Biochemistry

Question 1

Oxidation reactions

Answer 1

gain of O atoms
loss of H atoms
loss of e-

Question 2

Reduction reactions

Answer 2

loss of O atoms
gain of H atoms
gain of e-

Question 3

Catabolism

Answer 3

breaking down molecules

e.g., extract energy from glucose - oxidative catabolism

Question 4

Anabolism

Answer 4

building up molecules

generally reductive

Question 5

Bronsted-Lowry Acid

Answer 5

proton (H+) donor

Question 6

Bronsted-Lowry Base

Answer 6

proton (H+) acceptor
often OH- ions
any substance that can accept H+
any anion or neutral species w/ lone pair of e-

Question 7

Lewis Acid

Answer 7

e- pair acceptor

Question 8

Lewis Base

Answer 8

e- pair donor

Question 9

Acidic AAs

Answer 9

aspartic acid (Asp) - D
glutamic acid (Glu) - E

Question 10

Basic AAs

Answer 10

lysine (Lys) - K
arginine (Arg) - R
histidine (His) - H

Question 11

Hydrophobic/Nonpolar AAs

Answer 11

glycine (Gly) - G
alanine (Ala) - A
valine (Val) - V
leucine (Leu) - L
isoleucine (Ile) - I
phenylalanine (Phe) - F
tryptophan (Trp) - W
*methionine (Met) - M 
*proline (Pro) - P

Question 12

Polar AAs

Answer 12

serine (Ser) - S
threonine (Thr) - T
tyrosine (Tyr) - Y
asparagine (Asn) - N
glutamine (Gln) - Q
cysteine (Cys) - C

Question 13

Enzymes

Induced-fit model

Answer 13

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

Question 14

Enzymes

Active site model

Answer 14

lock and key hypothesis

substrate and active site are perfectly complementary

Question 15

Enzyme function

Answer 15

accelerate rate of reaction by stabilizing transition state

Question 16

Enzyme active sites

Answer 16

highly specific in its substrate recognition, including stereospecificity

found in humans: L AAs and D sugars

enzymes that act on hydrophobic substrates have hydrophobic AAs in their active sites, while hydrophilic/polar substrates will have hydrophilic AAs in their active sites

small alterations in active site structure can drastically alter enzymatic activity
both temp and pH have role in enzymatic function

Question 17

Proteases (protein-cleaving enzymes)

Answer 17

have active site with serine residue whose OH group can act as a nucleophile, attacking the carbonyl C of an AA residue in a polypeptide chain
e.g., trypsin, chymotrypsin, elastase
these enzymes usually have a recognition pocket near the active site - this is a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides

Question 18

Cofactors

Answer 18

metal ions or small molecules (not themselves a protein) - required for activity in many enzymes
majority of vitamins in diet are precursors for cofactors

Question 19

Coenzymes

Answer 19

when a cofactor is an organic molecule
often bind to the substrate during a catalyzed reaction
e.g., coenzyme A (CoA)

Question 20

Regulation of Enzyme Activity

Answer 20

1: covalent modification - proteins can have several different groups covalently attached to them, and this can regulate their activity, lifespan in the cell, and/or cellular location.
e.g., addition of a phosphoryl group from ATP by a protein kinase to hydroxyl (OH) of serine, threonine, or tyrosine residues.
phosphorylation of different sites on an enzyme can activate or inactivate the enzyme. protein phosphorylases also phosphorylate proteins, but use free-floating inorganic phosphate (Pi) in the cell instead of ATP. protein phosphorylation can be reversed by protein phosphatases.
2: proteolytic cleavage - many enzymes (and other proteins) are synthesized in inactive forms (zymogens) that are activated by cleavage by a protease.
3: association with other polypeptides - some enzymes have catalytic activity in 1 polypeptide subunit that is regulated by association with a separate regulatory subunit.
e.g., some proteins demonstrate continuous rapid catalysis if their regulatory subunit is removed - constitutive activity (continuous/unregulated).
e.g., other proteins that require association with another peptide in order to function.
4: allosteric regulation - modification of active-site activity through interactions of molecules with other specific sites on the enzyme (allosteric sites)

