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Biochem Flashcards

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1
Q

Which amino acid has an R absolute configuration and why?

A

Cysteine, because the -CH2SH group has priority over -COOH group

Still is an L amino acid

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2
Q

Which amino acids have alkyl side chains?

A

Alanine, valine, leucine, isoleucine

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3
Q

Which amino acids have amide side chains?

A

Asparagine and Glutamine (polar)

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4
Q

What is the effect of a point mutation changing E -> Y?

A 
E = glutamate 
Y = tyrosine

Acidic side chain to aromatic side chain

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5
Q

What is the effect of a point mutation changing D -> K?

A 
D = aspartate 
K = lysine

Acidic to basic side chain

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6
Q

At pH 7, what will be the protonation status of amino acids?

A

Carboxylate group unprotonated
(-COO-)
Amino group protonated (-NH3+)

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7
Q

What is the approximate pI of aspartate if pKa1=1.88, pKa2=3.65, and pKa3=9.60?

A

Aspartate is acidic so
pI = (pKa, R + pKa, COOH) / 2

Because acidic amino acids have 2 COOH groups that are deprotonated before NH3+

(1.88+3.65)/2 ~ (2+4)/2 ~ 3 (2.77)

Acidic side chains have low pI

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8
Q

What is the pI of arginine if pKa1=2.17, pKa2=9.04, pKa3=12.48?

A

Arginine is basic, extra amino group (+2 when fully protonated)

pI = (pKa, NH3+ + pKa, R) / 2

(9.04 + 12.48) / 2 ~ (9 + 13) / 2 ~ 11 (10.76)

Basic side chains have high pI

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9
Q

Explain the reason for the partial double bond character of the C-N amide bond in the peptide bond

A

Amide groups have delocalized pi electrons in carbonyl
Amino nitrogen has lone pair
Thus, resonance

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10
Q

At pH 7, the charge on glutamate is

A

-1

Both carboxyl groups are deprotonated

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11
Q

Which amino acid is most likely to be found in the transmembrane portion of an alpha helix?

  • Lysine
  • glutamate
  • aspartate
  • phenylalanine
A

Phenylalanine- has hydrophobic side chain (benzene ring)

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12
Q

True or false: bases can catalyze peptide bond hydrolysis

A

TRUE

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13
Q

In an oxidation reduction reaction, what is the role of the reductant?

A

Reductants donate electrons

Oxidants accept electrons

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14
Q

What class of enzyme are kinases, and what is the major function of this class?

A

Kinases are transferases, which catalyze functional group transfer

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15
Q

What reaction does aminotransferase catalyze?

A

Transfer of amino group from aspartate to alpha-ketoglutarate

Aspartate becomes glutamate, alpha-ketoglutarate becomes oxaloacetate

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16
Q

What class of enzyme are phosphatases and nucleases?

A

Hydrolases

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17
Q

What class of enzyme catalyzes conversion of ATP to cyclic AMP and Pi?

A

Lyase- cleavage of single molecule into 2, does not require water

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18
Q

Synthases are a more specific term for what class of enzyme?

A

Lyases- catalyze cleave of single molecule into two products, but also small synthesis reactions (then called synthases)

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19
Q

Can isomerases catalyze reactions between stereoisomers or constitutional isomers or both?

A

Both: isomerases catalyze bond rearrangement

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20
Q

What class of enzymes catalyze large synthesis reactions, often requiring ATP?

A

Ligases

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21
Q

What are the x and y axes of the Mechaelis-Menten plot?

A

Y axis: v, reaction velocity

X axis: [S], substrate concentration

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22
Q

Where is the Km of an enzyme found on the Michaelis-Menten plot?

A

Find the 1/2Vmax, then find the value on the x-axis directly below ([S])

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23
Q

What is the Michaelis- Menten equation?

A

v = Vmax [S]
————
Km + [S]

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24
Q

Finish this sentence: at 1/2Vmax in MM kinematics, Km =

A

At 1/2Vmax, Km=[S]

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25
Q

What effect does lowering the Km of an enzyme have on substrate binding?

A

lower Km = higher affinity for substrate

Increased enzyme activity

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26
Q

What does Kcat measure in MM kinematics?

A

Kcat = rate of substrate turnover

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27
Q

How is catalytic efficiency calculated?

A

Catalytic efficiency = Kcat/Km

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28
Q

What are the axes of the Lineweaver-Burk plot?

A

LB plot is double reciprocal of MM plot:
Y axis: 1/V
X axis: 1/[S], extrapolated to negative

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29
Q

What does a Hill coefficient <1 imply?

A

Negative cooperation

Further binding decreases ligand affinity

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30
Q

How does temperature affect enzyme activity?

A

Enzyme activity doubles in reaction velocity for every 10 degree C increase until temp is too high and enzyme denatures

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31
Q

Explain the following for competitive inhibition:

  • where does it bind
  • how does it affect Vmax and Km
  • what does its LB plot look like
A

Competitive inhibition binds active site - can be overcome by adding more substrate

Does not alter Vmax because adding more substrate can overcome it, so Vmax can still be reached eventually

Measured Km is increases because more substrate is needed to reach half Vmax

Lines cross on Y axis (1/V) on LB plot

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32
Q

Explain the following for no competitive inhibition:

  • where does it bind
  • how does it affect Vmax and Km
  • what does its LB plot look like
A

Noncompetitive inhibition binds allosteric site (conformation change)

Binds equally well to E and ES

Decreases Vmax because less enzyme is available to react due to altered conformation

Lines cross on -x axis (-1/[S]) on LB plot

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33
Q

Explain the following for mixed inhibition:

  • where does it bind
  • how does it affect Vmax and Km
  • what does its LB plot look like
A

Mixed inhibitors bind allosteric site, either E or ES with different affinity

Prefers E: increase Km
Prefers ES: decreases Km

Decreases Vmax

Intersect at point not on either axis on LB plot

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34
Q

Explain the following for uncompetitive inhibition:

  • where does it bind
  • how does it affect Vmax and Km
  • what does its LB plot look like
A

Uncompetitive inhibitors bind allosteric site, only bind ES

Decreases Km (binds ES)
Decreases Vmax

Parallel lines on LB plot

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35
Q

Compare alpha and beta anomers of glucose- what is different about their respective substituents?

