Amino Acids & Proteins

Question 1

Transmembrane proteins

Answer 1

Cross the phospholipid bilayer of cellular membranes; the surface consists mostly of hydrophobic amino acid residues

Question 2

Post-translational modifications

Answer 2

Covalent additions of non-amino acid groups to a protein; catalyzed by enzymes and generally only occur at specific amino acid residues

Question 3

Phosphorylation

Answer 3

Common post-translational modification that is facilitated by protein kinase enzymes; occurs at serine, threonine, and tyrosine, each of which contain a hydroxyl group in its side chain

Question 4

Asparagine and glutamine

Answer 4

Amide groups

Question 5

Cysteine

Answer 5

Thiol group

Question 6

Aspartate and glutamate

Answer 6

Carboxylic acids

Question 7

Proteases

Answer 7

(i.e., trypsin, pepsin) degrade proteins into smaller fragments by hydrolysis the peptide bonds that link amino acids in the polypeptide chain

Question 8

G proteins

Answer 8

Common signaling proteins in cells that are switched “on” when they bind GTP. After the G protein hydrolyzes GTP into GDP, the G protein switches “off” until the GDP is exchanged for a new GTP

Question 9

GTPase-activating proteins (GAPs)

Answer 9

Inhibit G protein signaling activity by enhancing their intrinsic hydrolase activity

Question 10

Guanine nucleotide exchange factors (GEFs)

Answer 10

Job is to catalyze G proteins and therefore stimulate G protein signaling activity

Question 11

Four substituents the α-carbon is bonded to, in order of stereochemical priority are:

Answer 11

1. An N atom, in the form of either an amine group or an amide group
2. A carbonyl carbon, in the form of either a carboxylic acid or an amide group
3. A variable R group that constitutes the amino acid’s side chain
4. A hydrogen atom

Question 12

L/S Configuration

Answer 12

Natural amino acids are typically L
Given priority rankings of N atom > carbonyl carbon > side chain > α-hydrogen, the absolute stereochemistry of amino acids is typically S
Two exceptions: glycine and cysteine

Question 13

Chiral amino acids, including cysteine

Answer 13

L configuration

Question 14

Achiral residue (glycine)

Answer 14

No D or L designation

Question 15

Tryptophan

Answer 15

An aromatic amino acid with extensive conjugation that allows for fluorescence (has pi orbitals)

Question 16

Ligand-binding

Answer 16

pH-independent

Question 17

Covalent attack

Answer 17

pH-dependent

Question 18

Positive charged amino acids

Answer 18

Lys and Arg, His is partially positive

Question 19

Aromatic amino acids

Answer 19

Try, Phe, and Trp

Question 20

Non-polar amino acids

Answer 20

Val, Ala, and Gly

Question 21

Negatively charged amino acids

Answer 21

Asp and Glu

Question 22

α-tubulin

Answer 22

Acts as a control to confirm that the same amount of cell lysates have been loaded into the cells during gel electrophoresis

Question 23

Contain hydroxyl groups and are able to hydrogen bond:

Answer 23

Serine, threonine, and tyrosine

Question 24

Approximate mass of one amino acid

Answer 24

110 daltons

Question 25

37 kDa = ? Da

Answer 25

37,000 Da

Question 26

Calculate amino acids

Answer 26

(37,000 Da) x (1 amino acid/100) = slightly fewer than 370 amino acids

Question 27

18 Carbons, how much NADH is produced? (Beta-oxidation)

Answer 27

The eighth oxidation of a C4 acid produces two molecules of acetyl-CoA. Thus, eight rounds of beta-oxidation are needed, and so only 8 molecules of NADH will be produced

Question 28

Five-membered cyclic amino acid, proline, prevents the alpha-amine nitrogen from participating in hydrogen bonding, what is true?

