Comprehensive Review > Biochemistry > Flashcards

Biochemistry Flashcards

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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
Monosaccharide Polymers
- polysaccharides | - condensation of 2 hydroxyls at various positions (1,2,4,6)
26
Glycogen (monosaccharide polymer example)
- next glucose added to 4 or 6 position -OH | - @ non-reducing end of existing chain
27
4 catalysis strategies (Covalent, Acid/Base, Approximation, Electrostatic)
Covalent - share electrons Acid/Base - share protons Approximation - orientation and proximity Electrostatic - noncovalent interactions
28
Induced Fit Model
active site changes to fit substrate
29
6 enzyme classes
1. oxidoreductase 2. transferase 3. lyase 4. hydrolase 5. isomerase 6. ligase
30
oxidoreductases
- redox - move electrons ex: dehydrogenase, reductases
31
transferases
- move functional group | ex: kinase, phosphatase
32
lyases
- break bond w/o water | ex: aldolase
33
hydrolases
- break bond w/water | ex: citrate synthase lactonase
34
isomerases
- rearrange atom order | ex: TPI
35
ligases
- make a covalent bond | ex: aldolase
36
Active Transport and examples
- move something against concentration gradient (use ATP) | ex: P-type ATPase, ABC transporter
37
P-type ATPase
- active transport (Na/K pump) - phosphorylates self - transports ions 4 domains: transmembrane, activator, nucleotide binding, phosphorylating
38
ABC transporter
- active transport (multidrug resistance protein) - does NOT phosphorylate self - transport small molecules dimeric, two copies of transmembrane domain and ATP binding cassette
39
secondary active transport
- Na/Glucose cotransport - use gradient established by primary active transport - moves ion/molecule against gradient w/o using ATP
40
Passive Transport and examples
- does NOT use ATP - moves something down concentration gradient 3 examples: ion channel, aquaporin, gap junction
41
Ion Channel
- passive transport selectivity filter or gated Gated = voltage or ligand gates
42
Aquaporin
- passive transport selectivity filter, NO gate
43
Gap Junction
- passive transport no selectivity filter, no gate
44
F-type ATP synthase
DOES NOT FALL INTO ANY OF THESE FAMILIES
45
Macromolecule Catabolic Pathways (8)
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
Glycolysis (NRG Production)
- cytoplasm - Rate Limiting Enzyme: phosphofructokinase - Regulated Enzymes: hexokinase, phosphofructokinase, pyruvate kinase
47
TCA Cycle (NRG Production)
- mitochondria - Rate Limiting Enzyme: Isocitrate dehydrogenase - Regulated Enzymes: PDH complex, Isocitrate dehydrogenase, a-ketoglutarate dehydrogenase
48
Oxidative Phosphorylation (NRG Production)
- 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
Glycogenolysis (Macromolecule Recycling)
- cytoplasm - Rate Limiting Enzyme: glycogen phosphorylase - Regulated Enzyme: glycogen phosphorylase
50
Amino Acid Catabolism (Macromolecule Recycling)
- in cytoplasm AND mitochondria | - Urea Cycle ONLY in Liver
51
B-Oxidation of Fatty Acids (Macromolecule Recycling)
- 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
Ketone Bodies (Macromolecule Recycling)
- only produced in LIVER - only broken down in NON-LIVER cells Acetoacetate --> D-3-hydroxybutyrate or acetone
53
Macromolecule Anabolic Pathways (7)
1. Macromolecule Synthesis (5) - Gluconeogenesis, Pentose Phosphate Pathway, Nucleotide Synthesis, Amino Acid Biosynthesis, Fatty Acid Synthesis 2. Storage Polymers (2) - Glycogenesis, TAG Synthesis
54
Gluconeogenesis (Macromolecule Synthesis)
- cytoplasm - Rate Limiting Enzyme: Fructose 1,6 Biphosphate - Regulated Enzymes: Pyruvate Carboxylase, PEP carboxykinase, Fructose 1,6 Biphosphate
55
Pentose Phosphate Pathway (Macromolecule Synthesis)
- cytoplasm - Rate Limiting Enzyme: Glucose 6 phosphate dehydrogenase - Regulated Enzymes: glucose 6 phosphate dehydrogenase
56
Nucleotide Synthesis (Macromolecule Synthesis)
- cytoplasm (dihydroorotate dehydrogenase in MITOCHONDRIA) - Feedback Regulation - Ribonucleotide Reductase --> activity and specificity site
57
Amino Acid Biosynthesis (Macromolecule Synthesis)
- cytoplasm AND mitochondrial matrix - Feedback Regulation - Regulated Enzyme: Glutamine Synthetase
58
Fatty Acid Synthesis (Macromolecule Synthesis)
- cytoplasm AND mitochondrial matrix - Rate Limiting Enzyme: Acetyl CoA carboxylase - Regulated Enzymes: ATP citrate lyase, Acetyl CoA carboxylase, Fatty Acid Synthase
59
Glycogenesis (Storage Polymer)
- cytoplasm - Rate Limiting Enzyme: glycogen synthase - Regulated Enzyme: glycogen synthase
60
TAG Synthesis (Storage Polymer)
in hepatocytes and adipocytes
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