Exam 2 Flashcards
(143 cards)
1
Q
Phototrophs
A
- trap and use sunlight
2
Q
Chemotrophs
A
-derive energy from oxidation of a chemical fuel
3
Q
Autotrophs
A
- can synthesize all of their biomolecules directly from CO2
4
Q
Heterotrophs
A
- Require some preformed organic nutrients made by other organisms
5
Q
What classification are all animals, most fungi, protists, and bacteria?
A
- chemoheterotrophs
- > we derive energy from the oxidation of a chemical fuel (chemotrophs) and require some pre-formed organic nutrients made by other organisms (heterotrophs)
6
Q
Basic tenants of Energy
A
- can neither be created nor destroyed, only transferred
- Energy is required for living cells and organisms to perform work, stay alive, and reproduce
- biochemistry aims to understand the transfer of this energy through metabolic processes and by which the energy is extracted, channeled, and consumed in living cells
7
Q
Living organisms differ from their surroundings by…
A
- molecules and ions contained within a living organism differ in kind and in concentration from those in the organism’s surroundings
8
Q
Living organisms exist in….
A
a dynamic steady state, never at equilibrium with their surroundings
-> maintaining this state requires a constant investment of energy
9
Q
System
A
- all the constituent reactants and products
- the solvent that contains them
- the immediate atmosphere
10
Q
Universe
A
- system plus its surrounding
11
Q
Isolated system
A
- If the system exchanges neither matter nor energy with its surroundings
12
Q
Closed system
A
- if the system exchanges energy but not matter with its surroundings
13
Q
Open system
A
- if the system exchanges both energy and matter with its surroundings
- > living organism
14
Q
Two ways that organ systems derive energy:
A
- Take up chemical fuels (glucose) from the environment and extract energy by oxidizing them
- Absorb energy from sunlight
15
Q
Oxidation
A
Loses electrons
16
Q
Reduction
A
gains electrons
17
Q
Where do electrons come from in photosynthesis?
A
- H2O
18
Q
The flow of electrons in nonphotosynthetic cells and organisms
A
- obtain energy by oxidizing the energy-rich products of photosynthesis and passing the acquired electrons to oxygen forming water, carbon dioxide, and energy
- glucose and oxygen → 6H2O + 6CO2 + energy
19
Q
First Law of Thermodynamics
A
- Principle of the conservation of energy
- In any physical or chemical change, the total amount of energy in the universe remains constant, although the form of energy may change
20
Q
Second Law of Thermodynamics
A
- The tendency in nature is toward ever-greater disorder in the universe
- The total entropy of the universe is continuously increasing
21
Q
Entropy (S)
A
- the randomness or disorder of the components of a chemical system
- delta S = increase in randomness
- delta S = decrease in randomness
22
Q
Free-energy constant (G)
A
- delta G = H-TS (determined by the change in enthalpy)
- Enthalpy (H) = reflecting the number and kinds of bonds
- Entropy (S)
- Absolute temperature (T) - in Kelvin
23
Q
When is a reaction spontaneous?
A
- when delta G is negative
24
Q
Exergonic
A
- neg delta G
- release free energy
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Endergonic
* pos delta G
* Energy must be put in
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What types of reactions are often coupled in biology?
