BioChem Flashcards
(310 cards)
1
Q
What is the sterochemistry of all chiral carbons in Eukaryotes?
A
L-amino acid (S configuration)
2
Q
What is the isoelectric point?
A
The pH when the molecule is electrically neurtral
3
Q
How does proline behave in secondary structres?
A
It si rigid so it introduced kinks into the alpha-helices or creates turns in the Beta-pleated sheets
4
Q
What is the difference between heat and solutes denaturing proteins?
A
heat: disrupts hydrophobic bonds
solutes: disrupt secondary, tertiary, and quaternary structures
5
Q
Is polypeptide formation a condensation or hydration rxn?
A
condensation
6
Q
What is a tightly bound cofactor or coenzyme that is necessary for enzyme function called?
A
prosthetic groups
7
Q
What are the two differences between the Michaelis-Menten plot and the Lineweaver-Burk plot?
A
- Michaelis-Menten plot is v vs. [S] and has a hyperbolic shaped curve
- Lineweaver-Burk plot is (1/v) vs. (1/[S]), which is a straight line
8
Q
What does a high kcat and a small Km mean?
A
high catalytic efficiency
9
Q
What is the ideal temp for most enzymes in the body?
A
37 degrees celcius=98.6 degrees F” 310 K
10
Q
What is the ideal pH for…
- Most enzymes
- Gastric enzymes
- Pancreatic enzymes
A
- 7.4
- 2
- 8.5
11
Q
Where can mixed inhibitors bind and how does the difference in binding change the Km of enzyme? How does Vmax change?
A
Binds to allosteric site
- Bind to enzyme–> increase Km value
- Bind to enzyme-substrate complex –> lower Km
Vmax for both decreases
12
Q
Where do uncompetitive inhibitors bind and how do they influence Km and Vmax?
A
They bind to an allosteric site. Bind to enzyme-substrate complex and lock the substrate in enzyme.
Km and Vmax both decrease
13
Q
What are two possible methods for irreversible inhibition?
A
- active site is made unavailable
- enzyme is permanently altered
14
Q
What are the two domains of zymogens and why do they have these domains?
A
They have a catalytic (active) and a regulatory domain
Zymogens are secreted in inactive form because dangerous and regulatory domain can be removed or alterd to expose active site
15
Q
What are the 5 structural proteins?
A
- Collagen: provide strength/flexibility, makes up extracellar matrix of connective tissue
- Elastin: stretch and recoil, component of extracelluar matrix of connective tissue
- Keratin: intermediate filament proteins in epithelial cells/mechanical integrity of cell/regulatory proteins
- Actin: microfilaments and thin filaments in myofibrils. Is polar to allow motor proteins to travel undirectionally/most abundant protein in eukaryotes
- Tubulin: makes up microtubules, have polarity (negative end is near nucleus and positive end is in the periphery of cell)
16
Q
What are three motor protons and their primary functions?
A
- Myosin: interact with actin/cellular transport/involved in thick filaments in myofibril
2/3. Kinesins and dyneins: vesicle transport
- Kinesin: align chromosoms during metaphase
- Dyneins: involved in sliding movement of cilia and flagella
-
17
Q
What are two difference between cytoskeletal and motor proteins?
A
- Cytoskeletal tend to be fibrous with repeating domains (motifs)
- Motor proteins have ATPase activity and binding heads
18
Q
What are the three major families of cell adhesion molecules?
A
- Cadherins: glycoproteins that mediate Ca-dependent cell adhesion
- Integrins: two membrane spanning proteins\play role in cell signaling (cell-cell adhesion)
- Selectins: bind to carbohydrates that project from cell surfaces/ play role in host defense
19
Q
Define opsonization?
A
antibody marks pathogen for destruction
20
Q
Define agglutinating?
A
clumbing together the antigen and antibody into a large insoluble protein complex that can be phagocytized
21
Q
What two types of bonds hold the heavy and light chains of antibodies together?
A
disulfide bonds and noncovalent bonds
22
Q
What are the two domains of an antibody? Function for each?
A
V-domain: bind to antigen
C-domain: activate complememt/phagocytosis
23
Q
What are four steps in GPCR pathway?
A
- Ligand binding enages the G protein
- GDP–> GTP, alpha unit dissociates from beta and gamma
- activated alpha subunit alters the activity of adenylate cyclase or phospholipase C
- GTP is dephosphorylated to GDP, alpha subunit rebinds to gamma and beta
24
Q
What are the three main types of G proteins?
A
- Gs=stimulates adenylate cyclase, increases cAMP in cell
- Gi=inhibits adenylate cyclase, decreases cAMP in cell
- Gq=activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2 –> cleaved inton DAG and IP3
25
What are two difference between a Native PAGE and SDS-PAGE?
1. Native maintains shape of protein so complete protein can be recoved after analysis and more accurately determines globular size of protein
2. SDS- denatures protein and masks charge to can compare size of protein
26
What is one important concept for Size exclusion chromatography?
larger molecules elute first bc small molecules are trapped in small pores of beads
27
What are two drawbacks to affinity chromatography?
1. protein of interest may not elute because affinity is too high
2. protein may be permanently bound to the free receptor in the elutent
28
What is the primary method of determining protein structure?
X-ray crystallography but NMR can be used as well
29
What are two ways amino acids that compose a protein can be determined?
1. amino acids that compose a protein can be determined by protein hydrolyisis and then chromatographic analysis
2. Use edman degradation: selectively and sequentially removes the N-terminal amino acids and then anaylze via mass spectroscopy
30
What are four ways protein concentration can be detemrined? Which one is most common?
1. UV spectroscopy: bc proteins can have aromatic side chains so do not need any treatment, but sensitive to contaminants
2. Colorimetric changes --\> BCA assay, Lowry reagent assay, _Bradford assay_
31
What die does Bradford Assay use and how does it work?
