amino acids , peptides and proteins (Dr Hawthorne)

Question 1

amino acids

Answer 1

they are the building blocks of proteins and peptides which makes them proteinogenic
peptides contain up to 50 amino acids + proteins but there can be more than 50 ( there can be several thousand amino acids in large complex proteins )
amino acids are organic compounds that contain an amine group ( NH2) and a carboxyl group ( COOH) along side an R group side chain which is specific to each amino acid .
the key elements to amino acids are C,H,N,O but other elements are found in the side chains such a sulphur.
there is about 500 naturally occurring amino acids but only 20 appear in genetic code ( proteinogenic)

Question 2

Naming amino acids

Answer 2

amino acid : 3 letter abbreviation : 1 letter abbreviation:
alanine ala A
arginine arg R
asparigine asn. N
aspartic acid. asp D
cysteine cys C
glutamic acid Glu E
glutamine gln Q
Glycine. gly G
Histidine His H
isoleucine ile. I
Leucine Leu L
lysine Lys. K
methionine. Met M
phenylalanine. Phe F
Proline Pro P
Serine Ser S
Threonine. Thr T
Tryptophan. Trp W
Tyrosine Tyr Y
Valine Val V

Question 3

The genetic code - DNA to amino acid

Answer 3

Twenty amino acids are encoded directly by tripletcodonsin thegenetic code
Most amino acids have more than 1 codon – some exceptions
Met (AUG is the start codon and therefore first amino acid on ALL proteins is Met) and Trp
3 stop codons – signals the end of a sequence
Genetic code is degenerate

Question 4

isomerism

Answer 4

with the exception of glycine , all amino acids adopt the L configuration
D amino acids are very rarely found in proteins

Question 5

Side chains of amino acids ( R group)

Answer 5

The R group is very important
Amino acids are classified by thepropertiesof their R group into four groups
Non-polar
Polar uncharged
Polar charged – basic or acidic

Question 6

Non polar amino acids

Answer 6

Gly has a proton for its R group – does not have a chiral centre
Ala, Val, Leu and Ile have non-cyclic alkyl hydrocarbon side chains
Met linear side chain that contains a sulphur
Phe and Trp have aromatic ring structures for side chains
Pro has a heterocyclic ring structure and is an imino acid, one of the N-H linkages is replaced by a N-C linkage - rigidity

Question 7

Polar uncharged amino acids

Answer 7

These amino acids are relatively hydrophilic as they possess polar functional groups i.e. oxygen and nitrogen, which can participate in hydrogen bonding with water
Ser, Thr and Tyr have hydroxyl (OH) groups
Asn and Gln are derived from Asp and Glu where the carboxyl is modified to become an amide group
Cys has an SH group which is weakly acidic

Question 8

Disulphide bond

Answer 8

Two thiol side chains (-SH) on cysteine amino acids can oxidise and cross-link to form a disulphide bond (-S-S-)
The two cysteines must be close together in the protein for this to occur
Hold the protein in its 3D conformation

Question 9

Polar charged – basic amino acids

Answer 9

Lys and Arg have functional groups that are positively charged at pH 7
His has an imidazole group with a pKa 6.5, so it is not fully ionised at pH 7
This means the side chain of His can be fully charged, uncharged or partially charged depending on the precise situation
His can serve as either a proton donor or acceptor

Question 10

Polar charged – acidic amino acids

Answer 10

Both Asp and Glu have carboxyl groups in their side chains which are negatively charged at pH 7
Asp pKa 3.46
Glu pKa 4.25

Question 11

Zwitterions

Answer 11

A zwitterion contains the same number of positively and negatively charged functional groups but has an overall net zero charge
At pH values between the two pKavalues, the zwitterion predominates

Question 12

Isoelectric point

Answer 12

At the exact midpoint between the two pKavalues, the amount of negative and positive ions exactly balance, so that average net charge of all forms present is zero
This pH is known as theisoelectric point,pI
pI=1/2(pKa1+ pKa2)
For amino acids with charged side chains, the pKaof the side chain is also involved
For example, for aspartate or glutamate with negative side chains, pI=1/2(pKa1+ pKa(R)), where pKa(R)is the side chain pKa