A

Alpha anomer of glucose has the OH group on C1 axial and trans to the CH2OH group

Beta anomer of glucose has the OH group on C1 equatorial and cis to the CH2OH group

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36
Q

What physical property of water allows for sweating to reduce body temperature?

A

High heat capacity- absorbs a lot of heat that is then evaporated off

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37
Q

Explain why competitive inhibition causes an increased Km and constant Vmax

A

Ligand analogue binds active site, causing increase in apparent Km—> more ligand needed to get half enzymes full because active sites are being filled

Competitive inhibition can be overcome by high substrate concentration, so Vmax is the same

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38
Q

What is the expression of probability of having 4 children, 2 girls and 2 boys in any birth order?

A

6 combinations of 2girls/2boys
1/2 chance of having a boy or girl
So each of 6 combinations is (1/2)^4 (4 children)

Multiple events possible (combinations) means adding probabilities

6 (1/2)^4

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39
Q

What does a phosphodiester bond do?

A

Links 3’ and 5’ carbons of 2 sugars

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40
Q

Do point mutations always affected secondary structure?

A

No, point mutants do not necessarily affect secondary or tertiary structure

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41
Q

What’s an enol?

A

C=C and OH group present

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42
Q

How does SDS PAGE work?

A

SDS detergent equalizes charge, then separates by size

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43
Q

What is ELISA used for?

A

Immunological technique to identify presence of protein

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44
Q

Hormones are found in low concentrations but have strong effects. Which type(s) of receptors are hormones likely to act on:

  • ligand gated ion channels
  • enzyme linked
  • GPCR
A

Enzyme linked and GPCR-

For low concentration to have strong effect, need to initiate second messenger cascade with amplification (both of these do this)

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45
Q

In Fischer projections, how do the hydroxides of the highest numbered chiral center differ in D and L sugars?

A

D sugars: hydroxide of highest numbered chiral center on the right

L sugar: hydroxide of highest numbered chiral center on the left

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46
Q

When converting a Fischer projection to a Hawthorn projection, any group on the right in the Fischer projection…

A

Groups on the right of a Fischer projection point down in a Hawthorn projection

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47
Q

Which type of glycerophospholipid has a single hydrogen atom as its head group?

  • cerebroside
  • ceramide
  • gangliosides
A

Ceremides- single H atom as head group

Cerebroside- glycosphingolipid with a single sugar as head group (no net charge at physiological pH)

Ganglioside- sphingolipid with oligosaccharide head group and 1+ NANA (sialic acid), négative charge

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48
Q

What is the structure of steroids?

A

Three cyclohexane and one cyclopentane

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49
Q

What’s a shortcut to determine if a molecule is polar?

A

Each polar group “overrules” 5 carbons

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50
Q

True or false: phosphate is nonpolar

A

FALSE: Phosphate is POLAR

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51
Q

What does a Keq of 1 indicate?

A

Keq of 1 means free energy change is 0 (delta G = 0)

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52
Q

Why would raising the temperature of a reaction in vivo not help increase reaction rate?

A

Increasing reaction temperature IN VIVO is not ideal… body needs ideal temp (you’ll kill everything!)

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53
Q

What type of linkage is created in formation of peptide bond?

A

Amide linkage

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54
Q

Double stranded RNA is marked for degradation. Which of the following strands of RNA would prevent mature mRNA in cytoplasm from being translated?

  • identical to mRNA being produced
  • antisense mRNA to one produced
  • sense mRNA to one produced
A

Antisense mRNA to one produced- needs to bind mRNA to make it double stranded RNA which will be degraded

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55
Q 
Which of the following will be low after an overnight fast?
Malate dehydrogenase 
Glucokinase 
Alpha-ketoglutarate dehydrogenase 
Phosphofructokinase-1
A

Glucokinase

PFK-1 will still be used with other sources of glucose (glycogen, gluconeogenesis)

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56
Q

When fatty acid beta oxidation is active in liver, mitochondrial pyruvate will be:

  • carboxylated to phosphoenolpyruvate for entry into gluconeogenesis
  • carboxylated to oxaloacetate for entry into gluconeogenesis
A

carboxylated to oxaloacetate for entry into gluconeogenesis

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57
Q

Patient presents with lysing RBC and Heinz bodies (oxidized hemoglobin). Which enzyme is defective:

  • fructose-1,6-biphosphate
  • glucose-6-phosphate dehydrogenase
  • pyruvate kinase
A

-glucose-6-phosphate dehydrogenase

Need NADPH from PPP

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58
Q

Name 3 uses for NADPH

A

Lipid biosynthesis
Bleach formation
Glutathione (ROS protection)

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59
Q

Match structure to link:
Linear, branched
alpha-1,6 and alpha-1,4

A

Linear- alpha-1,4 glycosidic link

Branched- alpha-1,6 glycosidic link

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60
Q

Match transporter to location and kinetics
GLUT2 and GLUT4
Liver, adipose-muscle
First order, zero order

A

GLUT2- liver (glucose sensor), first order kinetics (high Km)- not responsive to insulin

GLUT4- muscle/adipose, zero order kinetics (low Km)

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61
Q

What is the rate limiting step of glycolysis

A

PFK-1

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62
Q

What happens to UDP-glucose in glycogenesis?

A

Glycogen synthase + branching enzyme create glycogen

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63
Q

What 2 processes maintains blood glucose during fasting

A

Gluconeogenesis and glycogenesis

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64
Q

What is the net charge on lysine at pH 7.4 if pKa1=2.6, pKa2=9.06, pKaR=10.54?