Answer 28

Proline decreases the stability of beta-pleated sheets

Question 29

pI = pH

Answer 29

AA is neutral and will not bind to the negatively charged beads

Question 30

pI

Answer 30

ALWAYS higher than pKa1 pI lies between pKa1 and pKa2

Question 31

pI > pH

Answer 31

AA is positive and will be attracted to the negatively charged beads, inhibiting elution

Question 32

pI < pH

Answer 32

Elution is best, as it is the only type of AA that will be repelled to the beads due to the AA's negative charge

Question 33

Gel electrophoresis

Answer 33

Anode (+) larger Cathode (-) smaller

Question 34

Histidine

Answer 34

Basic and heterocyclic

Question 35

Heterocyclic

Answer 35

Ring is composed of different elements

Question 36

Homocyclic

Answer 36

Composed of rings made of the same element

Question 37

Misfolding of proteins

Answer 37

Protein folding is most likely to be disrupted at the level of tertiary structure (forming globules or fibers)

Question 38

Secondary or primary structure problems

Answer 38

Tend to result from translation errors or mutations of the gene encoding the protein

Question 39

Quaternary structure problems

Answer 39

Only impacted when there is more than one subunit

Question 40

Non-polar hydrophobic AA

Answer 40

Glycine

Question 41

Basic and hydrophilic AA

Answer 41

Histidine, Lysine, and Arginine

Question 42

Pyranoses

Answer 42

Sugar composed of six-membered rings

Question 43

Furanoses

Answer 43

Composed of 5-membered rings

Question 44

Glucogenic AA

Answer 44

Converted into glucose Arginine

Question 45

Ketogenic

Answer 45

Can be converted into acetyl-CoA or ketone bodies Lysine

Question 46

Both Keto and Gluco

Answer 46

Tyrosine and phenylalanine

Question 47

Isoelectric points of AA

Answer 47

Glycine and Lysine are 6.0 and 9.6, respectively, so they can be separated by gel electrophoresis at a pH of 6.0 and 9.6

Question 48

Myosin

Answer 48

Acts primarily as a protein motor, but also has secondary activity as an ATPase - Myosin binds to actin, which as motor activity, but does not hydrolyze ATP

Question 49

Troponin

Answer 49

A chaperone of actin, its activity is modulated by calcium, not ATP

Question 50

Kilocalories

Answer 50

Lipids = 9 kcal/g Carbs = 4 kcal/g Ethanol = 7 kcal/g Fats provide the most energy per gram of any fuel source used by mammals

Question 51

pI is calculated by averaging:

Answer 51

The pKa values for: the main chain carboxyl group and the side chain

Question 52

Metabolic difference between glucose and lactose

Answer 52

Lactose is a disaccharide, so it must be cleaved before it can be metabolized, while glucose does not

Question 53

Most of the lipids found in the two leaflets of the cell membrane of euk. are synthesized in the

Answer 53

Endoplasmic reticulum

Question 54

α-carbon

Answer 54

Each amino acid residue, except Gly, has a chiral α carbon

Question 55

β-carbon

Answer 55

With the exception of Ile and Thr, the β carbon in AA residues is achiral; CD spectra arise from the massively greater presence of α carbon chirality

Question 56

Indole

Answer 56

Trp

Question 57

Imidazole

Answer 57

Two AA residues blocking access to W15 are histidines, each with an imidazole ring-containing side chain

Question 58

Denaturation of proteins

Answer 58

Means that the protein is unfolded and exposed

Question 59

Tyr

Answer 59

Can form a π-stacking interaction

Question 60

Asp

Answer 60

Has a negatively charged side chain that will repel

Question 61

Ser

Answer 61

Not capable of π-stacking interactions

Question 62

Arg

Answer 62

Positively charged side chain, which can make a salt bridge

Question 63

Glycoprotein

Answer 63

Cannot cross the membrane and must bind to receptors on the cell surface; it is likely it would be located on the surface of the plasma membrane

Question 64

Glycoprotein

Answer 64

Cannot cross the membrane and must bind to receptors on the cell surface; it is likely it would be located on the surface of the plasma membrane

Question 65

GTP

Answer 65

Guanosine tri-phosphate, which is a nucleotide

Question 66

Transport affinity for substrates

Answer 66

Is an inherent property of transport proteins, and this transport affinity is independent of the concentration of transport protein