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Comprehensive Review > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

4 noncovalent interactions and examples of each

A
  1. ionic –> salt bridges
  2. hydrogen –> nucleic acid base pairing
  3. van derr Waals –> nucleotide stacking
  4. partial charge (dipole) –> K channel selectivity filter
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2
Q

What does Ka stand for?

A

how likely an acid is to donate its proton

  • dissocation constant
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3
Q

pH and pKa (3)

A

pH < pKa –> protonated

pH > pKa –> deprotonated

pH = pKa –> equal probability of pronation/depronation

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4
Q

3 electron carriers

A
  1. NAD –> NADH (reduced)
  2. FAD –> FADH2 (reduced)
  3. FMN —> FMNH2 (reduced)
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5
Q

What amino acid do you think of when you hear REDOX?

A

Cysteine (disulfide linkages)

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6
Q

Reduction vs Oxidation

A

Reduction –> gain electron (catabolic)

Oxidation –> lose electron (anabolic)

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7
Q

2 ways to drive an unfavorable reaction forward

A
  1. make a pathway and use up products

2. couple to a favorable reaction (ATP hydrolysis)

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8
Q

delta H

A

(-) = NRG released from system

(+) = energy added to system

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9
Q

delta S

A

(-) = decreasing disorder

(+) = increasing disorder

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10
Q

delta G

A

(-) = free NRG released, exergonic, favorable, spontaneous

(-) = free NRG required, endergonic, unfavorable, nonspontaneous

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11
Q

Catalysis

A
  • enzyme decreased activation energy
  • makes product formation more favorable
  • does NOT change delta G (more frequent = faster)
  • transition state more stable
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12
Q

What is an example of cooperative binding?

A

hemoglobin

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13
Q

cooperative binding (+, -, 0)

A

(+) = binding affinity INC w/every binding

(-) = binding affinity DEC w/every binding

(0) = binding sites independent (Michaelis-Menten enzyme –> 1st order enzyme)

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14
Q

Km

A

Michaelis Constant

  • [S] when rxn rate is half maximal or half of active sites are full
  • (K-1 + K2)/K1
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15
Q

Vmax

A

Maximum Velocity

  • maximum rate possible for a given [E], observed when enzyme is saturated
  • Kcat[E]t
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16
Q

Kcat/Km

A

Specificity Constant

  • measure of enzyme performance by predicting face of E*S
  • (Kcat/(K-1 + Kcat)) x K1
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17
Q

Competitive, Noncompetitive, Uncompetitive binding

A

Competitive: Vmax = constant, Km = varies

Noncompetitive: Vmax = varies, Km = constant

Uncompetitive = Vmax and Km = varies

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18
Q

Substrate vs Feedback lvls of control

A

Substrate:
- acts on single rxn (G6P and hexokinase, ACoA inhibits PDH)

Feedback:
- acts on different rxn in pathway (nucleotide synth, AA biosynth)

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19
Q

Activation vs Inhibition Regulation

A

Activation –> dephosphorylation of pyruvate kinase

Inhibition –> phosphorylation of pyruvate kinase

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20
Q

Reversible vs Irreversible Covalent Modification

A

Reversible:

  • addition/removal of small molecule (may be act or inhib)
  • histone modification, phosphorylation, adenylyl/uridylylation and glutamine synthetase

Irreversible:

  • proteolytic activity (always activating)
  • protease/digestive enzyme, insulin, blood clotting factors
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21
Q

Allosteric vs Competitive Effectors

A

Allosteric:

  • does not bind at active site, may be activating or inhibitory
  • binds at unique location and alters protein function
  • ACTase, ribonucleotide reductase, phosphofructokinase

Competitive:

  • binds at active site, always inhibitory
  • competes w/intended substrate to bind active site
  • methotraxate vs dihydrofolate for dihydrofolate reductase
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22
Q

Isozymes vs Enzyme Lvl of Control

A

Isozymes:

  • functional variants of single enzyme
  • hexokinase/glucokinase, LDH 1-4, sirtuins

Enzyme Lvl Control:

  • alter how much of enzyme is produced
  • hexokinase/glucokinase, LDH 1-4
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23
Q

Nucleic Acid Polymers

A
  • phosphodiester bond
  • between 5’ phosphate and 3’ hydroxyl
  • next nucleotide added to 3’ end
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24
Q

Amino Acid Polymers

A
  • peptide bond
  • between amine (N) and carboxyl (C)
  • next AA added to C end
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25
Q

Monosaccharide Polymers

A
  • polysaccharides

- condensation of 2 hydroxyls at various positions (1,2,4,6)

26
Q

Glycogen (monosaccharide polymer example)

A
  • next glucose added to 4 or 6 position -OH

- @ non-reducing end of existing chain

27
Q

4 catalysis strategies (Covalent, Acid/Base, Approximation, Electrostatic)

