biochemistry-secondary structure of proteins

ppt of primary and secondary structure of proteins

1. SECONDARY STRUCTURE OF PROTEINS
AZERBAIJAN MEDICAL UNIVERSITY
WRITTEN BY: ROYA BASSER
BIOCHEMISTRY

2. Amino acids
Peptide bonds
Primary structures
Secondary
structure
Type of secondary
structure

3. AMINO ACIDS
Amino acids are building units of proteins.
Proteins are polymers that participate in almost all biochemical
reactions in body as enzymes.
Amino acids are fundamental components of our bodies and
vital for physiological functions such as protein synthesis, tissue
repair and nutrient absorption.
There are 20 amino acids that make up proteins and all have the
same basic structure.
The amino acids join to each other to make proteins by a special
chemical bond which is called peptide bond.

4. AMINO ACID STRUCTURE
Parts
Carboxyl group
Amino group
Hydrogen
R(side chain)
It gives the amino acid, its
special feature such as
polarity
It is different in each
amino acid
It determines the chemical
behavior of amino acid

5. TYPES OF AMINO ACIDS
Essential amino acids
▪These amino acids can not be made by body.
▪They have to be in daily diet.
▪The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine,
tryptophan, and valine.
Nonessential amino acids:
▪These amino acids can be produced in body whether they are in diet or they are not.
▪Nonessential amino acids include: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine,
glycine, proline, serine, and tyrosine.
Conditional amino acids:
▪Conditional amino acids are usually not essential, except in times of illness and stress.
▪Conditional amino acids include: arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine

6. TYPES OF AMINO ACIDS ACCORDING TO SIDE CHAINS -OVERVIEW
Amino acids
Polar
Neutral
Charged
Acidic
Negatively
charged
Basic Positively charged
Nonpolar Neutral
Note: basic and acidic amino acids are charged in physiologic ph.

7. PEPTIDE BOND
This bond is formed between 2 amino acids and connect them to each other.
. It is formed between 2 non-side chain (carboxyl group and amino group of 2 DIFFRENET
and CONSECUTIVE amino acids).
The type of reaction is condensation reaction. It's a kind of combination of 2 molecules that
produces one single molecule and usually looses a small molecule such as water.
If the lost molecule is water it can be called dehydration synthesis. In this case the product
is known dipeptide.

8. TYPES OF AMINO ACID-BASED ON CARBON
The alpha amino acids:
The alpha carbon is the carbon which connects to the
functional group (R).The Amino group and the Carboxy
group are attached to "One Main" carbon which is called as
Alpha carbon and thus making it a alpha amino acid.
The beta amino acid:
The amino group is not attached to the carbon which has a
functional group. It is attached to the carbon adjacent to the
functional group one.

9. STRUCTURE OF PROTEINS-OVERVIEW
Proteins
One chain
Primary
Secondary
Tertiary
More than
one
Primary
Secondary
Tertiary
Quaternary

10. WHAT DETERMINES THE STRUCTURE OF PROTEINS?
Bonds and forces
Bonds Hydrogen bonds
It stabilize the
structure of
secondary structure
Forces
Hydrophobic effects
One of the strongest
forces in
determination of
proteins’sstructure
Van der vaalsforces
It stabilizes the
hydrophobic cores
Electrostatic forces

11. PRIMARY STRUCTURE OF PROTEINS
The simplest level of protein structure is primary structure.
It is the a simple sequence of amino acids.
Thus this sequence of amino acids has it’s own set that is determined by the
DNA that encodes the protein
it includes amino acid residues and peptide bonds.
Stages of production in body:
the primary structure is produced by a small molecular organelle that is called
ribosome.
1.Transduction
2.Transcription
3.Translation

12. SECONDARY STRUCTURE
The local dimensional segments of primary structure that are folded within
a polypeptide due to chemical interactions between atoms is called
secondary structure.
It is within one chain of polypeptide.
it describes how the main chain of a protein is arranged in space.
Formation :
it arises from the hydrogen bonds that are formed between atoms in
polypeptide strand.
The hydrogen bond is formed between the partially positive atom (nitrogen,
amino part) and partially negative (oxygen ,carboxyl part).

