenase phosphatase in response to high levels of ADP. By removing a phosphate from PDH, pyruvate dehydrogenase phosphatase is able to reactivate acetyl CoA production

Answer 336

ATP and NADH function as allosteric inhibitors of citrate synthase. Citrate also allosterically inhibits citrate synthase as does succinyl-CoA

Answer 337

This enzyme that catalyzes the CAC is likely to be inhibited by energy products: ATP and NADH. ATP and NAD+ function as allosteric activators for the enzyme and enhance it affinity for substrates

Answer 338

Reaction products of succinyl-CoA and NADH function as inhibitors of this enzyme complex. ATP also inhibitory and slows rate of cycle when cell has high levels of ATP. Stimulated by ADP and calcium ions

Answer 339

HIgh levels of ATP and NADH

Answer 340

High levels of ADP and NAD+

Answer 341

-NADH-CoQ oxidoreductase -Transfer of electrons from NADH to coenzyme Q is catalyzed in this first complex (complex has over 20 subunits) -First step involves NADH transferring its electrons over to FMN, becoming oxidized to NAD+ as FMN is reduced to FMNH2 -Flavoprotein becomes reoxidized while iron-sulfur subunit is reduced -Reduced iron-sulfur subunit donates electrons it received from FMNH2 to coenzyme Q -Coenzyme Q becomes CoQH2 (one of three sites where proton pumping occurs) Net effect is passing high energy electrons from NADH to CoQ to form CoQH2

Answer 342

Succinate-CoQ oxidoreductase -Complex 2 transfers electrons to coenzyme Q -While complex 1 received electrons from NADH, complex 2 actually receives electrons from succinate (CAC intermediate that is oxidized to form fumarate upon interacting with FAD) -FAD covalently bonded to complex 2 and once succinate is oxidized its converted to FADH2 then FADH2 gets reoxidized to FAD as it reduces iron-sulfur protein -Reoxidizing the iron sulfur protein as coenzyme Q is reduced -Succinate dehydrogenase part of complex 2 Net effect is passing high energy electrons from succinate to CoQ to form CoQH2

Answer 343

CoQH2-cytochrome c oxidoreductase - Complex facilitates transfer of electrons from coenzyme Q to cytochrome c - Only one electron is transferred per reaction but because coenzyme Q has two electrons to transfer, two cytochrome C molecules will be needed - Q Cycle: two electrons are shuttled from a molecule of ubiquinol near intermembrane space to a molecule of ubiquinone near the mitochondrial matrix - Another two electrons are attached to heme moieties reducing two molecules of cytochrome c - Carrier containing iron and sulfur help assist - 4 protons are also displaced to intermembrane space so the Q cycle continues to increase gradient of proton motive force across inner mitochondrial matrix

Answer 344

Complex facilitates the culminating step of ETC: transfer of electrons from cytochrome C to oxygen (the final electron acceptor) This complex includes subunits of cytochrome a, cytochrome a3, and Cu ions. Together a and a3 make up cytochrome oxidase which gets oxidized as oxygen becomes reduced and forms water. This is the final location on the ETC where proton pumping occurs as two protons are moved across membrane

Answer 345

Forms as electrons pass along the ETC; As H+ increases in the intermembrane space, pH drops and the voltage difference between the intermembrane space and matrix increases due to proton pumping. Together these two changes contribute to electrochemical gradient. ATP synthase responsible for harnessing this energy to form ATP from ADP and an inorganic phosphate

Answer 346

ATP yield per glucose is variable (30-32) because this variable efficiency is caused by the fact that cytosolic NADH formed through glycolysis cannot cross into the mitochondrial matrix. It must find alternate means of transportation. A shuttle mechanism transfers the high energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane. Either 1.5 or 2.5 ATP will end up being produced. Two mechanisms (glycerol 3-phosphate shuttle and malate aspartate shuttle)

Answer 347

- Cytosol contains isoform of glycerol-3-phosphate dehydrogenase which oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate (DHAP) - Outer face of inner mitochondrial membrane, there exists another isoform that is FAD dependent and is the oxidizing agent and ends up being reduced to FADH2. Once reduced, FADH2 proceeds to transfer its electrons to ETC via Complex 2 generating 1.5 ATP per molecule of NADH

