Download Proteins Introduction Aspects of a protein`s structure Primary

4/2/2012
Introduction
Proteins
• Proteins are essential parts of organisms and
participate in every process within cells.
• Many proteins are enzymes that catalyze
biochemical reactions and are vital to
metabolism.
• Through the process of digestion, animals
break down ingested protein into free amino
acids that are then used in metabolism.
Red blood cells contain the oxygen
transporting protein hemoglobin
1
Aspects of a protein's structure
2
Primary structure of proteins
• There are four distinct aspects of a protein's
structure:
• Primary structure,
• Secondary structure,
• Tertiary structure and
• Quaternary structure.
• This is the amino acid sequence
• An amino acid exists as a dipolar salt
H
H
H2N C COOH
H3N C COO
R
R
R = alkyl
• All amino acids have this general structure
3
4
1
4/2/2012
Classification of amino acids
Anatomy of an amino acid
• Non-polar with aliphatic R groups
Glycine
Alanine
Proline
Valine
5
Aromatic R groups
Non-polar with aliphatic R groups
Leucine
6
Isoleucine
Phenylamine
Methionine
7
Tyrosine
Tryptophan
8
2
4/2/2012
Polar Uncharged R groups
Serine
Threonine
Positively charged R groups
Cysteine
Arginine
Lysine
Asparagine
Glutamine
9
10
The origin of the single-letter code for
the amino acids
Negatively charged R groups
Aspartate
Histidine
Glutamate
11
Amino acid
3 letter
Single letter
Comment
Histidine
Isoleucine
Methionine
Serine
Valine
Alanine
Glycine
Leucine
Proline
Threonine
His
Ile
Met
Ser
Val
Ala
Gly
Leu
Pro
Thr
H
I
M
S
V
A
G
L
P
T
These amino acids
occur more frequently
in proteins than do
the other amino
acids having the same
first letters.
12
3
4/2/2012
Some of the other amino acids, are
phonetically suggestive
Amino acid
3 letter
Single letter
Arginine
Phenylalanine
Tyrosine
Tryptophan
Aspartic acid
Asparagine
Glutamic acid
Glutamine
Lysine
Arg
Phe
Tyr
Trp
Asp
Asn
Glu
Gln
Lys
R
F
Y
W
D
N
E
Q
K
Summary: Non-polar amino acids
Comment
Twyptophan
asparDic
asparagiN
glutamEke
Q-tamine
(K is near L in
alphabet)
13
Summary: Polar, non-charged amino acids
14
Summary: Negatively-charged amino acids
15
16
4
4/2/2012
Formation of a peptide bond
Summary: Positively-charged amino acids
• Amino acids are linked by PEPTIDE BONDS which are
covalent in nature
• Peptide bond is an amide linkage formed by a
condensation reaction (loss of water)
• Brings together the alpha-carboxyl of one amino acid
with the alpha-amino of another
• Portion of the amino acid left in the peptide is termed
the amino acid RESIDUE
– Amino acids sometimes called RESIDUES
• R groups remain UNCHANGED – remain active
• N-terminal amino and C-terminal carboxyl are also
available for further reaction
17
Amino acid residue
18
Formation of a peptide bond
• Definition of amino acid residue:
– an amino acid molecule that has lost a water molecule by becoming
joined to a molecule of another amino acid.
H
A peptide bond contains
19
C N
O
group
20
5
4/2/2012
Write the three-letter abbreviations for the
following tetrapeptide:
Example of a pentapeptide
Ser-Gly-Tyr-Ala-Leu
CH3
CH3
CH3 O
S
CH CH3
SH
CH2
CH2 O
CH2 O
CH2 O
NH3 CH C N CH C N CH C N CH C O
H
H
H
Ala-Leu-Cys-Met
**This is not the same as Met-Cys-Leu-Ala**
21
INSULIN
22
Insulin
• Insulin has 51 amino acids, divided between
two chains. One of these, the A chain, has
• 21 amino acids; the other, the B chain, has 30.
The A and B chains are joined by disulfide
• bonds between cysteine residues (Cys-Cys).
23
24
6
4/2/2012
Secondary structure of proteins
• This is the regularly repeating local structures
stabilized by hydrogen bonds
• Hydrogen bonds are electrostatic interactions
between a donor consisting of the dipole of a
polar O-H or N-H bond and an acceptor,
consisting of an available lone pair of
electrons on a neighbouring N or O atom.
• Typical hydrogen bonds are about 5 - 10% as
strong as a normal covalent bond, and are not
permanent bonds like covalent bonds.
• The dashed line - - - represents the hydrogen
bond.
Typical H-bond
donors
N-H - - -:N
typical H-bond
acceptors
N-H - - -:O
O-H - - -:N
O-H - - -:O
25
Hydrogen bonds in secondary
structures of proteins
26
Secondary structure of proteins:
a-helix
• Although each hydrogen bond is relatively
weak in isolation, the sum of the hydrogen
bonds in a helix makes it quite stable.