Exergonic and Endergonic
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Equilibrium constant (Keq)
aA + bB → cC + dD
Keq= ( [C]^c[D]^d ) / ( [A]^a[B]^b)
* large Keq : reaction contains mostly products
* small Keq : reaction contains mostly reactants
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Mass-Action Ratio, Q
Q = ratio of product concentrations to reactant concentrations at a given time
-can be calculated to determine how far the reaction is from equilibrium
29
Standard Free-Energy Change (delta Go)
* delta G= delta Go +RTln(Keq)
* delta G at equilibrium = 0
* Can also be calculated for overall reactions when we know the delta Go for each individual molecule
* delta Go = [(c)(delta GoC) + (d)(delta GoD)] - [(a)(delta GoA) + (b)(delta GoB)]
30
Enzymes
= biological catalyst
* greatly enhance reaction rates of specific chemical reactions without being consumed by the reaction
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Pathways
* sequences of consecutive reactions in which the products of one reaction becomes the reactant in the next
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Catabolism
* degradative, free-energy-yielding reactions
→ drives ATP synthesis
→ produces the reduced electron carriers NADPH
→ exergonic
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Anabolism
* synthetic pathways that require the input of energy
* endergonic
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Metabolism
* Overall network of enzyme-catalyzed pathways, both catabolic and anabolic
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Unity of life
* pathways of enzyme-catalyzed reactions that act on the main constituents of cells (proteins, fats, sugars, and nucleic acids) are nearly identical in all living organisms
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Feedback Inhibition
* keeps the production and utilization of each metabolic intermediate in balance
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Systems Biology
* tasked with understanding complex interactions among intermediates and pathways in quantitative terms
38
Lipids in water
* lipids are amphipathic (polar head and nonpolar tails)
* Can have one to three tails
* one: fatty acid
* two: membrane lipids
* three: storage lipids
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Types of lipids
* Storage lipids
* Fats
* Oils
* Structural Lipids
* Phospholipids
* Sterols
* LIpids as signals, cofactors, and pigments
* Enzyme cofactors
* Electron carriers
* Light absorbing pigments
* Hydrophobic anchors for proteins
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Storage Lipids
* Fats and oils are universally used as stored forms of energy in living organisms
* Derived from fatty acids
* Triacylglycerols (glycerol + 3 fatty acids)
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Fatty Acids
* Carboxylic Acid bound to long chains of hydrocarbons (4 to 36 carbons long)
* Have low oxidative states and are highly exergonic when burned
* Saturated: unbranched and fully saturated
* Unsaturated: chains contain double bonds (Cis-unsat are naturally occurring and Trans-unsat are synthetic/man-made)
* The most commonly occurring fatty acids have even numbers of carbon atoms in an unbranched chain of 12 to 24 carbons
*
42
Nomenclature of Fatty Acids
* The position of any double bonds are specified relative to the carboxyl carbon by superscript numbers following a delta (Δ)
* When numbering the double bonds from the methyl end of the fatty acids, the location of the double bonds is signified with an omega (ω) instead of a delta (these are the omega fatty acids)
* Each FA has three names: Carbon skeleton (12:0), Systematic (n-Dodecanoic acid), and Common (Lauric acid)
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Lauric Acid
12:0
n-Dodecanoic acid
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Myristic Acid
14:0
n-tetradecanoic acid
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Palmitric Acid
16:0
n-Hexadecanoic Acid
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Stearic Acid
18:0
n-octadecanoic acid
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Arachidic Acid
20:0
n-eicosanoic acid
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Lignoceric Acid
24:0
n-tetracosanoic acid
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Palmitoleic Acid
16:1 (Δ9)
cis-9-Hexadecenoic Acid
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Oleic Acid
18:1 (Δ9)
cis-9-octadecenoic acid
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Linoleic Acid
18:2 (Δ9,12)
cis-cis-9,12-Octadecadienoic acid
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a-Linolenic acid
18:3 (Δ9,12,15)
cis-cis-cis-9,12,15-Octadecatrienoic acid
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Arachidonic Acid
20:4(Δ5,8,11,14)
cis-cis-cis-cis-5,8,11,14-Eicosatetraenoic Acid
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Eicosapentaenoic Acid (EPA)
20:5(Δ5,8,11,14,17)
cis-cis-cis-cis-cis-5,8,11,14,17-Eicosapentaenoic acid