1. Coomassie Brilliant Blue dye (green-brown)
2. Gives up protons when bind to amino acids and will turn blue
3. more protein, stronger blue color
32
Equation for vmax?
vmax=[E]xkcat
33
What might be two plausible explainations if you detect a low activity with a high concentration of protein when using affinityn chromatography?
1. protein is inactive
2. Protein elutes off of an affinity collumn by binding free ligand. The binding might not have be reversed for the active site to be occupied for the free ligand so stayed on column
34
Name?
D-fructose
35
How do you find the number of steroisomers?
2^n
n=the number of chiral carbons
36
What is the difference between a diastereomers and epimers?
Epimers are diastereomers but epimers differ in configuration at exactly one chiral center
37
How can monosaccharides for cyclic hemiacetals or hemiketals?
the hydroxyl serves as a nucleophile and the carbonly group is the electrophile
38
What is the difference between and alpha-anomer and a beta-anomer?
Alpha: has the -OH of the C-1 trans to the CH2OH (axial)
Beta: has the -OH group of the C-1 cis to the -CH2OH (equitorial)
39
What is Mutarotation?
Hemiacetal rings ossilate btw either alpha or beta anomer
the alpha-anomer is less favored bc the hydroxyl of anomeric carbon is axial
40
What are oxidized aldehydes called? Are they strong reducing or oxidizing agents?
Aldonic acids --\> strong reducing agents
41
What two reagents are used to detect reducing sugars?
1. Tollens' reagent: Tollen's reagent is reduced to produce a silver mirror in the presence of aldehydes
2. Benedict's reagent: form a red ppt. This test is specific for glucose
42
Which one of the three most important disaccharides is this?
Sucrose (glucose alpha 1, 2 fructose)
43
Which one of the three most important disaccharides is this?
Lactose (galactose Beta 1,4 glucose)
44
Which one of the three most important disaccharides is this?
Maltose (glucose alpha 1,4 glucose)
45
What are three characteristics of cellulose?
1. Beta D glucose linked by B 1,4 glycosidic bonds
2. H-bonds holding polymer chains together for support--\> very strong
3. humans do not have cellulase
46
What are four characteristics of starch?
1. alpha D glucose linked by alpha 1,4 glycosidic bonds
2. plants store starch as amylose
3. amylopectin is a starch but has branches bia alpha 1,6 glycosidic bonds
4. Broken down by alpha and beta amylase
47
What are three characteristics of glycogen?
1. Similar to starch but with more alpha 1,6 glycosidic bonds
2. more branching --\> decrease intermolecular bonding --\> more soluble in water so more glucose to be stored in body
3. Branching allows gylcogen phosphorylase to cleave at mutliple nonreducing ends and phosyphorylate them
48
What are three types of structural lipids?
1. Phospholipids
2. Glycerophospholipids
3. Spingolipids
49
What are three components of Phospholipids?
1. a phosphate
2. alcohol which is joined to a 3)hydrophobic fatty acid by a phophodiester linkage
50
What are three components of Glycerophospholipids? How are they bonded together?
1. phospholipid that contains a glycerol back bone bonded by ester linages to two fatty acids and by a phosphodiester bond to a polar head group
51
What are the three components of sphingolipids?
1. sphingosine or sphingoid backbone instead of a glycerol one
2. long chain, non-polar fatty acid tails
3. polar head group
52
What are two traits of waxes?
1. esters of long chain fatty acids with long chain alcohols
2. help animals and plants prevent dehydration
53
What are four signaling lipids?
1. Terpenes/Terpenoids
2. Steroids
3. Prostaglandins
4. Fat-soluble vitamins
54
What are two traits of cholesterol?
1. amphipathic
2. a low temps keeps membrane from freezing and at high temps keeps memebrane intact
55
What is the defining structure of steroids?
three cyclohexane rings and one cyclopentane ring
56
What are 3 traits of prostaglandins?
1. paracrine and autocrine signaling molecules (not endocrine)--\> they affect regions close to where they are produced rather than affecting entire body
2. regulate synthesis of cAMP
3. affect smooth muscle contraction, body temp, fever, pain, sleepwake cycle
57
What are three main traits of vitamin A?
1. important for vision, growth, immune function
2. Vit A/carotene is metabolized to retinal
3. Retinol is the storage form of vit A and is oxidized to retinoic acid which regulate gene expression in epithelial development
58
What are three main traits of vitamin D?
1. can be consumed or formed in UV light driven rxn in skin
2. Vit D/cholecalciferol: in liver and kidney is converted into calcitriol which increases Ca and phosphate uptake in intestines to promote bone production
3. lack of vit D can result in **rickets**, which is curved long bones and impeded growth in children
59
What are three traits of vitamin E?
1. also known as tocopherols
2. act has biological antioxidants
3. aromatic rings destroy free radicles, preventing oxidative damage (ex:cancer)
60
What are three traits of vitamin K?
1. called phylloquinone and menaquinones
2. allows for postranslational modification of prothrombin (clotting factor in blood)
2. required to introduce Ca-binding sites on calcium dependent proteins
61
What are two lipids involved in energy storage?
1. Triacylglycerols
2. Free Fatty Acids
62
What are three traits of triacyglycerols?
1. three fatty acids bonded by ester linkages to glycerol
2. adipocytes store triaglycerides
3. the carbon atoms in lipids are more reduced than carbohydrates so they release 2x as much energy
63
What are two traits of free fatty acids?
1) esterfied fatty acids with a free carboxylate group
2) circulate in the blood by noncovalently bonding to albumin
64
What is saponification?
ester hydrolysis of trycylglycerols using a strong base (lye--\> NaOH/KOH)--\> leaving glycerol and fatty acid salt (soap)
65
What is the function of soap and how does it work?
It is a surfactant and lowers the surface tension of the liquid surface (detergent and emulsiferi)
aggregates of soap with hydrophobic tails turn inward with hydrophilic tails outward (micelles) to dissolve lipid-soluble molecules, watch away water and the formation of a colloid, combo of two phases
66
What two susbtances in body allow the formation of micelees?
fatty acids and bile salts secreted from gallbladder
67
What are topoismerases? What is one example?