Question 21

Allosteric regulation

Answer 21

biochemical switch - turn if on/off
binding of allosteric regulator to allosteric site generally noncovalent and reversible
when bound can alter conformation of enzyme to increase or decrease catalysis

Question 22

Feedback inhibition/Negative feedback

Answer 22

enzymes act as part of pathways - usually only around 2 key enzymes regulated, such as enzyme that catalyzes first irreversible step in pathway
e.g., A->B->C->D, if enough D can shut off enzyme early in pathway

Question 23

Feedforward stimulation

Answer 23

stimulation of an enzyme by its substrate or by a molecule used in the synthesis of the substrate
e.g., A might stimulate E3 (enzyme later in pathway)

Question 24

Reaction rate

Answer 24

V = velocity
amount of product formed per unit time, in moles per second (mol/s)
depends on:
- [S]
- [E]
if little S, rate V is directly proportional to amount of S added: double S and rxn rate doubles
if adding more S doesn’t increase V, enzyme is saturated - Vmax
Km = [S] at which rxn velocity if half its maximum (mark Vmax on y-axis, divide distance by 1/2 to find 1/2Vmax, Km found by drawing horizontal line to curve and vertical line down to x-axis)
low Km –> not much S required to get rxn rate to 1/2Vmax, so E has high affinity for S

Question 25

Cooperativity

Answer 25

type of allosteric interaction - 1 active site acts like allosteric regulatory site for other active sites
positive and negative
positive: binding of S to 1 subunit increases the affinity of other subunits for S (tense to relaxed)
sigmoidal curve results from positive cooperative binding:
- at low [S], E complex has low affinity for S, adding more S increses rate a little
- steep at [S]s where adding S greatly increases rxn rate, E complex in relaxed state
- levelling off where E saturated

cooperative enzymes must have more than 1 active site, usually multisubunit complexes, may be single-subunit enzyme

cooperativity not just applied to catalytic enzymes: hemoglobin (Hb) is protein complex of 4 polypeptide subunits, each contain heme prosthetic group w/ single O2 binding site, Hb is carrier (of O), not catalyst of reaction (not enzyme), exhibits positive cooperative O2 binding. Hb-O2 dissociation curve is sigmoidal.

Question 26

Competitive inhibition

Answer 26

compete with S for binding at active site
inhibition can be overcome by adding more S –> if [S] high enough, can outcompete inhibitor
Vmax not affected (can get same Vmax but takes more S)
Km increased

Question 27

Noncompetitive inhibition

Answer 27

bind at allosteric site, not active site
no matter how much S added, inhibitor not displaced from its site - Vmax decreases
Km same - S can still bind active site, but inhibitor prevents catalytic activity of E

Question 28

Uncompetitive inhibition

Answer 28

only able to bind to E-S complex (cannot bind before the S has bound)
binds allosteric sites - Vmax decreases (by limiting amount of available E-S complex which can be converted to product)
by sequestering E bound to S, this increases apparent affinity of E for S as it cannot readily dissociate - Km decreases

Question 29

Mixed-type inhibition

Answer 29

inhibitor can bind to either unoccupied E OR E-S complex
if E has greater affinity for inhibitor in free form, E will have lower affinity for S (similar to competitive inhibition) - Km increases
if E-S complex has greater affinity for inhibitor, E will have greater affinity for S (similar to uncompetitive inhibition) - Km decreases
if equal affinity = uncompetitive inhibitor
in each, inhibitor binds to allosteric site and additional S cannot overcome inhibition - Vmax decreases

