Proteins Flashcards
What are the 5 functions of proteins ?
- Provide Structure
- Transport molecules
- Defence
- Biological Catalysts
- Regulation of genes
What is the main component of connective tissues ?
Collagen fibres, which is the most abundant protein in the body.
In proteins what component provides structure ?
Collagen Fibres
Where is collagen fibre found ?
Skin, tendons, organs and bone
What is collagen known as ?
The protein of bone, skin and tendon
What protein is a transport molecule which carries oxygen?
Haemoglobin
What is the function of haemoglobin ?
Oxygen carrier
How many protein molecules are in haemoglobin ?
4 protein subunits per molecule
What does each protein subunit in haemoglobin contain ?
A haem group which can bind to 1 molecule of o2
The haem group (adult) consists of :
2 alpha subunits
2 beta subunits
In fetus :
2 alpha
2 gamma
What is an example of a prosthetic group ?
Haem
Which protein is a transport molecule that transports cholesterol ?
LDL and LDL receptors
What is the function of LDL and LDL receptors ?
LDL - Transport cholesterol molecules
LDLR - Co-ordinate cholesterol uptake into cells
What is LDL composed of ?
Phospholipid shell
Single molecule of apolipoprotein B
What is wrong with patients with familial hypercholesterolemia ?
They have a mutation in the LDL receptor gene.
Which proteins are involved in defence ?
Antibodies
What is the function of antibodies ?
Defence against infection
Structure of antibodies
2 identical heavy chains
2 identical light chains
They are covalently linked by disulphide bonds.
They have highly specific antigen recognition sites.
What proteins are biological catalysts ?
Enzymes
What is the function of enzymes ?
Regulation of all biological systems.
Lysozyme function
Catalyses the cutting of polysaccharide chains.
What proteins are involved in regulation of genes ?
Lac repressor
Function of the Lac repressor
Helps control gene expression of proteins metabolising lactose in bacteria.
How does the Lac repressor help control gene expression ?
The repressor binds to DNA and prevents the expression of the gene in the absence of lactose.
What changes the activity of proteins ?
Change in conformation
What are proteins ?
Large molecules, which are complex and are linear polymers.
Polymer
Amino acids joined together via peptide bonds
Protein structure hierarchy
Primary
Secondary
Tertiary
Quaternary Structures
What is the general structure of an amino acid ?
Central carbon atom
Amino group
Carboxyl group
H atom
Variable R group
What defines the structure and function of proteins ?
The chemical properties of each R group
Basic amino acid examples (3)
Lysine
Arginine
Histidine
Acidic amino acid examples (2)
Aspartate
Glutamate
Polar amino acid examples (4)
Serine
Threonine
Asparagine
Glutamine
Hydrophobic amino acid examples (4)
Alanine
Valine
Leucine
Tyrosine
What are the 3 special amino acids ?
Cysteine
Glycine
Proline
What is special about cysteine ?
Can form covalent disulphide bonds with other cysteine residues.
What is special about glycine ?
It is the smallest amino residue and can fit into tight spaces.
What is special about proline ?
The side chain of proline bends around to form a covalent bond with the nitrogen atom of the amino group.
By doing this, proline creates a kink in the protein chain.
Polypeptide
A polymer of amino acids joined by peptide bonds.
Amino acid residue
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
Prosthetic group
A non-protein unit, tightly bound to a protein and is essential for the protein’s function.
Conformation
The arrangement in space of the constituent atoms which determine the overall shape of the molecule.
Acid
Any molecule that tends to release a hydrogen ion.
Base
Any molecule that readily combines with a hydrogen ion.
pKa
The pKa of any acid is = to the pH at which half of the molecules are disassociated.
What can influence pKa ?
Local environment
When does disassociation occur ?
Over 2 pH units centred on the pKa.
What is the result of a change in pH on proteins conformation ?
A change in pH causes a change in conformation, so the substrate molecule cannot bind and is released into the lysosome.
What is a peptide bond ?
A covalent bond
Why is formation of a protein a condensation reaction ?
A molecule of water is lost.
What are some constraints of the peptide bond ?
It does not permit rotation.
Rotation can occur on the alpha carbon.
What is a disadvantage of the bulky R groups ?
They are positioned on either side of the backbone.
This limits the number of 3D conformations possible for a polypeptide.
Primary Structure function
The sequence where the amino acids are synthesised into the polypeptide, which determines the proteins function.