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Docosahexaenoic Acid (DHA)
22:6(Δ4,7,10,13,16,19)
cis-cis-cis-cis-cis-cis-4,7,10,13,16,19-Docosahexaenoic acid
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Polyunsaturated Fatty Acids (PUFAs)
* special importance in human nutrition
* The human body requires omega-3 fatty acids but does not have the enzymatic capacity to synthesize them
* Must obtain omega-3 fatty acids from the diet (essential fatty acids)
* Double bonds closer to the methyl end (over the carboxyl end)
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Water solubility of Fatty Acids
* dependent upon the length and degree of unsaturation
* Nonpolar hydrocarbon chains account for the poor solubility of fatty acids in water
* The longer the FA chain and the fewer the double bonds, the lower the water solubility
* Carboxylic acid head group is slightly polar, which allows short, saturated hydrocarbons chains to be semi-soluble in water
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Melting Points of Fatty Acids
* Strongly influenced by length and degree of unsaturation
* At room temp
* Saturated fats: waxy consistency
* cis-unsaturated fats: oily liquids
* Difference in melting points is due to different degrees of packing of the fatty acid molecules and the intermolecular forces that result
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Melting Points of Fatty Acids:
Fully Saturated Compounds
* free rotations around each carbon-carbon bond giving the hydrocarbon great flexibility
* most stable form is the fully extended form, which minimizes the steric hindrance of neighboring atoms
* The saturated molecules pack tightly together in a nearly crystalline array
* Have van der Waal interaction between molecules
60
Melting Points of Fatty Acids:
Unsaturated Compounds
* cis-double bonds force a “kink” in the chain
* the more “kinks”, the harder it is to pack tightly
* Neighboring FA are thereby unable to interact as readily and are therefore weaker
* Causes lower melting points
* Less thermal energy is needed to disorder arrays of unsaturated fatty acids
61
Triacylglycerols (TAGs)
* 1 glycerol + 3 fatty acids bound through ester linkages
* Nonpolar/Hydrophobic
* Insoluble in water
* Lower density than water (float on top of water)
* Provide stored energy and insulation
* Form oily droplets that serve as deposits for metabolic fuel when in the cytosol (polar environment)
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Adipocytes
* Fat cells
* Store large amounts of triacylglycerols droplets that fill the entire cell
* only found in vertebrates
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Energy storage in Plants
* energy is primarily stored as starches
* TAGs are stored in the seed
* Almond
* Coconuts
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Lipases
* Enzymes that catalyze the hydrolysis of stored TAGs releasing FAs for export to sites where they are required for fuel
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Advantages of TAGs as fuel source over saccharides
1. The C atoms of FAs are more reduced than those of sugars (reduction required for Kreb Cycle)
2. The oxidation of TAGs yields more than twice as much as much energy as the oxidation of saccharides
3. Because TAGs are hydrophobic and therefore unhydrated, the organism that carries fat as fuel does not have to carry the extra weight of water, which is associated with stored polysaccharides
* Saccharides are short term energy source
* TAGs are long term energy source
*
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Naming Simple TAGS
* Simple TAGs: TAGs containing the same kind of FA in all three positions
* Ex:
* Tripalmitin → 16:0
* Tristearin → 18:0
* Triolein → 18:1(Δ9)
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Fats in Nutrition: Types
* Natural Fats
* Mixtures of simple and mixed triacyglycerols
* Vary in chain length
* Vary in degree of saturation
* Vegetable Oils
* Corn oil, olive oil
* Composted of unsaturated fatty acids
* Melting temperature is below room temperature and is therefore liquid at room temp
* Beef Fats
* White, greasy, solid
* Saturated fats
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Fats in Nutrition
* When lipid-rich foods are exposed to oxygen too long, they spoil and become rancid
* Caused by the oxidative cleavage of double bonds producing aldehydes and carboxylic acids
* To increase the shelf life of unsaturated oils, they are subjected to partial hydrogenation to convert cis-double bonds to single bonds
* Hydrogenation increases the melting point, making the hydrogenated FAs solid at room temp
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Hydrogenation Negative Effects
* Some of the cis-double bonds spontaneously convert into trans double bonds, forming trans FAs
* Trans-FAs lead to higher incidents of cacardiovascular disease
70
Trans Fatty Acids
Lipids
* increase LDL-C
* increase Triglyceride
* decrease HDL-C
* decrease LDL-C particle size
* increase Apo lipoprotein (a)
71
LDL and HDL communication between Liver and Cell
