Download 2.4 Proteins

Essential Idea
• Proteins have a very wide range of functions in
living organisms.
Understandings
•
Amino acids are linked together by condensation to form polypeptides.
•
There are 20 different amino acids in polypeptides synthesized on ribosomes.
•
Amino acids can be linked together in any sequence giving a huge range of
possible polypeptides.
•
The amino acid sequence of polypeptides is coded for by genes.
•
A protein may consist of a single polypeptide or more than one polypeptide
linked together.
•
The amino acid sequence determines the three-dimensional conformation of a
protein.
•
Living organisms synthesize many different proteins with a wide range of
functions.
•
Every individual has a unique proteome.
Proteins have many structures, resulting in a wide
range of functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
[Animations are listed on slides that follow the figure]
Enzymes a type of protein
• Enzymes are a type of protein that acts as a
catalyst, speeding up chemical reactions
• Enzymes can perform their functions repeatedly,
functioning as workhorses that carry out the
processes of life
Enzymes
Substrate
(sucrose)
Glucose
Enzyme
(sucrose)
Fructose
Polypeptides --linear chain of Amino Acids
• Polypeptides are polymers of amino acids
• A protein consists of one or more polypeptides
Amino Acid Monomers
• Amino acids are organic molecules with carboxyl
(--COOH) and amino groups (--NH2)
• Amino acids differ in their properties due to
differing side chains, called R groups
• Cells use 20 amino acids to make thousands of
proteins
a carbon
Amino group
Carboxyl group
a carbon
Amino
group
Carboxyl
group
All living organisms using the same 20 Amino Acids.
Below are 9 nonpolar/ hydrophobic amino acids
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Nonpolar
Methionine (Met)
Phenylalanine (Phe)
Tryptophan (Trp)
Proline (Pro)
All living organisms using the same 20 Amino Acids.
Below are 6 polar/ hydrophilic amino acids
Polar
Serine (Ser)
Threonine (Thr)
Cysteine (Cys)
Tyrosine (Tyr)
Asparagine (Asn) Glutamine (Gln)
LE 5-17c
All living organisms using the same 20 Amino Acids.
Below are 5 VERY polar/ hydrophilic amino acids
Acidic
Basic
Electrically
charged
Aspartic acid (Asp) Glutamic acid (Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Ribsomes in the cytoplasm and on the E.R. make
proteins
• There are two types of ribosomes:
– Free Ribosomes (located in the cytoplasm)
– Bound Ribosomes (located on the Endoplasmic
reticulum)
Both ribosomes make proteins/ polypeptides by stringing
amino acids together.
Amino Acid Polymers
• Amino acids are linked by
peptide bonds
• A polypeptide is a polymer of
amino acids
• Polypeptides range in length
from a few monomers to
more than a thousand
• Each polypeptide has a unique
linear sequence of amino
acids
Protein Tutorial Below:
Click below for the protein tutorials
•http://www.wisconline.com/objects/ViewObject.aspx?ID=AP1
3304
•http://publications.nigms.nih.gov/structlife/c
hapter1.html#a1
Condensation reaction of amino acids to form
polypeptide bonds and thus proteins
Hydrolysis vs. Condensation
Hydrolysis
Condensation
• Adds water
• Removes water
• Breaks down polymers
into monomers
• Forms new bonds
between monomers
forming polymers
• Example: Breaks down
starch into glucose
• Example: glucose and
fructose are bonded
together to form sucrose
IB Assessment Statment
• 7.5.1 Explain the four levels of protein
structure, indicating the significance of each.
PRIMARY STRUCTURE
The sequence of amino
acids
© Anne-Marie Ternes
PRIMARY STRUCTURE
• The numbers of amino acids vary
(e.g. insulin 51, lysozyme 129, haemoglobin
574, gamma globulin 1250)
• The primary structure determines the folding
of the polypeptide to give a functional protein
• Polar amino acids (acidic, basic and neutral)
are hydrophilic and tend to be placed on the
outside of the protein.