They are involved in DNA replication and mRNA synthesis
ex: negative supercoils into the DNA molecules. facilitate DNA replication by keeping the strands separated and untangled
68
What is the main function of flippases?
Responsible for the movement of phospholipids between the layers of the plasma membrane because it is otherwise energetically unfavorable
69
What are the two structures phospholipids spontaneously form into?
micelles (monolayer vessicles) and liposomes (bilayer vessicles)
70
What are desmosomes and Hemidesmosomes?
1. Desmosomes: bind adjacent cells by anchoring to the cytoskeleton and are formed by interactions btw transmembrane proteins associated with intermediate filaments inside adjacent cells
2. Hemisomes: main function is to attach epithelial cells to underlying structures
71
What is osmotic pressure? How does it relate to the direction of water flow?
1. pressure applied to a pure solvent to prevent osmosis
2. water will move towards area with highest osmotic pressure
72
What is pinocytosis?
endocytosis of fluid and disolved substances
73
What 4 lipids make up the plasma membrane?
1. Triagylcerides and fatty acids--\> precursor for phospholipids
2. Glycerophospholipids: replace one fatty acid with phosphate group
3. cholesterol
4. wax
74
What is the difference between the inner mitochondrial membrane and other biological membranes? What is the pH gradient btw cytoplasm and intermembrane space?
1. Innermembrane space lacks cholesterol
2. no pH gradient bc the outer mitochondrial membrane has a high permeability for molecules
75
What is the Nernst Equation?
E=(61.5/z)log ([ion]out/[ion]in)
z=charge of ion
76
What are 4 difference/similarities between GLUT 2 and 4?
1. GLUT 2 is in hepatocytes and pancreatic cells and GLUT4 is in adipose and muscle cells
2. The Km for GLUT2 is higher (has first order kinetics) than for GLUT4 (zero order kinetics)
3. GLUT4 is responsive to insulin bit GLUT2 is not (but it serves as a glucose sensor to cause release of insulin in pacreatic B-cells)
4. GLUT4 is saturated when blood glucose levels are just a bit higher than normal (still only permit a constant flow of glucose so increase transport but increase number of transporters). GLUT2 cannot be saturated under normal conditions
77
What are the 2 difference between Hexokinase and Glucokinases?
1. Hexokinase found in most tissue and glucokinases present in hepacytes and pacreatic B-iselt cells
2. Hexokinase has low Km, glucokinase has high Km
78
What is the main function of lactate dehydrogenase?
1. reduce pyruvate to lactate and make more NAD+, which replenishes the oxidized coenzyme for glyceraldehyde 3 phosphate
79
What are the three steps for fructose metabolism?
1. liver phosphorylates fructose using furctokinase to trap inside cells.
2. Fructose 1-phosphate is cleaved into glyceraldehyde(can be phosphorylated into G3P and DHAP by aldolase
3. go to glycolysis, glycogenesis, glucoeogenesis
80
What are these called?
1. thiamine
2. pyrophosphate
3. lipoic acid
4. CoA
5. FAD
6. NAD+
cofactors
81
What are 4 traits of the Pyruvate dehydrogenase reaction?
1. Pyruvate enter mitochondira and converted to acetyl-CoA for entry into the citric acid cycle
2. pyruvate hydrolysis is inhibited by acetly-CoA and pyruvate is converted into oxaloacetate by pyruvate carboylase to enter gluconeogensis
3. pyruvate dehydrogenase in liver is activated by insulin
4. reactants are pyruvate, NAD+, CoA and products are NADH, CO2, and acetyl CoA
82
What is glycogenesis?
forming glycogen
83
What are 3 facts about glycogen synthase?
1. rate-limiting enzyme of glycogen synthesis and forms the alpha-1,4 glycosidic bond found in linear glucose
2. stimulated by G6P and insulin
3. inhibited by epinephrine and glucagon
84
What are 2 facts about branching enzyme?
1. introduces alpha 1-6 linked branches into the granile as it grows
2. role in glycogensis
85
What are 3 facts about glycogenolysis?
1. process of breaking down glycogen using glycogen phosphorylase
2. glycogen phosphorylase is activated by glucagon in the liver and by AMP/Epinephrin in the skeletal muscles
3. cannot break down alpha 1-6 bond so stops near the outmost branch points
86
What are 3 facts about debranching enzymes?
1. two enzyme complex that deconstructs the branches in glycogen that have been exposed to glycogen phosphorylase
2. breaks alpha 1,4 bonds adjacent to the branch points and moves the small oligo-glucose chains that is releases to exposed end of other chain, form new alpha 1,4 bond to a longer link.
3. role in glycogenolysis
87
What is the difference btw glucogenic and ketogenic amino acids?
Glucogenic aa (all except leucine and lysine) can be converted into intermediates and feed into gluconeogenesis
ketogenic aa can be converted into ketone bodies which can be used as alternative fuel
88
Under what two conditions should the body carry out gluconeogensis?
1. when a person is fasting for more than 12 hours
2. hepatic and renal cells must have enough energy to drive the process of glucose creation, which require succificent fat stores and B oxidation
mostly in the liver
89
How does acetyl-CoA shift the metabolism of pyruvate?
1. Acetly-CoA inhibits pyruvate dehyrogenase complex while activating pyruvate carboxylase. Shift from burning pyruvate in the citric acids cycle to creating new glucose molecules for the rest of the body. The acetle CoA from this regulations comes from B-oxidation (fatty acid oxidation)and not glycolysis (bc would just burn the glucose that is being generated)
90
What are the two main functions of the pentose phosphate pathway?
1. producetion of NADPH
2. source ofr ribose-5-phosphate for nucleotide synthesis
91
What is glutathione?
reducing agent that can help reverse radical formation before damage is done
92
What is the overall reaction of the pyruvate dehydrogenase complex?
