Biochemistry 1 Flashcards
catalysts
- increase the rate of the reaction by
- stabilizing the TS
- reduce Ea
- does not change ΔG. cannot make a nonspontaneous reaction spontaneous.
- kinetic not thermodynamic role.
- take an already spontaneous reaction and make it go faster.
3 defining characteristics of enzymes/catalysts
- must increase reaction rate
- must not be used up in the reaction - regenerated
- specific for a particular reaction
lock and key model
- substrate and active site are perfectly complementary
induced fit model
- binding of substrate causes conformational change in enzyme.
active site of an enzyme stereospecificity
- L amino acids (LA)
- D sugars/carbs (DC)
Vmax depends on
- enzyme concentration
- type of enzyme you have
Km
- the concentration of substrate required to reach 1/2 Vmax
- higher affinity has smaller Km
competitive inhibition
- binds reversibly at active site
- no change on Vmax
- increases Km
- overcome by adding more substrate
non-competitive inhibition
- binds at allosteric site
- reduces Vmax
- no change on Km
- adding more substrate does not help.
uncompetitive inhibition
- binds at allosteric site of ES complex
- reduces Vmax
- reduces Km
- limits amount of ES to be converted to product
mixed inhibition
- binds at allosteric site of E alone or ES complex
- reduces Vmax
- Km varies
if inhibitor has affinity for ES complex
- looks more like uncompetitive
if inhibitor has affinity for enzyme
- looks like competitive
if inhibitor has equal affinity for enzyme and ES complex
- looks like non competitive.
4 biologically relevant macromolecules
- proteins
- carbohydrates
- lipids
- nucleic acids
- all polymers
- enzymes that make them are called polymerases
- run in polymerization reactions or dehydration synthesis
pH < pka
will be positively charged
ph > pka
will be negatively charged
ph = pka
will be neutral (zwitterion)
acidic amino acid has
(-) charge at physiological pH
basic amino acid has
(+) charge at physiological pH
2 covalent bonds in proteins
- peptide bond
- disulfide bridge between cysteines.
primary structure of protein
- amino acid sequence
- determined by peptide bond
secondary structure of protein
- hydrogen bonding interactions between backbone atoms
- alpha helix
- beta pleated sheet
why is proline not found in the alpha helix
- will cause kink
same direction beta sheet
- parallel
opposite direction beta sheet
- antiparallel
denatured protein
- improperly folded
denaturation
- disruption of protein structure without breaking peptide bonds
- urea
- extreme pH and temp
- change in salt concentration (tonicity)
tertiary structure
- due to side chain interactions within a peptide
- noncovalent and covalent
noncovalent interactions in tertiary structure
- polar/polar
- nonpolar/nonpolar
- acidic/basic
- electrostatic
covalent interactions in tertiary structure
- disulfide bridge
- found in extracellular protein
- stabilizes tertiary protein structure.
quaternary structure
- structure due to side chain interactions between different polypeptide subunits
- no peptide bonds found
monomer of carbs
- monosaccharide
- CnH2nOn
3 common sugars
- glucose - 6 membered
- fructose - 5 membered
- galactose
C6H12O6
3 common disaccharides
- maltose (glucose + glucose) alpha 1-4
- sucrose (glucose + fructose) alpha 1-2
- lactose (glucose + galactose) beta 1-4
formula for disaccharides
C12H22O11
C12H24O12 - H2O
multiple monosaccharides
- polysaccharides
3 common polysaccharides
- glycogen - animal storage (alpha 1-4 for residues, 1-6 for linking)
- starch - plant storage (alpha)
- cellulose - plant structure (beta 1-4, 1-6)
functions of polysaccharides
- energy
- cell surface markers
- cell adhesion
hydrocarbon
- monomer of lipid
- long unsubstituted alkane that ends in a carboxylic acid
- synthesized 2 carbons at a time
saturated fatty acid
- covalently bound to maximum number of hydrogen
- solid at room temperature (worse for body)
- no double bonds
- more rigid less fluid
unsaturated fatty acid
- one or more double bonds
- Z or cis
- liquid at room temperature (better for body)
- disrupts packing
amphoteric
- acts as acid or base
amphiphilic
- both polar and nonpolar
triglyceride
- stored energy
- glycerol
- 3 fatty acids
why are fats more more efficient for energy storage than carbs
- packing - hydrophobicity allows great, close packing
- energy content - more energy carbon for carbon. more reduced so when they are oxidized produce more energy.
phospholipids
- barrier between intracellular and extracellular environments
- form lipid bilayer
- driven by hydrophobic interactions. stabilized by van der waals forces between tails
what determines fluidity
- saturation
- tail length
- amount of cholesterol
how many isoprenes to make a terpene?
- 3
- must have 2 isoprenes minimal to make a terpene
function of terpenes
- precursor to cholesterol, ear wax
- vitamin A terpenoid
cholesterol
- 666 + 5
- obtained from diet
- synthesized in liver
- carried in blood w/ fats and proteins (lipoproteins)
functions of cholesterol
- cell membranes
- precursors to steroids
- bile
cholesterol at low temps
cholesterol at high temps
- increases fluidity
- decreases fluidity
- paradox
solving for enthalpy
ΔH = E + PΔV
reduced form of the disulfide bond
- broken
- cysteine’s acquiring H’s
exergonic
- (-)ΔG
- products lower in energy than reactants
endergonic
- (+)ΔG
- reactants lower in energy than products
squalene is how many isoprenes
- 6
- 3 terpenes
ATP hydrolysis
- 30.5 kJ
- 12 kcal/mol
how fast something will happen?
- kinetics
cofactor
- metal ions or small molecules
coenzyme
- cofactor that is an organic molecule
to switch an enzyme to on/off
- phosphorylation
- allosteric regulation
allosteric regulation
- bind somewhere other than active site (allosteric site) to modify enzyme function.
positive feedback regulator
- must have external regulator.
y intercept in LB
1/vmax
x intercept in LB
-1/Km