A

+1

At this pH, carboxyl group has -1 charge, both amino and R group have +1 charge—> +1 net charge

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65
Q

In an aromatic ring system, each carbon atom must be what hybridization?

A

Sp2

Needed to be planar, so that each atom will have p orbital available for overlap

Also sp2 has 120* bond angles which reduce ring strain

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66
Q

Given a genome with 50% AT content, the probability of AUUUA sequence is one in every how many nucleotides?

A

50% AT means 50% GC. 25% (1/4) of having the necessary base at each position. There are 5 nucleotides in this sequence, so it’s (1/4)^5 or 1/1024, or 1 in every 4^5 bases

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67
Q

What are loading controls for in western blots?

A

Ensure the same quantity of protein was loaded for all samples

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68
Q

Where X represents the conjugate base, which of these acids will have the smallest H-X bond dissociation energy:
Acid A, pKa of 4.10
Acid B, pKb of 10.90

A

Stronger acids will have smaller dissociation energy

14 = pKa + pKb

So Acid B is stronger because 14-10.90 = 3.10 pKa

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69
Q

If 2 solutions are separated by biological membrane with 100mM Na3PO4 on one side and 200mM NaCl on the other side (with equal amounts of water)- where will water go?

A

No net movement of water because Na3PO4 has van’t Hoff factor of 1 while NaCl has van’t Hoff factor of 2 (2 ions produced when dissociated)

(Osmotic pressure P=iMRT)

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70
Q

If germ cells of an organism divide without DNA replication that normally occurs before meiosis, what type of chromosome will be found at the metaphase plate during Meiosis I?

A

DNA replication produces dyads

So this organism will have no sister chromatids- it will have monads on the metaphase plate

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71
Q

How does impurity affect the melting point range?

A

Lowers and widens the melting point range

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72
Q

Why are glycogen stores in skeletal muscle critical during prolonged exercise?

  • myosin hydrolyzes ATP during muscle contraction
  • actin requires ATP for polymerization
  • exposure of myosin binding site requires ATP
A

myosin hydrolyzes ATP during muscle contraction

ATP is required for sliding filament model- ATP hydrolysis needed to cock the myosin head, binding of ATP to myosin head necessary to release myosin head from actin filament for next contraction

(Calcium binds troponin to move tropomyosin and expose actin filament binding site)

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73
Q

Following ingestion of meal high in simple carbs, primary metabolic process is:

  • glycolysis
  • gluconeogenesis
  • glycogenesis
A

Glycogenesis: building glycogen stores

Glycolysis only partially contributes because it shuts down after cell has enough energy

Glycogen built can grow to any size

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74
Q

A women who is a heterogenous carrier for Duchenne MD has a son with a normal man- what is probability son will have MD?

A

50%

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75
Q

Which of these is true:

  • prions can be inherited
  • prions can cause pathology outside of the CNS
A

Prions are usually acquired through food but can be inherited

Only cause pathology within the CNS

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76
Q

After pyruvate enters the mitochondrion via active transport, it is?
Decarboxylated
Oxidized

A

Both

Via PDH complex in mito matrix

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77
Q

What is pyruvate cleaved into? Is this reversible?

A

2-carbon acetyl group and CO2

Not reversible (can’t make glucose from acetyl co-A)

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78
Q

Which of these is (are) required for PDH complex?
Vitamin B1
Mg2+
NAD+

A

All of them

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79
Q

In the formation of acetyl-coA, lipoic acid’s disulfide group acts as a ___ agent, then FAD acts as a ____ agent of lepoic acid

A

Disulfide groups in lipoic acid act as oxidizing agent to create acetyl group (bonded to lipoic acid via thioester linkage)

FAD reoxidizes lipoic acid for figure acetyl-CoA formation

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80
Q

Because fatty acyl-CoA Cabot cross inter mito membrane, the fatty acyl group is transferred to _____? What kind of reaction is this?

A

Fatty acyl group transferred to carnitine via transestérification reaction

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81
Q

Alcohol dehydrogenase can convert alcohol to acetyl-CoA, but also causes NADH buildup. How does this effect metabolism?

A

TCA is inhibited

Acetyl-CoA used for fatty acid synthesis

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82
Q

Why can’t the TCA be run under anaerobic conditions, even if it doesn’t require oxygen?

A

If ETC isn’t running, NADH and FADH2 build up, inhibit cycle

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83
Q

What’s the rate limiting enzyme in TCA?

A

Isocitrate dehydrogenase

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84
Q

What’s the difference between a synthase and a synthetase?

A

Synthetases require significant energy input

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85
Q

Dehydrogenases are a subunit of what type of enzyme?

A

Oxidoreductases

Transfer hydride ion to electron acceptor

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86
Q

Which provides more ATP?
NADH
FADH2

A

NADH (2.5 ATP vs 1.5)

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87
Q

In Complex I of the ETC, what does electron transfer occur between?

A

NADH —> coenzyme Q (ubiquinone)

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88
Q

Which ETC complex is a part of 2 distinct pathways simultaneously?

A

Complex II, succinate-CoQ oxidoreductase

Part of TCA and ETC

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89
Q

Which ETC complex uses cytochrome c?

A

Complex III

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90
Q

What is a cytochrome?

A

Protein with heme group in which iron is reduced to Fe2+ (and reoxidized to Fe3+)

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91
Q

What are the 2 NADH shuttles and which one is more efficient?

A

Glycerol 3-phosphate shuttle (produces FADH2)

Malate-aspartate shuttle (produces NADH, more efficient)

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92
Q

How does DHAP link glycolysis and fat metabolism?

A

DHAP is intermediate in glycolysis

Glycerol of triglycerides can be shunted into glycolysis for energy

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93
Q

What happens to long chain fatty acids in micelles?

  • diffusion across intestine to lymphatic system
  • transport into chylomicrons releases into lymph system
A

transport into chylomicrons releases into lymph system

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94
Q

True or false: adipocytes cannot undergo gluconeogenesis

A

TRUE. they cannot

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95
Q

Statin drugs inhibit HMG-CoA reductase. What are they used for?

