test 2: protein structure

Question 1

covalent bonds are present in what protein structure level

Answer 1

primary

Question 2

what bonds do secondary protein structure have

Answer 2

covalent and hydrogen bonds

Question 3

what bonds are more prevalent in tertiary and quaternary protein structuer

Answer 3

hydrophobic effect

Question 4

what is significant about covalent bonds in protein strucutre

Answer 4

• shows in amino acid sequence
• location of s-s bonds

Question 5

H bonds

Answer 5

• interaction of amino acids close to each other
• form specific patterns

Question 6

hydrophobic effect level

Answer 6

• 3d structure of polypeptide
  quat
• arrangement of multiple folded molecules

Question 7

what % of DB character does a peptide bond have

Answer 7

40

Question 8

what are the characteristics of a peptide bond

Answer 8

• planar
• no rotation around peptide bond
• cis/ trans isomerism

Question 9

what isoermism are peptide bonds

Answer 9

• nearly 90% are trans
• 10% are cis

Question 10

why is trans configuration better than cis

Answer 10

steric hinderance and interactions

Question 11

in peptide bond where can rotation occur

Answer 11

around the alpha carbon but there is no rotation at all

Question 12

what does a ramachandran plot show

Answer 12

• sterically allowed alpha and beta angles for a polypeptide chain
• limited amount of allowed configurations

Question 13

2nd protein structure is found where

Answer 13

• local segments of biopolymers
• proteins and nucleic acids (DNA/ RNA)
• local conformations

Question 14

what is an example of a secondary protein structure

Answer 14

• alpha helix
• beta strnad
• beta bend
• collagen triple helix
• loops and turns

Question 15

what bonding is present in secondary

Answer 15

• H bonding between backbone amide NH of one AAand the carbonyl of another

Question 16

who proposed the alpha helix

Answer 16

linus pauling

Question 17

what bonds are present in alpha helix

Answer 17

• h bonds between n and n+4 residue

Question 18

where do R groups poin on alpha helix

Answer 18

outward, perpendicular to the axis

Question 19

what are some characteristics of alpha helix structure

Answer 19

• h bonds are parallel
• pitch = 5.4 angstrom
• 3.6 residue/ turn
  1.5 Rise/AA
• right hand
  -charged AA
• dipole polarity

Question 20

how is alpha helix dipole polarity

Answer 20

• all c=O grpups point toward C and give dipole with + N, (-) C termini

Question 21

how can you make a stable alpha helix

Answer 21

• end C term with a charged AA to neutralize

Question 22

which protein has predominantly alpha helices

Answer 22

myoglobin

Question 23

what does proline do to alpha helix

Answer 23

• detabilizes the alpha helix that why it is not found

Question 24

do alpha helices like bulky things

Answer 24

no

Question 25

what are the alpha helix detablilizers

Answer 25

- proline - bulkiness - R groups to large( tryptophan and tyrosine) - too small (glycine)

Question 26

what is an amphipathic helics

Answer 26

hydrophonic residues on one side - hydrophi8llic resides on opposite sides

Question 27

what is keratin

Answer 27

-key structural material in hair skin and nails - coiled coil - 2 amphipathic alpha helices

Question 28

what amino acid is kertatin rich in

Answer 28

- cys to form s-s bonds

Question 29

what does a perm do

Answer 29

- reduce s-s bonds--> 2RSH ; then reoxidize to s-s

Question 30

why is keratin important

Answer 30

used to detect heavy metal poisoning

Question 31

what are B strands

Answer 31

polypeptide chain almost fully extended found in B sheets

Question 32

what is a beta sheet

Answer 32

multiple b strands arranged side by side

Question 33

what are charactersitcs of B strands and B sheets

Answer 33

- h bonds occur between aa on adjacent stands and perp to the strand direction - side chains R-gps alternate in pointing above and below plane perp to b bonds and stands

Question 34

do beta sheets like bulky

Answer 34

yes they do

Question 35

what is an antiparallel b sheet

Answer 35

stand runs in opposite direction

Question 36

parallel

Answer 36

run in the same N to C direction

Question 37

what is the beta sheet structure

Answer 37

- zig zag - 6-12 residue - repeat 2AA distance 7A - may be amphipathic

Question 38

what is silk fibroin

Answer 38

antiparallel B sheets of Gly-ser-gly

Question 39

what does ala do in a silk fibroin

Answer 39

interlocksw/ ala from another sheett

Question 40

what is collagen

Answer 40

- main sturctural protein in the extracellular matrix in connective tissues - most abundant protein in mamels

Question 41

where is collagen present

Answer 41

- bone matrix - tendonds -cartilage - blood vessesl

Question 42

what is the repeating AA in collagen

Answer 42

G-P-P proline helix

Question 43

where are the gly residues located in collagen

Answer 43

- invariant - central axis of triple helix, other can't fit

Question 44

does interchain H bonds occur in collagen

Answer 44

no

Question 45

what helps stabilize the helix

Answer 45

- interchain H bonds w/ Hydroxypro

Question 46

what is osteogenesis imperfecta

Answer 46

- mutation in a gene for collagen - gly is substituted for another AA - prevents normal production of collagen - leads to brittle bones

Question 47

to form hydroxypro what is required

Answer 47

O2 and ascorbic acid(vitamin c)

Question 48

what is scurvy

Answer 48

vitamin c deficiency - lack of hydroxypro - not enough interchain h bonding - tweaking collagen

Question 49

how are collagen fibrils strengthened

Answer 49

- interchain lysine-lysine interaction hydroxypyrindium covalent cross links

Question 50

increase in cross links =

Answer 50

less eslatic collagen= more brittle bones = sign of old age

Question 51

why are loops and turns important

Answer 51

- allow chain reversal - found on the surface of globular protein