• The H-bonds result in a strong but temporary
attraction between H-bonding partners.
27
28
7
4/2/2012
Secondary structure of proteins:
a-helix
An α -helical secondary structure.
• Hydrogen bonds between ‘ backbone ’ amide NH and
C= O groups stabilize the α -helix.
• Hydrogen atoms of OH, NH or SH group
(hydrogen donors) interact with free
electrons of the acceptor atoms such as
O, N or S
29
Hydrogen bonds in secondary
structures of proteins : b-pleat
30
The parallel β -sheet
secondary structure.
• If the H-bonds are formed between peptide bonds in
different chains, the chains become arrayed parallel or
antiparallel to one another in what is commonly called
a β -pleated sheet.
• That is: When the zigzag polypeptide chains are
arranged side by side, they form a structure resembling
a series of pleats.
• The β -pleated sheet is an extended structure as
opposed to the coiled α -helix.
• It is pleated because the carbon—carbon (C—C) bonds
are tetrahedral and cannot exist in a planar
configuration.
31
32
8
4/2/2012
• In an antiparallel arrangement, the successive
β-strands alternate directions of the N and Cterminus. This is the most stable β-sheet
arrangement.
• In a parallel arrangement, the N-termini of
successive strands are oriented in the same
direction, generating a less stable β-sheet due
to the non-planarity of the inter-strand Hbonds.
33
34
Examples of amino acid side chain interactions
contributing to tertiary Structure
Tertiary Structure of Proteins
• T he three-dimensional, folded and biologically
active conformation of a protein is referred to as
its tertiary structure.
• This structure reflects the overall shape of the
molecule.
• T he three-dimensional tertiary structure of a
protein is stabilized by interactions between side
chain functional groups: covalent disulfide bonds,
hydrogen bonds, salt bridges, and hydrophobic
interactions.
35
36
9
4/2/2012
Stabilizing interactions responsible for the
tertiary structure of a protein.
Tertiary Structure of Proteins
• These complex structures is held together by a
combination of several molecular interactions
that involve the R-groups of each amino acid in
the chain.
• These interactions include
–
–
–
–
hydrogen bonds between polar R- groups
ionic bonds between charged R-groups
hydrophobic interactions between non-polar R-groups
covalent bonds: The disulfide bond
37
38
Tertiary Structure of Proteins…
Tertiary Structure of Proteins…
• The importance of disulfide bonds in the structure of
certain proteins is demonstrated by hair. Hair is made
of the protein apha-keratin. The particular structure of
your hair (straight, curly, etc.) is based on specific
disulfide bonds that naturally form in the hair protein.
This should help explain why an individual with straight
hair cannot simply heat their hair, denature the protein
(keratin), put in curlers and make it curly. The disulfide
bonds are covalent bonds and thus are very strong.
Heating these bonds will not break them, so simply
heating hair will not change straight hair to curly.
• Instead, it is necessary to break these bonds
chemically, reform the hair to the desired shape,
and make new disulfide bonds to maintain the
new shape.
• If an individual goes to the hairdresser for a
permanent, the beautician must first treat the
hair with a reagent that reduces (and thus
breaks) the disulfide bond, then put in curlers (to
get the desired shape), and add an oxidizing
agent to form new disulfide bonds to maintain
the new shape.
39
40
10
4/2/2012
Tertiary structures are quite varied
Tertiary structure is important!
The function of a protein (except as food)
depends on its tertiary structure. If this is
disrupted, the protein is said to be denatured
and it loses its activity. For example:
• denatured enzymes lose their catalytic power
• denatured antibodies can no longer bind
antigen
A mutation in the gene encoding a protein is a
frequent cause of altered tertiary structure.
41
Quaternary structure of proteins
42
Examples of quaternary structures
Tetramer
Hexamer
SSB
Allows coordinated
DNA binding
DNA helicase
Allows coordinated DNA binding
and ATP hydrolysis
Filament
• It is the shape or structure that results from
the interaction of more than one protein
molecule, usually called protein subunits,
which function as part of the larger assembly
or protein complex.
43
Recombinase
Allows complete
coverage of an
44
extended molecule
11
4/2/2012
Different structures of proteins
• Some proteins (such as hemoglobin) have more than one
peptide chain (these are multimeric proteins). The manner
in which these chains fit together is the quaternary
structure.
• The subunits of a multimeric protein may be identical
(homomultimeric protein), homologous or totally dissimilar
(heteromultimeric protein ) and dedicated to disparate
tasks. In some protein assemblies, one subunit may be
referred to as a "regulatory subunit" and another as a
"catalytic subunit."
• The protein hemoglobin is made up of four polypeptide
chains, two apha chains and two beta chains
45
46
Major Classes of proteins
• The number of subunits in an oligomeric complex is
described using names that end in –mer (Greek for
"part, subunit")
• 1 = monomer, 2 = dimer, 3 = trimer, 4 = tetramer, 5 =
pentamer 6 = hexamer, 7 = heptamer, 8 = octamer, 9 =
nonamer, 10 = decamer, 11 = undecamer, 12 =
dodecamer etc
• Although complexes higher than octamers are rarely
observed for most proteins, there are some important
exceptions: A capsid is the protein shell of a virus. It
consists of several oligomeric (e.g. 60) structural
subunits made of protein called protomers.
