BG7004: Advanced Cell Biology

Lecture 2: Protein structure and function

Dr Noreen Ishak

Learning Outcomes:
Shape and structure of proteins
How proteins work
How the functions of proteins are controlled

Amino acids are the subunits of proteins or

polypeptides

There are 20 amino acids which are grouped into 4 classes

according to their side chains

hydrophilic

hydrophobic

Amino acids are joined together by a peptide bond

Condensation

 Proteins are built up by amino acids that are linked by peptide bonds to form a
polypeptide chain
The shape of a protein is determined by its amino acid sequence
Each type of protein differs in its sequence and number of amino acids hence the
sequence of the chemically different side chains make each protein different from each
other

3D structure of a protein is stabilised by noncovalent bonds

between different parts of the protein

Four types of noncovalent bonds important in

biological systems
Ionic bonds: Formed when electrons are transferred from one
atom to the other
Hydrogen bonds: Formed by electrical attractions between a
positively charged hydrogen atom in one
molecule with a negatively charged oxygen
or nitrogen in another molecule
Van der Waals attractions: Formed by electrical attractions
between two atoms that are close to
each other
Hydrophobic interaction: Hydrophobic groups are forced together
by repulsion from water

Three types of noncovalent bonds help proteins to fold

Hydrophobic forces help proteins fold into compact

conformations

Polar amino acid side chains

tend to gather on the outside of
the folded protein where they can
interact with water

Nonpolar amino acid side

chains are buried inside to form a
highly packed hydrophobic core of
atoms that are hidden from water

Most proteins are folded by noncovalent bonds into only

one stable conformation in which free energy is minimised

Protein can be denatured and renatured

When protein folds improperly, they can form aggregates

that can damage cells even whole tissues

Aggregated proteins have been

associated with diseases such as
Huntingtons disease, Alzheimers
disease and prion disease
In the case of prion disease, prion
protein can adopt a special misfolded
form that is considered infectious due to
its ability to convert normal protein into
an abnormal conformation

Proteins are in different shapes and sizes

Globular shape

Fibrous shape

Four levels of organization in the structure of a

protein
Primary structure (amino acid sequence)
Secondary structure ( helices, sheets)

Tertiary structure (3D structure of a polypeptide)

Quartenary structure (3D structure of a protein complex consisting of
more than one polypeptide)

 helix generated when a single polypeptide chain

turns around itself to form a cylindrical structure

In an helix, a hydrogen bond is made between every fourth

peptide, linking the C=O of one peptide bond to the N-H of
another
Hydrogen bond

Peptide bonds

Video Clip: 04.2 Alpha helix

Peptide bonds

Lipid
bilayer

The sheets are made when hydrogen bonds form

between segments of polypeptide chains lying side by
side
oxygen

Video Clip: 04.4 Beta sheet

Both types of sheets are common in proteins

Antiparallel sheet

Parallel sheet

Many proteins are composed of separate functional

domains made with helix and sheet

Proteins can bind to each other through the binding sites

on the surface of a protein to form dimers or multimers

Proteins can assemble into filaments, sheets or spheres

based on the differences in their binding sites

Extracellular proteins such as collagen are stabilised by

cross linking through disulfide bonds

Collagen is a triple helix formed by three extended protein chains that wrap around
one another
Many rod-like collagen molecules are cross-linked together in the extracellular
space to form collagen fibrils that have the tensile strength of steel

 Extracellular proteins such as collagen are stabilised by cross linking through

disulfide bonds
Disulfide bonds can form between adjacent cysteine side chains
A disulfide bond can have a major stabilising effect on a protein since it requires
high energy to be disrupted
Video Clip: 04.6 Disulfide bonds

General protein functions

Proteins have many functions such as:
Enzyme catalyses enzymatic reactions (pepsin, DNA polymerase)
Structural protein provides mechanical support (collagen, elastin)
Transport protein carries small molecules or ions (haemoglobin,
transferrin)
Motor protein generates movement in cells (myosin, kinesin)
Storage protein stores small molecules or ions (ferritin, casein)
Signal protein carries signals from cell to cell (insulin, epidermal growth
factor)
Receptor protein detects signals and transmits them to the cells
response machinery (acetylcholine receptor, insulin
receptor)
Gene regulatory protein binds to DNA to switch genes on and off (lactose
repressor)

