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IB Biology - Curriculum Notes 

2.4 Proteins  

∑ - Understandings:

∑ - Amino acids are linked together by condensation to form polypeptides.



Amino acids are then combined to create large polypeptides through condensation reactions which produce many molecules of water (i.e. polypeptides - Hemoglobin and Insulin).


B  Skill: Drawing molecular diagrams to show the formation of a peptide bond.



A basic dipeptide is shown to the right. Students should practice drawing  with a variety of different amino acids (different “R” groups)
Every peptide bond should be between the NH2 (amine group) and the COOH (carboxyl group). One H comes from the NH2 and an –OH group comes from the –COOH group to produce H2O
Condensation reaction



∑ - There are 20 different amino acids in polypeptides synthesized on ribosomes.



Twenty different amino acids are used by the ribosomes to create polypeptides in our body
They all contain an amine (NH2) group, a carboxyl (-COOH) group which combine to form the peptide bond and an “R” group
The different “R” groups are what makes the amino acids different and allow the proteins to form a wide array of structures and functions
Some are charged or polar, hence they are hydrophilic
Some are not charged and are non-polar, hence they are hydrophobic





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∑ - Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.



Ribosomes link amino acids together forming a peptide bond according to the mRNA sequence copied from the gene or genes (DNA) for a particular polypeptide
Since there are 20 amino acids, an enormous variety of polypeptides can be produced
Basically, the number of different polypeptides that can be produced is 20^n, where 20 represents the number of amino acids that can be used and n represents the number of AA’s in a particular polypeptide.
So if a protein has 200 AA’s, the number of different combinations would be 20^200, which is an astronomically large number. Some proteins can be in the thousands or tens of thousand



∑ - The amino acid sequence of polypeptides is coded for by genes.



The sequence of amino acid in polypeptides is coded by the base sequence in an organism’s genes
Each 3 bases codes for 1 amino acid in a polypeptide
So if a polypeptide is 300 amino acids in length, 900 bases actually code for that polypeptide (not including the 3 base pairs that code for the stop codon). Also, the genes are actually longer as they contain non-coding regions that don't code for the polypeptide.
The actual coding region is called the reading frame



∑ - A protein may consist of a single polypeptide or more than one polypeptide linked together.



Some proteins consist of a single polypeptide, while some contain more than one polypeptide
Hemoglobin, for example, has 4 linked polypeptides, which are folded into a globular protein to carry oxygen in the blood
Collagen consists of 3 polypeptides wound together like a rope (a structural protein in tendons)
Keratin consists of 2 polypeptides twisted into a double helix (a structural protein in hair and fingernails). Insulin also has two polypeptides
Glucagon consists of only 1 alpha-helix polypeptide. Glucagon breaks down glycogen into glucose when the body needs sugar for energy



∑ - The amino acid sequence determines the three-dimensional conformation of a protein.



There are 4 levels of proteins, primary, secondary, tertiary and quaternary
How protein twists and folds to form secondary and tertiary structures is determined by the primary sequence of amino acids
Secondary structures for fibrous proteins such as collagen and keratin are determined by repeating sequences in the amino acid sequence. They are formed by the interactions between the amine and carboxyl groups
Tertiary structures that form globular proteins are still determined by the original amino acid sequence. They form from interactions between the different “R” groups causing them to fold to create an active protein



Video on Protein Structure https://www.youtube.com/watch?v=hok2hyED9go





∑ - Living organisms synthesize many different proteins with a wide range of functions.

Protein Functions

Enzymes - catalyze biochemical reactions by lowering the activation energy needed for the reaction to take place



Examples
    Pepsin – breaks down protein in the stomach

    Amylase – breaks down the starch in the mouth and small intestine

Hormones – chemical messengers that help coordinate certain regulatory activities



Example
    Insulin – regulates glucose metabolism by controlling blood sugar concentration

Structural Proteins – fibrous proteins provide support and structure within the body

Example


    Collagen – main protein in connective tissues such as tendons and ligaments

Transport Proteins – move molecules from one place to another around the body



Example
    Hemoglobin – transports oxygen throughout the blood system

Muscle Contractions



Example
    Actin and myosin – used in the contraction of a muscle in location and transport

Cytoskeletons



Example
​    Tubulin – subunit of microtubules in the spindle to pull apart chromosomes and give animal cells their shape

Receptors



Example
    Binding sites in the membrane for hormones, neurotransmitters and light in the retina

Immunity



Example
    Antibodies – for defence against pathogens

∑ - Every individual has a unique proteome.



A proteome is all of the different kinds of proteins produced by a genome, cell, tissue or organism at a certain time.
This is completed by extracting mixtures of proteins and using gel electrophoresis with antibodies specific to those proteins with fluorescent markers
Proteomes vary in different cells (different cells make different proteins) and at different times within the same cell (cell activity varies)
Proteomes vary between different individuals because of not only cell activity but slight variations in amino acid sequences
Within a species, there are strong similarities between proteomes



Applications and skills:

β - Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

Rubisco

- Catalyzes the reaction in the Calvin cycle that fixes CO2 into organic carbon to be used by living organisms to produce the carbon compounds need for life.
- Full name is ribulose bisphosphate carboxylase
- It is one of the most abundant and important enzymes in the world

Insulin

- a hormone produced by the beta cells of the pancreas that reduces the blood glucose levels by promoting the absorption of glucose from the blood to the skeletal muscles and tissue
- Insulin binds reversibly to receptors in the cell membrane to promote uptake

Immunoglobulins

- these are also known as “antibodies”
- They are Y shaped proteins produced by the plasma B cells to identify and neutralize foreign pathogens like bacteria and viruses
- they act as markers to identify these pathogens for destruction by large white blood cells called Phagocytes
- each antibody is specific for a specific pathogen

Rhodopsin

- rhodopsin is a biological pigment in the photoreceptor cells of the retina
- rhodopsin consists of a retinal molecule surrounded by an opsin polypeptide
- When the retinal absorbs light through the eye, it changes its shape and the shape of the opsin. This sends a nerve impulse through the optic nerve to the brain
- essential in low light

Collagen

- main structure molecule in various connective tissues such as skin, blood vessels, and ligaments
- They are fibrous rope-like proteins made from 3 polypeptides


Most abundant protein in the body (about ¼ of all the proteins)


Spider silk

- spider silk consists of many different types with different functions
Eg. dragline silk is stronger than steel and tougher than Kevlar used in bulletproof vests)
- used in the spokes of web and when a spider suspends itself
- very extensible and resistant to breaking

β - Application: Denaturation of proteins by heat or by the deviation of pH from the optimum. (studied in further detail in enzyme section)



Tertiary or 3D structure of proteins is held together by bonds between the “R” groups
Heat causes proteins to denature because vibrations caused by the KE break the intermolecular bonds or interactions
Different proteins can tolerate different temperatures. Most of the proteins in the humans work best at body temperature, but some organisms like bacteria in hydrothermal vents or volcanic hot springs can tolerate extreme temperatures without denaturing (Thermus aquaticus – the optimal temperature is 80 Celsius
Different pH’s away from a protein's optimal pH can also cause denaturation
Alkaline or acidic solutions can break the ionic bonds between R groups causing the protein to lose its 3D shape
Pepsin – Enzyme in the stomach works best at about 1.5 pH but will denature as the pH gets higherType