A

Covalent - share electrons

Acid/Base - share protons

Approximation - orientation and proximity

Electrostatic - noncovalent interactions

28
Q

Induced Fit Model

A

active site changes to fit substrate

29
Q

6 enzyme classes

A
  1. oxidoreductase
  2. transferase
  3. lyase
  4. hydrolase
  5. isomerase
  6. ligase
30
Q

oxidoreductases

A
  • redox
  • move electrons

ex: dehydrogenase, reductases

31
Q

transferases

A
  • move functional group

ex: kinase, phosphatase

32
Q

lyases

A
  • break bond w/o water

ex: aldolase

33
Q

hydrolases

A
  • break bond w/water

ex: citrate synthase lactonase

34
Q

isomerases

A
  • rearrange atom order

ex: TPI

35
Q

ligases

A
  • make a covalent bond

ex: aldolase

36
Q

Active Transport and examples

A
  • move something against concentration gradient (use ATP)

ex: P-type ATPase, ABC transporter

37
Q

P-type ATPase

A
  • active transport (Na/K pump)
  • phosphorylates self
  • transports ions

4 domains: transmembrane, activator, nucleotide binding, phosphorylating

38
Q

ABC transporter

A
  • active transport (multidrug resistance protein)
  • does NOT phosphorylate self
  • transport small molecules

dimeric, two copies of transmembrane domain and ATP binding cassette

39
Q

secondary active transport

A
  • Na/Glucose cotransport
  • use gradient established by primary active transport
  • moves ion/molecule against gradient w/o using ATP
40
Q

Passive Transport and examples

A
  • does NOT use ATP
  • moves something down concentration gradient

3 examples: ion channel, aquaporin, gap junction

41
Q

Ion Channel

A
  • passive transport

selectivity filter or gated

Gated = voltage or ligand gates

42
Q

Aquaporin

A
  • passive transport

selectivity filter, NO gate

43
Q

Gap Junction

A
  • passive transport

no selectivity filter, no gate

44
Q

F-type ATP synthase

A

DOES NOT FALL INTO ANY OF THESE FAMILIES

45
Q

Macromolecule Catabolic Pathways (8)

A
  1. Macromolecule Recycling (5)
    - Glycogenolysis, Amino Acid Catabolism, Nucleotide Catabolism + Salvage, B-Oxidation of FA, Ketone Bodies
  2. NRG Production (3)
    - Glycolysis, OxPhos, TCA Cycle
46
Q

Glycolysis (NRG Production)

A
  • cytoplasm
  • Rate Limiting Enzyme: phosphofructokinase
  • Regulated Enzymes: hexokinase, phosphofructokinase, pyruvate kinase
47
Q

TCA Cycle (NRG Production)

A
  • mitochondria
  • Rate Limiting Enzyme: Isocitrate dehydrogenase
  • Regulated Enzymes: PDH complex, Isocitrate dehydrogenase, a-ketoglutarate dehydrogenase
48
Q

Oxidative Phosphorylation (NRG Production)

A
  • mitochondria
Complex 1 inhib: amytal, retenone
Complex 2 inhib: malonate
Complex 3 inhib: antimycin
Complex 4 inhib: CO, cyanide, H2S
Complex 5 inhib: oligomycin
49
Q

Glycogenolysis (Macromolecule Recycling)

A
  • cytoplasm
  • Rate Limiting Enzyme: glycogen phosphorylase
  • Regulated Enzyme: glycogen phosphorylase
50
Q

Amino Acid Catabolism (Macromolecule Recycling)

A
  • in cytoplasm AND mitochondria

- Urea Cycle ONLY in Liver

51
Q

B-Oxidation of Fatty Acids (Macromolecule Recycling)

A
  • Phase 1: FA activation (cytoplasm)
    • outer mito NOT permeable: FA
    • inner mito NOT permeable: FA CoA
  • Phase II: Beta Oxidation (mitochondria)
  • Rate Limiting Enzyme: perilipins
  • Regulated Enzymes: perilipins –> phosphorylation promotes TAG release by inhibiting perilipins
52
Q

Ketone Bodies (Macromolecule Recycling)

A
  • only produced in LIVER
  • only broken down in NON-LIVER cells

Acetoacetate –> D-3-hydroxybutyrate or acetone

53
Q

Macromolecule Anabolic Pathways (7)

A
  1. Macromolecule Synthesis (5)
    - Gluconeogenesis, Pentose Phosphate Pathway, Nucleotide Synthesis, Amino Acid Biosynthesis, Fatty Acid Synthesis
  2. Storage Polymers (2)
    - Glycogenesis, TAG Synthesis
54
Q

Gluconeogenesis (Macromolecule Synthesis)

A
  • cytoplasm
  • Rate Limiting Enzyme: Fructose 1,6 Biphosphate
  • Regulated Enzymes: Pyruvate Carboxylase, PEP carboxykinase, Fructose 1,6 Biphosphate
55
Q

Pentose Phosphate Pathway (Macromolecule Synthesis)

A
  • cytoplasm
  • Rate Limiting Enzyme: Glucose 6 phosphate dehydrogenase
  • Regulated Enzymes: glucose 6 phosphate dehydrogenase
56
Q

Nucleotide Synthesis (Macromolecule Synthesis)

A
  • cytoplasm (dihydroorotate dehydrogenase in MITOCHONDRIA)
  • Feedback Regulation
  • Ribonucleotide Reductase –> activity and specificity site
57
Q

Amino Acid Biosynthesis (Macromolecule Synthesis)

A
  • cytoplasm AND mitochondrial matrix
  • Feedback Regulation
  • Regulated Enzyme: Glutamine Synthetase
58
Q

Fatty Acid Synthesis (Macromolecule Synthesis)

A
  • cytoplasm AND mitochondrial matrix
  • Rate Limiting Enzyme: Acetyl CoA carboxylase
  • Regulated Enzymes: ATP citrate lyase, Acetyl CoA carboxylase, Fatty Acid Synthase
59
Q

Glycogenesis (Storage Polymer)

A
  • cytoplasm
  • Rate Limiting Enzyme: glycogen synthase
  • Regulated Enzyme: glycogen synthase
60
Q

TAG Synthesis (Storage Polymer)

A

in hepatocytes and adipocytes

Comprehensive Review (7 decks)

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