Question 30

Inhibition summary

Answer 30

Competitive:
Vmax same, Km inc

Noncompetitive:
Vmax dec, Km same

Uncompetitive:
Vmax dec, Km dec

Mixed:
Vmax dec, Km varies

Question 31

Lineweaver-Burk plot

Answer 31

x-axis = 1/[S]
y-axis = 1/V

slope = Km/Vmax
y-int = 1/Vmax
x-int = -1/Km

inc in [S] = dec in 1/[S] - dec in value on x-axis
inc in rxn rate (V) = dec in 1/V - as V inc, value on y-axis dec

Question 32

Inhibitors and L-B plot

Answer 32

Competitive:
y-int same, x-int dec (b/c Km inc)

Noncompetitive:
y-int inc (Vmax decreases so slope inc), x-int same

Uncompetitive:
y-int inc, x-int inc

Question 33

Cellular respiration

Answer 33

glucose oxidized to produce CO2 and ATP - 4 step process
2,3 - require O in cell, but neither use O directly
1: glycolysis - glucose partially oxidized while its split in half into 2 identical pyruvate molecules (pyruvic acid), produces small amount ATP and NADH
- occurs in cytoplasm
- O not required
2: pyruvate dehydrogenase complex (PDC) - pyruvate produced in glycolysis is dearboxylated to form acetyl group, acteyl group then attached to coenzyme A (carrier that can transfer acetyl group into Krebs cycle), small amount NADH produced
3: Krebs cycle (tricarboxylic acid cycle [TCA cycle] or citric acid cycle) - acetyl group from the PDC is added to oxaloacetate to form citric acid. citric acid decarboxylated and isomerized to regenerate original oxaloacetate. modest amount of ATP, large amount of NADPH, and small amount FADH2 produced.
4: e- transport/oxidative phosphorylation - high-energy e- carried by NADH and FADH2 are oxidized by the ETC in inner mito membrane. the reduced e- carriers dump e- at beginning of chain, and O is reduced to H2O at end. e- energy libertated by the ETC is used to pump protons out of innermost compartment of mito. H+ allowed to flow back into mito, and energy of this proton flow used to produce the high-energy triphophate group in ATP.
- oxidative –> refers to use of O to oxidize the reduced e- carriers NADH and FADH2)

Question 34

Glycolysis

Answer 34

universal 1st step in glucose metabolism, all cells from all domains possess enzymes in this pathway
2 net ATP produced

Question 35

PDC

Answer 35

2 3C pyruvates oxidized to 2 2C
pyruvate –> acetyl-CoA
2NADH produced
1 CO2 released (oxidized)

Question 36

Krebs cycle

Answer 36

2C from acetyl-CoA + oxaloacetate = citrate (6C)
2 CO2 released
NADH, FADH2 produced
oxaloacetate regenerated

Question 37

ETC

Answer 37

oxidation of the high-energy e- carriers NADH and FADH2 coupled to the phophorylation of ADP to produce ATP
5 e- carriers
proton gradient used to drive phosphorylation of ADP to ATP

Question 38

Gluconeogenesis

Answer 38

when dietary sources of glucose are unavailable and when liver had depleted its stores of glycogen and glucose
occurs primarily in liver (and a bit in kidneys)
converts non-carb precursor moleculess into intermediates where they eventually become glucose
glycolysis-in-reverse
requires 4 ATP, 2 GTP, 2 NADH
made thermodynamically stable by coupling rxns to the hydrolysis of high-energy phosphate bonds of GTP and ATP

Question 39

Pentose Phosphate Pathway

Answer 39

G6PDH = primary point of regulation
6-phosphogluconate –> ribulose-5-P
2x NADPH generated

Question 40

FA Metabolism

FA oxidation

Answer 40

free FAs can undergo B-oxidation
begins at outer mito membrane with activation of the FA
rxn catalyzed by acyl-CoA sythetase
requires 2 ATP to generate fatty acyl-CoA, then transported into mito, undergoes 4 rxns to liberate acetyl-CoA, also produce FADH2 and NADH
acetyl-CoA can go to Krebs cycle

unsat FA: less energy produced, skip step of generating FADH2 (b/c don’t need to create double bond)