Answer 348

Cytosolic oxaloacetate which cannot pass trough inner mitochondrial membrane is reduced to malate which can (accomplished by cytosolic malate dehydrogenase) Accompanying this is oxidation of cytosolic NADH to NAD+ once malate crosses into matrix, mitochondrial malate dehydrogenase reverses reaction to form mitochondrial NADH which passes its electrons to Complex 1 and generates 2.5 ATP per molecule of NADH -Recycling malate requires oxidation to oxaloacetate which can be transaminated to form aspartate which crosses into cytosol and can be reconverted to restart the cycle

Answer 349

F0 functions as an ion channel so protons travel through here along their gradient back into the matrix. As this happens chemiosmotic coupling also occurs

Answer 350

Allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP thus forming ATP. ETC generates a high concentration of protons in the intermembrane space which then flow through the F0 ion channel of ATP synthase back into the matrix. As this happens the other portion of ATP synthase which is called the F1 portion, utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP

Answer 351

Another mechanism suggests that the relationship between the proton gradient and ATP synthesis is indirect. ATP is released by the synthase as a result of conformational change caused by the gradient. The F1 portion of ATP synthase is similar to a turbine, spinning within a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding

Answer 352

Regulation of these pathways: - O2 and ADP are key regulators of oxidative phosphorylation. If o2 is limited o.p. will decrease and the concentration of NADH and FADH2 will increase. Accumulation of NADh in turn inhibits the citric acid cycle. - In the presence of adequate O2, O.P. rate is dependent on availability of ADP - Accumulation of ADP accompanied by decrease in ATP and amount of energy available to cell - ADP accumulation signals need for ATP synthesis - ADP allosterically activates isocitrate dehydrogenase inc rate of CAC and production of NADH and FADH2 inc rate of electron transport

Answer 353

Dietary fat mostly triacylglycerols with the remainder being cholesterol, cholesteryl esters, phospholipids, and free fatty acids. Lipid digestion is minimal in the mouth and stomach; lipids are transported to the small intestine essentially intact. Upon entry into duodenum, emulsification occurs which is the mixing of two normally immiscible liquids (fat and water). Formation of emulsion increases the SA of the lipid which permits greater enzymatic interaction and processing. Emulsification aided by bile which contains bile salts pigments and cholesterol

Answer 354

Secreted by the liver and stored in the galbladder; has bile salts, pigments, and cholesterol

Answer 355

Secretes pancreatic lipase, colipase, and cholesterol esterase into the small intestine; these enzyme hydrolyze the lipid components to 2-monoacylglycerol, free fatty acids, and cholesterol

Answer 356

Absorption of fats by intestinal cells

Answer 357

Free fatty acids, cholesterol, 2 -monoacylglycerol and bile salts contribute to formation of micelles which are clusters of amphipathic lipids that are soluble in the aqueous environment of the intestina lumen

Answer 358

Water soluble spheres with a lipid soluble interior. Micelles are vital in digestion, transport, and absorption of lipid soluble substances starting from the duodenum all the way to the end of the ileum. At the end of the ileum, bile salts are reabsorbed and recycled; any fat that remains in the intestine will pass into colon and end up in stool

Answer 359

Micelles diffuse to the brush border of the intestinal mucosal cells where they are absorbed into the mucosa and re-esterified to form triacylglycerols and cholesteryl esters and packaged along with certain apoproteins, fat soluble vitamins, and other lipidsinto chlymicrons

Answer 360

Leave the intestine via lacteals, the vessels of the lymphatic system and re-enter the bloodstream via the thoracic duct, a long lymphatic vessel that empties into the left subclavian vein at the base of the neck. More water soluble short chain fatty acids can be absorbed by simple diffusion into blood stream

Answer 361

At night body is in this state using energy stores instead of food for fuel. Fatty acids are released from adipose tissue and used for energy. A fall in insulin levels activates a hormone sensitive lipase (HSL) that hydrolyzes triacylglycerols yielding fatty acids and glycerol. Epinephrine and cortisol can also activate HSL. Released glycerol from fat may be taken to liver for glycolysis or gluceneogenesis. HSL is effective within adipose cells but lipoprotein lipase is necessary for metabolism of chylomicrons and very low density lipoproteins. LPL is an enzyme that can release free fatty acids from triacylglyerols in these lipoproteins

