Proteins

Rut Klinger
MIS IB DP SL Biology
 Proteins have a very
wide range of
Essential idea
functions in living
organisms
Proteins are a very diverse class of compounds and may
serve a number of different roles within a cell, including:

Structure
Collagen: A component of the connective tissue of animals (most abundant protein in mammals)
Spider silk: A fiber spun by spiders and used to make webs (by weight, is stronger than kevlar and steel)

Hormones
Insulin: Protein produced by the pancreas and triggers a reduction in blood glucose levels
Glucagon: Protein produced by the pancreas that triggers an increase in blood glucose levels

Immunity
Immunoglobulins: Antibodies produced by plasma cells that are capable of targeting specific antigens

Transport
Haemoglobin: A protein found in red blood cells that is responsible for the transport of oxygen
Cytochrome: A group of proteins located in the mitochondria and involved in the electron transport chain

Sensation
Rhodopsin: A pigment in the photoreceptor cells of the retina that is responsible for the detection of light

Movement
Actin: Thin filaments involved in the contraction of muscle fibres
Myosin: Thick filaments involved in the contraction of muscle fibres

Enzymes
Rubisco: An enzyme involved in the light independent stage of photosynthesis
proteins Made of Amino Acids subunits
Amino Acids

There are 20 different amino acids in polypeptides synthesised

on ribosomes
Proteins are comprised of long chains of recurring monomers
called amino acids
There are 20 different amino acids which are universal to all
living organisms
A further two – selenocysteine and pyrrolysine – are modified
variants found only in certain organisms
Amino acids all share a common basic structure, with a central
carbon atom bound to:
An amine group (NH2)
A carboxylic acid group (COOH)
A hydrogen atom (H)
A variable side chain (R)
Amino  acids are
linked together by
condensation to form
polypeptides

Polypeptides are chains of amino

acids that are made by linking
together amino acids by
condensation
The condensation reaction involves
the amine group (-NH2) of one
amino acid and the carboxyl
group (-COOH) of another. Water is
removed as in all condensation
reactions, and a new bond is
formed between the two amino
acids, called a peptide bond
Polypeptide chains can be broken
down via hydrolysis reactions,
which requires water to reverse the
process
Drawing molecular diagrams to show the formation of a peptide
bond
Amino acids can be linked together in any sequence giving
a huge range of possible polypeptides

Polypeptides are molecule consisting of many amino acids linked by peptide bonds - this
happens on ribosomes by a process called translation
The polypeptides can contain any number of amino acids through chains of fewer than 20
amino acids are usually referred to as oligopeptides rather than polypeptides
Ribosomes link  amino acids together on at a time until a polypeptide is fully formed
Ribosome can make peptide bonds between any pair of amino acids
amount of amino acid sequences can be calculated starting with dipeptides:
The amino acids in a dipeptide can be any of the 20 so there are 20 times 20 possible
sequences
There are 20 x 20 x 20 possible tripeptide sequences
for a polypeptide of n amino acids there are 20 n possible sequences # of amino acids in a
polipeptide – e.g. 400 amino acids there are 20^400 possible amino acid sequences
Amino Acids’
properties

Each type of amino acid

differs in the composition of
the variable side chain
These side chains will have
distinct chemical properties
(e.g. charged, non-polar, etc.)
and hence cause the protein
to fold and function differently
according to its specific
position within the polypeptide
chain
 Polar amino acids have hydrophilic R groups, while
non-polar amino acids have hydrophobic R groups
The localisation of polar and non-polar amino acids will be
determined by the type of protein and its function:
Amino acids Water soluble proteins:
may be either Non-polar amino acids tend to be found in the centre of
polar or the molecule (stabilise the structure)
Polar amino acids tend to be located on the protein
non-polar surface (capable of interacting with water molecules)

depending on Membrane-bound proteins:

Non-polar amino acids tend to be located on the regions
the composition of the surface in contact with the membrane

of their side Polar amino acids will generally line interior pores (to
create hydrophilic channels)
chain Enzymes:
The active site specifically depends on the location and
distribution of polar and non-polar amino acids as
hydrophobic and hydrophilic interactions can play a role
in substrate binding to the active site
Levels of protein
structure:
The amino acid
sequence
determines the
three-dimensional
conformation of a
protein
 Sequence and number of amino acids in the
Primary polypeptide
Directly encoded by codons in mRNA
structure Joined by covalent peptide bonds
 Secondary structure

Alpha helices - amino acid

sequence folds into a coil / spiral
arrangement
Beta sheets - a
directionally-oriented staggered
strand conformation
Formed by neighbouring amino
acids
Stabilized by hydrogen bonds
between non-adjacent amine and
carboxyl groups

Present in structural proteins

Where no secondary structure
exists, the polypeptide chain will
form a random coil
 3D structure of polypeptide determined by the
interactions between the variable side chains
Distant parts of the polypeptide chain joined
Interactions between R groups
The affinity or repulsion of side chains will affect
Tertiary the overall shape of the polypeptide chain and
are determined by the position of specific
structure amino acids within a sequence
Imay include hydrogen bonds, disulphide bridges,
ionic interactions, polar associations, etc.
This structure determines function of active
proteins
There are two main classes of protein tertiary
structure: Fibrous and Globular
Fibrous proteins are generally composed of long and narrow
strands and have a structural role (they are something)

ibrous proteins such a collagen are elongated usually

with a repeating structure
many proteins are globular with an intericate shape that
oftern includes parts that are helical or sheet like
amino acids are added one by one to form a
polypeptide
they are always added in the same sequence to make a
particular polypeptide
In Fibrous proteins amino acid sequence prevents folding
up and ensures the chain remains in an elongated form
Globular proteins generally have a more compact and rounded
shape and have functional roles (they do something)

in globular proteins the polypeptides gradually fold up as they are

made to develop the final conformation= this is stabilized by
bonds between the R groups of the amino acids that have been
brought together by the folding
globular proteins that are soluble in water- there are hydrophilic R
groups on the outside of the molecules and there are usually
hydrophobic groups on the inside
in globular membrane proteins there are regions with hydrophobic
R groups on the outside of the molecules which are attracted to
the hydrophobic centre of the membrane
A protein may consist of a
single polypeptide or more
than one polypeptide linked
together