Pyruvate +CoA-SH +NAD+--\> Acetyl-CoA +CO2+NADH+H+
93
What is the main purpose of the citric acid cycle?
complete oxidation of carbons in intermediates to CO2 so can have reductions coupled with CO2 formation to form NADH and FADH2 for ETC
94
What are the three main sites of regulation for citric acid cycle? Which one is the rate limiting enzyme?
1. Citrate synthase: Inhibitors are ATP, NADH, succinyl-CoA and citrate/ no activators
2. Isocitrate dehydrogenase (rate limiting enzyme): Inhibitors are ATP and NADH, activators are ADP and NAD+
3. Alpha-ketoglutarase complex: Inhibitors are ATP, NADH, succinyl-CoA/ activiators are ADP, Ca2+
95
What are the the 3 products yeilds from citric acid cycle? How many ATPs do they produce?
1. 3 NADH--\> 10 ATP
2. 1FADH2--\> 1.5 ATP
3. 1 GTP--\> 1ATP
(mutliple by two for one glucose molecule)
96
What are the 4 different complexes in the ETC?
1. Complex I: transfer of electrons from NADH to CoQ. First site of proton pump (4 protons)
2. Complex II: FADH2 reduced by iron-sulfate protein in CoQ. No hydrogen pumping here
3. Complex III: transfers of electrons from CoQ to cytochrome c. proton pump here (4 protons)
4. Complex IV: transfer of electron from cytochrome c to oxygen. proton pump here (two protons)
97
What are the two important subunits of CoQ out of the 20 subunits?
1. proteins that has a iron-sulfer cluster
2. Flavoprotein that oxidizes NADH. Flavoprotein has a coenzyme called FMN.
98
What are the 2 shuttle mechanisms that cause a range of 30-32 ATPs to be produced?
Shuttle mechanism: transfers high energy electrons of NADH to a carrier than can cross the inner mitochondrial membrane because NADH cannot cross inner mitchondrial membrane
Gylcerol 3-phosphate Shuttle: allow NADH produces in cytosol to be used in ETC. Created RADH2 to contributed to complex II
Malate-asparate shuttle: cystolic oxalacetate, cannot pass through inner mitochondrial membrane and is reduced into malate, which can. Once malate crosses into matrix, mitochondrial malate dehydrogenase reverse the reaction to form mitochondrial NADH and pass electrons to complex I.
99
What is the difference between chemiosmotic and conformational coupling?
1. Chemiosmotic: H+ flow into F0 protions of ATP synthase and chemical energy of gradient is harnessed to convert ADP into ATP in F1 portion
2. conformational: proton gradients and ATP synthesis is indirect. ATP releases by synthase as a result of conformational changes caused by gradient (turbine)
100
How is cystein different from other amino acids?
It is in the R configuration while the rest of amino acids are in the S
101
How are peptide bonds formed and cleaved?
Formed by condensation reactions and cleaved by strong acids and based
102
Why is the C-N bond in an amide planar?
it is a partial double bond character due to resonance
103
What are the two ways amino acids are synthesized?
1. Strecker synthesis
2. Gabriel Synthesis
104
What are two characteristics that make inorganic phosphates have so much energy?
1. contain negative charge, so when bonded to other phosphate groups, this creates repulsion with adjacent phosphate groups
2. can be resonance stabilized
105
What is an organic phosphate?
are carbon containing compounds that also have phosphate groups (ATP,GTP, DNA)
106
What are two traits of phosphoric acids?
1. three acidic hydrogens with unique pKa
2. wide variety of pKa act as a moderate buffer over a large range of pH values. can pick up or donate H+
107
What 4 substances contributes to chemical digestion of lipids in small intestine?
1. bile
2. pacreatice lipase
3. colipase
4. cholesterol esterase
108
What is one difference between how large and small fatty acid chains are absorbed?
1. Small: absorbed across intesting into blood
2. long: are absorbed as micelles and assembled into chylomicrons for releases in lymphatic system
109
What are 3 traits of hormone-sensitive lipase (HSL)?
1. insulin activates it/ also epinephrine and cortisol can activate it
2. hydrolyzes triacylgerols, yeilding fatty acids and glycerol --\> releases glycerols can go to liver for glycolysis or glucogenesis
3. effective within adipose tissue
110
What are the 5 different types of lipoproteins? Function?
1. Chylomicrons: transport triacylglycerols, cholesterol, and cholesteryl esters from intestine to tissue
2. VLDL: transports triaglycerols and fatty acids from liver to tissue/ produced and assembled in liver cells
3. IDL: picks up cholesteryl esters from HDL to become LDL
4. LDL: delivers cholesterol into cells
5. HDL: picks up cholesterol accumulating in blood vessesl/delivers cholesterol to liver and steroidogenic tissues/transfers apoliproteins to other lipoproteins. synthesized in liver and intestines
111
What are apoproteins?
they are receptor molecules and are involved in signaling/control interactions between lipoproteins
112
What is the primary method of transporting free fatty acids in blood?
free fatty acids remain in blood, bonding to albumin and other carrier proteins. Much smaller amount will remain unbonded
113
Order the 5 lipoproteins from greated percentage to least?
HDL\>LDL\>IDL\>VLDL\>chylomicrons
114
where are lipoproteins primarly synthesized?
liver and intestine
115
Where does fatty acid synthesis take place?
cytosol, mostly in liver
116
How do fatty acids enter mitrochondria for beta oxidation?
Small and medium sized chains can freely diffuse. Long chains need carnitine acyltransferase I (rate-limiting enzyme of oxidation)
117
What what are three product generated by beta oxidation?