A

Hypercholesterolemia

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96
Q

Which is the correct order of fatty acid synthesis?

  • activation followed by bond formation, reduction, dehydration, reduction
  • two reductions followed by dehydration and bond formation
A

activation followed by bond formation, reduction, dehydration, reduction

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97
Q

Majority of triacylglycerols stored in adipose originate from

A

Synthesis in liver

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98
Q

What is hormone sensitive lipase (HSL) used for?

A

HSL hydrolyzes triacylglycerols

Adipose does not respond directly to glucagon, so HSL is activated by fall in insulin

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99
Q

Lipoprotein lipase (LPL) does what?

A

Releases free fatty acids from triacylglycerols in lipoproteins

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100
Q

Which lipoproteins have the highest protein to fat ratio?

A

HDL

“Good”- cleans up excess cholesterol

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101
Q

Which chylomicron delivers cholesterol to tissues for biosynthesis?

A

LDL

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102
Q

Which shuttle is crucial for cholesterol synthesis?

A

Citrate shuttle- carries mito acetyl-CoA to cytoplasm (where synthesis occurs)

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103
Q

Fatty acids are long chain ____

A

Carboxylic acids

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104
Q

Double bonds in natural fatty acids are generally in what configuration?

A

Cis

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105
Q

What are the 2 major enzymes of fatty acid biosynthesis?

A

Acetyl-CoA carboxylase (rate limiting)

Fatty acid synthase

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106
Q

What is the rate limiting enzyme in beta oxidation?

A

Carnitine acetyltransferase I

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107
Q

What are the 4 repetitive steps of beta oxidation?

A

Oxidation (forms double bond)
Hydration (forms hydroxyl)
Oxidation (of hydroxyl to form carbonyl)
Split (into shorter acyl-CoA and acetyl-CoA)

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108
Q

All amino acids are glucogenic except for:

A

Leucine and lysine

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109
Q

Why are cells considered closed systems?

A

Constant pressure and volume —> no work can be done

DeltaU (internal energy) = Q (heat)

110
Q

Can a reaction with negative deltaS and negative deltaH be spontaneous?

A

At low temp

deltaG = deltaH - TdeltaS

111
Q

A spontaneous redox reaction will have a negative deltaG and a (negative/positive) value of E (electromotive force)

A

Positive value

112
Q

After a meal, most of the energy needs of the liver are met by…

A

Oxidation of excess amino acids

113
Q

Which happens first, gluconeogenesis or glycogenolysis?

A

Glycogenolysis (almost immediately at beginning of postabsorptive state)

114
Q

What tissue is least able to change its fuel source in periods of starvation?

A

RBC- can only use glucose anaerobically

115
Q

Which work faster, peptide hormones or steroid hormones?

A

Peptide hormones are fast, rapidly adjust metabolism

Steroid hormones have longer effects by modifying transcription

116
Q

Which tissues require insulin for glucose uptake?

A

Adipose, resting skeletal muscle

117
Q

Muscle cannot release glucose into the blood because it lacks this enzyme:

A

Glucose-6-phosphate

118
Q

What effect do catecholamines have on metabolism?

A

Muscle/ liver glycogenolysis

Adipose lipolysis

119
Q

After a meal, the liver extracts excess glucose to replenish its glycogen stores. What happens to any remaining glucose in the liver?

A

Converted to acetyl-CoA for fatty acid synthesis

120
Q

Which tissue does not prefer glucose?

A

Cardiac- prefers fatty acids (think prolonged muscle use)

121
Q

How is respiratory quotient depicted to change when you start exercising?

A

Approaches 1–> increased use of glucose for energy

RQ = (CO2 produced)/(O2 consumed)

122
Q

What characteristic makes antioxidants effective?

A

Low reduction potential, so they can reduce other molecules and become oxidized themselves

123
Q

Which of these is unique to or shared between fatty acids and triglycerides?
Carboxylic acids
Esters
Carbonyl

A

Fatty acids- long chain carboxylic acids
Triglycerides- esters
Both- carbonyls

124
Q

Which amino acid is not chiral?

A

Glycine- does not have 4 unique substituents (R group is just H atom)

125
Q

Most L-amino acids are S, but one L-amino acid is R- which one

A

cysteine (S has higher priority)

126
Q

What do the amino And carboxylic acid groups look like for isoleucine in its zwitterion form?

A

NH3+, COO-

127
Q

In peptide bond formation, the amine group nitrogen acts as ___ while the carbonyl carbon acts as ___

A

Nitrogen- nucleophile

Carbon- electrophile (on c terminus)

128
Q

Trypsin and chymotrypsin cleave proteins on what side?

A

Carboxyl

129
Q

What is Strecker synthesis?

A

Form amino acids from aldehydes and ketones (via imine, C=N)

Use KCN or NH4Cl

130
Q

What reagents can effectively form amino acids from aldehydes and ketones (Strecker synthesis)?

A

KCN

NH4Cl

131
Q

What is Gabriel synthesis good for?

A

Making primary amines using protected amine (phthalimide) in SN2 rxn

Does not undergo over-alkylation

Only works well for primary alkyl halides

132
Q

How many residues apart are hydrogen bonds in alpha hélices?

A

4

A-B-B-A where A and A share hydrogen bond

133
Q

Can you more easily overdose Vitamin D or Vitamin C?

A

Vitamin D- fat soluble vitamins can be stored and accumulate

Water soluble vitamins are easily excreted

134
Q

What is the MM equation?

A

V0 = (Vmax)([S])
——————
Km + [S]

135
Q

Why are uncompetitive inhibitors uncommon?

A

Bind only to enzyme- substrate complex

Limited time window

(Decrease Vmax and Km)

136
Q

When a mixed inhibitor has high affinity for ES over E, it’s acting like what other inhibitor?

