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Topic 2: Molecular Biology (Student)
2.4
Essential Idea: Proteins have a very wide range of functions in living organisms.
 2.4 Proteins
Protein basics:
- Monomer is the amino acid (there are 20 types), R group
is unique to the type of amino acid (some polar and some
non polar) creating different properties
- Many functions including:
o Communication in body: hormones, receptors for
chemical signaling
o Antibodies
o Transport: hemoglobin carries oxygen
o Structure: collagen
o Catalyst: Enzymes that speed up reactions (often end in –ase)
i.
Amino acids are linked together by condensation to form polypeptides.
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Chains of many amino acids are called polypeptides.
Amino acids are linked by condensation reactions forming a peptide bond. This involves the
amine group (-NH3) of one amino acid and the carboxyl group (-COOH) of another. Water is
lost.
Amino acids are linked in the ribosomes during translation.
Dipeptide contains 2 amino acids, polypeptide contains many.
SKILL: Drawing molecular diagrams to show the formation of a peptide bond.
Draw the condensation reaction here:
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To form a dipeptide, two amino acids are linked by a condensation reaction (lose water)
between the amine group of one amino acid and carboxyl group of another.
Peptide bond is the same, the R group of the amino acid will differ.
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
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ii.
There are 20 different amino acids in polypeptides synthesized on ribosomes.
o Amino acids have three parts: amine groups (NH2), a carboxyl group (-COOH) and a R
group. The R group is unique to each amino acid and gives a polypeptide its character
allowing for a wide array of structures and functions of proteins.
o Twenty different amino acids are used by ribosomes to make polypeptides.
How are the amino acids separated into 3 different groups. Explain: _______________________________
_________________________________________________________________________________________________
iii.
Amino acids can be linked together in any sequence giving a huge range of possible
polypeptides.
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iv.
Ribosomes link the amino acids together and they can be arranged in any order
The number of amino acids in a polypeptide be from 20 to tens of thousands.
Basically the number of different polypeptides that can be produced is 20n, 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 20200, 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.
o The sequence that each polypeptide needs to have is stored in a coded form in the bases of
a gene (DNA).
o Each 3 bases codes for 1 amino acid in a polypeptide
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v.
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.
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vi.
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 (structural protein in tendons)
Keratin consists of 2 polypeptides twisted into a double helix (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
Integrin consist of two polypeptides with hydrophobic portion embedded in membrane. Used
to connect between structures inside and outside the cell.
The amino acid sequence determines the three-dimensional conformation of a protein.
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Conformation is the three-dimensional structure of a protein and it is determined by the amino
acid sequence of a protein.
Fibrous protein like collagen, elongated protein with repeating structure, usually have
repeating structure
Globular proteins often have parts that are helical or sheet-like.
vii. Living organisms synthesize many different proteins with a wide range of functions.
o No other carbon compounds can compare with the versatility of proteins.
Function
Catalysis: speed up specific chemical reactions within the cell or
outside of it. Do this by lowering activation energy needed for
reaction
Muscle Contraction: cause the contractions used in locomotion
and transport in body
Function
Amylase: breaks down
starch in the mouth and
small intestine.
Actin and Myosin
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Cytoskeletons: microtubules that give animals cells shape and
pull chromosomes during mitosis.
Tensil Strengthening: fibrous proteins that give strength to skin,
tendons, ligaments and blood vessel walls.
Blood clotting: plasma proteins act as clotting factors that cause
blood to turn from liquid to a gel in wounds
Transport of nutrients and gasses: transport oxygen, carbon
dioxide, iron and lipids
Cell adhesion: membrane proteins cause adjacent animal cells
to stick to each other within tissues
Membrane transport: used for facilitated diffusion and active
transport, and electron transport during cell respiration and
photosynthesis
Hormones: control actions in the body
Receptors: binding sites in membranes and cytoplasm for
hormones, neurotransmitters, tastes and smells, and receptors for
light in eye and in plants.
Packing DNA: help chromosomes to condense during mitosis
Immunity: most diverse group, cells can make huge numbers of
different antibodies.
viii.
Tubulin: subunit of
microtubules in the spindle
to pull apart chromosomes
Hemoglobin: transports
oxygen in blood
Insulin: regulates glucose
metabolism by controlling
blood sugar concentration
Antibodies: the defense
against pathogens
Every individual has a unique proteome.
o Proteome is all the proteins produced by a cell, tissue, or organism
o This is completed by extracting mixtures of proteins and using gel electrophoresis is with
antibodies specific to those proteins with florescent markers.
o Proteomes very in different cells (because they need different protein), and at different times
within the same cell (cell activity varies)
o Proteomes vary between different individuals because of not only cell activity but slight
variations in amino acid sequences.
o Within species there are strong similarities between proteomes.
APPLICATION: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of
the range of protein functions.
Rubisco
Insulin
Immunoglobulins
- 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 enzyme in the world
- 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
- 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
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Rhodopsin
Collagen
Spider silk
- 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 it’s shape and the shape of
the opsin. This sends a nerve impulse through the optic nerve to the brain
- essential in low light
- 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 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 a web and when a spider suspends itself
- very extensible and resistant to breaking
APPLICATION: Denaturation of proteins by heat or by deviation of pH from the optimum. (studied in
further detail in enzyme section)
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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 – optimal
temperature is 80 Celsius
Different pH’s away from a proteins 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
higher
How are the proteins of humans and bacteria in hydrothermal vents different?
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