Answer 362

Free fatty acids are transported using albumin, carrier protein but triacylglycerol and cholesterol are transported in the blood as lipoprotein

Answer 363

aggregates of apolipoproteins and lipids. Named according to density which increaes in direct proportion to the percentage of protein in the particle

Answer 364

Highly soluble in lymphatic fluid and blood and function in transport of dietary triacylglycerols, cholesterol and cholesteryl esters from intestine to other tissues. They are the least dense with the highest fat to protein ratio

Answer 365

Very low density lipoprotein - Metaboism is similar to that of chylomicrons but VLDL is produced and assembled in liver cells - Main function is transport of triacylglycerols to other tissues and it also contains fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants

Answer 366

Intermediate Density Lipoprotein - One triacylglycerol removed from VLDL to form IDL - Some reabsorbed by liver b apolipoproteins on its exterior and some processed in the bloodstream. Some IDL picks up cholesteryl esters from HDL to become LDL so it exists as a transition particle between triacylglycerol transport and cholesterol transport

Answer 367

Low density lipoprotein - Majority of cholesterol measured in blood is associated with LDL - Normal role is to deliver cholesterol to tissues for biosynthesis - Cholesterol plays important role in cell membranes - Bile acids and salts made from cholesterol in liver

Answer 368

High density lipoprotein -Synthesized in the liver and intestines and released as dense protein rich particles into the blood HDL contains apolipoproteins used for cholesterol recovery (cleaning up excess cholesterol from blood vessels for excretion) Also delivers cholesterol to steroidogenic tissues

Answer 369

Form the protein component of the lipoproteins described above. They are receptor molecules and are involved in signaling.

Answer 370

activates LCAT, an enzyme that catalyzes cholesterol esterification

Answer 371

mediates chylomicron secretion

Answer 372

permits uptake of LDL by the liver

Answer 373

activates lipoprotein lipase

Answer 374

permits uptake of chylomicron remnants and VLDL by th eliver

Answer 375

- Occurs in liver and is driven by acetyl CoA and ATP - Citrate shuttle carries mitochondrial acetyl CoA into the cytoplasm where synthesis occurs - NADPH supplies reducing equivalents - Synthesis of mevalonic acid in the SER is the rate limiting step in cholesterol biosynthesis and is catalyzed by 3-hydroxy-3-methylglutaryl CoA reductase

Answer 376

Increased levels of cholesterol can inhibit further synthesis by a feedback inhibition mechanism Insulin promotes cholesterol synthesis. Control is also dependent on regulation of HMG-CoA reductase gene expression in the cell

Answer 377

Lecithin cholesterol acetyltransferase is an enzyme found in the bloodstream that is activated by HDL apoproteins. It adds a fatty acid to cholesterol which proudces soluble cholesteryl esters such as those in HDL which can be distributed to other lipoproteins like IDL. CETP facilitates transfer process

Answer 378

These poly-unsaturated fatty acids as well as other acids formed from them are important in maintaining cell membrane fluidity which is critical for proper functioning of the cell

Answer 379

Fatty acids used for fuel are primarily synthesized in diet. Excess carb and protein acquired from diet can be converted to fatty acids and stored as energy reserves in the form of triacylglycerols. Lipids and carbs called nontemplate synthesis because they do not rely directly on coding of a nucleic acid unlike proteins or nucleic acids occurs in liver and its products are transported to adipose tissue for storage palmitic acid is the primary end product of fatty acid synthesis

Answer 380

acetl CoA carboxylase and fatty acid synthase and they are stimulated by insulin

Answer 381

After a large meal, acetyl-CoA accumulates in the mitochondrial matrix and needs to be moved to the cytosol for fatty acid biosynthesis. IT couples with OAA to form citrate. Isocitrate dehydrogenase is the rate limiting enzyme so as cell becomes energetically satisfied it slows the CAC causing citrate accumulation. In the cytosol citrate lyase splits citrate back into acetyl CoA and oxaloacetate which then returns to mitochondrion to continue moving acetyl CoA