1. FAD--\> FADH2
2. (NAD+--\> NADH)
3. acetyl-CoA
118
what does acetyl-CoA stimulate in the liver?
glucogensis by activating pyruvate carboxylase
119
How does Beta oxidation of unsaturated fatty acids differ from that of saturated fatty acids?
additional isomerase and reducatasewhich provide the sterochemistry necessary for futher oxidation
120
What is ketogenesis? What is the main enzyme?
occurs in the mitochondria of liver cells when there is excess acetyl-CoA acculating during fasting
HMG-CoA synthase main enzyme
121
What is ketolysis?
aim to regain energy via oxidation of ketone bodies, which takes place in mitochondria. stimulated by low energy states in muscle and brain tissue
122
What is ketolysis of brain?
during prelonged fast, the brain gets 2/3 of its energy from ketone bodies are metabilized in acetyl-CoA.
123
Why are fatty acids used to create ketone bodies instead of creating glucose?
fatty acid degradation results in large amounts of acetyl-CoA, which cannot enter the gluconeogenic pathway to reproduce glucose. only odd numbered fatty acids can act as a source of carbon for gluconeogenesis
fatty acid synthesis is used to store energy
124
Where does proteolysis occurs and what enzymes are involveed?
Stomach: pepsin
small intestine: trypsin, chymotrypsin, carboxypeptidases A and B
125
How are proteins used for energy?
amino acids are released from proteins through transamination or deamination and carbon skeleton is used for energy
amino acids are fed into urea cycle in liver
126
What can glucogenic and ketogenic amino acids be converted into?
Glucogenic(all but luecine and lysine) can be converted into glucose through gluconeogensis
ketogenic (leucine and lysine, isoluecine, phenylalanine, threaonine, tryptophan, and tyrosine) can be converted into acetyl-CoA and ketone bodies
longest carbon change--\> most energy
127
What is the only fatty acid humans can synthesize?
palmitic acid, which is fully saturated and contained 16 carbons and synthesized from 8 molecules of acetyl-CoA
128
Where do the majority of triacylglcerols stores in adiposecytes come from?
liver
129
Why is ATP an ineffecient molecule for long term energy storage?
The higher energy bonds in ATP and the presence of a significant charge make it an inefficient molecule to pack into a small space. long term energy sotrage molecules are dense and stable, nonrepulsive bonds
130
What are three facts about flavoproteins? What are two examples?
1. derived from vitamin B2 or riboflavin
2. either in the form of FAD or FMN
3. primarly in mitochondira and chloroplasts as e carriers
131
What are three traits about the Postsprandial state (absorptive state)?
1. occurs shortly after eating
2. greater anabolism (synthesis of molecules) and fuel storage than catabolism (break down of molecules for energy)
3. increase in insulin to promote glycogen formation in muscle and liver and triacylglycerol synthesis in adipose tissue.
132
What five types of cells are insensitive or insulin
1. nervouse tissue
2. kidney tubules
3. intestinal mucosa
4. RBCs
5. beta-cells of the pancreas
133
What are three traits of the postabsorptuve (fasting) state?
1. counterregulatory hormones increase (glucagon, cortisol, epinephrin, norepinephrine, GH)
2. glycogenolysis increases
3. release of amino acids from skeletal muslces and fatty acids from adipose tissues are stimulated by decrease in insulin and increase in epinephrine
134
What are three traits of the prolonged fasting (Starvation) state?
1. levels of glucagon and epinephrine are elevated
2. liver glycogen storage is depleted
3. lipolysis occurs to make ketone bodies
135
Which tissue is least able to change its fuel source in periods of prolonged starvation?
cells that rely solely on anaerobic respiration are the least adaptable to different energy sources. RBCs are least flexible and rely on glucose
136
What is one fact about insulin?
1. increases rate of anabolic rxn such as (glycogen synthesis), increase amino acid uptake by muscle cells so increase protein synthesis, triacylglycerol synthesis
137
What are 7 facts about glucagon?
1. secretede by alpha cells in pancrease
2. primary target are hepatocytes
3. increases glycogenolysis/inactives glycogen synthase
4. increase in gluconeogenesis
5. increase liver ketogensis and decreases lipogensis
6. increase lipolysis in liver and actives hormone sensitive lipase in liver
7. increase release when higher basic amino acids in blood
138
What are glucocorticoids and what is one example?
1. increase blood glucose in response to stress by mobilizing fat stores and inhibiting glucose uptake. Increase the impact of glucogon and catecholamins
2. cortisol increase lipolysis and amino acid mobilization, while decreasing glucose uptake in certain tissue and enhacing activity of counterregulatory hormones
139
What are catecholamines and what are two examples?
1. catecholamines are secreted by adrenal medulla/promote glycogenolysis and increase basal metabolic rate through their sympathetic nervouse system activity. increase lipolyisis by increasing activity of hormone sensitive lipase in adipose tissue
2. epinephrine and norepinephrine
140
What are thyroid hormones and what are two specific ones?
1. modulate the impact of other metabolic hormones and have a direct impact on basal metabolic rate. main effect on lipid and carb metabolism
2. T3 is more potent that T4
141
When is hormone sensitive lipase released?
release in fat cells during fasting state to release fatty acids into circulation
142
What is a very short lived source of energy in active muscle?
creatine phosphate, transfers a phosphate group to ADP to form ATP
143
How is cardiac muscle different from skeletal muslce?
prefers fatty acids as their major fuel in both well fed anf fasting states
144
How to skeletal muscle metabolism differ bases on activity?
1. resting muscle conserved carbs in glycogen stores and uses free fatty acids from blood stream
2. active muscle may use anaerobic metabolism, oxidative phosphorylation of glucose, creatine phosphate, fatty acid oxidation
145
What organ consumes the greatest amount of glucose relative to percent of body mass?
brain
146
What is the respiratory quotient? What does it measure? What are respiratory quoients of lipids, carbs?
RQ=(CO2 produced)/(O2 consumed)
composition of fuel thay is actively consumed by the body
lipid: 0.7
carbs: 1
147
What three hormones influence appetite and how?
1. Ghreline is secreted by stomach in response to signals of impendeing meal (sight, sound, taste smell). increases appetite and stimualted orexin
2. Orexin: futher increases appetite, involved in alertness and sleep-wake cycle
3. leptin is secreted by fat cells that decrease appetite by supressing orexin production
148
What is the charge within a sodium channel?