72
Waxes
* serve as energy stores and water repellents
* Biological waxes are esters of long-chain (C14 to C36) saturated and unsaturated FAs with long-chain alcohols (C16 to C30)
* Fatty Acid + Alcohol → wax
* Melting points of waxes are much higher than fatty acids and TAGs (60 to 100C)
* When a candle melts, the wax is being burned as the hydrocarbon energy source in the combustion reaction
73
Functions of Waxes
* Vertebrates secrete waxes to protect hair and skin to keep it pliable, lubricated, and waterproof (like ear wax)
* Birds secrete wax from their preen glands to keep feathers water-repellent
* Leaves of plants are coated with thick layers of wax which
* Prevents excessive evaporation of water
* Protects against parasites
* Beeswax
* wax is formed into scales by eight wax-producing glands in the abdominal segments of worker bees, which discard it in or at the hive
* The hive workers collect and use it to form cells for honey storage and larval and pupal protection within the beehive
74
Structural Lipids
* This central architectural feature of biological membranes is a double layer of lipids that acts as a barrier to the passage of polar molecules and ions
* Membranes are amphipathic
* one end of the molecule is hydrophobic while the other is hydrophilic
* the hydrophobic interaction of the lipids orient the membrane into a bilayer
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Glycerophospholipids
* General membrane lipid
* Hydrophobic regions are composed of two fatty acids joined to the first and second Cs of glycerol
* A highly polar or charged group is attached through a phosphodiester linkage to the third carbon
* The addition of phosphate converts glycerol into a chiral compound
* The polar alcohol bears a negative charge at a neutral pH
* Primarily found in animals
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Galactolipids and Sulfolipids
* contain two fatty acids esterified to glycerol
* Lack the characteristic phosphate group found in phospholipids
* Predominate in plant cells (located in chloroplast)
* Galactolipids:
* Make up 70 to 80% of the total membrane of plants
* most abundant lipid in the biosphere
* Have one or two galactose residues that are connected by a glycosidic linkage to C-3
* Sulfolipids
* galactolipids with a sulfate group off the saccharide
* adds negative charge on the galactolipid head
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Archaeal Tetraether Lipids
* Two very long alkyl chains are ether-linked to glycerol at both ends
* Live in extreme conditions
* high temp, hot water, low pH, high ionic strength
* Typically have long chain (32 C) branched hydrocarbons and twice the length of phospholipids and sphingolipids
* Linkages through ether bongs which increase stability
* Each end has a glycerol polar head (and it can span the entire membrane)
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Sphingolipids
* A single fatty acid is joined to a fatty amine-sphingosine
* Do NOT contain glycerol (has sphingosine instead)
* Has three subclasses: Sphingomyelin(+ at pH=7), Glycosphingolipids(neutral at pH=7), and Gangliosides(negative at pH=7)
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Sterols
* compounds characterized by a rigid system of four fused hydrocarbon rings
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Sphingomyelin
* Positive charge at pH = 7
* Contain phosphocholine of phosphoethanolamine as a polar head group
* Classified with glycerophospholipids and looks like phosphatidylcholine
* Present in the plasma animal cells (vertebrates)
* Prominent in myelin
* membraneous sheath that surrounds and insulates the axon of some neurons
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Glycosphingolipids
* Neutral at pH = 7
* Occur largely in the outer face of the plasma membrane
* Have head groups with one or more sugars connected directly to the -OH on Carbon-1 of the ceramide moiety
* Cerebrosides: contain one sugar
* Globosides: contain two or more sugars
* Does NOT contain a phosphate
* The blood type antigens on the surface of RBCs
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Gangliosides
* Negative charge at pH = 7
* Most complex sphingolipids
* Have oligosaccharides as polar head groups
* Contain a Neu5Ac (Sialic acid) that gives a negative charge at a pH = 7
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Sialic Acid
* Binds selectin in humans and other organisms
* Overexpression of sialic acid creates a negative charge on cell membranes
* Bacterial cells use sialic acid to help evade the innate immune response of the host
* Viruses use Sialic acid to bind and transfect cells
* In humans, the brain has the highest sialic acid concentration, where they play an important role in neural transmission and ganglioside structure in synaptogenesis
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Sphingolipids on Cell Surfaces:
Biological Recognition
* at least 60 different sphingolipids have been identified in cell membranes of humans
