protein structure

1. BASIC STRUCTURE OF
BIOINFORMATICS
PRESENTED BY
GOKILA.K
MSFBI1802
Bioinformatics

2. TOPIC
 PROTEIN AND ITS STRUCTUREAND
ITS STRUCTURE

3. Proteins are polymers of amino acids….Proteins have a
variety of function in cells. Major functions include acting as
enzymes, receptors, transport molecules,
regulatory proteins for gene expression, and so on.
Enzymes are biological catalysts that speed up a chemical
reaction without being permanently altered.
Protein is found throughout the body—in muscle, bone, skin,
hair, and virtually every other body part or tissue.
It makes up the enzymes that power many chemical reactions
and the haemoglobin that carries oxygen in your blood. At least
10,000 different proteins function in our body.

7. What Are Proteins Made Of?
The building blocks of proteins are amino acids, which are small
organic molecules that consist of an alpha (central) carbon atom
linked to an amino group, a carboxyl group, a hydrogen atom, and a
variable component called a side chain .
Within a protein, multiple amino acids are linked together
by peptide bonds, thereby forming a long chain.
Peptide bonds are formed by a biochemical reaction that extracts a
water molecule as it joins the amino group of one amino acid to the
carboxyl group of a neighbouring amino acid.
The linear sequence of amino acids within a protein is considered
the primary structure of the protein.

8. CHIRAL PROPERTIES OF AMINO ACIDS:
With the exception of glycine, all the 19 other common
amino acids have a uniquely different functional group
on the central tetrahedral alpha carbon (i.e. Cα).
The Cα is termed "chiral" to indicate there are four
different constituents and that it is asymmetric. Since
the Cα is asymmetric there exists two possible, non-
super imposable, mirror images of the amino acids.

10. Chirality essentially me
ans 'mirror-image, non-
super imposable
molecules', and to say
that a molecule is chiral
is to say that its mirror
image (it must have
one) is not the same as it
self.
The term chirality is
derived from the
Ancient Greek word
.Chemists call the
chirality is enantiomers
or optical isomers.

11. There are two important nomenclature systems for enantiomers.
The D/L system is based on optical activity and refers to the
Latin words dexter for right and laevus for left, reflecting left-
and right-handedness of the chemical structures.
An amino acid with the dexter configuration (dextrorotary)
would be named with a (+) or D prefix, such as (+)-serine or D-
serine.
An amino acid having the laevus configuration (levorotary)
would be prefaced with a (-) or L, such as (-)-serine or L-serine.
The amino acids are most commonly named using the (L) and
(D) system.

13. Isomerism of Natural Amino Acids:
All amino acids found in proteins occur in the L-configuration
about the chiral carbon atom. The exception is glycine because it
has two hydrogen atoms at the alpha carbon, which cannot be
distinguished from each other except via radioisotope labeling.
D-amino acids are not naturally found in proteins and are not
involved in the metabolic pathways of eukaryotic organisms,
although they are important in the structure and metabolism of
bacteria. For example, D-glutamic acid and D-alanine are
structural components of certain bacterial cell walls.
It's believed D-serine may be able to act as a brain neurotransmitter.
D-amino acids, where they exist in nature, are produced via post-
translational modifications of the protein.

14. Properties of the Amino Acids:
The characteristics of the amino acids depend on the
composition of their R side chain. Using the single-letter
abbreviations:
Polar or Hydrophilic: N, Q, S, T, K, R, H, D, E
Non-Polar or Hydrophobic: A, V, L, I, P, Y, F, M, C
Contain Sulfur: C, M
Hydrogen Bonding: C, W, N, Q, S, T, Y, K, R, H, D, E
Ionizable: D, E, H, C, Y, K, R

15. Cyclic: P
Aromatic: F, W, Y (H also, but doesn't display much UV
absorption)
Aliphatic: G, A, V, L, I, P
Forms a Disulfide Bond: C
Acidic (Positively Charged at Neutral pH): D, E
Basic (Negatively Charged at Neutral pH): K, R

17. The four levels of protein structure are distinguished from
one another by the degree of complexity in the polypeptide
chain. protein structure types:
Primary structure
Secondary structure
Territory structure &
Quantanary structure

18. Protein primary structure is the linear sequence of amino
acids in a peptide or protein.
By convention, the primary structure of a protein is
reported starting from the amino-terminal (N) end to the
carboxyl-terminal (C) end.
Protein biosynthesis is most commonly performed by
ribosome's in cells. In primary structure , A change in the
gene's DNA sequence may lead to a change in the amino acid
sequence of the protein.
Even changing just one amino acid in a protein’s sequence
can affect the protein’s overall structure and function.

