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MCAT Biology > Biochemistry > Flashcards

Biochemistry Flashcards

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1
Q

Hydropathy index

A

measure of polarity of amino acid residue; how hydrophobic vs how hydrophilic an amino acid is

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2
Q

higher the hydropathy value (kJ/mol) –> the more ______ the amino acid

A

hydrophobic

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3
Q

lower the hydropathy value (kJ/mol) –> the more ______ the amino acid

A

hydrophilic

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4
Q

hydropathy value of peptide chain

A

sum of individual hydropathy value of each residue

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5
Q

primary structure of protein

A

sequence of amino acids, held together by peptide bonds

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6
Q

secondary structure of protein

A

local folding, only relatively close residues interact, held together by backbone interaction (H-bonds between amine H and carbonyl O of the backbone)

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7
Q

tertiary structure of protein

A

global folding, held together by side group interaction (disulfide bonds, ionic bonds, H-bonds, hydrophobic interaction)

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8
Q

quaternary structure of protein

A

different peptides/proteins interacting, held together by side group interactions

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9
Q

forms of denaturation

A

heat, pH, salts, detergents

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10
Q

Lineweaver-Burke Plot:

Equation

A
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11
Q

Lineweaver-Burke Plot:

x-intercept

A
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12
Q

Lineweaver-Burke Plot:

y-intercept

A
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13
Q

competitive inhibitor

A

binds E, Km increases, Vmax stays the same

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14
Q

uncompetitive inhibitor

A

binds ES, Km decreases (more ES formed), Vmax decreases

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15
Q

noncompetitive inhibitor

A

binds to E and ES, Km stays the same, Vmax decreases

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16
Q

allosteric inhibitor

A

binds to a site other than the substrate binding site

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17
Q

bind to a specific amino acid in the active site

A

group specific reagents

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18
Q

similar size and shape as substrate, binds covalently in active site

A

affinity labels (substrate analogs)

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19
Q

very similar to substrate (in size, shape, and charge), bind in active site with noncovalent bonds, causes reaction to happen, product is made that covalently binds to active site (blocking it)

A

suicide inhibitors

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20
Q

amino acids found in active sites

A

catalytic residues

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21
Q

types of enzymes

A

OTHLIL: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases

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22
Q

optimal pH and temperature of enzymes

A

optimal pH varies greatly, temperature is 37 ºC

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23
Q

the non-protein component of an enzyme required for catalysis, some enzymes require them but not all; two types: essential ions and coenzymes

A

cofactor

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24
Q

type of cofactor:

organic molecules that contribute to catalytic function of enzymes; include NAD+/NADH

A

coenzymes

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25
Q

glycosidic bond

A

links monosaccharides together; anomeric C of one MS bonded to an OH on a second MS

26
Q

maltose

A

glucose + glucose, 1 => 4, both in α, homoglycan

27
Q

cellobiose

A

glucose + glucose, 1 => 4, first glucose in β; released on breakdown of cellulose, homoglycan

28
Q

lactose

A

galactose + glucose, 1 => 4, heteroglycan

29
Q

sucrose

A

glucose + fructose, 1 => 2, heteroglycan

30
Q

amylose

A

contains α (1 => 4) linkage between glucose

31
Q

amylopectin

A

contains α (1 => 4) linkage between glucose, with occasional branching of α (1 => 6) linkage between glucose

32
Q

pectin

A

contains α (1 => 4) linkage between galactose

33
Q

cellulose

A

β (1 => 4) linkage between glucose, 300 to 15000 MS homoglycan, plays more of a structural role, made in the plant cell then is secreted

34
Q 
polysaccharide:
α (1 => 4) and β (1 => 6) linkages
glucose subunits, breakdown into maltose
storage of energy in animals
have branching
glucose is larger, >5000 MS
branching every 8-12 MS
branches are shorter
A

glycogen

35
Q 
polysaccharide:
α (1 => 4) and β (1 => 6) linkages
glucose subunits, breakdown into maltose
storage of energy in plants
have branching
glucose is smaller, <6000 MS
branching every 25ish MS
branches are 15-25ish MS long
A

starch

36
Q 
polysaccharide:
β (1 => 4) linkages
glucose subunits, breakdown into cellobiose
structure in plants
no branching
has rotation
made in the cell, then secreted
A

cellulose

37
Q

O linkage

A

carbohydrate attaches to protein through Ser or Thr

38
Q

N linkage

A

carbohydrate attaches to protein through Agn, first attachment in ER (not golgi)

