Week 1 part 2

Question 1

Protein

Answer 1

Linear polymer of a.a. joined by peptide bond (polypeptide)

Made by translation mRNA transcribed from genomic DNA

Biologic point of DNA/RNA allow synthesis of specific protein

Functions of P r determined by overall shape

Question 2

Scale

Answer 2

Genome-DNA
|
v
P primary structure (Sequence)
|
v
P 3D structure
|
v
Function
|
v
Cell biology

Question 3

Hydrophobic vs hydrophilic

Answer 3

Hydrophilic:
Polar electronic charge distribution (might carry a net +/- charge)
Interact well w/ polar solvent water

Hydrophobic:
Non-polar chain distribution
Do not interact well as polar solvent water
-Hydrophoic effect

Question 4

Hydrophobic effect

Answer 4

WAter molecule adopt a constrained (cage-like) organization

If hydrophobic molecule coalesce, the # of water molecule is reduced(less water when hydrophobic mol. is bigger)

Lower intropy–>Higher entropy

“oil drop”=impo becasues cytoplasm is an aqueous solution… each protein has only one structure… if there’S more=conformations

Question 5

What determined the path of the peptide backbone (shape of mol.)

Answer 5

2ndary and tertiary structure

Question 6

The molecular structure of protein

Answer 6

Primary (sequence)

Secondary (local folding and hydrogen bonding… involve peptide backbone)

TErtiary (overall conformation)

Quaternary (multimetric structure=many polyp)

Supramolecular (large-scale assembly… they can assemble and unassemble)

Question 7

Function of Protein

Answer 7

Determined by structure

Structure
Movement
Molecular transformation
Transport
Signaling
Binding
Catalysis
REgulation

Question 8

Primary structure

Answer 8

A.A. squence determine structure and function
so DNA inderctly determin the P function

Question 9

SEcondary structure

Answer 9

only looking at backbon(no side chain)

a helix and B sheet

both r based on H-bonding between

peptide bond carbonyl O atoms one aminio residue
&
amino group hydrigens on a diff. amino acid residue

60% of P corrsponds to these structure… others have a definite one but not those

Question 10

a-helix

Answer 10

Periodicity of 3.6 residue/turn (titlted axis)
…every 36 a.a.=10 turn…

H-bond between N and N+4

Gross structure straight rod

Surface properties depend on side chain becasue they are the one that interacts with other part of P… so it is there that the propensity for the helox to form is decided

Question 11

B-sheet

Answer 11

H-bond between 2 adj. B-strands

Can creat large surface

Side chai=above and below sheet’S plane and they determine the propensity of the sheet to form by interactin with other part of the P

Antiparallel or parallel

Question 12

Tertiart structure

Answer 12

OVerall conformation of the polypeptide (spatial organization of the multipel secondary structure element)…ex: a-helix+B-sheet+side chains

Amino acid side-chain mediate interaction (non-convalent)
between diff. part of the P and between the P and its lgand GDP

IMPO: COVALENT BOND: CYSTEINE

Question 13

Cysteine

Answer 13

Contains a sulfhydryl group that form convalent S-S(disulfide) bonds w/ other cysteine side chains

In P, disulfide bonds can be intrachain (teritary structure) or interchain (quaternary structure)

Question 14

Quaternary structure

Answer 14

Check image

Question 15

Motids of P structure

Answer 15

Coiled-coil motif

EFhand/helix-loop-helix-motif

Zinc-finger motif

Question 16

Coiled-coil motif

Answer 16

Comb of 2 a-helix
Hydrophobic side-chain dacing each other inside (oil drop)

Heptad reapeat:
HxxHxxxHxxHxxx
(every 7 residues=2 Hydrophobic)

7/2=3.5 (vs pitch helix 3.6)

Involved in P interactions

Question 17

EFhand/helix-loop-helix motif

Answer 17

2 a-helix at 90°
w/ loop of a.a. between them

A Ca2+ binding motif

Question 18

Zinc-finger motif

Answer 18

a-helix + 2 B-sheet

Common in transcription factors (binds to DNA/RNA)

Side chain binding w/ Zn

Question 19

Motifs vs domains

Answer 19

Motif is not a whole P (too small)…
it has to be embedded in smthg holding it tgtr (NOT STRUCTURALLY INDEPENDANT)

Domain(larger(: 40 a.a. + contain 2ndary struc.

have enought bonds to hold itself tgtr even if cut out from P (compactly folded),
can be made of manny motifs (STRUCTURALLY INDEPENDANT ENTITIE)

Question 20

4 major structural classes of P

Answer 20

Fibrous protein: fibesr

Globular protein (oild rop)

Integral membrane proteins (hydrophobic region)

Intrinsically disorded P: random coils under physiological conditions… may adop specefic 2/3 stru. upon binding to a well structured partner P

Question 21

Molecular nature of P domain

Answer 21

Domains can be found in unrelated P