Biochemistry Flashcards
4 noncovalent interactions and examples of each
- ionic –> salt bridges
- hydrogen –> nucleic acid base pairing
- van derr Waals –> nucleotide stacking
- partial charge (dipole) –> K channel selectivity filter
What does Ka stand for?
how likely an acid is to donate its proton
- dissocation constant
pH and pKa (3)
pH < pKa –> protonated
pH > pKa –> deprotonated
pH = pKa –> equal probability of pronation/depronation
3 electron carriers
- NAD –> NADH (reduced)
- FAD –> FADH2 (reduced)
- FMN —> FMNH2 (reduced)
What amino acid do you think of when you hear REDOX?
Cysteine (disulfide linkages)
Reduction vs Oxidation
Reduction –> gain electron (catabolic)
Oxidation –> lose electron (anabolic)
2 ways to drive an unfavorable reaction forward
- make a pathway and use up products
2. couple to a favorable reaction (ATP hydrolysis)
delta H
(-) = NRG released from system
(+) = energy added to system
delta S
(-) = decreasing disorder
(+) = increasing disorder
delta G
(-) = free NRG released, exergonic, favorable, spontaneous
(-) = free NRG required, endergonic, unfavorable, nonspontaneous
Catalysis
- enzyme decreased activation energy
- makes product formation more favorable
- does NOT change delta G (more frequent = faster)
- transition state more stable
What is an example of cooperative binding?
hemoglobin
cooperative binding (+, -, 0)
(+) = binding affinity INC w/every binding
(-) = binding affinity DEC w/every binding
(0) = binding sites independent (Michaelis-Menten enzyme –> 1st order enzyme)
Km
Michaelis Constant
- [S] when rxn rate is half maximal or half of active sites are full
- (K-1 + K2)/K1
Vmax
Maximum Velocity
- maximum rate possible for a given [E], observed when enzyme is saturated
- Kcat[E]t
Kcat/Km
Specificity Constant
- measure of enzyme performance by predicting face of E*S
- (Kcat/(K-1 + Kcat)) x K1
Competitive, Noncompetitive, Uncompetitive binding
Competitive: Vmax = constant, Km = varies
Noncompetitive: Vmax = varies, Km = constant
Uncompetitive = Vmax and Km = varies
Substrate vs Feedback lvls of control
Substrate:
- acts on single rxn (G6P and hexokinase, ACoA inhibits PDH)
Feedback:
- acts on different rxn in pathway (nucleotide synth, AA biosynth)
Activation vs Inhibition Regulation
Activation –> dephosphorylation of pyruvate kinase
Inhibition –> phosphorylation of pyruvate kinase
Reversible vs Irreversible Covalent Modification
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
Allosteric vs Competitive Effectors
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
Isozymes vs Enzyme Lvl of Control
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
Nucleic Acid Polymers
- phosphodiester bond
- between 5’ phosphate and 3’ hydroxyl
- next nucleotide added to 3’ end
Amino Acid Polymers
- peptide bond
- between amine (N) and carboxyl (C)
- next AA added to C end
Monosaccharide Polymers
- polysaccharides
- condensation of 2 hydroxyls at various positions (1,2,4,6)
Glycogen (monosaccharide polymer example)
- next glucose added to 4 or 6 position -OH
- @ non-reducing end of existing chain
4 catalysis strategies (Covalent, Acid/Base, Approximation, Electrostatic)
Covalent - share electrons
Acid/Base - share protons
Approximation - orientation and proximity
Electrostatic - noncovalent interactions
Induced Fit Model
active site changes to fit substrate
6 enzyme classes
- oxidoreductase
- transferase
- lyase
- hydrolase
- isomerase
- ligase
oxidoreductases
- redox
- move electrons
ex: dehydrogenase, reductases
transferases
