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)

Enzyme(sucrose)

Fructose

Glucose

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

Amino group Carboxyl group

carbon

Aminogroup

Carboxylgroup

carbon

All living organisms using the same 20 Amino Acids.

Below are 9 nonpolar/ hydrophobic amino acids

Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

Leucine (Leu)Valine (Val)Alanine (Ala)

Nonpolar

Glycine (Gly)

Asparagine (Asn) Glutamine (Gln)Threonine (Thr)

Polar

Serine (Ser) Cysteine (Cys) Tyrosine (Tyr)

All living organisms using the same 20 Amino Acids.

Below are 6 polar/ hydrophilic amino acids

LE 5-17c

Electricallycharged

Aspartic acid (Asp)

Acidic Basic

Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

All living organisms using the same 20 Amino Acids.

Below are 5 VERY polar/ hydrophilic amino acids

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.wisc-online.com/objects/ViewObject.aspx?ID=AP13304

•http://publications.nigms.nih.gov/structlife/chapter1.html#a1

Condensation reaction of amino acids to form polypeptide bonds and thus proteins

Hydrolysis vs. Condensation

Hydrolysis

• Adds water

• Breaks down polymers into monomers

• Example: Breaks down starch into glucose

Condensation

• Removes water

• Forms new bonds between monomers forming polymers

• 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 uselessNatural 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

© Science Student

© Text 2007 Paul Billiet ODWS

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)

© Dr Gary Kaiser © Text2007 Paul Billiet ODWS

TERTIARY STRUCTURE

The folding of the polypeptide into domains whose chemical properties are determined by the amino acids in the chain

MIL1 protein

© Anne-Marie Ternes © 2007 Paul Billiet ODWS

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.

© Max Planck Institute for Molecular GeneticsChain B of Protein Kinase C

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 nonpoly-peptide (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.