13. TYPES OF SECONDARY STRUCTURE -OVERVIEW
Types
Main
Alpha helix
Beta
sheets
Others
Turns
Loops

14. ALPHA HELIX
The alpha-helix is a right-handed helical coil.
held together by hydrogen bonding between almost every fourth amino acid(3\6)
shape ; spiral, in 3 dimensional
and the most predictable from a sequence.
It is formed because of the forces and bonds between amino acids of one chain.
3 dimensional form of it, doesn’t mean that is formed of 2-3 chains.
These stable folding patterns make up the secondary structure of a protein.
In this helix, the amino acids which are 3-4 amino acids away (distance) can become
close together.

15. HOW TO DETERMINE THE TYPE OF AMINO ACID?
a)The thumb goes toward the upper side and the 4 other
fingers shows the rotate direction.
b)The “screw sense” of an alpha helix can be right-handed
(clockwise) or left-handed (counter-clockwise).
c)the left handed pattern can be seen too but the right one is
more common and favorable.
d)These stable folding patterns make up the secondary
structure of a protein.
e)In the helix, the external distance between each pitch is
0/54 nanometers therefore It can be inferred that the
aminoacyl roots that were 3 or 4 roots apart, are spatially
close to each other.

16. BONDS AND FORCES OF ALPHA HELIX
Bonds and forces
Hydrogenic bond
It is the most important bond of
secondary structure and stabilize the
building.
Van der waalseffect
It has a vital role in the center of helix.
The amino acids are very close to each
other and based on their chemical
properties, have van der waalsforce.
Peptide bond
It is normally between amino acids
It is made between amino group of one
amino acids and carboxyl group of other
amino acids

17. STABILITY OF ALPHA HELIX-OVERVIEW
Factors
Amino acids
Too large
group
Too small
group
Steric
hindrance
Interactions
Electrostatic
Hydrophobic
Van der
waals
Hydrogen
bond
Destabilize
Stabilize

18. STABILITY OF ALPHA HELIX-AMINO ACIDS
Amino acids:
amino acids with too large R group such as (tryptophan, tyrosine) or too small like (glycine)
destabilize the structure of alpha helix.
Proline also destabilizes α-helices because of its strange structure. Proline is an alpha imino
acid. its R-group bonds back to the nitrogen of the amide group and it is a part of a strong
circular structure and rotation around the N-C bond is impossible.in addition, the lack of a
hydrogen on Proline's nitrogen prevents it from participating in hydrogen bonding.
Steric hindrance: it destabilize the structure of protein and usually happens between the
amino acids that are adjacent to each other such as aromatic groups in side chains.

19. STABILITY OF ALPHA HELIX-INTERACTIONS
Interactions:
Hydrophobic and hydrostatic interactions between R groups that are situated 3 to 4
amino acids away. For instance the positively charged amino acids are situated 3-4 amino
acids away from negatively charged amino acids.
Van der Waals: There are van der Waals connections at the center of the alpha helix due
to the density of the atoms, which contributes to their stability.
Hydrogen bonds: Interestingly, due to the H-bond pattern, the right hand helix is much
more stable than the left hand helix (for L-amino acids)

20. FORMATION OF ALPHA HELIX
The alpha helix is a regular protein secondary structure.A
regular protein secondary structure means the dihedral angles φ
(phi) and Ψ(psi) are nearly same throughout the
structure.Residuesin α-helices typically adopt (φ, ψ),dihedral
angles around (-57°, -47°)in general they adopt dihedral angles
such that the ψdihedral angle of one residue and the φdihedral
angle of thenextresidue sum to roughly -105. ranging from (-
90°, -15°) to (-35°, -70°),(-60°, -45°)
How good an amino acid can form the alpha helix is dependent
on, how good an amino acid can take up the characteristic i.e.
required φand Ψangles (i,eit is solely dependent upon the
structure of amino acid weather they will be able to form a
good alpha helix or not).