Certain proteins possess a fourth level of

structural organisation called a quaternary
structure
Quaternary structures are found in proteins
that consist of more than one polypeptide
chain linked together, e.g. haemoglobin
consists of 4 polypeptides
Alternatively, proteins may have a
quaternary structure if they include inorganic
prosthetic groups as part of their structure
Not all proteins will have a quaternary
structure – many proteins consist of a single
polypeptide chain
 Denaturation of proteins involves the disruption and possible
destruction of both the secondary and tertiary structures.
Since denaturation reactions are not strong enough to break
the peptide bonds, the primary structure (sequence of amino
acids) remains the same after a denaturation process.
Denaturation disrupts the normal alpha-helix and beta sheets
Protein in a protein and uncoils it into a random shape

denaturation
pH - ‘power of hydrogen’ - represents
the concentration of hydrogen ions in
a water-based solution

pH is expressed on a logarithmic scale, whereby pH

= –log10c  (c = concentration of H+ in moles per litre) 
The pH scale typically ranges from 0 – 14 and
measures how acidic or basic a substance is
Substances with a pH less than 7 are acidic and will
donate hydrogen ions (i.e. high H+ concentration)
Substances with a pH greater than 7 are basic /
alkaline and will accept hydrogen ions (i.e. high OH–
concentration)
Substances with a pH of 7 are neutral (there is an
equal number of H+ and OH– ions)
Denaturation of proteins can usually be caused by
two key conditions – temperature and pH

pH Temperature

Amino acids are zwitterions, neutral

molecules possessing both negatively
(COO–) and positively (NH3+) charged High levels of thermal energy may disrupt the
regions  hydrogen bonds that hold the protein
together
Changing the pH will alter the charge of the
protein, which in turn will alter protein As these bonds are broken, the protein will
solubility and overall shape begin to unfold and lose its capacity to
function as intended
All proteins have an optimal pH which is
dependent on the environment in which it Temperatures at which proteins denature
functions (e.g. stomach proteins require an may vary, but most human proteins function
acidic environment to operate, whereas optimally at body temperature (~37ºC)
blood proteins function best at a neutral pH)
The amino acid sequence of polypeptides is coded for by
genes

A gene is a sequence of DNA which encodes a polypeptide sequence

A gene sequence is converted into a polypeptide sequence via two processes:
Transcription – making an mRNA transcript based on a DNA template (occurs within the nucleus)
Translation – using the instructions of the mRNA transcript to link amino acids together (occurs at the
ribosome)

Typically, one gene will code for one polypeptide – however there are exceptions to this rule:
Genes may be alternatively spliced to generate multiple polypeptide variants
Genes may be mutated (their base sequence is changed) and consequently produce an alternative
polypeptide sequence
 Every individual has a unique proteome

The proteome is the totality of proteins expressed within a cell, tissue or organism at a certain time. The
proteome of any given individual will be unique, as protein expression patterns are determined by an
individual’s genes
Genome - all of the genes of a cell, a tissue or an organism
The genome of an organism is fixed, but the proteome is variable because different cells in an
organism make different proteins
Even in a single cell the proteins that are made vary over time depending on its activities – the
proteome therefore reveals what is actually happening in an organism, not what potentially could
happen
Within a species there are both strong similarities and differences in the proteome of all individuals
Proteome of each individual is unique partly because of differences of activity, but also because of
differences in the amino acid sequence of proteins - with the possible exception of identical twins,
none of us have identical proteins, so each of us has a unique proteome, even the proteome of
identical twins can become different with age
The proteome is always significantly larger than the number of genes in an
individual due to a number of factors:

Gene sequences may be

alternatively spliced
following transcription to
generate multiple protein
variants from a single
gene

Proteins may be modified

(e.g. glycosylated,
phosphorylated, etc.)
following translation to
promote further variations
Examples of proteins

Rubisco Insulin Immunoglobulins

Rhodopsin Collagen Spider silk

Rubisco - catalysis

RuBP Carboxylase / Oxydase

Crucial enzyme in light-independent
phase of photosynthesis
Binds CO2 from the air

Sigmaaldrich.com
Insulin -
regulation

Animal hormone
Produced by b cells of
pancreas
Lowers glucose level in
blood
Triggers glucose uptake by
various cells
Immunoglobulins
- immunity

Antibodies
Produced by lymphocytes
Recognize specific
molecules in foreign cells
or substances
Participate in destroing of
dangerous molecules and
microorganisms
Rhodopsin - reception

Light-sensitive protein
Produced by rods (photoreceptor
cells) in retina
Enables B&W (monocolour) vision
Collagen - elasticity

Structural protein in animals

Elastic
Present in connective tissues
Skin, bones, tendons, ligaments, hair, nails

www..jsd.claremont.edu
Spider silk -
resistance

Produced by spiders to
make webs
Incredibly resistant to
pulling forces

http://www.scienceinschool.org/
Resources

Textbook chapter 2.4 pages 87-95

https://www.thoughtco.com/proteins-373564
https://www.youtube.com/watch?v=2Jgb_DpaQhM
https://ib.bioninja.com.au/
https://www.youtube.com/watch?v=hok2hyED9go
https://youtu.be/ys4VXmgmC2g