39
Q

nucleotides

A

building blocks of nucleic acids; three parts: nitrogenous base, 5 C MS, 1-3 phosphates

40
Q

nucleoside

A

nitrogenous base + 5 C MS

41
Q

phosphodiester bonds

A

primary structure of nucleic acids; link nucleotides together; nucleophilic attack, 3’ OH attacks first phosphate; create sugar-phosphate backbone

42
Q

secondary structure of nucleic acids

A

characteristics of DNA (base pairing and double helix) and RNA (base pairing, ss or ds, and flexibility which allows for more folding)

43
Q

double helix characteristics of B-DNA

A

normal form helix takes; antiparallel, complementary, R-handed, major groove and minor groove, 10 bp per turn, d = 2.0 nm

44
Q

RNA molecules with enzymatic activity

A

ribozymes

45
Q

tertiary structure of nucleic acids

A

organized packing of a very large amount of material into a very small, yet accessible and functional, space

46
Q

tertiary structure of prokaryote nucleic acids

A

single, circular chromosome (haploid) allows for supercoiling

47
Q

tertiary structure of eukaryote nucleic acids

A

more than one, linear chromosomes (diploid); organized by histones

48
Q

basic proteins; contain many Lys and Arg AAs giving a positive charge that attracts negative DNA; five types (H1, H2A, H2B, H3, and H4), 2 copies of each type

A

histones

49
Q

histone octomer (including two H2A, H2B, H3, and H4) wrapped with DNA, octomers are linked by DNA strings containing H1 linker histones (which pulls them closer together)

A

nucleosome

50
Q

are nonpolar and sometimes amphipathic; have diverse chemistry, no one universal building block

A

lipids

51
Q

melting point of fatty acids

A

increases with more C and less C=C due to packing (more packing allows for more interactions); unsaturated are liquid at room temp, saturated are solid at room temp

52
Q

glycerol

A

can function as backbone, 3 C

53
Q

triglyceride

A

glycerol + 3 FA; storage of fatty acids, neutral lipid

54
Q

phospholipid

A

glycerol + 2 FA (hydrophobic) + 1 phosphate (hydrophilic); amphipathic, steric hindrance from phosphate normally causes rotation around single bond

55
Q

molecules with distinctly hydrophilic and hydrophobic portions
e.g. phospholipids and phosphosphingolipids

A

amphipathic

56
Q

phospholipids and phosphosphingolipids in water

A

arrange to where hydrophilic (heads + water) things are together and hydrophobic (tails) things are together; form micelle which becomes liposome which becomes bilayer sheet

57
Q

steroids/sterols

A

3 six-membered rings, 1 five-membered ring, 2 methyl groups; attachments at top right (OH, hydrocarbon, etc.) and bottom left (distinguishes between steroid (=O) and sterol (-OH))

58
Q

cholesterol

A

a sterol, -OH will align with edge of membrane, the hydrophobic ring structure will stick into the hydrophobic middle of the membrane; more cholesterol leads to less fluidity of membrane

59
Q

is responsible for cholesterol recovery from the blood; increased levels will lead to increased cholesterol in tissues

A

HDL (high-density lipoprotein)

60
Q

catalyzed the rate determining step of de novo cholesterol synthesis; decreasing this enzyme will lead to a decrease in cholesterol in tissues

A

HMG-CoA reductase

61
Q

medications that lower cholesterol levels; decreasing medication levels would lead to an increase in cholesterol levels in tissues

A

glucagon or statin medications

62
Q

drive de novo synthesis of cholesterol; increased levels would lead to increased cholesterol in tissues

A

ATP and NADPH

MCAT Biology (19 decks)

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