AAs and Proteins

Question 1

Functional Group

Answer 1

Amino
carboxyl
R

Question 2

R group

Answer 2

determines
the biochemical
properties of the
amino acids.
* Charge
* Polarity
* Size
POLAR, and
POLAR, and
and uncharged

Question 3

Chiral Carbon

Answer 3

4
different groups/atoms
attached to it

Question 4

amino acid
DOES NOT
have a chiral centre?

Answer 4

GLYCINE

Question 5

naturally occurring amino acids

Answer 5

classified as left-handed or L-amino
acids.

Question 6

D Amino Acids

Answer 6

found in bacterial cell
walls and in some secondary
metabolites.

Question 7

Properties of Core Region

Answer 7

At the pH levels
typically found in
cells (usually pH
7.0–7.4 - neutral
pH), both the
carboxyl and amino
groups of amino
acids are ionized

Question 8

What happens at the carboxyl end?

Answer 8

the carboxyl group loses a hydrogen ion -COOH -COO- + H+ ACID

Question 9

What happens at the amino end?

Answer 9

the amino group
gains a hydrogen ion

-NH2 + H+ -NH3+ BASE

Question 10

What happens at the overall core region?

Answer 10

Amino Acids exist as ZWITTERIONS.

They show the properties of acids and bases at the same time!
At neutral pH, the core of an amino
acid has no net charge.

Question 11

Non Polar AAs (10)

Answer 11

Glycine (Gly,G)
Cysteine ( Cys, C)
Alanine (Ala, A)
Proline ( Pro, P)
Isoleucine (Ile, I)
Leucine (Leu, L)
Methionine (Met, M)
Tryptophan (Trp, W)
Valine (Val, V)
Phenylalanine (Phe, F

Question 12

Polar Uncharged AAs (5)

Answer 12

Serine (Ser, S)
Threonine (Thr, T)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Tyrosine (Tyr, Y)

Question 13

Positively Charged Polar AAs

Answer 13

Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)

Question 14

Negatively Charged Polar AAs

Answer 14

Aspartic acid (Asp, D)
Glutamic acid (Glu, E)

Question 15

Non-polar amino acids - hydrophobic

Answer 15

They have hydrocarbon
chains and/or rings.

Question 16

Non-polar amino acids – special amino acid

Answer 16

Cysteine contains a thiol group
(SH)
Glycine is the smallest amino acid
and is not chiral
Proline forms a ring – which is
NOT a benzene ring

Question 17

Polar – uncharged amino acids

Answer 17

They all have a C-O or C=O bonds

Question 18

Primary protein structure

Answer 18

 Specified by the genetic code of the organism.
 The sequence in which amino acids are linked by
peptide bonds in a protein.

Question 19

Peptide bonds

Answer 19

Two amino acids are joined by condensation reaction
forming a peptide bond

Question 20

Oligopeptide

Answer 20

2 -25 amino acids

Question 21

polypeptide

Answer 21

More than 25 amino acids

Question 22

Short oligopeptides have specific names

Answer 22

2 amino acids – dipeptide
3 amino acids – tripeptide
4 amino acids - tetrapeptide

Question 23

Linear arrays of amino acids can make a huge number of different molecules

Answer 23

Consider a peptide with
two amino acids (AAs) AA1 AA2 20 × 20 = 400 different molecules
Consider a peptide with
three amino acids AA1 AA2 AA3 20 × 20 × 20 = 8000 different molecules
For any protein that is made of 100 amino acids, the number of possibilities is:
20100 = 1.267 × 10130

Question 24

Secondary protein structure

Answer 24

 Secondary structure refers to 3D form of local segments
of proteins, stabilised by intramolecular and sometimes
intermolecular hydrogen bonding.
 Hydrogen bonds form between the R groups of amino acids.
 This bonding causes coiling or folding of the polypeptide.

Question 25

Coiling

Answer 25

Coiling results in
formation of alpha (a)
helices – spiral,
cylindrical (helical)
shape.

Question 26

Folding

Answer 26

in formation of almost
flat, but kinked sheet
of amino acids called
beta (b) pleated
sheets.

