Biochemistry

Question 1

Hydropathy index

Answer 1

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

Question 2

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

Answer 2

hydrophobic

Question 3

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

Answer 3

hydrophilic

Question 4

hydropathy value of peptide chain

Answer 4

sum of individual hydropathy value of each residue

Question 5

primary structure of protein

Answer 5

sequence of amino acids, held together by peptide bonds

Question 6

secondary structure of protein

Answer 6

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

Question 7

tertiary structure of protein

Answer 7

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

Question 8

quaternary structure of protein

Answer 8

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

Question 9

forms of denaturation

Answer 9

heat, pH, salts, detergents

Question 10

Lineweaver-Burke Plot:

Equation

Answer 10

Question 11

Lineweaver-Burke Plot:

x-intercept

Answer 11

Question 12

Lineweaver-Burke Plot:

y-intercept

Answer 12

Question 13

competitive inhibitor

Answer 13

binds E, Km increases, Vmax stays the same

Question 14

uncompetitive inhibitor

Answer 14

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

Question 15

noncompetitive inhibitor

Answer 15

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

Question 16

allosteric inhibitor

Answer 16

binds to a site other than the substrate binding site

Question 17

bind to a specific amino acid in the active site

Answer 17

group specific reagents

Question 18

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

Answer 18

affinity labels (substrate analogs)

Question 19

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)

Answer 19

suicide inhibitors

Question 20

amino acids found in active sites

Answer 20

catalytic residues

Question 21

types of enzymes

Answer 21

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

Question 22

optimal pH and temperature of enzymes

Answer 22

optimal pH varies greatly, temperature is 37 ºC

Question 23

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

Answer 23

cofactor

Question 24

type of cofactor:

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

Answer 24

coenzymes

Question 25

glycosidic bond

Answer 25

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

Question 26

maltose

Answer 26

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

Question 27

cellobiose

Answer 27

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

Question 28

lactose

Answer 28

galactose + glucose, 1 => 4, heteroglycan

Question 29

sucrose

Answer 29

glucose + fructose, 1 => 2, heteroglycan

Question 30

amylose

Answer 30

contains α (1 => 4) linkage between glucose

Question 31

amylopectin

Answer 31

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

Question 32

pectin

Answer 32

contains α (1 => 4) linkage between galactose

Question 33

cellulose

Answer 33

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

Question 34

``` 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 ```

Answer 34

glycogen

Question 35

``` 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 ```

Answer 35

starch

Question 36

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

Answer 36

cellulose

Question 37

O linkage

Answer 37

carbohydrate attaches to protein through Ser or Thr

Question 38

N linkage

Answer 38

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

Question 39

nucleotides

Answer 39

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

Question 40

nucleoside

Answer 40

nitrogenous base + 5 C MS

Question 41

phosphodiester bonds

Answer 41

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

Question 42

secondary structure of nucleic acids

Answer 42

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

Question 43

double helix characteristics of B-DNA

Answer 43

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

Question 44

RNA molecules with enzymatic activity

Answer 44

ribozymes

Question 45

tertiary structure of nucleic acids

Answer 45

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

Question 46

tertiary structure of prokaryote nucleic acids

Answer 46

single, circular chromosome (haploid) allows for supercoiling

Question 47

tertiary structure of eukaryote nucleic acids

Answer 47

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

Question 48

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

Answer 48

histones

Question 49

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)

Answer 49

nucleosome

Question 50

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

Answer 50

lipids

Question 51

melting point of fatty acids

Answer 51

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

Question 52

glycerol

Answer 52

can function as backbone, 3 C

Question 53

triglyceride

Answer 53

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

Question 54

phospholipid

Answer 54

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

Question 55

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

Answer 55

amphipathic

Question 56

phospholipids and phosphosphingolipids in water

Answer 56

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

Question 57

steroids/sterols

Answer 57

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))

Question 58

cholesterol

Answer 58

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

Question 59

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

Answer 59

HDL (high-density lipoprotein)

Question 60

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

Answer 60

HMG-CoA reductase

Question 61

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

Answer 61

glucagon or statin medications

Question 62

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

Answer 62

ATP and NADPH