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Princeton Bio > Biochemistry 1 > Flashcards

Biochemistry 1 Flashcards

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1
Q

catalysts

A
  • 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.
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2
Q

3 defining characteristics of enzymes/catalysts

A
  • must increase reaction rate
  • must not be used up in the reaction - regenerated
  • specific for a particular reaction
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3
Q

lock and key model

A
  • substrate and active site are perfectly complementary
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4
Q

induced fit model

A
  • binding of substrate causes conformational change in enzyme.
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5
Q

active site of an enzyme stereospecificity

A
  • L amino acids (LA)

- D sugars/carbs (DC)

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6
Q

Vmax depends on

A
  • enzyme concentration

- type of enzyme you have

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7
Q

Km

A
  • the concentration of substrate required to reach 1/2 Vmax

- higher affinity has smaller Km

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8
Q

competitive inhibition

A
  • binds reversibly at active site
  • no change on Vmax
  • increases Km
  • overcome by adding more substrate
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9
Q

non-competitive inhibition

A
  • binds at allosteric site
  • reduces Vmax
  • no change on Km
  • adding more substrate does not help.
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10
Q

uncompetitive inhibition

A
  • binds at allosteric site of ES complex
  • reduces Vmax
  • reduces Km
  • limits amount of ES to be converted to product
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11
Q

mixed inhibition

A
  • binds at allosteric site of E alone or ES complex
  • reduces Vmax
  • Km varies
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12
Q

if inhibitor has affinity for ES complex

A
  • looks more like uncompetitive
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13
Q

if inhibitor has affinity for enzyme

A
  • looks like competitive
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14
Q

if inhibitor has equal affinity for enzyme and ES complex

A
  • looks like non competitive.
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15
Q

4 biologically relevant macromolecules

A
  • proteins
  • carbohydrates
  • lipids
  • nucleic acids
  • all polymers
  • enzymes that make them are called polymerases
  • run in polymerization reactions or dehydration synthesis
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16
Q

pH < pka

A

will be positively charged

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17
Q

ph > pka

A

will be negatively charged

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18
Q

ph = pka

A

will be neutral (zwitterion)

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19
Q

acidic amino acid has

A

(-) charge at physiological pH

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20
Q

basic amino acid has

A

(+) charge at physiological pH

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21
Q

2 covalent bonds in proteins

A
  • peptide bond

- disulfide bridge between cysteines.

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22
Q

primary structure of protein

A
  • amino acid sequence

- determined by peptide bond

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23
Q

secondary structure of protein

A
  • hydrogen bonding interactions between backbone atoms
  • alpha helix
  • beta pleated sheet
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24
Q

why is proline not found in the alpha helix

A
  • will cause kink
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25
Q

same direction beta sheet

A
  • parallel
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26
Q

opposite direction beta sheet

A
  • antiparallel
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27
Q

denatured protein

A
  • improperly folded
28
Q

denaturation

A
  • disruption of protein structure without breaking peptide bonds
  • urea
  • extreme pH and temp
  • change in salt concentration (tonicity)
29
Q

tertiary structure

A
  • due to side chain interactions within a peptide

- noncovalent and covalent

30
Q

noncovalent interactions in tertiary structure

A
  • polar/polar
  • nonpolar/nonpolar
  • acidic/basic
  • electrostatic
31
Q

covalent interactions in tertiary structure

A
  • disulfide bridge
  • found in extracellular protein
  • stabilizes tertiary protein structure.
32
Q

quaternary structure

A
  • structure due to side chain interactions between different polypeptide subunits
  • no peptide bonds found
33
Q

monomer of carbs

A
  • monosaccharide

- CnH2nOn

34
Q

3 common sugars

A
  • glucose - 6 membered
  • fructose - 5 membered
  • galactose

C6H12O6

35
Q

3 common disaccharides

A
  • maltose (glucose + glucose) alpha 1-4
  • sucrose (glucose + fructose) alpha 1-2
  • lactose (glucose + galactose) beta 1-4
36
Q

formula for disaccharides

A

C12H22O11

C12H24O12 - H2O

37
Q

multiple monosaccharides

A
  • polysaccharides
38
Q

3 common polysaccharides

A
  • glycogen - animal storage (alpha 1-4 for residues, 1-6 for linking)
  • starch - plant storage (alpha)
  • cellulose - plant structure (beta 1-4, 1-6)
39
Q

functions of polysaccharides

A
  • energy
  • cell surface markers
  • cell adhesion
40
Q

hydrocarbon

A
  • monomer of lipid
  • long unsubstituted alkane that ends in a carboxylic acid
  • synthesized 2 carbons at a time
41
Q

saturated fatty acid

A
  • covalently bound to maximum number of hydrogen
  • solid at room temperature (worse for body)
  • no double bonds
  • more rigid less fluid
42
Q

unsaturated fatty acid

A
  • one or more double bonds
  • Z or cis
  • liquid at room temperature (better for body)
  • disrupts packing
43
Q

amphoteric

A
  • acts as acid or base
44
Q

amphiphilic

A
  • both polar and nonpolar
45
Q

triglyceride

A
  • stored energy
  • glycerol
  • 3 fatty acids
46
Q

why are fats more more efficient for energy storage than carbs

A
  • packing - hydrophobicity allows great, close packing

- energy content - more energy carbon for carbon. more reduced so when they are oxidized produce more energy.

47
Q

phospholipids

A
  • barrier between intracellular and extracellular environments
  • form lipid bilayer
  • driven by hydrophobic interactions. stabilized by van der waals forces between tails
48
Q

what determines fluidity

A
  • saturation
  • tail length
  • amount of cholesterol
49
Q

how many isoprenes to make a terpene?

A
  • 3

- must have 2 isoprenes minimal to make a terpene

50
Q

function of terpenes

A
  • precursor to cholesterol, ear wax

- vitamin A terpenoid

51
Q

cholesterol

A
  • 666 + 5
  • obtained from diet
  • synthesized in liver
  • carried in blood w/ fats and proteins (lipoproteins)
52
Q

functions of cholesterol

A
  • cell membranes
  • precursors to steroids
  • bile
53
Q

cholesterol at low temps

cholesterol at high temps

A
  • increases fluidity
  • decreases fluidity
  • paradox
54
Q

solving for enthalpy

A

ΔH = E + PΔV

55
Q

reduced form of the disulfide bond

A
  • broken

- cysteine’s acquiring H’s

56
Q

exergonic

A
  • (-)ΔG

- products lower in energy than reactants

57
Q

endergonic

A
  • (+)ΔG

- reactants lower in energy than products

58
Q

squalene is how many isoprenes

A
  • 6

- 3 terpenes

59
Q

ATP hydrolysis

A
  • 30.5 kJ

- 12 kcal/mol

60
Q

how fast something will happen?

A
  • kinetics
61
Q

cofactor

A
  • metal ions or small molecules
62
Q

coenzyme

A
  • cofactor that is an organic molecule
63
Q

to switch an enzyme to on/off

A
  • phosphorylation

- allosteric regulation

64
Q

allosteric regulation

A
  • bind somewhere other than active site (allosteric site) to modify enzyme function.
65
Q

positive feedback regulator

A
  • must have external regulator.
66
Q

y intercept in LB

A

1/vmax

67
Q

x intercept in LB

A

-1/Km

Princeton Bio (14 decks)

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