Answer 382

- Acetyl-CoA activated in the cytoplasm for incorporation into fatty acids by acetyl-CoA carboxylase - Acetyl CoA carboxylase requires biotin and ATP to function and adds CO2 to acetyl CoA to form malonyl-CoA. - Activated by insulin and citrate - CO2 added to form malonyl-COA is never incorporated into fatty acid because it is removed by fatty acid synthase

Answer 383

- Palmitate synthase - Only fatty acid that human can synthesize de novo - Large multienzyme complex found in cytosol that is rapidly induced in liver following meal high in carbs bc of elevated insulin levels - Enzyme complex contains acyl carrier protein that requires pantothenic acid (vitamin B5) - NADPH is also needed to reduce the acetyl groups added to the fatty acid - 8 acetyl CoA groups are required to proudce palmitate - Fatty acl-CoA may be elongated and desaturated using enzymes associated with the SER

Answer 384

formed by attaching three fatty acids (fatty acyl-CoA) to glycerol. Occurss primarily in the liver and somewhat in adipose tissue with small contribution from diet. In the liver triacylglycerols are packaged and sent o to adipose tissue as VLDL leaving only a small amount of stored triacylglycerols

Answer 385

Two additional enzymes are needed because double bonds can disturb the stereochemistry needed for oxidative enzymes to act on the fatty acid. To function, these enzymes can have at most one double bond in their active site (between C 2 and 3). Enoyl-CoA isomerase rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl CoA has been liberated to isolate double bond within the first 3 carbons. Permits B oxidation to proceed

Answer 386

In the fasting state, the liver converts excess acetyl CoA from B oxidation of fatty acids into the ketone bodies acetoacetate and 3-hydroxybutyrate which can be used for energy in various tissues. Cardiac and skeletal muscle, renal cortex can metabolize these to acetyl CoA. During fasting periods, the muscle will metabolize ketones as rapidly as the liver releases them preventing accumulation in the bloodstream

Answer 387

Occurs in the mitochondria of liver cells when excess acetyl-CoA accumulates in the fasting state. HMG-CoA synthase forms HMG-CoA and HMG-CoA lyase breaks down into HMG-CoA into acetoacetate which can be reduced to 3-hydroxybutyrane

Answer 388

Acetoacetate picked up from blood is activated in the mitochondria by succinyl-CoA acetoacetyl-CoA transferase an enzyme present only in tisues outside the liver. During this reaction, 3-hydroxybutyrane is oxidized to acetoacetate. -Stimulated by low energy state in muscle and brain tissues

Answer 389

Protein rarely used as energy because it is so important for other functions. Under conditions of extreme energy deprivation however it can be used for energy. Digestion of proteins begins in stomach with pepsin and then pancreatic proteases trypsin, chymotrypsin,and carboxypeptidases A and all which secreted as zymogens. Digestion completed by small intestinal brush border enzymes dipeptidase and aminopeptidase. Main end proudce are amino acids, dipeptide,s and tripeptdies. Absorption of amino acids and small peptides through luminal membrane accomplished by secondary active transport linked to sodium Protein Catabolized primarily in muscle and liver. Amino acids released usually lose their amino group through transamination or deamination. Remaining carbon skeleton can be used for energy. Amino groups removed by transamination constitute toxin to body in form of urea and must be excreted safely (urea cycle)

Answer 390

Amino acids classified by ability to turn into specific metabolic intermediates. Glucogenic (all but leucine and lysine) can be converted to glucose through gluconeogenesis. Ketogenic (leucine, lysine, isoleucine, phenylalanine, threonine, tryptophan, and tyrosine can be converted into acetyl CoA and ketone bodies

Answer 391

- It is a mid level energy carrier and is formed form substrate level phosphorylation as well as oxidative phosphorylation - ATP cannot get back the leftover free energy after a reaction so it's bet to use a carrier with a smaller free energy - ATP in a cell most produced by mitochondrial ATP synthase but some produced during glycolysis and CAC - ATP is consumed through hydrolysis or the transfer of a phosphate group to another molecule

Answer 392

Its high energy phosphate bonds. The negative charge on phosphate groups experience repulsive forces with one another and the ADP and P molecules that form after hydrolysis are stabilized by resonance. ATP doesn't rapidly break down on its own in the cell, it is much more stable after hydrolysis

Answer 393

most likely to be encountered in context of coupled reactions. Many coupled reactions use ATP as an energy source.