21. ALPHA HELIX BREAKER-PROLINE
A helix breaker is a type of amino acid that Unstable the structure of alpha
helix like proline.
Proline is a cyclic, nonessential amino acid (actually, an iminoacid) in humans
(synthesized from glutamic acid and other amino acids), Proline is a
constituent of many proteins.
Found in high concentrations in collagen, proline constitutes almost a third
of the residues.
Collagen is the main supportive protein of skin, tendons, bones, and
connective tissue and promotes their health and healing

22. WHY IS PROLINE A HELIX BREAKER?
1-side chain: as I said before the side chain of amino acids has important
role in the participation in alpha helix. The side chain in proline is a rigid
circle chemical group and the rotation around the N-C bond is impossible
(because the sidechain is circle)
2-lack of hydrogen bond: in previous slides I explained that the base alpha
helix’s formation is hydrogen bond.
In chemistry the hydrogen bond is a force of attraction between
ahydrogen(H) atom which iscovalently boundto a
moreelectronegativeatom or group such as elements F.O.N.
when proline residues are incorporated, no hydrogen atoms remain on
the nitrogen atom that takes part in peptide bonding.
Rotation around this bond is impossible

23. AMINO ACIDS OF ALPHA HELIX
Amino
acids
Participant
Alanine Glu Methionine
Non
participant
Glycine Tyrosine Tryptophan

24. AMPHIPATHIC STRUCTURE
The amino acids in alpha helixes are divided into 2 groups:
1-hydrophobic (hate water)
2-hydrophylic(love water)
In alpha helix structure, the hydrophilic amino acids are in
one face and the hydrophobic structure is in opposite face.
In this structure the residues are changed in 3-4 amino
acids from hydrophilic to hydrophobic.
this structure can be seen in the environments that both
polar and none polar are present such as protein channels.
The hydrophilic side chain is facing outward (toward the
aqueous solvent) and the hydrophobic side chain is facing
inward (toward the hydrophilic interior).

25. BETA STRANDS
Beta strands:
A beta strand is a chain of polypeptides that are formed by
3-10 amino acids which completely stretch in 180 degree.
Each beta strand is a polypeptide chain which has 2 ends.
1-N-terminus:it is referring to the free amino group (-NH2)
located at the end of a polypeptide
2-C-terminus:it is the end of anamino acid chain
(proteinorpolypeptide), terminated by a free carboxyl
group(-COOH)
Ends of beta
sheet
N-terminus C-terminus

26. FORMATION OF BETA STRANDS
Formation of beta strands:
the primary structure has an alternating pattern of
hydrophobic (H) and polar (P)amino acids. This leads to
an extended structure where theamino acidside-chains
alternate between the two faces of the strand,
extending into space ( both outward and inward) at an
angle of approximately 90degrees from the face of the
strand.
This is one strand which forms hydrogen
bond with the strand in front of it

27. BETA SHEETS:
The beta sheet, (β-sheet) (also β-pleated sheet) is a
common motif of the regular protein secondary
structure. Beta sheets consist of beta strands (β-strands)
connected laterally by at least two or three backbone
hydrogen bonds, forming a generally twisted, pleated
sheet. A β-strand is a stretch of polypeptide chain
typically 3 to 10 amino acids long with backbone in an
extended conformation.
Several beta strands can form hydrogen bonds together
and make beta sheets.

28. FORMATION OF BETA SHEETS
According to the (just like alpha helix) the
hydrogen bond is the base of secondary
structure.
In the beta sheets the hydrogen bond is
formed between O element of carboxyl
group (C=O) in one strand and N element
pf amino group (N-H) in the opposite
strand.
allhydrogen bondsin abeta-sheetare
between different segments of polypeptide

29. TYPES OF BETA SHEETS
Types
Parallel
In parallel the
terminals of the
opposite beta strands
are same.
The angle of hydrogen
bonds in parallel is
diagonal.
The stability of parallel
structure is less than
anti parallel.
Antiparallel
In antiparallel the
terminals of the beta
strands are NOT
same.
The angle of hydrogen
bonds in anti parallel
structures is 90
degree (vertical)
The stability of anti
parallel structure is
more than parallel
Antiparallel Parallel

30. STABILITY OF BETA SHEET:
parallelbetasheetsareless
stablethananti-parallelbetasheets,
because the geometry of the individual
amino acid molecules forces the inter
chain hydrogen bonds in parallel beta-
pleatedsheetsto occur at an angle, making
them longer and thus weaker than those
inanti-parallelbeta-pleatedsheets, where
the inter strand hydrogen bonds are
aligned directly opposite each other,
resulting in stronger and more stable
bonds.
The C-terminus and N-
terminus in the opposite
strand
The angle is 90
The C-terminus and N-termnusin opposite
chain aren’t in front of each other
The angle is diagonal