Question 13

Proteogenic amino acids

Answer 13

These amino acids are components of peptides and proteins
Proteins are encoded by DNA which is transcribed into mRNA which is then translated into protein
Amino acids are joined together by a peptide bond
The 3D conformation of a protein is dependent on the R groups of the amino acids contained within it

Question 14

Peptide bond formation

Answer 14

Amino acids can link together by a covalent bond between the -carboxyl end of one amino acid and the -amino end of another
Peptide bond (type of amide bond)

Question 15

Peptide bond

Answer 15

The peptide bond is rigid and planar
Peptide backbone
Can be broken by hydrolysis (addition of water)
Digestive enzymes such as trypsin and elastase break down proteins in food by hydrolysing the peptide bonds

Question 16

Non-proteinogenic amino acids

Answer 16

Either not found in proteins or not produced directly from the genetic code
Examples not found in proteins
GABA - neurotransmitter
Examples not produced directly from the genetic code
Formed by post-translational modification
Hydroxyproline – formed by hydroxylation of proline

Question 17

Non-protein functions of amino acids

Answer 17

Tryptophanis a precursor of the neurotransmitterserotonin
Tyrosine(and its precursor phenylalanine) are precursors of thecatecholamineneurotransmittersdopamine,adrenalineandnoradrenaline
Glycineis a precursor ofporphyrinssuch ashaem
Arginineis a precursor ofnitric oxide

Question 18

Protein structure

Answer 18

There are four levels of structure in proteins
Primary, secondary, tertiary and quaternary

Question 19

Primary structure

Answer 19

Linear sequenceofamino acidsin apolypeptideorprotein
The primary structure of a protein is written as a string of letters starting from theamino-terminal (N) end to thecarboxyl-terminal (C) end
The primary structure of a protein is determined by thegenecorresponding to the protein
The sequence of a protein is unique to that protein, and defines the structure and function of the protein

Question 20

Post-translational modifications

Answer 20

A wide variety of modifications can take place
The N-terminal amino group of a protein can be modified
Acetylation – addition of a –CH3 group
Phosphorylation - a phosphate group can be attached to the sidechain hydroxyl group of serine, threonine and tyrosine* most important modification *
Glycosylation – addition of sugars to sidechain hydroxyl groups of serine and threonine

Question 21

secondary structure

Answer 21

Highly regular local structures on the polypeptide backbone chain
A polypeptide will spontaneously fold into a regular and defined shape – dependent on the primary structure
Three main types of secondary structure have been found in proteins
Alpha helix
Beta pleated sheet
Beta bend/turn
These secondary structures are defined by patterns ofhydrogen bondsbetween the polypeptide R groups

Question 22

Alpha helix

Answer 22

Right hand-helixconformation in which every backboneN−Hgrouphydrogen bondsto the backboneC=Ogroup of theamino acidlocated three or fourresidues along the protein sequence
Most prevalent secondary structure in proteins

Question 23

Beta pleated sheet

Answer 23

H-bonding is achieved by stretching out the polypeptide chain, and laying it side by side to form H-bonds between lengths of polypeptide chain

Question 24

Beta bend/turn

Answer 24

Allows the peptide chain to reverse direction
Carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away
Proline and glycine are prevalent in beta turns

Question 25

Tertiary structure

Answer 25

3D structure created by a singlepolypeptide chain
The secondary structures are folded into a compact 3D structure
The folding is driven by thenon-specifichydrophobic interactions and the burial ofhydrophobic amino acids in the inside of the protein
The structure is stable only when the parts of aprotein domainare locked into place byspecifictertiary interactions, such assalt bridges, disulphide bonds and hydrogen bonds

Question 26

Quaternary structure

Answer 26

3D structure consisting of the aggregation of two or more individual polypeptide chains that operate as a single functional unit (multimer)
It is stabilised by the same interactions that hold the tertiary structure together
Forms two types of proteins
Globular – polypeptide chains interact to form a spherical shape
Fibrous – polypeptide chains lie parallel to each other to form a fibre
Not found in all proteins

Question 27

Globular protein - haemoglobin

Answer 27

Two alpha and two beta chains
Come together to form quaternary structure
Only active in quaternary form

Question 28

Fibrous protein - collagen

Answer 28

Three linear polypeptides are twisted together and held by H-bonds
Provides strength to the collagen