Secondary structure function
The initial folding pattern of the linear polypeptide.
3 main types of 2ndary structure : alpha helix, beta pleated sheets, turns
How is the secondary structure stabilised ?
By Hydrogen bonding along the backbone of the polypeptide strand.
Features of alpha helix
The R group sticks out
The H bonds are between the carboxyl groups of every 4th amino acid.
What are beta strands ?
Extended stretches of >5 amino acids
Features of Beta sheets
Beta strands organised next to each other.
The R group sits above and below.
How are turns formed ?
Polypeptide chains can fold upon themselves forming a bend or a loop.
Usually 4 amino acids are require d to form a turn.
What residues are frequently found in turns ?
Proline
What happens in tertiary structure ?
The 3D folding of secondary structure.
Hydrophobic residues are buried and hydrophilic residues are buried outwards to the aqueous environment.
What is tertiary structure ?
It can be the final folded 3D shape caused by interactions between R groups.
Arrangement of an entire polypeptide to form a globular structure.
What are the different interactions between R groups ?
Disulphide bonds
H-Bonds
Ionic interactions
Van der Waals interactions
Hydrophobic interactions
What is the function of turns in tertiary structure ?
They connect regions of alpha helix and beta pleated sheets so that the polypeptide can fold into a globular domain.
In cysteine how are disulphide bonds formed ?
The SH groups of 2 neighbouring cysteine residues form a covalent S-S bond.
Where does quaternary structure exist ?
It exists in proteins with 2 or more connected polypeptide sub-units.
What stabilises the quaternary structure ?
Disulphide bonds
What is quaternary structure ?
Arrangement of more than one polypeptide to form an oligomeric, functional protein.
What is tertiary structure affected by ?
High temperature
Changes in pH
What does high temperature do to tertiary structure ?
It destabilises the structure and weak bonds break.
What do changes in pH do to tertiary structure ?
Affects the ionisation of acidic and basic R groups.
The conformation of the protein changes until the protein is denatured.
What happens when a molecule of oxygen binds to a haem group ?
1 molecule of oxygen binds to a haemoglobin subunit.
Change in conformation.
Other subunits have an increased affinity for the remaining oxygen.
What is the binding of oxygen affected by ?
High temperatures
Low pH
What does a high temperature do to oxygen binding ?
Lowers the affinity of haemoglobin for oxygen.
This means that binding of oxygen is reduced, so increased oxygen delivery to the tissues.
What does a low pH do to oxygen binding ? (Bohr effect)
Lowers the affinity of haemoglobin for oxygen.
What happens during exercise ?
Tissues generate heat and CO2 + H2O —> carbonic acid. This promotes increased oxygen delivery to tissues.
What causes sickle cell anaemia ?
Mutation at primary structure
A single amino acid change at position 6 in the beta chain of haemoglobin.
Hydrophilic glutamic acids to hydrophobic valine.
What is a result of sickle cell anaemia ?
Sickling of erythrocytes
What is adult haemoglobin composed of ?
2 alpha and 2 beta subunits
What is foetal haemoglobin composed of ?
2 alpha and 2 gamma subunits
Why are foetal red blood cells unaffected by sickle cell disease ?
Due to the absence of beta chains.
What is the function of the protein collagen ?
It helps bind cells together to form tissues.
It assembles in long, extremely strong fibres.
What is the building block of collagen fibre ?
Tropocollagen
What is vital for formation of tropocollagen ?
Glycine, as it is has a small side chain that allows tight turns.
Proline, as it imposes left hand twist in the helix which provides main stabilising force.
What is the structure of tropocollagen ?
Triple helix structure
How is hydroxyproline formed ?
When prolines become hydroxylated.
What is the function of hydroxyproline ?
Hydroxyproline forms strong hydrogen bonds that help to stabilise the triple helix
Formation of collagen fibre
Molecules are stitched together by covalent crosslinks
Gaps provide access sites for lysyl oxidase
Osteogenesis imperfecta cause
Gly-Cys mutation
Scurvy cause
Lack of proline hydroxylation (Vitamin C)
Elhers-Danloss syndrome causes
lack of Lysyl oxidase
What builds strength in collagen fibres ?
Close packing of subunits
(Glycine every 3rd residue)
Opposing twists of subunits and superhelix
(high proline content)
Hydrogen bonding
(Hydroxyproline)
Cross-linking
(Lysine derived aldehydes)