+ because Na+
149
What are two facts about disulfide bonds?
1. they can only be between two cystein amino acids
2. the formation involves oxidation of S and breaking involves reduction of S
150
How do you find the isoelectric point of histadine with a pKa of 6?
Caboxylic acid has a pKa of 2, amino group has a pKa of 9. Since hsitadine is basic, use the two basic pKas
(9+6)/2
151
What is the turnover number and how do you calculate it?
1. kcat: it is the time it takes one enzyme to turnover a maximum amount of substrate molecules per unit time
2. kcat=Vmax/[E]
152
How do you find catalytic efficiency?
kcat/Km
153
What is a coenzyme? Cofactor?
nonprotein/ organic compound necessary for function of enzyme. Coenzyme is a type of cofactor. cofactor can be organic or inorganic
154
What is are prosthetic groups?
type of coenzymes tightly bound to enzyme
155
Where does an uncompetitive inhibitor bind? How do Km and Vmax change?
Enzyme-substrate complez
both decrease
156
What is vitamin B?
coenzyme, cofactor
157
What is homotropic regulation?
molecule serves as a substrate and a regulatory molecule
158
What is aconitase?
converts citrate into cis aconitate in citric acid cycle
159
What is Mg the cofactor of?
glycolysis
160
What is rate limiting step in citric acid cycle?
generation of a five carbon molecule
161
Where is glucokinase located? what is it responsive to?
1. liver and pancrease P cells
2. responsive to insulin
162
What are the 4 things PFK1 is inhibited by?
ATP, low Ph, PEP, citrate
163
What are two difference between microtubules and microfilaments?
1. actin filaments are assembled from monomeric units of actin. Microtubules are assembled by dimeric tubulin heterodimers
2. GTP is used for Tubulin synthesis and ATP is used for actin synthesis
164
How do actin filaments move?
1. Myosin
165
What is axoplasmic transport and what are the two motor proteins used?
1. movement of membrane bound organelles
2. Microtubules associated motor proteins:
Kinesin (antereograde transport: towards cell membrane)
Dyneisin (retorgrade transport: toward the center of cell)
166
How many heavy chains and light chains in Ig?
two heavy chains and 2 light chains
167
How are G protein decativates?
GTP hydrolysis
168
What are carboxylases?
add carboxyls
169
What are two characteristics of conjugated systems?
1. alternating double and single bonds
2. absorb UV light
170
What are pyridine, imadazole, pyrrole?
1. pyridine: 6 member ring with N
2. imadazole: 5 member ring with O
3. pyrrole: 5 member ring with -NH
171
What is collagen compassed up?
triple helix formed by 3 proteins
they cross link with eachother in extracellular space
172
Under what conditions with disulfide links break?
reducing conditions
173
What is salting in? Salting out?
1. Salting in: addition of salt to a solution, salt intercts with charged amino acids side chains, decreases protein's ability to aggregate with other proteins so increase solubility
2. salting out: when salt concentrations are high, protein solubility decreases
174
What are the signs of anode and cathode in electrophoresis?
like an electrolytic cells so anode is + and cathode is -
175
What drives fatty acid oxidation? Fatty acid synthesis?
1. Higher NAD+ /NADH ratio will drive catabolism
2. lower NAD+/NADH ratio will drive anabolism
176
Where does fatty acid oxidation occur and how does it get there?
occurs in the mitochondria, following transport by carnitine shuttle via beta oxidation
177
How is resting muscle different from active muscle and cardiac muscle?
1. Resting muscle uses free fatty acids
2. active muscle uses carbs, fatty acid oxidation
3. cardiac muscle uses fatty acid oxidation
178
What are Hormone sensitive lipases and where are they expressed?
1. expressed in adipose tissue and adrenal cortex, ovaries, testies
2. catelyze the breakdown of tracylglycerols and glycerol through hydrolysis of ester linkages
179
What are three facts about Acyl-CoA dehydrogenase?
1. enzymes involved in the first step of beta oxidation
2. break down fatty acids in mitochondria--\> broken down into ketone bodies when freely diffuse across the blood brain barrier, then converted into Acetyl CoA
3. glucogenic amino acids can be converted into glucose during extended fasting
180
How are LDLs different from chylomicrons and VLDL?
LDLs transport cholesterol to tissue and others transport triglycerols
181
Where does glucokinase located and what is it responsive to?
In liver and pancreatic Beta cells
responsive to insulin
182
How does cAMP cascade influence PFK2? Where does it happen?
1. deactivates kinase functions which turns off PFK2 so glycolysis decreases
2. happens in liver so gluconeogensis can occur, which is restricted to liver
3. insulin activates protein phosphatase which depholsphorylates PFK2
183
What is the pentose pathway? What is the Rate limiting enzyme?
1. occurs in the cytoplasm in most cells generating NADH and sugars for biosynthesis
2. G6P dehydrogenase is activated by NADP+ and insulin
184
Where is palmitic produced and from where?
in cytoplasm from acetyl-CoA transported out of mitochondria
185
How does miRNA alter expression?
single nucleotide strands incorporates into an RNA structure with a hairpin loop
186
What are lysases?
cleave bonds through non-hydrolysis mech
187
What does aldosterone do? Where does it work?
1. Increase HB, [NA+], excreation of K+/H+
2. works in convuluted tubule and collecting duct
188
How does ADH work?
increase permeability of collecting duct
189
How and where does ANP work?
1. decrease BP, NA+ absorption/ inhibits aldosterons, increases glomerula filtration
2. works in distal convuluted tubule and collecting duct
190
What is the rate law of an enzyme that is completly saturated
zero-order
191
During the introduction of a substrate to an enzyme, what rate law describes the rxn?
first-order
192
What is beta oxidation?
fatty acids are broken down into acetyl-CoA and fed into citric acid cycle and generate NADH and FADH2
fatty acid is oxidized to CO2
193
What is the pKa of carboxylic groups? amino groups?