20. For instance, a single amino acid change is associated with
sickle cell anaemia, an inherited disease that affects red
blood cells.
In sickle cell anaemia, one of the polypeptide chains that
make up haemoglobin, the protein that carries oxygen in
the blood, has a slight sequence change.
The glutamic acid that is normally the sixth amino acid
of the haemoglobin β chain (one of two types of protein
chains that make up haemoglobin) is replaced by a valine.
This substitution is shown for a fragment of the β chain in
the diagram below.

22. The next level of protein structure, secondary structure, refers
to local folded structures that form within a polypeptide due to
interactions between atoms of the backbone.
(The backbone just refers to the polypeptide chain apart from
the R groups – so all we mean here is that secondary structure
does not involve R group atoms.)
The most common types of secondary structures are the α helix
and the β pleated sheet. Both structures are held in shape by
hydrogen bonds, which form between the carbonyl O of one
amino acid and the amino H of another.

24. In an α helix, the carbonyl (C=O) of one amino acid is
hydrogen bonded to the amino H (N-H) of an amino
acid that is four down the chain.
(E.g., the carbonyl of amino acid 1 would form a
hydrogen bond to the N-H of amino acid .)
This pattern of bonding pulls the polypeptide chain
into a helical structure that resembles a curled ribbon,
with each turn of the helix containing 3.6 amino acids.
The R groups of the amino acids stick outward from
the α helix, where they are free to interact..

25. In a β pleated sheet, two or more segments of a polypeptide
chain line up next to each other, forming a sheet-like structure
held together by hydrogen bonds.
The hydrogen bonds form between carbonyl and amino groups
of backbone, while the R groups extend above and below the
plane of the sheet.
The strands of a β pleated sheet may be parallel, pointing in the
same direction (meaning that their N- and C-termini match up),
or antiparallel, pointing in opposite directions (meaning that
the N-terminus of one strand is positioned next to the C-
terminus of the other).
Many proteins contain both α helices and β pleated sheets,
though some contain just one type of secondary structure.

27. The overall three-dimensional structure of a polypeptide is called
its tertiary structure. The tertiary structure is primarily due to
interactions between the R groups of the amino acids that make
up the protein.
R group interactions that contribute to tertiary structure include
hydrogen bonding, ionic bonding, dipole-dipole interactions,
and London dispersion forces – basically, the whole gamut of
non-covalent bonds.
For example, R groups with like charges repel one another,
while those with opposite charges can form an ionic bond.
Similarly, polar R groups can form hydrogen bonds and other
dipole-dipole interactions.

28. Also important to tertiary structure are hydrophobic
interactions, in which amino acids with non polar, hydrophobic
R groups cluster together on the inside of the protein, leaving
hydrophilic amino acids on the outside to interact with
surrounding water molecules.
Finally, there’s one special type of covalent bond that can
contribute to tertiary structure:
The disulfide bond. Disulfide bonds, covalent linkages between
the sulfur-containing side chains of cysteines, are much stronger
than the other types of bonds that contribute to tertiary structure.
They act like molecular "safety pins," keeping parts of the
polypeptide firmly attached to one another.

31. Many proteins are made up of a single polypeptide chain and
have only three levels of structure.
However, some proteins are made up of multiple polypeptide
chains, also known as subunits. When these subunits come
together, they give the protein its quaternary structure.
An example of a protein with quaternary structure
is haemoglobin. In haemoglobin, one protein binds to oxygen
while another binds carbon dioxide. This is how one protein
can serve two functions.

32. What bonds are in quaternary structure of proteins?
These chains are held together to form the
larger protein by bonds that exist between the side groups of
different chains. As with tertiary structure, the bonds involved in
holding these separate chains together can be vander Waals bonds,
hydrogen bonds, ionic bonds, or at times covalent bonds.
Why is quaternary structure important?
Quaternary structure allows a protein to have multiple functions.
It also allows for a protein to undergo complicated conformational
changes. This has several mechanisms. An individual subunit can
change shape.

38. REFERENCE:
 Protein structure and function :(DAVID WHITFORD)
 The protein book :(LYLE MCDONALD)
 https://www.thoughtco.com/
 www.news-medical.net
 www.ncbi.nlm.nih.co
 www.khanacademy.org ›