AAs and Proteins Flashcards
Functional Group
Amino
carboxyl
R
R group
determines
the biochemical
properties of the
amino acids.
* Charge
* Polarity
* Size
POLAR, and
POLAR, and
and uncharged
Chiral Carbon
4
different groups/atoms
attached to it
amino acid
DOES NOT
have a chiral centre?
GLYCINE
naturally occurring amino acids
classified as left-handed or L-amino
acids.
D Amino Acids
found in bacterial cell
walls and in some secondary
metabolites.
Properties of Core Region
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
What happens at the carboxyl end?
the carboxyl group loses a hydrogen ion -COOH -COO- + H+ ACID
What happens at the amino end?
the amino group
gains a hydrogen ion
-NH2 + H+ -NH3+ BASE
What happens at the overall core region?
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.
Non Polar AAs (10)
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
Polar Uncharged AAs (5)
Serine (Ser, S)
Threonine (Thr, T)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Tyrosine (Tyr, Y)
Positively Charged Polar AAs
Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)
Negatively Charged Polar AAs
Aspartic acid (Asp, D)
Glutamic acid (Glu, E)
Non-polar amino acids - hydrophobic
They have hydrocarbon
chains and/or rings.
Non-polar amino acids – special amino acid
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
Polar – uncharged amino acids
They all have a C-O or C=O bonds
Primary protein structure
Specified by the genetic code of the organism.
The sequence in which amino acids are linked by
peptide bonds in a protein.
Peptide bonds
Two amino acids are joined by condensation reaction
forming a peptide bond
Oligopeptide
2 -25 amino acids
polypeptide
More than 25 amino acids
Short oligopeptides have specific names
2 amino acids – dipeptide
3 amino acids – tripeptide
4 amino acids - tetrapeptide
Linear arrays of amino acids can make a huge number of different molecules
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
Secondary protein structure
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.
Coiling
Coiling results in
formation of alpha (a)
helices – spiral,
cylindrical (helical)
shape.
Folding
in formation of almost
flat, but kinked sheet
of amino acids called
beta (b) pleated
sheets.
Tertiary protein structure
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.
Hydrophobic
interactions
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
ionic bonds
Salt Bridges
Disulfide Bridges
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.
Importance of protein folding in biological systems
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
Quaternary protein structure
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.
In a dimer When both polypeptides are the same =
homodimer
polypeptides are different
heterodimer
Protein Folding in the cell
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.
What happens if a protein is misfolded?
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.
Globular
vast majority of proteins
function:
catalysis of reactions (enzymes)
transport
hormones
amino acid order: irregular
Fibrous
less common type
function:
structural support
amino acid order: repetitive sequences
Globular Proteins
Insulin
One of the smallest proteins.
Functions as a hormone.
A complex of 2 polypeptides
connected with disulfide bonds.
Haemoglobin
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.
SCA
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.
Histone
Proteins involved in supercoiling
(storage of DNA).
The surface of histones is very
positively charged – remember
DNA is negatively charged.
Fibrous Proteins
Collagen
> 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)
Hydroxyproline
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).
Vit C deficiency
Vitamin C Deficiency
Lack of Hydroxyproline
Defective collagen structure