* Prominent in the plasma membrane of neurons
* Recognition sites on the cell surface
* Carbohydrate moieties of certain sphingolipids define the human blood groups
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Phospholipases
* Enzymes that hydrolyze bonds
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Phospholipase A
* removes one of the two fatty acid chains
* produces a lysophospholipase that removes the remaining fatty acid
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Phospholipase C/D
splints one of the phosphodiester bonds in the head group
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Phospholipids and Sphingolipids are degraded in …
* Lysosomes
* Most cells continually degrade and replace their membrane lipids
* Each of the hydrolysable bonds in a glycerophospholipid has a specific hydrolytic enzyme in the lysosome
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Sterols
* Structural lipids present in the membranes of most eukaryotic cells
* Characteristic Structures:
* Steroid nucleus
* Four fused rings
* 3 6C rings and 1 5C ring
* Steroid nucleus is almost planar and is relatively rigid (fused rings do not allow rotation about the C-C bonds)
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Cholesterol
* Major sterol in animal tissues
* Amphipathic
* Polar head group and nonpolar hydrocarbon body (steroid nucleus and hydrocarbon side chain)
* Side chain is 16C fatty acid
* Serves as a precursor for a variety of products with specific biological activities
* Fat soluble vitamins
* Quinones
* Dolichols
* Bile Acid
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Stigmasterol
Found in plants
92
Ergosterol
Found in fungi
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Bile Acid
* Polar derivative of cholesterol that acts as detergents in the intestines
* Emulsifies dietary fats to make them more readily accessible to digestive lipases
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Steroids
* Oxidize derivatives of sterols
* Have the sterol nucleus
* lack the alkyl chains attached to cholesterol
* Travel through the blood stream to the target tissue
* Function via the endocrine system
* Enter cells to the target tissue and bind to the receptors that translocate to the nucleus and initiate transcription by binding to the DNA in the nucleus
* Have very high affinity and specificity for the receptor
* Require a very low concentration to function
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Steps of Steroid Hormone Cell Signaling
1. lipid-soluble hormone diffuses through plasma membrane
2. hormone binds with receptor in cytoplasm, forming a receptor-hormone complex
3. Receptor-hormone complex enters the nucleus adn triggers gene transcription
4. Transcribed mRNA is translated into proteins that alter cell activity
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Three Main Classes of Steroids
1. Sex hormones (testosterone (males) and estradiol (females))
2. Adrenal Cortex Hormones (Cortisol and Aldosterone)
3. Steroid Drugs (Prednisone and Cortisone are examples as anti-inflammatory medications)
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Estradiol
98
Progesterone
99
Testosterone
100
Cortisol
101
Aldosterone
102
Cortisone
103
Prednisone
104
What is vitamin D derived from?
Sterols
105
How much of dry mass of cell is made up of membrane lipids?
5 to 10%
106
Storage lipids make up what percent of the dry mass of adipocytes?
80%
107
Passive functions of lipids
* storage and membrane lipids
108
Active functions of lipids
* Roles in metabolic traffic as metabolites and messengers
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Lipids as Pigment
* lipids in a system of conjugated double bonds serve as pigment molecules that absorb visible light
* produce natural colorations and capture light through pigments for vision
110
Lipids as cofactors
* enzyme cofactors in electron-transfer reaction in the chloroplasts and mitochondria
111
IP3
* water soluble
* triggers the release of Ca2+ from the ER
112
DAG
* Remains associated with the plasma membrane
* a combo of DAG and elevated cytosolic calcium ions activate the enzyme protein kinase C (PKC)
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Membrane Sphingolipids
* Can serve as a source of intracellular messengers
* Ex: Ceramide and Sphingomyelin
* potent regulators of protein kinases
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Ceramide Regulates…
* cell division
* cell differentiation
* cell migration
* apoptosis
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Protein Kinase C (PKC)
* Phosphorylates downstream proteins
* activates downstream signaling
* Promotes activity of:
* SM contraction
* sperm ejaculation
* gastric juice secretion
* csf secretion
* H+ secretion
* Na+ reabsorption
* broncoconstriction
116
Principles of Membrane Dynamics
1. Bio membrane is a lipid bilayer with various proteins embedded in or associated with the bilayer
2. All internal membranes of the cell are part of an interconnected, functionally specialized, and dynamic endomembrane system