A

Uncompetitive

Decreases Km

137
Q

When a mixed inhibitor has high affinity for E over ES, it’s acting like what other inhibitor?

A

Competitive

Increases Km

138
Q

Prothrombin is an example of what?

A

Zymogen- inactive enzyme precursor

139
Q

In a Fischer projection, the hydroxyl group attached to the highest numbered chiral carbon is on the right. What kind is it?

A

D

Left = L

140
Q

When differentiating between a reducing and non-reducing sugar, what functional group should you look for?

A

Aldehyde = reducing sugar (can do redox)

141
Q

Fatty acids are the only lipids that have what functional group?

A

Carboxylic acid, -COOH

142
Q

What’s an easy way to recognize an alpha-1,4 linkage (which glycogen phosphorylase cleaves)?

A

Remember that glycogen is used for glucose storage- it’s a homopolymer

All monomers will be identical

143
Q

pKa + pKb =

A

14

144
Q

How many protons do NADH and FADH2 pump?

A

NADH- 10. 4 from complex I, 4 from complex III, 2 from complex IV

FADH2- 6. 4 from complex III, 2 from complex IV

145
Q

Is anomeric carbon fixed stereocenter or invertible epimer

A

Anomeric carbon of sugar is invertible epimer

Epimers are beta vs alpha sugar, which anomeric carbon can convert between

146
Q

Anhydrase =

A

Removal of water

147
Q

Enzymes catalyze reactions in both directions (T/F)

A

TRUE

148
Q

Kinetic factors determine __

Thermodynamics determine ___

A

Kinetics- rate of reaction

Thermodynamics- rxn equilibrium

149
Q

Give graph units for first and second order reaction

A

First- ln[A]

Second- 1/[A]

150
Q

What is produced each round of beta oxidation

A

An acetyl CoA generated each round, fatty acid chain shortened by 2 C
Final round generates 2 acetyl CoA

Odd numbered fatty acid chains cleave 5C chain in final step into acetyl CoA (2C) and succinyl CoA (3C)

151
Q

Difference between prosthetic and coenzyme groups

A

Prosthetic tightly/ covalently bound

Coenzymes loosely bound

152
Q

Name 3 major mechanisms of controlling blood pH (increasing blood pH)

A
  1. Exhale CO2
  2. Conversion of CO2 into HCO3- (bicarbonate, buffer system)
  3. Exertion of blood through kidneys
153
Q

What effect will releasing H3PO4 (phosphoric acid) in blood have

A

Decrease blood pH

Dissociâtes into H2PO4- and H+, further dissociates into HPO4^2- and H+

154
Q

T/F calcium is necessary for blood clotting

A

TRUE

155
Q

What’s used as template during DSB repair

A

Sister chromatid

Can’t use template strand because in DSB both strands are damaged

156
Q

Is amino or carboxyl terminus translates first

A

Amino

Translation is 5’-3’ and amino terminus is at 5’ end

157
Q

Which will never affect reaction rate?

  • putting reactants into aqueous solution
  • increasing pressure in closed container
  • removing product of irreversible reaction
A

removing product of irreversible reaction

Rate law doesn’t depend on concentration of reactants

158
Q

What chemical mechanism allows biochemical reactions to proceed despite positive deltaG*’ values?

A

Reaction coupling

159
Q

What does deltaG*’ represent

A

Free energy change of proceeding from standard state concentration to equilibrium

160
Q

deltaG =

deltaG*’ =

A

deltaG = deltaG*’ + RTlnQ

deltaG*’ = -RTlnKeq
Because at equilibrium, Q=Keq and deltaG=0

161
Q

If Keq=1, deltaG*=

A

0

deltaG*’ = -RTlnKeq

ln(1)=0

162
Q

If Q=1, deltaG*=

A

DeltaG* = deltaG when Q=1

deltaG = deltaG*’ + RTlnQ
deltaG*’ = -RTlnKeq
163
Q

T/F: substrate level phosphorylation must be coupled to an exergonic reaction

A

TRUE

164
Q

Irreversible enzymes of glycolysis

Which is committed step

A
  1. Hexokinase
  2. PFK1 (phosphofructokinase)
  3. Pyruvate kinase

PFK1 is committed step

165
Q

How does DHAP become incorporated into glycolysis?

A

Dihydroxyacetone phosphate (DHAP) —> glyceraldehyde 3-phosphate

Via enzyme triose phosphate isomerase

166
Q

How is glycogen funneled into glycolysis?

A

Glycogen phosphorylase produces glucose 1-phosphate

Phosphoglucomutase converts glucose 1-phosphate to glucose 6-phosphate, which is funneled into step 2

167
Q

How is fructose funneled into glycolysis? Say how for both muscles/kidneys and liver

A

In muscles and kidneys, hexokinase converts fructose to fructose 6-phosphate, which is then funneled into 3rd step of glycolysis
(After glucose 6-phosphate converted via isomerase to fructose 6-phosphate)

In liver, fructokinase converts fructose to fructose 1-phosphate, then an aldolase converts it to glyceraldehyde 3-phosphate and DHAP (DHAP funneled in by triose phosphate isomerase)

168
Q

What makes ethanol fermentation unique to lactic acid fermentation

A

Carbon skeleton changes

Pyruvate (3C) broken to ethanol (2C) and CO2

169
Q

Irreversible steps of gluconeogenesis

A

Glucose 6-phosphatase

Fructose 1,6-biphosphatase (F-1,6-BP)

Phosphoenol pyruvate (PEP) carboxylase (+GTP)

Pyruvate carboxylase (+ATP) produces oxaloacetate

170
Q

Major products of pentose phosphate pathway

A

NADPH

ribose 5 phosphate

171
Q

What are the 3 destinations of pyruvate

A

PDH complex —> acetyl CoA

Lactate dehydrogenase —> lactate

Pyruvate carboxylase —> oxaloacetate (gluconeogenesis)

172
Q

Where are 3 places you can get acetyl CoA

A

PDH complex

Beta oxidation

Amino acid metabolism

173
Q

Where are the 3 places that produce NADH in TCA?