All proteins must bind to particular ligands to

carry out their various functions
Any substance that can bind to a
protein is referred to as a ligand for
that protein
A ligand can be an ion, a small
molecule, or a macromolecule
The binding between a protein and its
ligand is highly selective and requires
the formation of noncovalent bonds

Example 1 - Antibody

Example 1 Antibody can bind tightly with its

antigen through the binding site

Video Clip: 04.7 Antibodies

Example 2 Enzymes bind to substrates and convert

them into chemically modified products

Lysozyme cleaves a polysaccharide chain

Video Clip: 04.8 Lysozyme reaction

Mechanisms that regulate the activity of

proteins and enzymes
1) The catalytic activity of enzymes in cells are often regulated by
other molecules in several ways:
The production of an enzyme can be regulated by gene
expression
The availability of an enzyme can be controlled by subcellular
localization of the protein
The activity of an enzyme can be negatively regulated by
feedback inhibition
The enzyme activity can be stimulated by a regulatory molecule
through a positive regulation

Feedback inhibition regulates the flow

through biosynthetic pathways

In this negative feedback inhibition, the

end product Z inhibits the production of
the first enzyme that is required for the
synthesis of X and thereby controls the
concentration of its final product
Feedback inhibition can work almost
instantaneously and is rapidly reversed
when product levels fall

Many enzymes have two binding sites: one for the

substrate and the other for the regulator (negative
control)

Aspartate transcarboxylase is an allosteric enzyme from E.coli. It catalyses an important

reaction that begins the synthesis of the pyrimidine ring of C,U and T nucleotides. One of
the final products of this pathway, cytosine triphosphate (CTP), binds to the enzyme to
turn it off whenever CTP is plentiful. CTP can thus act as a negative regulator. The
binding of CTP changes the protein confirmation and inactivates the enzyme.

In a positive regulation, a regulator (ADP) can bind

to the enzyme to lock them in the active form

2) Protein phosphorylation is a very common mean to

regulate protein activity

Thousands of proteins in a typical eukaryotic cell are modified by the covalent addition of
a phosphate group
A phosphate group is transferred from ATP to an amino acid side chain of the target
protein by a protein kinase
Removal of the phosphate group is catalyzed by a protein phosphatase
The phosphorylation of a protein by a protein kinase can either increase (ON) or decrease
(OFF) the proteins activity depending on the site of phosphorylation and the protein
structure

3) The activity of GTP-binding protein is also regulated by

the cyclic gain and loss of a phosphate group

Guanosine Triphosphate (GTP)

GTP-binding proteins can function as molecular switches

The activation of a GTP-binding protein generally requires the presence of a tightly bound
GTP molecule (switch on)
Hydrolysis of this GTP molecule by GTPase produces GDP and inorganic phosphate (Pi),
and it causes the protein to convert to an inactive conformation (switch off)
Resetting the switch requires the tightly bound GDP to dissociate, a slow step that is
greatly accelerated by specific signals
Once GDP dissociates, a molecule of GTP quickly replaces it and returns the protein to its
active conformation

4) ATP hydrolysis allows motor proteins to produce large

movement in cells

ATPase

ATP binding shifts a motor protein from

confirmation 1 to 2
The bound ATP is then hydrolysed to
produce ADP and inorganic phosphate
(Pi), causing a change from confirmation
2 to 3
The release of the bound ADP and Pi
drives the protein back to confirmation 1

Summary
Each type of protein has a unique amino acid sequence which determines both its
3D shape and biological activity
The folded structure of a protein is stabilized by multiple noncovalent interactions
between different parts of the polypeptide chain
There are four levels of organisation in the structure of a protein
Activities of most enzymes are strictly regulated
Properties

Fibrous protein

Globular protein

Shape

Long and narrow

Rounded/spherical

Role

Structural (strength and support)

Functional (catalytic, transport, etc)

Solubility

(Generally) insoluble in water

(Generally (soluble in water)

Sequence

Repetitive amino acid sequence

Irregular amino acid sequence

Stability

Less sensitive to changes in heat, pH, etc

More sensitive to changes in heat, pH, etc

Examples

Collagen, myosin, fibril, elastin, keratin, actin

Catalase, haemoglobin, insulin, immunoglobulin

Follow-up tasks for Lecture 2

Chapter 4 of Essential Cell Biology
Essential concepts and Key terms
Attempt questions 10, 11, 15, 19