3. Cell membrane has transporters to allow for the movement of specific solutes to their desired location
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Functions of Biological Membranes
* Permit shape changes that accompany cell growth and movement
* Permit exocytosis, endocytosis, and cell division
* Serve as molecular gatekeepers
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Transporters
Move specific organic solutes and inorganic ions across the membrane
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Receptors
Sense extracellular signals and trigger molecular changes in the cell
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Ion Channels
Mediate electrical signaling between cells
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Adhesion Molecules
Hold neighboring cells together
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Membrane Trafficking
* Process by which membrane lipids and proteins that are synthesized in the ER move to their destination organelles or to the plasma membrane
* Lipids and proteins undergo covalent modifications in the Golgi apparatus
* dictates the eventual location of the mature protein
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Lipid Transfer Proteins (LTPs)
* soluble proteins that contain a hydrophobic lipid-binding pocket to carry a lipid from one membrane to another
* can be bispecific
124
Posttranslational Modification of Membrane Proteins
* glycosylation
* attachment of oligosaccharides to proteins
* Typically on the outer face of the plasma membrane
* attachment of 1+ lipids
* serve as hydrophobic anchors or targeting tags
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Peripheral Membrane Proteins
* Associate with the membrane through
* electrostatic interactions
* hydrogen bonding with the hydrophilic domains of integral proteins
* Associate with polar head groups of membrane lipids
* Can be released by relatively mild treatments that interfere with electrostatic interactions or breaking hydrogen bonds (ex: change in pH)
126
Amphitrophic Proteins
* Found in both the cytosol and in association with membranes
* Affinity for membranes result in some cases from the protein's noncovalent interactions with a membrane protein or lipid
* From the presence of one or more lipids covalently attached to the amphitrophic protein
* Generally the reversible association of amphitrophic proteins with the membrane is regulated
* Phosphorylation or ligand binding can cause a conformational change, thereby exposing new binding sites that were previously inaccessible
127
Integral Membrane Proteins
* Very firmly associated with the lipid bilayer
* Are removable ONLY by agents that interfere with hydrophobic interactions
* Detergents
* Organic solvents
* Denaturants
128
Transmembrane Proteins
* Proteins that span the hydrophilic outsides of the lipid bilayer and the hydrophobic inside of the lipid bilayer
* Polar amino acids outside the membrane
* Nonpolar acids inside the membrane
129
Monotopic Proteins
* Have small hydrophobic domains that interact with only a single leaflet of the membrane
130
Bitopic Proteins
* Span the bilayer once, extending on either surface
* Have a single hydrophobic sequence somewhere in the molecule
131
Polytopic Proteins
* Cross the membrane several times
* have multiple hydrophobic sequences of ~20 residues that each cross the membrane when in the alpha helical conformation
132
Hydropathy Index
* The relative polarity of each amino acid determined experimentally by measuring the free-energy change accompanying movement of that amino acid from a hydrophobic solvent into water
133
Beta Barrel
* Structural motif in which 20= transmembrane segments form beta sheets that line a cylinder (stabilized by intrachain hydrogen bonds)
134
Porins
* proteins that allow certain polar solutes to cross the outer membrane of gram-negative bacteria
* have beta barrels lining the transmembrane passage
135
β Strands of Membrane Proteins:
in β conformation
* 7 to 9 residues are needed to span a membrane
* alternating side chains project above and below the sheet
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β Strans of Membrane Proteins:
in β strands of membrane proteins
* every second residue in the membrane-spanning segment is hydrophobic and interacts with the lipid bilayer
* aromatic side chains are commonly found at the lipid-protein interface
137
Tyr and Trp side chains
serve as membrane interface anchors
138
Positive-inside rule
* positively charged Lys and Arg residues in the extramembrane loop of membrane proteins occur more commonly on the cytoplasmic face
139
GPI-anchored protein
* exclusively on the outer face and are clustered in certain regions
140
Antiport
* Orrcurs when substrates move in opposite directions
141
Symport
* Two substrates are moved simultaneously in the same direction
142
Uniport
* Carries only one substrate
143
Cotransports
* simultaneously carry two solutes across the membrane (antiport and symport)