A

Isocitrate -> alpha ketoglutarate via isocitrate dehydrogenase (CO2 produced here too)

Alpha ketoglutarate -> succinyl CoA via alpha ketoglutarate dehydrogenase complex (CO2 produced)

Malate -> oxaloacetate via malate dehydrogenase

174
Q

Where are GTP and FADH2 produced in TCA? (Hint: back to back)

A

Succinyl CoA -> succinate produces GTP

succinate -> fumarate produces FADH2

175
Q

Each NADH produces how many ATP, what about FADH2

A

NADH- 3 ATP

FADH2- 2 ATP

176
Q

What happens in malate aspartate shuttle

Why do we need it

What anti porter and other shuttle is involved in this cycle

A

NADH can’t pass through inner mito membrane

NADH donates 2 e- to oxaloacetate, converting it to malate. Malate enters matrix via

Malate alpha-ketoglutarate anti porter

Converted back to oxaloacetate in matrix and NADH generated

Oxaloacetate converted to aspartate and goes back to cytosol via glutamate-aspartate shuttle

177
Q

Why is glycerol 3 phosphate shuttle less favorable than malate aspartate shuttle

What does it do

A

NADH donates 2 e- to DHAP to form glycerol 3-phosphate. In the mito matrix G3P turned back into DHAP and e- go to FAD to make FADH2

Less efficient because it makes FADH2 instead of NADH

178
Q

What does carnitine shuttle transport

A

Carnitine acyltransferase attaches fatty acyl group from acyl-CoA to hydroxyl group of carnitine

To get fatty acids through inner mito matrix for beta oxidation

179
Q

What does citrate acetyl CoA shuttle (tricarboxylate transport system) do?

A

Acetyl CoA in mitochondria are used for fatty acid synthesis in cytosol but can’t pass membrane

Acetyl CoA combines with oxaloacetate to form citrate which passes through membrane and is converted to oxaloacetate and acetyl CoA in cytosol

180
Q

How do peroxisomes aid in fat metabolism

A

Extra long chain fatty acids are catabolized to smaller pieces here

181
Q

What does beta oxidation require, and what does it produce?

A

Requires: 1 FAD, 1 H2O, 1 NAD+, 1 CoA-SH

Produces: 1 FADH2 (2 ATP), 1 NADH (3 ATP), 1 acetyl CoA (12 ATP)

182
Q

How many cycles of beta oxidation require for 14-C FA? For 17-C FA?

A

14-C: divide by 2, subtract 1–> 6 rounds

17-C: 7 rounds, odd numbered C uses last 5 C to make acetyl CoA (2C) and succinyl CoA (3C)

183
Q

What type of enzyme is used for oxidation of odd numbered FA?

A

Isomerase (enoyl-CoA isomerase)

Catalyzes movement of double bond to 2-3 position

184
Q

4 steps of beta oxidation

A

Dehydrogenation
Hydration
Dehydrogenation
Thiolase (cleavage)

185
Q

Which of these ketone bodies CANNOT be used for energy by the heart and the brain?
Acetone
Acetoacetate
3-hydroxybutyrate

A

Acetone CANNOT be used for energy

186
Q

Transamination in protein metabolism

A

Exchange of amine group of one molecule for a carbonyl group on another

187
Q

What fuel does heart prefer

A

Fatty acids

Like the endurance muscle it is
Can use ketones in fasting

188
Q

Primary location of FA synthesis

Source of acetyl CoA?

A

Cytosol of liver cells

Always makes 16-C palmitic acid

Citrate shuttle provides acetyl CoA

189
Q

Steps of FA synthesis

A

Condensation
Reduction
Dehydration
Reduction

190
Q

Which provides more energy, glucose or glucose 1-phosphate?

A

G1P is product of glycogenolysis. G1P is converted to G6P (via phosphoglucomutase) and funneled into glycolysis. This skips the first step which requires ATP (glucose to G6P via hexokinase- the investment step)

So G16 is more efficient

191
Q

Which requires ATP:
Alcohol dehydrogenase
Decarboxylases
Phosphofructokinase

A

Phosphofructokinase

Kinases needs ATP for phosphorylation

Other two options use NADH

192
Q

Where does oxidative phosphorylation occur

A

Inner mitochondrial membrane and matrix to a degree (O is final e- acceptor, in matrix)

NOT intermembrane space

193
Q

Where is coenzyme Q in ETC

A

Complex I gives e- from NADH to coenzyme Q (via NADH dehydrogenase)

194
Q

Where does TCA take place

A

Mitochondria

195
Q 
Which of these is endergonic
Glycolysis 
Gluconeogenesis 
Glycogenolysis
Glycogen synthesis
A

Gluconeogenesis- requires coupling to ATP hydrolysis

196
Q

How does insulin affect GLUT2?

A

Not directly. GLUT2 (liver and pancreas) is bidirectional glucose transporter- requires glucose release via gluconeogenesis at same time as glucose uptake towards glycolysis

197
Q

What molecule connects glycolysis and PPP

A

Glucose 6-phosphate

198
Q

What percentage of beta oxidation is redox reactions?

A

50%

  1. Dehydrogenation (oxidation)
  2. Hydration
  3. Dehydrogenation (oxidation)
  4. Thiolysis
199
Q

When comparing 2 LB plots, enzyme that produced steepest slope will have:

A

Higher Km value, low Vmax value

Slope is Km/Vmax

200
Q

How do peptide bonds form

A

Amino terminus of one amino acid attacks carbonyl terminus of another

201
Q

Only amino acid without chirality center

A

Glycine (just an H R group)

202
Q

Atomic oxygen is not found naturally because it is a free radical. It has 8 electrons. Why is it a radical?

A

E- configuration of oxygen:
1s2 2s2 2p4

4 e- in p orbital.
2 will be paired in -1
1 will be in 0
1 will be in +1

These unpaired electrons are free radicals

203
Q

All monosaccharides are reducing sugars?

