EXAM 1

Question 1

what happens to a the hydrophobic aa in a polypep chain when exposed to water

Answer 1

they cluster towards the interior

Question 2

what happens to a the hydrophilic aa in a polypep chain when exposed to water

Answer 2

they hydrogen bond with water

Question 3

what is the formation that most amino acids are found in nature

Answer 3

L

Question 4

what is the isoelectric point (pI)

Answer 4

the pH at which the amino acids carries no net charge

Question 5

which amino acids are negatively charged

Answer 5

aspartate and glutamate

Question 6

which amino acids are positively charged

Answer 6

lysine, arginine, and histidine

Question 7

which amino acids are hydrophilic

Answer 7

serine, theronine, cysteine, asparagine, glutamine

Question 8

which amino acid makes disulfide bonds

Answer 8

cysteine

Question 9

which amino acids are hydrophobic

Answer 9

glycine, alanine, proline, valine, leucine, isoleucine, methionine

Question 10

what are the aromatic amino acids

Answer 10

phenylalanine, tyrosine, and tryptophan

Question 11

what is a misense mutation

Answer 11

a mutation that changes the amino acid in a protein

Question 12

what is a nonsense mutation

Answer 12

a mutation that results in a termination codon

Question 13

what is a frameshift mutation

Answer 13

an insertion or deletion in a DNA sequence

Question 14

what is the primary protein structure

Answer 14

the amino acid sequence

Question 15

what is the secondary protein structure

Answer 15

alpha helices, beta strands, and beta turns

Question 16

what is the tertiary protein structure

Answer 16

spatial location of the atoms

Question 17

what is the quartnary protein structure

Answer 17

the arrangement of multiple subunits

Question 18

what direction does hte alpha helix normally follow

Answer 18

right handed

Question 19

what weak interaction stabilizes alpha helices

Answer 19

hydrogen bonding

Question 20

what is the dipole moment on an alpha helix

Answer 20

positive towards the n terminus and negative towards the c terminus

Question 21

how many residues wihthin one 360 turn of an alpha helix

Answer 21

3.6

Question 22

difference between parallel and antiparallel beta sheets

Answer 22

parallel strands are oriented in the same amino to carboxyl direction

Question 23

what is more stable: antiparallel or parallel beta strand

Answer 23

antiparallel

Question 24

where do you find alpha helices on the ramchadran plot

Answer 24

towards the bottom cluster

Question 25

where do you fund beta strands and turns in the ramchadran plot

Answer 25

towards the top cluster

Question 26

what is a four-helix bundle

Answer 26

a protein fold that contains four alpha helices linked together

Question 27

what is a greek key fold

Answer 27

A protein fold that contains 4 beta strands linked together

Question 28

what is a rossman fold

Answer 28

two regions of alternating aplha helices and beta strands

Question 29

what is a TIM barrel fold

Answer 29

alternating alpha and beta that was identified in glycolytic enzyme

Question 30

what are two ways tertiary structures can be stabilized

Answer 30

disulfide bonds and metal ions

Question 31

what is a homodimer

Answer 31

a protein complex containing two identical protein subunits

Question 32

what is a coiled coil

Answer 32

two helices that are wrapped around each other

Question 33

what kind of protein is keratin made up of

Answer 33

homodimer called a coiled coil that is stabilized by disulfide bonds

Question 34

what kind of protein is silk made up of

Answer 34

heterotrimer of beta sheets

Question 35

what kind of protein is collagen made up of

Answer 35

3 left handed helixes that intertwine to form an right handed triple coil

Question 36

what drives the hydrophobic effect in protein folding

Answer 36

the increase of disorder in water molecules

Question 37

what kind of conditions are invitro protein folding experiments done in

Answer 37

dilute

Question 38

can in vivo protein folding occur while the polypeptide is being synthesized

Answer 38

yes

Question 39

clamp type chaperone proteins are represented by what kind of proteins

Answer 39

heat shock

Question 40

what are the purines

Answer 40

adenine and guanine

Question 41

what are the pyrimidines

Answer 41

thymine cytosine and uracil

Question 42

what form of DNA is mostly found in physiology

Answer 42

B form

Question 43

how does the amount G-C base pair effect the Tm of a DNA strand

Answer 43

it increases the Tm because G-C base pairs make the DNA strand more stable

Question 44

how does the length of a DNA strand effect the Tm

Answer 44

as length increases so does the Tm

Question 45

how does the concentration of ions in solution effect Tm

Answer 45

the more ionic solution the higher the Tm

Question 46

which molecule contains an extra hydroxyl group on the 2' carbon

Answer 46

rna

Question 47

why is rna more easily degradable

Answer 47

because of the extra oh group on the sugar

Question 48

why is there no uracil in dna

Answer 48

because a cytosine deamination will occur and cuase mutations

Question 49

how do histone proteins bind to dna

Answer 49

the positive regions in the histone proteins bind the negative charged backbone of dna

Question 50

what is euchromatin

Answer 50

lossley packed chromatin around histone proteins where the dna is being transcribed

Question 51

what is heterochromatin

Answer 51

tightly packed chromatin that is not being transcribed