• Non-polar (hydrophobic) amino acids tend to
be placed on the inside of the protein
© 2007 Paul Billiet ODWS
Infinite variety
• The number of possible sequences is
infinite
• An average protein has 300 amino acids,
• At each position there could be one of 20
different amino acids
= 10390 possible combinations
• Most are useless
Natural selection picks out the best
© 2007 Paul Billiet ODWS
SECONDARY STRUCTURE
The folding of the
N-C-C backbone of the
polypeptide chain using
weak hydrogen bonds
© Text 2007 Paul Billiet ODWS
© Science Student
SECONDARY STRUCTURE
• This produces the alpha helix and beta pleating
• The length of the helix or pleat is determined by certain
amino acids that will not participate in these structures
(e.g. proline)
© Text2007 Paul Billiet ODWS
© Dr Gary Kaiser
TERTIARY STRUCTURE
The folding of the polypeptide into domains
whose chemical properties are determined
by the amino acids in the chain
MIL1 protein
© 2007 Paul Billiet ODWS
© Anne-Marie Ternes
TERTIARY STRUCTURE
• This folding is sometimes held together by strong
covalent bonds
(e.g. cysteine-cysteine disulphide bridge)
• Bending of the chain takes place at certain
amino acids (e.g. proline)
• Hydrophobic amino acids tend to arrange
themselves inside the molecule
• Hydrophilic amino acids arrange themselves on
the outside
© 2007 Paul Billiet ODWS
Disulfide bonds of tertiary structures of proteins
• Covalent bonds can form
between two adjacent
cysteine amino acids.
• The bond is covalent.
• The covalent bond stabilises
the tertiary shape of a
protein.
Chain B of Protein Kinase C
© Max Planck Institute for Molecular Genetics
QUATERNARY STRUCTURE
Some proteins are
made of several
polypeptide subunits
(e.g. haemoglobin has
four)
Protein Kinase C
© Max Planck Institute for Molecular Genetics
© Text 2007 Paul Billiet ODWS
QUATERNARY STRUCTURE
• These subunits fit together to form the
functional protein
• Therefore, the sequence of the amino acids
in the primary structure will influence the
protein's structure at two, three or more
levels
© 2007 Paul Billiet ODWS
Result
Protein structure depends upon the amino acid
sequence
This, in turn, depends upon the sequence of
bases in the gene
© 2007 Paul Billiet ODWS
QUATERNARY STRUCTURE
• In some cases proteins consist of nonpolypeptide (non-protein) chain called a
prosthetic group
• Example: haemoglobin is linked to a heme
group (iron contain molecule)
• Proteins with a prosthetic group are called
conjugated proteins.
© 2007 Paul Billiet ODWS
PROTEIN FUNCTIONS
• Protein structure determines protein function
• Denaturation or inhibition which may change
protein structure will change its function
• Coenzymes and cofactors in general may
enhance the protein's structure
© 2007 Paul Billiet ODWS
IB Assessment Statement
• 7.5.2 Outline the difference between fibrous
and globular proteins with references to two
examples of each protein type
Fibrous proteins
• Involved in structure: tendons ligaments
blood clots
(e.g. collagen and keratin)
• Contractile proteins in movement: muscle,
microtubules
(cytoskelton, mitotic spindle, cilia, flagella)
© 2007 Paul Billiet ODWS
Globular proteins
• most proteins which move around (e.g.
albumen, casein in milk)
• Proteins with binding sites:
enzymes, haemoglobin, immunoglobulins,
membrane receptor sites
© 2007 Paul Billiet ODWS
Examples to know
1. Rubisco
2. Insulin
3. Immunoglobulin
4. Rhodopsin
5. Collagen
6. Spider silk
Proteomes
• The total of all the proteins produced by a cell, a tissue or an
organism.
Gel electrophoresis is used to identify the proteins in a sample –
florescent markers are attached to antibodies for specific
proteins.
Proteomes vary, because different cells produce different
proteins. The proteome for each individual is unique.
Application:
• Denaturation of proteins by heat or by deviation
of pH from the optimum.