31. AMINO ACIDS OF BETA SHEETS:
Large aromatic residues
(tyrosine, phenylalanine,
tryptophan) andβ-
branchedamino
acids(threonine, valine,
isoleucine) are favored to
befound in β-strandsin
the middle ofβ-sheets.
Tryptophan Phenylalanine Tyrosine
Threonine Valin Isoleucine

32. LOOPS:
loopsare irregularstructureswhich connect
two secondarystructureelements
inproteins. They often play important roles in
function, including enzyme reactions and
ligand binding. Despite their importance,
theirstructureremains difficult to predict.
loops are more likely to be found near the
surface of the protein. Not surprisingly, loops
tend to be rich in hydrophilic sidechains. The
hydrophilic in loops make hydrogen bonds
with the surrounding water more than with
adjacent amino acids, helping make loops
more flexible than helices and sheets.

33. PLACE OF LOOPS
Place
In molecule
Between alpha
helixes and beta
sheets in proteins
are loop regions.
In the 3
rd
structure
Near the surface
of protein
There is a loop between alpha
helix and beta sheet in the
molecule

34. GENERAL INFORMATION OF LOOPS
A general classification of loops is made that divides loops into three classes Strap, Omega, and Zeta
Function of loops:
They are located usually on the surface of protein.
They are made up of hydrophilic amino acids.
Due to these 2 reasons they help to intractbetween water and protein through forming hydrogen bonds.
Amino acids of loops:
They are usually hydrophilic amino acids.
theamino acidsthat have the highest average ΔGwithin all interfaceloopsare tryptophan, phenylalanine,
histidine, aspartate, tyrosine, leucine, glutamate, isoleucine, and valine. Theseamino acidsspan charged,
hydrophobic, and aromatic residues, and contain several striking features.

35. TURNS
Turns are type of loops that are made up of 4
or 5 residues.
Turns refer to short segments of amino acids
that join 2 secondary structures together such
as 2 adjacent of anti parallel strands of beta
sheets.
Beta turn:
A beta turn involves four aminoacyl residue
that the 4th aminoacyl forms hydrogen bonds
with 1st aminoacyl which results in a tight 180
degree turn.

36. AMINO ACIDS OF BETA TURNS
proline and Glycine are frequently found
in beta turns, proline because its cyclic
structure is ideally suited for the beta
turn cause it easily can make the cis
configuration and it is perfectly suitable
for circulation , and glycine because, with
the smallest side chain of all the amino
acids, it is the most sterically flexible.
Cis and trans conversion of proline
Glycine

37. OVERVIEW OF TERTIARY AND QUATERNARY STRUCTURE
Tertiary structure refers to the overall
three-dimensional arrangement of all
atoms in a protein. Tertiary structure
deals with long-range aspects of the fold
of a protein, including interactions that
form between isolated elements of
secondary structure. Both noncovalent
and covalent interactions are included in
the tertiary structure. Quaternary
structure refers to the contacts between,
and overall arrangement in three-
dimensional space of the individual
subunits of a multisubunitprotein.
Example of the tertiary structure of
proteins.
enzyme triose phosphate isomerase

38. TERTIARY STRUCTURE
Tertiary structureis the next level of complexity
inprotein folding.
Tertiary structure is the three-dimensional structure of
several chains . It is the arrangement of the secondary
structures into this final 3-dimensional shape.
Important point about tertiary structure is that in this
folding shape the amino acyl residues that were far from
each other or were in different parts in secondary
structure ,get near to each other.

