Week 4 - Amino acid and protein structures

Question 1

amino acid structures

Answer 1

1

Question 2

protein structure, conformation, and functions

Answer 2

1

Question 3

protein analysis techniques

Answer 3

1

Question 4

Amino acids

Answer 4

amino group + alpha-carbon atom + carboxyl group + side-chain group

at pH 7, both amino group (positive) and carboxyl groups (negative) are ionized

Question 5

Amino acids are building blocks of proteins

Answer 5

grouped based on their side chains

• neutral - nonpolar
• neutral - polar
• acidic
• basic

Question 6

Cystein

Answer 6

Cys, C
form disulfide bonds
- CH2 - S - S- CH2 -
paired cystaines allow disulfide bonds to form in proteins;
reactive with other cystein and form covalent bonding
ex. hair perm

Question 7

Formation of peptide bond

Answer 7

planar amide linkage
OH + H -> H2O (condensation) :::: C end and N end will be combined
Always N added onto C end

Question 8

polypeptide - protein

Answer 8

1. linear polymers from ~100 - 1000 amino acid residues in length; may be a few times larger/smaller
2. avg amino acid molecular weight of 110 Da; range from 10 to 100kDa
3. adjacent amino acids covalently bonded by peptide bonds

Question 9

R groups

Answer 9

side chains
determine the folding
1. Polar amino acid - on the protein surface
2. Non-polar (hydrophobic) - internal
3. Two cysteins - form covalent disulfide bonds
4. Hydrogen bonding between C=O group bond with N-H group of different peptide bond

Question 10

Protein conformation

Answer 10

Native conformation
Denaturation
Renaturation-restoration

Question 11

native conformation

Answer 11

normal folding structure of a protein - functional and most stable

Question 12

denaturation

Answer 12

partial or complete disruption or unfolding of the native protein conformation
treated with heat, detergent, or strong salts (ions)

Question 13

renaturation - restoration

Answer 13

denature by heat -> slowly cooling to allow proper refolding

** chaperones assist in protein folding

Question 14

chaperones

Answer 14

assist in protein folding;

nearly the last to be denatured

Question 15

four levels of protein structure

Answer 15

primary
secondary
tertiary
quarternary

Question 16

primary structure

Answer 16

amino acid sequence

linear sequence of amino acids from N- to C- terminus

Question 17

secondary structure

Answer 17

folding and local repetitive contiguous

arrangement of segments of the polypeptide chain into regular structures

Question 18

tertiary structure

Answer 18

whole polypeptide chain folded into 3D; one polypeptide chain
overall 3D conformation (shape) polypeptide resulting from folding of secondary structures and unstructured regions

Question 19

quarternary structure

Answer 19

composition of several polypeptide chains
association of two or more polypeptides (called subunits) fo fomr a functional protein (complex)

dimer, trimer, tetramer…
Homo-dimer, hetro-dimer…

not all proteins have quarternary structure

Question 20

alpha helix

Answer 20

secondary structure
H-bonding between C=O group of one peptide (n) and N-H group of another(n+3)
* regular H-bond; 1(O)-4(H), 2(O)-5(H), 3-6, 4-7 …
3.6 amino acids
5.4A per turn
2.3A diameter
*** DNA helix is 20A in diameter
side chains protrude outward from alpha-helix

Question 21

beta sheet

Answer 21

secondary structure
H-bonding between C=O group of one peptide and N-H group of another

two types: parallel sheet and antiparallel sheet
same orientation of N- and C- termini or alternate
R groups project up and down in alternation

Question 22

prolines

Answer 22

disrupt alpha-helices
alpha helices need to be regular zigzag
proline R group (O) would flip back and form bond with previous amino acid’s H
* due to ring structure

cf. alanine, would simply form zigzag

Question 23

joining secondary structures

Answer 23

stretches of turns
glycine (has no side chain) and proline (has a natural bend) frequently found in turns

ex. hairpin loop

Question 24

motif

Answer 24

locally connected 2 degree structures form motifs
a design or figure consist of recurring shapes or colors as in architecture or decoration
theme that is repeated or elaborated in a piece of music

ex. zinc-finger (binds DNA)
ex. coiled coils

Question 25

modular domain

Answer 25

domain - part of the tertiary structure
module = functional module (engine)
motif = repeating structure (cylinders/pistons)
contiguous segments of proteins
independently maintain structure/function
different domain/modules combined to create a protein with two or more discrete functions

Question 26

protein structure

Answer 26

structure & motifs
can be predicted from the primary sequence
3D structure can be predicted using ::
1. X-ray crystallograph - high resolution structure; a protein crystal ( very hard to form )
2. NMR useful; limited to small proteins (<20kDa)

similar primary sequence likely to have similar 3D structure

Question 27

protein function

Answer 27

catalysis
DNA binding/regulation
Structural 
Signaling
Recognition
Others

Question 28

catalysis function of protein

Answer 28

metabolism, macromolecule synthesis, modification of protein structure/ function

Question 29

DNA binding/regulation function of protein

Answer 29

DNA compaction, replication, transcription, recombination

Question 30

structural function of protein

Answer 30

cell structure, scaffolds for enzymes,

Question 31

signaling function of protein

Answer 31

hormones, intracellular signal transduction

Question 32

recognition function of protein

Answer 32

cell-cell interactions, immune response

Question 33

DNA binding proteins

Answer 33

interact with specific DNA sequence (ex. restriction enzyme) / or non specifically – interaction stabilized by weak interactions
most common structure interacting with DNA is alpha helix
negatively charged phosphate backbone of DNA mediate non-specific interaction

Question 34

major and minor grooves of DNA

Answer 34

in major groove, all four base-paring can be distinguished
in minor groove, only two of four can be distinguished
* sequence specific DNA binding proteins recognize the major groove
* hydrogen bonding acceptor and donor not different in minor groove to tell the direction

Question 35

regulation of protein structure and function

Answer 35

allostery
cooperativity
covalent modification of amino acid side chains

Question 36

allostery

Answer 36

change of conformation of one site by binding ligand (or covalent modification) at second (allosteric) site

Question 37

cooperativity

Answer 37

facilitated binding of one molecule to ligand (through interaction with another molecule)

ex. DNA binding protein bind another protein recruiting second protein to DNA
ex. tRNA?

Question 38

allosteric regulation

Answer 38

activation

repression

Question 39

covalent modification of amino acid side chains

Answer 39

act as a switch (on/off/alter binding properties/target for degradation…)
result in an allosteric change in the protein
modification may directly affect ligand binding/cooperative interactions