A

TRUE

204
Q

T/F: a reaction step that follows second order kinetics MUST have only 2 reactants

A

TRUE

205
Q

Oxidation number of C in

(NH2)2CO

A

N is -3 (look at periodic table)
2 x -3 = -6

H is +1
4 x 1 = 4

Oxygen is -2

-6+4-2 = -4 for carbon

206
Q

For a buffer, the pH varies LEAST where?

A

Around the pKa

So a triprotic acid could be a buffer over several pH ranges because of 3 pKa’s

207
Q

On a globular protein, where will leucine and phenylalanine each be?

A

Both interior- Hydrophobic side chains

208
Q

Which will have a lower melting point, valine or ethanol?

A

Ethanol

Valine CAN hydrogen bond because of amino and carboxyl groups
And valine is bigger then ethanol

209
Q

When tittering HCl with NaOH, what pH range should the indicator transition?

A

Strong acid + strong base will neutralize around pH7

Indicator for titration should have transition range around equivalence point

210
Q

Uracil is purine?

A

FALSE. Uracil is pyrimidine

211
Q

Can you separate enantiomers by physical properties?

A

NO- same physical properties, just polarize light in opposite directions

212
Q

What is Ksp expression for

Ca3(PO4)2

A

Ksp = [Ca2+]^3[PO4]^2

213
Q

How will an isotope differ in electron configuration?

A

It won’t

214
Q

The only elements that are exceptions to filing order in electron configurations

A

Transition metals

215
Q

solvents should solubilize all compounds of reaction, and can also act as reagents of reaction. How could you tell if a solvent acts as a reagent? how could you tell if it acts as a catalytic base?

A

if solvent is used as reagent, its functional groups will be present in products
if solvent acts as catalytic base, reaction will begin with abstraction of a proton

216
Q

pKa 1 represents __

pKa1 represents __

A 
pKa1 = carboxyl
pKa2 = amino
217
Q

on LB plot, inverse of x-intercept represents

A

Km

218
Q

intravenous sucrose (C12H22O11) solutions contain 0.34 mol of sucrose per liter. how many grams of sucrose are in 500mL (MW sucrose ~350g/mol)

A
  1. 34mo/L = 0.17mol/0.5L

0. 17mol/0.5L x 350g/mol = 60g / 500mL

219
Q

pKa of citric acid 3.13, what is pH of buffer made of 0.005M citric acid and 0.5M sodium citrate?

A 
pH = pKa + log[base/acid]
pH = 3.13 + log[0.5/0.005]
pH = 3.13 + log(100)
pH = 3.13 + log(1x10^2)
pH = 3.13 + (2) = 5.13
220
Q

how to find enthalpy change of a reaction

A

enthalpy change of rxn = enthalpy(products) - enthalpy (reactions)

221
Q

if Ksp of Cu2S is 5x10^-29, what is [Cu]?

A 
Ksp = [Cu2+]2[S2-] = (2x)^2(x) = 4x^3
5x10^-29 = 4x^3 (->divide by 4)
12.4x10^-30 = x^3
cube root of 12.5 somewhere between 2 and 3
x ~ 2.3x10^-10
222
Q

what does Keq < 1 mean

A

Keq = kforward/ kreverse

Keq < 1 means reverse rate is larger than forward rate

223
Q

how can you tell if a sugar is the beta anomer

A

all substituents are equatorial

224
Q

on a cyclic sugar, which is C1 and which is C6

A

C1 is CW to ring oxygen C6 is CCW to ring oxygen

225
Q

which is least likely to form ionic bond: iron, sodium, helium, magneisum

A

helium- noble gas

226
Q

compare position of oxygen on anomeric carbon in alpha and beta anomers

A

beta- anomeric C on same side of ring as CH2OH

Alpha- anomeric C Anti to CH2OH

227
Q

break starch down to its smallest component

A

starch (poly) - > maltose (di) -> glucose (mono) via pancreatic amylase

228
Q

lactose and its linkage

A

lactose = galactose + glucose
beta linkage

exception to the rule that humans cannot hydrolyze beta-linkages (via lactase)

229
Q

explain how to go from Fischer to Hawthorn projection

A

all groups on RIGHT are DOWN
all groups on LEFT are UP
NEXT TO LAST C (on bottom of Fischer) isn’t included because this hydroxyl becomes ring oxygen upon closure

230
Q

facilitated diffusion uses or releases energy?

A

releases. molecule moves down concentration gradient and does not require energy

231
Q

how does partial pressure of oxygen at high altitude vary, and how does this affect blood pH?

A

partial pressure of O is reduced at high altitude
does not directly affect blood pH
might make you breathe rapidly, which would cause you to blow of CO2 and blood would become more basic (but this is indirect)

232
Q

acetycholinesterase does what?

A

catalyzes hydrolysis of ester functional group

233
Q

ATP is an effective source of energy coupling because hydrolysis of phosphoanhydride bond occurs at low energies. why?

A

resonance stabilized

234
Q

how can there be 63 codons and only 20 amino-acyl tRNA synthase enzymes?

  • wobble allows for +1 amino acids to be paired to same tRNA molecule
  • wobble allows for same amino acid to be paired with +1 tRNA molecule
A

wobble allows for same amino acid to be paired with +1 tRNA molecule

same amino acid can be loaded onto multiple tRNA molecules with different anticodons

235
Q

bonds of cellulose

A

beta(1-4), why we can’t digest it

only beta sugar we can digest is lactose

236
Q

why does Bohr effect cause more oxygen to be released in active muscle tissue?