39. PROPERTIES OF THIS STRUCTURE
Here are some properties of tertiary structure.
1-it is 3 dimensional(Primary is a line and secondary is 1 dimensional)
2-it is the first functional unit of the proteins. if the tertiary structure is destroyed due to several reasons such as
high temperature ,the protein will not be able to do its job anymore.
3-if the high temperature becomes normal again, this structure can be achieved again.
4-in the stage of tertiary structure the protein can start its interaction with other molecules because the
functional groups are shown up on the surface of protein.
5-Protein tertiary structures are the result of weak interactions.
6-the base of this structure is interactions between sidechains.
7-it is folding up of secondary structure.
8-The tertiary structure is the structure at which polypeptide chains become functional

40. FORMATION-OVER VIEW
serine,threonine,cysteine,asparagine,glutamine
phenylalanine, valine, or tryptophan

41. FORMATION OF TERTIARY STRUCTURE
Protein tertiary structures are the result of weak interactions.
The base of this structure is interactions between sidechains.
▪In the formation of this structure 2 factors are involved:
▪1-amino acids
▪Nonpolar amino acids
▪Acidic and basic amino acids
▪cysteine
▪2-chemical interactions
▪Hydrophobic interactions
▪Ionic bonds
▪Hydrogen bonds
▪Disulfide bridges

42. NONPOLAR AMINO ACIDS IN THE FORMATION OFF TERTIARY STRUCTURE
The non-polar amino acids are type of amino
acids that the side chain of them mostly consist
of hydrocarbons (hydrogen + carbon)
The chemical behavior of these amino acids is
that are not tend to react in watery
environment.
The side chain of these amino acids are divided
in to 2 groups:
1-aliphatic:chmical groups without cycle or with
cycles that are not aromatic such as methyl.

43. AROMATIC AMINO ACIDS-FORMATION OF TERTIARY STRUCTURE
▪Aromatic amino acids are relatively
nonpolar. To different degrees, all aromatic
amino acids absorb ultraviolet light.
Tyrosine and tryptophan absorb more than
do phenylalanine; tryptophan is responsible
for most of the absorbance of ultraviolet
light (ca. 280 nm) by proteins. Tyrosine is
the only one of the aromatic amino acids
with an ionizable side chain. Tyrosine is one
of three hydroxyl containing amino acids.

44. BEHAVIOR OF TERTIARY STRUCTURE –FORMATION
Under physiologic conditions, the hydrophobic
side-chains of neutral, non-polar amino acids such
as phenylalanine or isoleucine tend to be buried on
the interior of the protein molecule, thereby
shielding them from the aqueous medium. The alkyl
groups of alanine, valine, leucine and isoleucine
often form hydrophobic interactions between one
another, while aromatic groups such as those of
phenylalanine and tyrosine often stack together.

45. ACIDIC AND BASIC AMINO ACIDS –FORMATION
The two amino acids in this group areaspartic acidandglutamic acid. Each has acarboxylic acidon its side chain that
gives it acidic (proton-donating) properties. In an aqueous solution at physiological pH, all three functional groups on
these amino acids will ionize. thus giving an overall charge of −1. In theionicforms, the amino acids are called aspartate
and glutamate.
The side chains of aspartate and glutamate can form ionic bonds (“salt bridges”)
Acidic are(negatively charged) amino acids
Basic;
The three amino acids in this group arearginine,histidine, andlysine. Each side chain is basic
Lysine and arginine both exist with an overall charge of +1 at physiological pH.
Theimidazoleside chain of histidine allows it to function in bothacid and base catalysisnear physiological pH values.
Basicare (positvelycharged) amino acids.
▪Acidic:

46. BEHAVIOR OF ACIDIC AND BASIC AMINO ACIDS
▪Acidic or basic amino acid side-chains will generally be
exposed on the surface of the protein as they are
hydrophilic.
▪Basicare (positvelycharged) amino acids and Acidicare
(negatively charged) amino acids.
These amino acids are usually seen on the surface of protein

47. BONDS OF TERTIARY STRUCTURE

48. TERTIARY STRUCTURE-CHAPRONINE
At this level, every protein has a specific three-dimensional
shape and presents functional groups on its outer surface,
allowing it to interact with other molecules, and giving it its
unique function. The arrangement is made with the help of
chaperones, which move the protein chain around, bringing
different groups on the chain closer together in order to
help them form bonds. These amino acids interacting are
usually far away from each other on the chain. Eukaryotic
chaperonins such as the TriCcomplex are large multimeric
complexes related to the bacterial GroELand GroES
proteins. These complexes take up unfolded proteins into an
internal chamber for folding ATP hydrolysis drives folding

49. DOMAINS
A domain is a section of
the protein structure sufficient to perform a
particular chemical or
physical task such as binding of a substrate or
other ligand.
Several motifs are packed to each other and
make a compact unit which is called domain.
each domain containing an individual hydrophobic
core built from secondary structural units
connected by loop regions