1. 2
2. 9-10.5
194
What is the function of NADPH?
important function in anabolic pathways such as lipid and nucleic acid synthesis
have more NADPH compared to NADP+ unlike NAD where have more NAD+ than NADH
195
What is the function of transketolase in pentose pathway?
responsible for catalyzing the production of G3P and F6P to go into glycoylsis
196
What are antisense strands?
complemenatary strand (form double stranded product, such as DNA)
197
Is the anomeric carbon a reducing sugar?
yes, attached to two O
198
What are the bonds in sucrose? fructose? maltose?
1. Sucrose: glucose alpha 1,2 fructose
2. Lactose: galactose beta 1,4 glucose
3. Maltose: glucose beta 1,4 glucose
199
What is 2 mecaptoethanol?
BME
reducing agent of disulfide bonds
200
What are coenzymes?One Exp?
donate functional groups
ATP
201
What is one inorganic and one organic cofactor?
Inorganic: metal oxides
Organic: ATP
202
Does inhibition of enzyme inhibit overall rxn?
no
203
What 4 compounds does the gluconeogenic pathway act on? What is the one compound it does not act upon?
pyruvate, lactate, glycerol, glucogenic amino acids
does not act on even-chain free fatty acids
204
Where should you inhibit an enzymatic pathway to minimize side effects?
the last possible enzyme
205
If protein is denatured, what bonds are left?
the covalent bonds between amino acids
206
How can you detect the first mRNA strand in RT-PCR? (if the RNA primers do not have repeats)
with a poly T probe because will have a poly A tail that will not get copied
207
What nucleotides are telomers made of?
G and C
208
What is the difference between a thioester, thioether, and thioketon?
209
What are three products of beta oxidation?
NADH, FADH, acetly CoA
210
What are fatty aacid/cholesterol derivatives?
Terpenes/terpenoids (Repeating C5H8)
VDL/LDL/HDL/IDL
211
What are two components of ATP?
pentose +Purine
212
What 4 substanves produce free radicals?
FADH2, NADH, Vit E, Ubiquinone
213
What is a calorie?
amount of heat required to raise temp of one gram of water by one degrees C
214
How are cellulose and glycogen different?
Glycogen had alpha 1, 4 glycosidic lonks
cellulose has beta 1,4 glycosidic links
215
Is glycogen more branched than amylopectin?
yes
216
What type of hormone is ACTH?
peptide
217
In TCL, what elute second?
polar
218
What is the apoprotein?
unbound to prosthetic group(non protein component)
219
What is the function of vitamin K?
coagulation
220
What are the three usual endings of steroid hormone names?
-ol, -one, -en
221
What is the role of vitamine C?
collagen
222
What can a vitamin B deficiency lead to?
deficiency can lead to memory dysfunction (karsakoff) and cardiovascular problems
223
Besides vision, what does vitamin A play a role in?
immune function and normal growth
224
Are SnRNA, SnoRNA, and HnRNA non-coding or coding?
SnRNA and SnoRNA are non coding and play a role in RNA biogensis and modification of rRNA and tRNA (Found in nucleus)
hnRNA are precursor for mRNA so are coding --\> do turn into protein
225
Does lysine have a larger or smaller pKa compared to histadine?
larger
226
What is the net ATP after glycoylsis? How many ATPs in investment steps?
2 ATPs
2 ATP (1ATP required to phosphorylate)
227
What will build up when an aerobic organism is in a O2 poor environment?
bult up NADH+ because undergoing excessive glycolysis
228
What happens when a protein cannot fold into secondary, teritary, and quatanary structures?
it will maximize its entropy
229
What is the average weight of an amino acid?
110 Da
230
If you want to maintain a tetromer or dimer configurations with anSDS page, should you denature and reduce?
no, just reduce
231
What is another name for proteolytic cleavage?
hydrolysis rxn
232
What is rate limiting step in gluconeogensis?
oxalacetate in mitochondira is converted to malate to export from mitochondria and then converted and rexoidized back into oxolacetate when in cytoplasm
233
What is homotropic regulation?
molecules serves as a substrate and a regulatory molecule
234
What is a lipase?
catalyzes the break down of fatty acids, glycerol, alcohols
235
What is the difference btw ribose and fructose?
236
What is nicotinamide?
NAD+
237
What structure is this?
GTP
238
What does an SDS page remove?
quatenary protein structures
239
What is a glycoside bond?
links monosaccharides togethers in oligosaccharides
240
What type of chromatography is histine tagging and nickel column?
affinity chromatography
241
What does GADPH catalyze?
the reversible conversion of G3P to 1,3 biphosphoglycerate
242
What mediates the internalization of viral particled through endocytosis?
endosomes
243
Where do microtubules orginate from?
centrosomes
244
What is deamination? which amino acids can undergo deamination?
the removal of an amide group (asparagine and glutamine)
245
What are the three differences between a noncompetitive and an uncompetitive inhibitor?
1. uncompetitive inhibitors bind to enzyme-substrate complex only(need substate to bind) but noncompetitive bind to enzyme and enzyme-substrate complex)
2. for noncompetitive inhibitors Vmax decreases and Km stays the same, but for uncompetitive both Km and Vmax decrease
246
What does a Hill coffecient of 1 mean?
not cooperative
247
What are five important steps in krebs cycle?
1. D-isocitrate--\> alpha ketoglutarate creates NADH
2. Alpha Ketoglutarate to succinyl-Coa create NADH
3. Sucinyl-Coa to Succitate create GTP
4. Succinate to Fumerate creates FADH2
5. Malate to oxaloacetate creates NADH
248
What is one enzyme that catalyzes both gluconeogenisis and glycogenolysis?
glucose 6 phosphatase
249
What is Kcat used to describe?
used to describe the rate limiting step of catalysis under staturating conditions of substrate
250
How many H-bond donors and acceptors in A, T, G, C?
