Structures, Properties of 20 Amino acids

Question 1

Define Proteins

Answer 1

Large biomolecules made of amino acids that are found in every cell of the body.
They are involved in most of the body function and life processes
The DNA determines the sequence of amino acids.

Question 2

List the 7 functions of proteins in biochemistry

Answer 2

1. Catalysts - enzyme proteins quick up reactions in metabolic pathways
2. Transport - transport proteins transport molecules in different environments such as hemoglobin which transports oxygen through blood
3. Structural - structural proteins provide mechanical supports to cells in the body, For example, collagen proteins provide the skin strength and elasticity.
4. Contraction - contractile proteins make up the cytoskeleton which provides mechanical support to cells. For example, tubulin proteins make up the cytoskeleton.
5. Decoding information - Gene expression proteins such as polymerase and helicase.
6. Regulation - Protein Hormone and Protein hormone receptor regulate metabolism such as insulin which regulates glucose metabolism
7. Antibodies - antibody proteins are part of the adaptive immune system that binds to foreign pathogens
8. Others - hormone precursor, metabolic pathways

Question 3

Protein structure

Answer 3

Made up of chains of amino acids 
Peptides : Less than 50
Dipeptide : 2
Polypeptide : 10 or more
Proteins : Typically 100 to 10000

Question 4

Amino Acids classification and structure

Answer 4

• Building blocks of proteins
• 20 standard types based on 20 different R groups
• 4 chemical groups are bound to the alpha carbon. Amino group, Carboxyl group, R side chain and Hydrogen atom
• R groups will create different chemicals properties

Question 5

List the Abbreviations (short form and long form)
Alanine
Cysteine 
Aspartic acid
Glutamic acid
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Proline 
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine

Answer 5

A, ala
C, cys
D, asp
E, glu
F, phe
G, gly
H, his
I, ile i-l-e
K, lys
L, leu
M, met
N, asn
P, pro
Q, gln
R, arg
S, ser
T, thr
V, val
W, trp
Y, tyr
D(asp) is for aspartic acid, E(glu) for glutamic acid, F(phe) for phenylalanine, K(lys) for lysine, N(asn) for asparagine, Q(gln) for glutamine, , W(trp) for tryptophan and Y(tyr) for tyrosine

Question 6

4 major classes of amino acids based on side chains

Answer 6

Non-polar
Polar
Acidic
Basic

Question 7

What are the non-polar amino acids

Answer 7

Glycine (R group H),
Alanine (R groups CH3),
Valine (R group CH double branched to 2 CH3),
Leucine (R group CH2-CH double branched to 2 CH3), Methionine (R group CH2-CH2-S-CH3),
Isoleucine (R group C bonded to a H, CH3 and a CH3 bonded to CH3)
Proline (R group CH2, CH2, H2C bond to H2N the amino group in a ring)
Phenylalanine (R group CH2 to Phenyl ring)
Tryptophan (R group CH2 to C=CH2-NH-C=C back to C in a ring and the 2 C-C is part of a phenyl ring)

Question 8

What are the properties of non-polar amino acids?
Gly, Ala, Val, Leu, Ile, Phe, Met, Pro, Trp
Total 9

Answer 8

• Neutral charge
• No O and N atoms in side chain or low compared to other side chains
• Unable to H bond with water
• Poorly soluble in water, hence these side chains cluster inside the protein due to hydrophobicity
• Special ones are proline which R group binds to the amino group.
  Proline is rigid and inflexible
  Proline interrupt alpha helices in globular proteins and gives fibrous structure of collagen.

Question 9

What are the polar amino acids?

Answer 9

Serine (R group CH2OH)
Threonine (R group C bonded to H, OH and CH3)
Asparagine (R group CH2 bonded to C double branched to =O and H2N)
Glutamine (R group CH2-CH2-C double branched to =O and H2N
Tyrosine (R group CH2-Phenyl ring-OH)
Cysteine (R group CH2-SH)
Note asparagine and glutamine may have extra amino group but does not make them more alkaline as the H2N is non-ionizable
Cysteine can form disulfides bonds with other cysteine

Question 10

Properties of polar side chains

Total 6 Serine, threonine, tyrosine, asparagine, glutamine, cysteine

Answer 10

• Neutral charge
• Soluble in water due to containing O and N, form H bonds with water
  Aromatic side chains are non-polar so they participate in hydrophobic interactions.
  Side chains with aromatic group - absorb light at wavelength 280nm, a property exploited by researchers for the characterization of proteins

Question 11

What are the acidic amino acids?

Answer 11

Aspartate (R group CH2-COO-)

Glutamate (R group CH2-CH2-COO-)

Question 12

What are the properties of acidic amino acids?

Answer 12

Polar due to O atoms that can H bond with water

Acidic due to -COO carboxylate group at physiological pH

Question 13

What are the basic amino acids?

Answer 13

Histidine (R group CH2-CH2-CH2-CH2-NH3),
Lysine(R group CH2-CH2-CH2-NH-C double branched to NH2 and = NH2+)
Arginine (R group CH2-C-NH-CH=N-CH=back to C)
Arginine is more basic, but only 1 of the R amino group is ionizable.

Question 14

Drawing them

Answer 14

Proline, arginine and tryptophan is special because of a ring
Arginine and lysine is more basic due to 2 NH2+ groups
Aspartate and Glutamate have COO- at the end of their R groups.
Draw alpha carbon - H3N+ and COO- and H and R group