  • active muscle consumes CO2, causes local decrease in pH
  • active muscle produces CO2, causes local decrease in pH
  • active muscle produces CO2, causes local increase in pH
  • active muscle consumes CO2, causes local increase in pH
A

active muscle produces CO2, causes local decrease in pH
TCA produces CO2, which shifts bicarbonate equilibrium left towards H+

decrease in pH leads to decreased affinity for O2, facilitating oxygen release

237
Q

what is the purpose of washing with cold solvent in recrystallization

A

removes soluble inpurities

238
Q 
which of these amino acids is nonpolar:
T
Q
F
S
A 
T = threonine = polar
Q = glutamine = polar
F = phenylalanine = nonpolar 
S = serine = polar
239
Q

in muscles, action potential triggers calcium channels to open in ___

A

sarcoplasmic reticulum

240
Q

D and L convention, and how to distinguish

A

D/L distinguishes enantiomers of chiral monosaccharides and amino acids
most oxidized position at top, D will have OH on right, L will have OH on Left

241
Q

stearic acid is C17H35CO2H requires how many beta oxidation steps

A

18 C total

(18/2)-1 = 8 rounds

242
Q

what does increase in Km indicate when an inhibitor is present

A

inhibited binding, decreased substrate binding

243
Q

Zn2+ forms quaternary coordination compound- what is bond angle?

A

quaternary = tertiary = 109.5*

octahedral = 90*
trigonal planar = 120*

244
Q

what do NADH/NADPH donate

A

hydride ions (H-)

245
Q

what does SDS page do

A

coats proteins in negative charge so they migrate towards positive terminal
it’s also a pseudo detergent, so it will denature noncovalent bonds but covalent bonds (so not disulfide bonds)
once all proteins are negatively charged, separation will be based on size of protein only

246
Q

what direction does gel electrophoresis run

A

negative to positive (proteins coated in negative charge by SDS page or other substance)

247
Q

carboxylation often use which cofactor

A

biotin

248
Q

buildup of AMP would:
decrease rate of triacylglycerol synthesis
increase rate of enzymatic breakdown of triacylglycerol?

A

buildup of AMP would decrease triacylglycerol synthesis (enzymatic breakdown doesn’t involve phosphate group transfers)

249
Q

myelin acts as conductor T/F?

A

FALSE: myelin is insulator (from outside of axon)

250
Q

how do fat soluble vitamins travel through body

A

DEAK: fat soluble vitamins

travel attached to binding protein (does not need vesicle because it can freely diffuse through cell membrane)

251
Q

compare roles of PCT and DCT

A

PCT- reabsorption of caloric substances (glucose, amino acids, proteins) and secretion of non-ionic substances
DCT- concentration of urine, some ion regulation (acid-base)

252
Q

T/F PPP is stimulated by NADPH

A

FALSE, PPP generates NADPH from NADP+

253
Q

what types of vascular are low pressure systems

A

capillaries and veins

254
Q

heterozygote advantage

A

tendency of carrier of dangerous condition to have survival advantage
ex- sickle cell anemia conveys advantage to malaria

255
Q

substituent of sphingomyelin?

A

phosphocholine

256
Q

what causes menstruation, what causes ovulation?

A

ovulation (day 14)- LH surge

menstruation (end and beginning)- period of lowest FSH/LH secretion

257
Q

aspartate transaminase

A

transfers amino group to alpha-ketoglutarate to form glutamate and oxaloacetate

258
Q

muscarinic acetylcholine receptors

A

throughout CNS and postsynaptic parasympathetic nervous system

259
Q

only two amino acids that are ketogenic but not glucogenic

A

leucine and lysine

260
Q

what do molecule scavengers do

A

inhibit, like sponges- consume molecule

261
Q

if mitochondria is malfunctional, how will CO2 concentration in cell change

A

will rely on anaerobic metabolism- glycolysis

decrease in CO2 because CO2 is product of TCA, which is part of aerobic respiration (takes place in mito matrix)

262
Q

Triglycerides undergo base-catalyzed transesterification with either methanol or ethanol, involving:

a. Attack of carbonyl carbon by alcohol proton
b. Attack of carbonyl carbon by methoxide or ethoxide ion

A

b. Attack of carbonyl carbon by methoxide or ethoxide ion-> correct. During transesterification, base extracts a proton to generate RO- ion (methanol-> methoxide or ethanol-> ethoxide). RO- ion is nucleophile that attacks carbonyl carbon. Product is 3 fatty acid esters and glycerol

(a not correct because protons are not nucleophiles capable of attacking a carbonyl)

263
Q

adrenal medulla releases ___ hormones, posterior pituitary releases ___ hormones

A

adrenal medulla- steroid

posterior pituitary- peptide

264
Q

state of amino acids at physiological pH

A

carboxylic acid deprotonated, amine group positively charged, net charge of 0

265
Q

to do RT-PCR, you need to lyse the cells, then:
isolate and stabilize genomic DNA
or
isolate and stabilize RNA, and generate cDNA

A

isolate and stabilize RNA, and generate cDNA

its RT-PCR! so RNA is reverse transcribed to form cDNA, upon which PCR is performed

266
Q

which is true in skeletal muscle:

  • reduced ATP results in high intracellular Ca2+
  • Ca+ binds calmodulin
  • shorter sarcomere length is stronger contraction
A

only true that reduced ATP results in high intracellular Ca2+–> persistent contraction
(Ca2+ binds calmodulin in cell signaling, but not in muscles- binds troponin)
(sarcomere length follows length-tension relationship, if it’s shorter there’s less space to create potential energy by overlap)

267
Q

exogenous corticosteroids would do what to the hypothalamic-pituitary-adrenal axis?

A

decrease CRH (hypothalamus) and ACTH (anterior pituitary) due to negative feedback

268
Q

where does FADH2 donate its electrons in the ETC

A

ubiquinone (CoQ)

269
Q

what effect will changing FA tails in bilayer from saturated to unsatruated?

A

kinks due to unsaturation increases membrane fluidity and decreases melting point because they can’t pack as tightly

270
Q

how many calories do you get per gram of carb, protein, fat?

A

carb- 4kcal/g
protein- 7kcal/g
fat- 9kcal/g

MCAT (6 decks)

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