Answer 394

transfer of a high energy phosphate from ATP to another molecule. This activates or inactivates the target molecule. With these phosphoryl group tansfers, the overall free energy of the reaction will be determined by taking the sum of the free energies of the individual reactions

Answer 395

ATP is an intermediate energy storage molecule and is not energetically dense. The high energy bonds in ATP and the presence of a significant charge make it an inefficient molecule to pack into a small space. Long term storage molecules are characterized by energy density and stable, nonrepulsive bonds primarily seen in lipids

Answer 396

Soluble and include: NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione, Some of these electron carriers are used by the mitochondrial electron transport chain which leads to oxidative phosphorylation of ADP to ATP. As electrons are passed down ETC, they give up their free energy to form proton motive force across inner mitochondrial membrane. There are membrane bound electron carriers embedded within inner mitochondrial membrane

Answer 397

Bonded to complex 1 of the ETC and can act as a soluble electron carrier. Proteins with prosthetic groups containing an iron sulfur cluster are well suited for transport of electrons

Answer 398

Contain a modified vitamin 2, or riboflavin. They are nucleic acid derivatives. More noticeable for their presence in the mitochondria and chloroplasts as electron carriers. Also involved in modification of other B vitamins to active forms. Functions as coenzmes in the oxidation of fatty acids, decarboxylation of pyruvate, and reduction of glutathione

Answer 399

Equilibrium is a fixed state which prevents us from storing any energy for later use or creating an excitable environment. Homeostasis is a physiological tendency toward a relatively stable state that is maintained and adjusted often with the expenditure of energy. Most compounds in body are stored as homeostatic level which allows us to store potential energy

Answer 400

Occurs shortly after eating. Marked by greater anabolism or synthesis of biomolecules and fuel storage than catabolism or breakdown of biomolecules for energy. Nutrients flood in from the gut and make way via hepatic vein to the liver where they can be stored or distributed to other tissues of body. Lasts 3-5 hours after meal. Just after eating blood glucose levels rise and stimulate release of insulin to liver, muscle, and adipose tissue. Insulin promotes glycogen synthesis in liver and muscle. After glycogen stores are filled liver converts excess glucose to fatty acids and triacylglyercols. After a meal most of energy needs of liver are met by oxidation of excess amino acids

Answer 401

Nervous tissue and red blood cells. Nervous tissue derives energy fro oxidizing glucose to CO2 and water. RBC use glucose anaerobically for all their energy needs

Answer 402

Glucagon, cortisol, epinephrine,norepinephrine, and growth hormone oppose the actions of insulin. These hormones are termed counterregulatory. - Hepatic gluconeogenesis is stimulated by glucagon but the response in slower than glycogenolysis. Glycogenolysis begins almost immediately after postabsorptive state, gluconeogenesis takes about 12 hours o hit max velocity - Release of amino acids from skeletal muscle and fatty acids from adipose tissue stimulated by decrease of insulin and increase of epinephrine. thee can provide energy needed for gluconeogenesis

Answer 403

- Levels of glucagon and epinephrine are elevated during starvation result in rapid degradation of glycogen stores in the liver - As liver glycogen stores are depleted, gluconeogenic activity continues and plays an important role in maintaining blood glucose levels during prolonged fasting - Lipolysis is rapid resulting in excess acetyl-Co that is used in the synthesis of ketone bodies. Once levels of fatty acids and ketones are high enough in the blood, muscle tissue will use fatty acids as its major fuel source and the brain will adapt to using ketones for energy - The shift from glucose to ketones as the major fuel reduces the quantity of amino acids that must be degraded to support gluconeogenesis which spares proteins that are vital for other functions

