bg7004 lecture 2 student copy
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BG7004: Advanced Cell Biology
Lecture 2: Protein structure and function
Learning Outcomes:
• Shape and structure of proteins
• How proteins work
• How the functions of proteins are controlled
Dr Noreen Ishak
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
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
Four types of noncovalent bonds important in
biological systems
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 Huntington’s disease, Alzheimer’s 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
Primary structure (amino acid sequence)
Secondary structure (α helices, β sheets)
Tertiary structure (3D structure of a polypeptide)
Quartenary structure (3D structure of a protein complex consisting of more than one polypeptide)
Four levels of organization in the structure of a
protein
α helix – generated when a single polypeptide chain
turns around itself to form a cylindrical structure
In an α helix, a hydrogen bond is made between every fourth
peptide, linking the C=O of one peptide bond to the N-H of
another
Video Clip: 04.2 Alpha helix
Hydrogen bond
Peptide bonds Peptide bonds
Lipid bilayer
oxygen
Video Clip: 04.4 Beta sheet
The β sheets are made when hydrogen bonds form
between segments of polypeptide chains lying side by
side
Both types of β sheets are common in proteins
Antiparallel β sheet
Parallel β sheet
Many proteins are composed of separate functional domains made with α helix and β 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
Video Clip: 04.6 Disulfide bonds
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
General protein functionsProteins 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 cell’s 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
Video Clip: 04.7 Antibodies
Example 1 – Antibody can bind tightly with its
antigen through the binding site
Example 2 – Enzymes bind to substrates and convert
them into chemically modified products
Lysozyme cleaves a polysaccharide chain
Video Clip: 04.8 Lysozyme reaction
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
Mechanisms that regulate the activity of
proteins and enzymes
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 reversedwhen product levels fall
Feedback inhibition regulates the flow
through biosynthetic pathways
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 protein’s 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
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
Guanosine Triphosphate (GTP)
4) ATP hydrolysis allows motor proteins to produce large
movement in cells
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
ATPase
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
Chapter 4 of Essential Cell Biology
Essential concepts and Key terms
Attempt questions 10, 11, 15, 19
Follow-up tasks for Lecture 2