Question 27

Tertiary protein structure

Answer 27

 Tertiary structure is the overall 3-dimensional shape
formed from a single protein chain.
 Arises due to interactions between amino acids that are
far away (usually 10 aa or more).
 These amino acids come in to contact with each other
through the process of protein folding.

Question 28

Hydrophobic
interactions

Answer 28

amino acids
with nonpolar,
hydrophobic R
groups cluster
together on
the inside of
the protein,
leaving
hydrophilic
amino acids on
the outside to
interact with
surrounding
water
molecules

Question 29

ionic bonds

Answer 29

Salt Bridges

Question 30

Disulfide Bridges

Answer 30

Covalent bonds
between the sulfur-
containing side
chains of cysteines.
They are much
stronger than the
other types of
bonds that
contribute to
tertiary structure.

Question 31

Importance of protein folding in biological systems

Answer 31

Changing an amino acid in the primary sequence will
change the structure of the protein.
This change in the structure may produce a change in
protein function (depending on where the change
occurs).
The amino acid change can have damaging effects if the
new amino acid has different biochemical properties

Question 32

Quaternary protein structure

Answer 32

 Quaternary structure is formed from the association of
more than 1 polypeptide chain.
 It is very common for proteins to consist of multiple
subunits.
 Quaternary structures are stabilised by the same bonds
that stabilise tertiary structures.

Question 33

In a dimer When both polypeptides are the same =

Answer 33

homodimer

Question 34

polypeptides are different

Answer 34

heterodimer

Question 35

Protein Folding in the cell

Answer 35

 Protein folding takes place in the Endoplasmic reticulum
 Special proteins called chaperones ensure that newly
made proteins do not interact with each other randomly
 Important types of chaperone proteins are the Heat
Shock Proteins (HSPs).
 Chaperone proteins come in many shapes and sizes.

Question 36

What happens if a protein is misfolded?

Answer 36

 Misfolded
proteins can
cause
disease.
 Example: Mad cow disease (prions)
Creutzfeldt-Jakob disease (CJD) and Bovine Spongiform Encephalopathy (BSE)
Correctly folded
name: PrPC
function:
maintain the myelin
sheath in nerve cells.
Misfolded
name: PrPSc
abnormality: cannot be
degraded - form large
aggregates – destroy
nerve cells.

Question 37

Globular

Answer 37

 vast majority of proteins
 function:
 catalysis of reactions (enzymes)
 transport
 hormones
 amino acid order: irregular

Question 38

Fibrous

Answer 38

 less common type
 function:
 structural support
 amino acid order: repetitive sequences

Question 39

Globular Proteins

Question 40

Insulin

Answer 40

One of the smallest proteins.
Functions as a hormone.
A complex of 2 polypeptides
connected with disulfide bonds.

Question 41

Haemoglobin

Answer 41

Has quaternary structure – formed
from 4 polypeptides (called a tetramer).
Each polypeptide has a heme molecule
containing an iron atom.
Oxygen atoms bind to histidine amino
acids close to the iron atoms, for
transport in the blood.

Question 42

SCA

Answer 42

example of a disease caused by a single base mutation in the nucleotide sequence.
The change causes the hydrophilic amino acid, glutamic acid (E) to be substituted for a
hydrophobic amino acid, valine (V).
Sickle blood
cells live 10-20
days instead of
90-120 days.

Question 43

Histone

Answer 43

Proteins involved in supercoiling
(storage of DNA).
The surface of histones is very
positively charged – remember
DNA is negatively charged.

Question 44

Fibrous Proteins

Question 45

Collagen

Answer 45

> 25% of the total body protein.
Found in skin, tendon, bone, dentin,
cartilage, vitreous humor, muscle, blood
vessels.
There are at least 16 types. Most
common are types I, II and III.
Excellent example of repetitive
amino acid sequence
Most common alternating sequence:
Gly-Pro-Hyp
(Hyp is hydroxyproline)

Question 46

Hydroxyproline

Answer 46

a version of proline with
an extra OH (hydroxyl) group.
 This extra OH group allows for many
hydrogen bonds between collagen molecules =
holds collagen molecules together.
 Formation of hydroxyproline from proline
is assisted by vitamin C (ascorbic acid).

Question 47

Vit C deficiency

Answer 47

Vitamin C Deficiency
Lack of Hydroxyproline
Defective collagen structure