Answer 404

- For carbs, insulin increases uptake of glucose and increases carb metabolism in muscle and fat - Increased glucose in muscle can be used as additional fuel to burn during exercise or can be stored as glycogen - Increases glycogen synthesis in the liver by increasing the activity of glucokinase and glycogen synthase while decreasing activity. - Insulin increases levels of protein synthesis and decreasing breakdown of essential proteins - Decreaes triacylglycerol breakdown in adipose tissue - Decreases formation of ketone bodies by liver

Answer 405

- Increase liver glycogenolysis, glucagon activates glycogen phosphorylase and inactivates glycogen synthase - Increased liver gluconeogenesis. glucagon promotes the conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase and phoshpenolpyruvate carboxykinase. glucagon increases the conversion of fructose 1,6-bisphosphate to fructose 6 phosphat by fructose 1,6 bisphosphatase - Increased liver ketogenesis and decreased lipogenesis - Increased lipolysis in the liver

Answer 406

From the adrenal gland are responsible for part of the stress response. Glucose must be rapidly mobilized from the liver in order to fuel actively contracting muscle cells while fatty acids are released from adipocytes. Glucocorticoids especially cortisol is released with many forms of stress

Answer 407

Steroid hormone that promotes mobilization of energy stores through degradation and increased delivery of amino acids and increased lipolysis. Cortisol also elevates blood glucose levels increasing its availability for nervous tissue through 2 mechanisms. First cortisol inhibits glucose uptake in most tissues (muscle, lymphoid, fat) and increases hepatic output of glucose via gluconeogenesis particularly from amino acids. Cortisol enhances activity of glucagon, epinephrine, and other catecholamines

Answer 408

Secreted by adrenal medulla and include epinephrine and norepinephrine. Catecholamines increase the activity of liver and muscle glycogen phosphorylase promoting glycogenolysis. Increasing glucose output by liver. Also increases in skeletal muscle but muscle lacks glucose 6 phosphate so glucose cannot be released by skeletal muscle into bloodstream but it is metabolized by the muscle tissue itself. Catecholamines act on adipose tissue to increase lipolysis by increasing activity of lipase.

Answer 409

Increase the basal metabolic rate with increased O2 consumption and heat production when secreted. T3 provides more rapid increase in metabolic rate and has a shorter duration of activity. Thyroid hormones have their primary effects in lipid and carb metabolism. They accelerate cholesterol clearance from plasma and increase rate of glucose absorption from the small intestine

Answer 410

Maintains a constant level of blood glucose under wide range of conditions and to synthesize ketones when excess fatty acids are being oxidized. The liver extracts excess glucose and uses it to replenish glycogen stores. Any glucose remaining is converted to acetyl-CoA and used for fatty acid synthesis. Fatty acis are converted to triacylglycerols and releaed into blood as VLDL

Answer 411

Insulin triggers fatty acid release from VLDL and chylomicrons which carry triacylglycerols absorbed from the gut. Lipoprotein lipase an enzyme found in capillary bed of adipose tissue is also induced by insulin. The fatty acids that are released from lipoproteins are taken up by adipose tissue and re-esterified to triacylglycerols for storage. During fasting state, decreased levels of insulin and inc epinephrine activate hormone sensitive lipase in fat cells allowing fatty acids to be released into circulation

Answer 412

Allows accurate measurement of the respiratory quotient, which differs depending on the fuels being used by the organism. Respiratory quotient: RQ= CO2 produced/O2 produced -For carbs around 1 -For lipids around 0.7 -In resting individuals, usually around 0.8 indicating that both fat and glucose are consumed -Changes under conditions of high stress, starvation, exercise as predicted by actions of different hormones

Answer 413

Measure basal metabolic rate based on heat exchange with the environment. Makes use of insulated chambers with specialized heat sinks to determine energy expenditure.

Answer 414

Secreted by the stomach in response to signals of an impending meal. sight sound taste and smell act as signals for its release. increases appetite and also stimulates secretion of orexin

Answer 415

Further increases appetite and is also involved in alertness and the sleep wake cycle

Answer 416

Hormone secreted by fat cells that decreases appetite by suppressing orexin production. Genetic variations have been implicated in obesity

Biochem Flashcards

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