- move functional group
ex: kinase, phosphatase
lyases
- break bond w/o water
ex: aldolase
hydrolases
- break bond w/water
ex: citrate synthase lactonase
isomerases
- rearrange atom order
ex: TPI
ligases
- make a covalent bond
ex: aldolase
Active Transport and examples
- move something against concentration gradient (use ATP)
ex: P-type ATPase, ABC transporter
P-type ATPase
- active transport (Na/K pump)
- phosphorylates self
- transports ions
4 domains: transmembrane, activator, nucleotide binding, phosphorylating
ABC transporter
- active transport (multidrug resistance protein)
- does NOT phosphorylate self
- transport small molecules
dimeric, two copies of transmembrane domain and ATP binding cassette
secondary active transport
- Na/Glucose cotransport
- use gradient established by primary active transport
- moves ion/molecule against gradient w/o using ATP
Passive Transport and examples
- does NOT use ATP
- moves something down concentration gradient
3 examples: ion channel, aquaporin, gap junction
Ion Channel
- passive transport
selectivity filter or gated
Gated = voltage or ligand gates
Aquaporin
- passive transport
selectivity filter, NO gate
Gap Junction
- passive transport
no selectivity filter, no gate
F-type ATP synthase
DOES NOT FALL INTO ANY OF THESE FAMILIES
Macromolecule Catabolic Pathways (8)
- Macromolecule Recycling (5)
- Glycogenolysis, Amino Acid Catabolism, Nucleotide Catabolism + Salvage, B-Oxidation of FA, Ketone Bodies - NRG Production (3)
- Glycolysis, OxPhos, TCA Cycle
Glycolysis (NRG Production)
- cytoplasm
- Rate Limiting Enzyme: phosphofructokinase
- Regulated Enzymes: hexokinase, phosphofructokinase, pyruvate kinase
TCA Cycle (NRG Production)
- mitochondria
- Rate Limiting Enzyme: Isocitrate dehydrogenase
- Regulated Enzymes: PDH complex, Isocitrate dehydrogenase, a-ketoglutarate dehydrogenase
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
Glycogenolysis (Macromolecule Recycling)
- cytoplasm
- Rate Limiting Enzyme: glycogen phosphorylase
- Regulated Enzyme: glycogen phosphorylase
Amino Acid Catabolism (Macromolecule Recycling)
- in cytoplasm AND mitochondria
- Urea Cycle ONLY in Liver
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
Ketone Bodies (Macromolecule Recycling)
- only produced in LIVER
- only broken down in NON-LIVER cells
Acetoacetate –> D-3-hydroxybutyrate or acetone
Macromolecule Anabolic Pathways (7)
- Macromolecule Synthesis (5)
- Gluconeogenesis, Pentose Phosphate Pathway, Nucleotide Synthesis, Amino Acid Biosynthesis, Fatty Acid Synthesis - Storage Polymers (2)
- Glycogenesis, TAG Synthesis
Gluconeogenesis (Macromolecule Synthesis)
- cytoplasm
- Rate Limiting Enzyme: Fructose 1,6 Biphosphate
- Regulated Enzymes: Pyruvate Carboxylase, PEP carboxykinase, Fructose 1,6 Biphosphate
Pentose Phosphate Pathway (Macromolecule Synthesis)
- cytoplasm
- Rate Limiting Enzyme: Glucose 6 phosphate dehydrogenase
- Regulated Enzymes: glucose 6 phosphate dehydrogenase
Nucleotide Synthesis (Macromolecule Synthesis)
- cytoplasm (dihydroorotate dehydrogenase in MITOCHONDRIA)
- Feedback Regulation
- Ribonucleotide Reductase –> activity and specificity site
Amino Acid Biosynthesis (Macromolecule Synthesis)
- cytoplasm AND mitochondrial matrix
- Feedback Regulation
- Regulated Enzyme: Glutamine Synthetase
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
Glycogenesis (Storage Polymer)
- cytoplasm
- Rate Limiting Enzyme: glycogen synthase
- Regulated Enzyme: glycogen synthase
TAG Synthesis (Storage Polymer)
in hepatocytes and adipocytes