50. DOMAINS
Each domain has a solid-like core and a fluid-
like surface. Core residues are often conserved
in a protein family, whereas the residues in
loops are less conserved.
Domains are distinct functional and/or
structural units in a protein responsible for a
particular function or interaction
milardomains can be found in proteins with
different functions

51. CLASSIFICATION OF PROTEINS

52. FIBROUS PROTEINS
Fibrous proteins are made of fibers often consisting
of repeated sequences of amino acids, resulting in a
highly ordered, elongated molecule. theyare made
up of polypeptide chains that are elongated and
fibrous in nature or have a sheet like structure.
The polypeptide chainsrun parallel to one another
and are stabilized by cross-linkages
fibrous proteinsgenerally have periodicalamino
acid

53. FEATURES OF PROTEINS
Properties
1-mechanically strong
2-water insoluble
3-built up from single elements of secondary structure which
are repeated
4-rope like proteins
5-durability:less sensitive to Ph and temperature
6-sequence of amino acids: repeatetive
7-made up of long, narrow strands
8-examples:actin,myosine,collagen
9-roles:structural,involve in forming reactions

54. INSTANCES
Collagen
Most abundant protein
The main structural protein found in connective tissue
Appear as triple helix structure
actin
It exists in two forms:G actin (monomeric globular actin)andF actin(polymeric fibrous actin)
Role: muscle contraction and stabilize the shape of cell, Cytoskeletal structure and scaffolding for signal transduction
processes, Cell Motility
myosin
total of six subunits
having a long tail and two globular heads.
Role: contraction of skeletal muscles

55. GLOBULAR PROTEINS
Globular proteins have a 3D molecular structure that has a shape
that is anywhere from a sphere to a cigar.
The tertiary structure of many globular proteins can be
characterized by the number of layers of peptide backbone which
are present and the attractive forces which are generated by these
layers.
Globular proteins are build from combinations of secondary
structure elements.
This type of folding increases solubility of proteins in water
Polar groups on the protein’s surface
Hydrophobic groups in the interior
Although Fibrous proteins are mainly insoluble structural proteins.

56. CHEMICAL FEATURES OF GLOBULAR PROTEINS
1-have compact and spherical shape
2-they are water soluable
3-have functional roles
4-they have irregular amino acids sequence
5-more sensetiveto changes in heat and ph.
6-compact structure
7-globular proteins are held together by weak interactions
(hydrogen bonds)
8-they also can be seen in the quarternitystructure of protein.

57. DUTIES OF GLOBULAR PROTEINS
1-enzymes
2-messengers:they transport the biochemical messages to organs such as
insulin.
3-transporters:they do transport as other molecules through membranes
4-storage of molecules and ions(myoglobin)
5-defeanse against pathogenes(antibodies)
6-biological cathalyst(lysosome)

58. STABILITY OF GLOBULAR PROTEINS
Hydrogen bonds
Salt bridges
Cofactores
Disulfide bonds
Hydrophobic interactions

59. DIFFRANCESBETWEEN GLOBULAR AND FIBROUS PROTEINS

60. QUATERNARY STRUCTURE
The quaternary structure of a protein is the association of several protein
chains or subunits into a closely packed arrangement.
This level of protein structure applies only to those proteins that consist of
more than one polypeptide chain, termedsubunits.
These proteins are calledoligomersbecause they have two or more subunits
In this structure not only the amino acids are involved but also non amino
acid groups such as metals can be seen.

61. STABILITY OF QUATERNARY STRUCTURE
Subunits are held together by noncovalent forces; as
a result, oligomeric proteins can undergo rapid
conformational changes that affect biological activity.
disulfide bonds as the tertiary structure can also
stabilize the structure.
The quaternary structure can also be affected by
formulation conditions

62. LEVELS OF QUATERNARY STRUCTURE
In general we call the quaternary structure oligomer because they consist of several sub units.

63. LEVEL OF QUATERNARY STRUCTURE

64. EXAMPLES OF QUATERNARY STRUCTURE
Hemoglobin Antibody
Myoglobin

65. THANK YOU FOR YOUR ATTENTION