Protein types
• Proteins fall into three general classes, based
on their overall three-dimensional (tertiary)
structure and on their functional role:
– fibrous,
– membrane,
– globular
47
48
12
4/2/2012
Fibrous Proteins
Fibrous Proteins
• Fibrous proteins tend to be long, narrow molecules.
Fibrous proteins are used to construct macroscopic
structures, especially structures outside of cells.
Fibrous proteins tend to have a structural role,
although some have more active functions as well.
• Fibrous proteins are elongated molecules in which the
secondary structure (either a-helices or b-pleated
sheets) forms the dominant structure.
• Fibrous proteins are insoluble, and play a structural or
supportive role in the body, and are also involved in
movement (as in muscle and ciliary proteins).
• One feature of fibrous tissues is that they often have
regular repeating structures.
49
• Keratin, for example, which is found in hair, horns, wool,
nails, and feathers, is a helix of helices (2 pairs of a-helices
wound around one another) and has a seven amino acid
repeating structure. Other keratins are found in skin, fur,
hair, wool, claws, nails, hooves, horns, scales, beaks,
feathers, actin and mysin in muscle tissues and fibrinogen
needed for blood clots.
• Fibroin is the fibrous protein that makes up silk cloth and
spider webs.
• Silk is a fibrous protein that is composed only of bsheets. It too has a repeating pattern: layers of glycine
alternate with layers of alanine and serines in the b-sheets.
• Collagen, is the major protein component of connective
tissue. In collagen, every third amino acid is glycine and
many of the others are proline.
• fibrous proteins generally have only primary and secondary
structure whereas
50
Globular Proteins
Membrane proteins
• Globular proteins are by far the most abundant class of
proteins. Many of the most heavily studied proteins are
members of this class of proteins.
• They are a highly diverse group of proteins that are soluble
and form compact spheroidal molecules in water.
• All have tertiary structure and some have quaternary
structure in addition to secondary structure. Regular
secondary structures generally comprise less than half the
average globular protein.
• Globular proteins typically consist of relatively straight runs
of secondary structure joined by stretches of polypeptides
that abruptly change direction.
• Major examples include insulin, hemoglobin, most
enzymes, transport proteins and receptor proteins.
• Membrane proteins typically have a
hydrophobic region (frequently α-helical) that
interacts with the non-polar interior of
membranes.
• Membrane proteins often serve as receptors
or provide channels for polar or charged
molecules to pass through the cell membrane.
51
52
13
4/2/2012
Membrane proteins
• A membrane protein is a protein molecule that is
attached to, or associated with the membrane of
a cell or an organelle (a specialized subunit within
a cell that has a specific function, and is usually
separately enclosed within its own lipid bilayer - a
thin membrane made of two layers of lipid
molecules).
• Examples of organelles include: chloroplasts (in
plants, algae etc), mitochondria (in almost all
eukaryotes i.e. one of the structurally complex
cell types) and cell nucleus
• Example of a membrane protein
53
Some terminology
54
Cellular functions of proteins
• Cell contains genome = complete set of DNA
• Genes = specific sequences that encode
instructions for making proteins
• Protein = molecules of (20) amino acids that
perform much of life’s function
• Proteome = set of all proteins in a cell
• Proteins are the chief actors within the cell,
said to be carrying out the duties specified by
the information encoded in genes
• The set of proteins expressed in a particular
cell or cell type is known as its proteome
55
56
14
4/2/2012
Enzymes
Enzymes …
• The best-known role of proteins in the cell is as
enzymes, which catalyze chemical reactions.
• Enzymes are usually highly specific and accelerate
only one or a few chemical reactions.
• They carry out most of the reactions involved in
metabolism, as well as manipulating DNA in
processes such as DNA replication, DNA repair,
and transcription.
• The molecules bound and acted upon by
enzymes are called substrates.
• Although enzymes can consist of hundreds of
amino acids, it is usually only a small fraction of
the residues that come in contact with the
substrate, and an even smaller fraction - 3-4
residues on average - that are directly involved in
catalysis.
• The region of the enzyme that binds the
substrate and contains the catalytic residues is
known as the active site.
57
58
Cell signaling and ligand binding of
proteins
Structural proteins
• Many proteins are involved in the process of
cell signaling.
• Antibodies are protein components of
adaptive immune system whose main function
is to bind antigens (foreign substances in the
body) and target them for destruction.
• Receptors and hormones are highly specific
binding proteins.
• Structural proteins confer stiffness and rigidity
to otherwise-fluid biological components
• Most structural proteins are fibrous proteins;
for example, actin and tubulin are globular
and soluble as monomers, but polymerize to
form long, stiff fibers that comprise the
cytoskeleton, which allows the cell to maintain
its shape and size.
59
60
15