A: 1 donor, 1 acceptor
T: 1 donor, 1 acceptor
G: 2 donors and 1 acceptor
C: 1 donor and 2 acceptors
251
What are three things that affect thermal denaturation?
1. pH of solution
2. Ionoic strength of Solution
3. length of DNA strand
252
What type of phosphate is involved in phosphoryl tranfers from kinases?
gamma phosphate in ATP
253
What is a dehydrogenase?
remove H to form a double bond (oxireducatate)
254
Where is phosphoglucose isomerase inolved?
glycolysis
255
Do neutral side chains of amino acids influence pKa?
no
256
What is the size of prokaryotic and a eukaryotic ribosome?
70s/80s
257
What does monocistronic mean?polycistronic?
monocistronic: when mRNA contains a coding sequence for a single protein (eukaryotes)
polycistronic: Carry many ORFs and each is coded into a protein, they are regulated by a single promoter and operator
258
What type of primers does PCR use?
DNA
259
How do you find association constant of enzyme? Dissociation constant?
[Es]/([E]x[S])
inverse
260
What is photoreactivation? What do eukayrotics use in replacement?
a prokaryotic process to reverse the damage done by UV light. Base exicision repair (prokaryotics can use this too)
261
What is oposonization?
antibodies bind to and recognize antigens on the surface of a pathogen. these antibodies then attrack macrophages
262
do macrophages release cytokines?
yes
263
What is the difference between amphoteric and amphipathic?
Amphoteric: able to act as an acid or base/ amphipathic: both hydrophilic and hydrophobic
264
What vitamins are fat soluble?
vitamin BEAK
265
What is/are the most electrons exchnages in ETC?
1
266
Do type two diabetics have higher or lower than normal insulin?
higher than normal because not responsive to insuline, bllod sugar is not lowering
267
Can reversible reactions be committed steps?
no
268
Where does fatty acid catabolism (beta oxidation) occur and then end?
start in cytosol and end in mitochondria
269
What is the difference between beta oxidation and cell rep?
The cell requires more than twice the number of NAD+ electron carriers compared to FAD electron carriers, in order to harvest ATP from fatty acids
270
What happens to lipolysis when eat?
decreases
271
What reducing agent aids in glutathione reduction?
NADPH as it relieves oxidative stress by aiding in the conversion of hydrogen peroxide to water
272
What are two hormones that can increase gluconeogensis?
glucagon and norepinephrine
273
What are three things the pentose pathway produces?
G3P, NADPH, and nucleic acids
274
What is the difference between allosteric modulators and inhibitors?
modulators change the affinity but inhibitors change V max
275
How would an alloesteric modulators impact kinetics of a rxn?
allosteric activation would increase the initial rate and allosteric inhibition will decrease the initial rate but for both the Vmax will stau the same
276
What are two water soluble vitamins?
B (coenzyme, prosthetic group) and C (antioxidant)
277
What is a Carotenoids?
vitamin A
278
What are the two difference between hexokinase and glucokinase?
Hexokinase has a higher affinity for glucokinase. Glucokinase works in pancreas and liver
279
How many carbons in acetly Coa?
two
280
Do HDLs or LDLs contain more cholesterol?
LDLs
281
What is the purpose of glycosyltransferase enzym?
intiation and longation of glycogen
282
What is glycogen phosphorylase?
release glucose from alpha 1,4 linkages and is rate limiting step
283
What does two rounds of ATP hydrolysis lead to?
AMP
284
What enzyme is required to make GTP?
Nucleoside diphosphate kinase
285
What is a ketone body you can smell from one's breath?
acetone
286
Does an enzyme reduce the activation for both the forward and reverse rxn?
yes, The direction of reaction in this case is governed by the relative amounts of reactants and products, i.e. the difference between the reaction quotient and equilibrium
287
What are the two ways a competetive inhibitor acts?
can simulate substrate and also the transition state because enzymes have a strong affinity for the transition state
288
What is the role of transketolase?
involved in non-oxidative step in pentose pathway to produce G3P and F6P
289
Do enzymes that display cooperative binding display michaelis-menten kinetics?
no
290
What hormone stimulates fatty acid oxidation? What does fatty oxidation fuel?
glucagon
gluconeogenesis
291
What type of carbon chain has the most energy?
longest and most saturated
292
How many NADHs, FADHs and GTPs are created from acetyl CoA?
3NADH, 1 FADH, 1GTP
293
What is the first molecule involved in pentose phosphate pathway?
G6P
294
What is the difference between allosteric activation and allosteric inhibitor?
Allosteric inhibition: slow the initial rate but same Vmax
Allosteric activation: increase initial rate but same Vmax
295
What is the shape of graph of alloesteric enzyme?
sigmoidal
296
Does Vmax change if add mor enzyme?
yes
297
Compare coenzyme and prosthetic groups?
are cofactos but prosthetic groups bind to enxyme
coezymes released from active site (NADH)
298
What are three substances gluconeogenesis can directly use?
pyruvate, glycerol, lactate
299
How is lactate converted into pyruvate?
through the cori cycle
300
Where do phosphates come from and inorganic phosphates?
ATP: phosphates
NADH: inorganic phosphates
301
What is catabolism?
breakdown
302
What is hormone sensitive lipase?
breakdown into fatty acids
303
How to transferases work with glycogen?
tak a segment of the branched chain that is one unit away from the branch point and relocated it to parent chain
304
What do you need for fatty acid synthesis?
acetly CoA and NADPH
305
What happens during starvation?
decrease pentose phosphate pathway bc was G6P
306
What is AMP?
low energy state
307
What are 4 types of nucleotides?
cAMP, GTP, ATP, cGMP
308
What does pyruvate dehydrogenase do?
convert pyruvate into acetly CoA
309
What is a coenzyme of hemoglobin?
iron (dissociate after rxn, can transfer functional groups)
310
Where does gluconegensis occur?
kidney and lover
