Amino Acids & Proteins

Question 1

4 major types of macromolecules

Answer 1

proteins
nucleic acids
lipids
carbohydrates

Question 2

How do proteins contribute to the cell?

Answer 2

enzymes to catalyse reactions
stuructural proteins in connective tissue
interact with DNA and RNA - control nucleic acids
lipid bound proteins act as transport systems
glycosylated or interact with sugars

Question 3

Lactofernin & flexibility & function?

Answer 3

binding to iron, lactrofernin undergoes conformational change
allows other molecules to distinguish between iron free and iron bound forms

Question 4

structure of amino acid

Answer 4

all proteins are linear polymers
simple unit is an amino acid

contain:
variable group, amino group, carboxyl group and a H

Both acid and amine bonded to alpha carbon

Question 5

how do you define an alpha carbon

Answer 5

the carbon next to the carboxyl group

Question 6

variation of amino acids

Answer 6

variation in the side chain distinguish them
identity and properties of amino acid dependent on nature of R group

Question 7

what is chirality

Answer 7

molecules that are distinguishable in their mirror form

have potentially different chemical properties

alpha carbon has 4 different substituents - making it chiral

Question 8

what amino acids are chiral

Answer 8

all apart from glycine

Question 9

chiral isomers

Answer 9

L isomer carboxyl group on the Right
D isomer carboxyl group on the L

Amino acids in proteins are always in L form

Question 10

4 main group of amino acids?

Answer 10

Hydrophobic with non-polar R groups

Polar with neutral R groups, charge not evenly distributed

Positively charged with positive R groups at physiological pH

Negatively charged with negative R groups at physiological pH

Question 11

Key properties of: Glycine

LOOK UP STRUCTURE

Answer 11

No chirality as R group is H
Flexible
Acts to provide flexibility to proteins when other side chains too bulky

Gly, G

Question 12

Key properties of: Alanine

LOOK UP STRUCTURE

Answer 12

CH3 R group
Ala, A

Question 13

Alanine scanning directed mutagenesis

Answer 13

change of functional group to alanine
see if any changes on properties
see if protein driven by structure

Question 14

Key properties of: Proline

LOOK AT DIAGRAM

Answer 14

Unusual amino acid
side chain bonds to amino group
tight restraints on conformation of protein
peptide bind forms cis & trans conformations
in proteins that need to be rigid

Question 15

Key properties of: Histidine

LOOK AT DIAGRAM

Answer 15

in active site of many enzymes
only amino acid with pKa of side chain near neutral
side chain can alter charge
His, H

Question 16

Histidine side chain

LOOK AT DIAGRAM

Answer 16

can alter its charge at physiological pH
modulated by other amino acids surrounding It
often found in active sites of enzymes
imidazole ring can bind to release protons

Question 17

Key properties of: Cysteine

LOOK AT DIAGRAM

Answer 17

contains free thiol group (SH)
form covalent bonds with another cysteine
disulphide bond formed
only covalent bond found to hold chain in correct fold
pKa of 8.4 so found in active sites

residues form a covalent bond in some proteins to form cystine

Question 18

Define: zwitterionic

Answer 18

in solution at ph 7
amino acids exist predominantly as zwitterions

Amine group is protonated NH3+
Carboxyl group is deprotonated COO-

Question 19

pH raised with zwitterions

LOOK AT DIAGRAM

Answer 19

Carboxylic acid first group to give up a proton
pHA of near 2

dipolar persists until pH approaches 9
protonated amine group then loses a proton

Question 20

titration curve of glycine

LOOK AT DIAGRAM

Answer 20

carboxyl group pKa 2.0
amino group pKa 10.0

R carries no charge the aa has isoelectric point of 6

Question 21

define: isoelectric point

Answer 21

amino acid electrically neutral
acidic charge neutralised by basic charge

Question 22

charged r groups

LOOK AT DIAGRAMS

Answer 22

some (Lys) carry a basic charge
some (Glu) carry an acidic charge

due to charge on the R group

Question 23

A.A with aromatic side chains

LOOK AT DIAGRAMS

Answer 23

Phenylalenine
Tyrosine
Tryptophan

Absorb strongly near 280nm

Rich in aromatic residues = detect for presence of proteins up to 80n m

Bulky side chains

Question 24

pKa value of: terminal alpha carboxyl group

Answer 24

3.1

Question 25

pKa value of: aspartic acid and glutamic acid

Answer 25

4.1

Question 26

pKa value of: histidine

Answer 26

6.0

Question 27

pKa value of: terminal alpha amino group

Answer 27

8.0

Question 28

pKa value of: cysteine

Answer 28

8.3

Question 29

pKa value of: tyrosine

Answer 29

10.9

Question 30

pKa value of: lysine

Answer 30

10.8

Question 31

pKa value of: arginine

Answer 31

12.5

Question 32

pKa values dependent on?

Answer 32

temperature
ionic strength
microenvironment
ionisable group

not exact as biological systems can change

Question 33

Peptide bond formation

LOOK AT DIAGRAM

Answer 33

aa join together to make peptide bond
loss of a molecule of water

one O- combines with H3- to create peptide bonds
carboxyl and amino groups join

Question 34

trans peptide bond

Answer 34

peptide chain in proteins in trans formation

R group on different sides of the protein
avoiding steric clashes

Question 35

cis peptide bond

LOOK AT TYPICAL BOND LENGTHS

Answer 35

R group on same sides of protein

proline found in cis formation