proteins Flashcards
What kinds of proteins provide support?
Collagen (the protein of the bone), skin and tendon
Tell me about collagen fibres
These are the main component of connective tissue
Found in skin, tendons, organs and bone
What are erythrocytes
This is another name for a red blood cell
Tell me about haemoglobin
Selective delivery of O2 to metabolic tissues
4 protein subunits per molecule
Each subunit contains a haem group that can bind one oxygen molecule
Haem is an example of a prosthetic group
What are LDLs composed of?
a phospholipid shell and a single molecules of apolipoprotein
What are LDLs used for?
To transport cholesterol between cells via the circulatory system
What is the uptake of LDL particles mediated by
the LDL receptor that binds LDL and facilitates internalisation
What condition is associated with a mutation in the LDL receptor gene
Hypercholesterolemia
Describe the structure of antibodies
There are two identical heavy chains and two identical light chains covalently linked by disulphide bonds
The antigen recognition site is highly specific and tightly binds the complementary antigen allowing recognition of foreign proteins by the immune system
Lysozyme is an exmpale of a biological catalyst: describe it
It catalyses the cutting of polysaccharide chains
Lysozyme binds to the polysaccharide chain, catalyzes the cleavage of a specific covalent bond and releases the cleaved products
lysozyme remains unchanged at the end of the reaction
What kind of protein regulates genes?
the lac repressor - helps controls gene expression
Describe the lac repressor
Controls production (expression) of proteins metabolising lactose in bacteria The repressor binds to DNA and prevents expression of the gene in the absence of lactose
what do the functions of protein come down to
SPECIFIC BINDING = CHANGE OF CONFORMATION = CHANGE OF ACTIVITY
What bonds are proteins joined by
peptide bonds
Whats the structure hierarchy of proteins
PRIMARY - SECONDARY - TERTIARY - QUATERNARY
What is the general structure of an amino acids
An amino group, a carboxylic acid and a unique side chain
What does the r-group determine
the structure and function of the protein
Name the hydrophilic amino acids
Lysine, arginine, histidine - basic
aspartate, glutamate - acidic
Serine, threonine, asparagine, glutamine - polar uncharged r-groups
Name the hydrophobic amino acids
alanine, valine, isoeucine, leucine, methionine, phenylalanine, tyrosine, tryptophan
Name the special amino acids
Cysteine, glycine, proline
what is special about cysteine
it can form covalent disulphide (-s-s-) bons with other cysteine residues
What is special about glycine
It is the smallest amino residue and can fit into tight spaces
Why is proline special
he side chain of proline bends around to form a covalent bond with the nitrogen atom of the amino group. By doing this creates a kink in the protein chain
What is an acid
any molecule that tends to release a hydrogen ion
What is a base
a base is a molecule that readily combines with a hydrogen ion
Whats the equilibrium constant:
Ka = [H+][A-] / [HA]
Whats the pH equation
pH = pKa + log [A-]
[HA]
What is the pKa rule
•The pKa of any acid is equal to the pH at which half the molecules are disassociated
What does the charge of an amino acid vary with
pH
What is pKa
pKa is the pH at which dissociation is 50% complete
What can influence pKa
Local enviroment
Describe the receptor mediated endocytosis process in relation to the uptake of LDL
A reduction in pH in the endosome causes a change in conformation of the LDL-
receptor due to the presence of histidine residues within the protein (pK 6.5)
LDL can no longer bind and is released to the lysosome
Patients with familial hypercholesterolemia frequently have mutations in the
histidine residues of the LDL-receptor.
What is a peptide bond
- A covalent bond formed when the carbon from the carboxylate group (red) shares electrons with the nitrogen atom from the amino group (blue) of a second amino acid
- A molecule of water is lost so this is called a condensation reaction
Describe the constraints on a peptide bond
The peptide bond (grey shading) does not permit rotation
Rotation can occur on the a-carbon
The conformation of the folded polypeptide chain is determined by one pair of angles for each amino acid residue
Bulky R-groups are positioned on either side of the backbone
This limits the number of 3-dimensional conformations possible for a polypeptide
What is secondary structure
- Secondary structure is the initial folding pattern (periodic repeats) of the linear polypeptide
- 3 main types of secondary structure: α-helix, β-sheet and bend/loop
- Secondary structures are stabilized by hydrogen bonds
tell me about the alpha helix
- The α-helix is right-handed and each turn has 3.6 amino acid residues
- The helix is stabilized by H-bonds between amino and carboxyl groups of every 4th amino acid
Tell me about beta sheets
- Extended stretches of 5 or more amino acids are called β-strands
- β-strands organized next to each other make β-sheets
- H-bonding pattern varies depending on type of sheet
parallel and anti-parallel beta sheets
If adjacent strands are oriented in the same direction (N-end to C-end), it is a parallel β-sheet, if adjacent strands run opposite to each other, it is an anti-parallel β-sheet. There can also be mixed β-sheets
Describe the bend/loop or a turn
- Polypeptide chains can fold upon themselves forming a bend or a loop.
- Usually 4 amino acids are required to form the turn
- Proline residues frequently found in bends / loops
What is amino acid resdue
When two or more amino acids combine to form a peptide
What are the function of loops and turns in tertiary structure
connect regions of α-helix and β-sheet so that the polypeptide can fold into a globular domain.
What kind of bonds stabilise tertiary structure
Di-sulphide bonds H-bonds Ionic interactions Van der Waals interactions Hydrophobic interactions
What is a haem group
A porphyrin ring with coordinated Fe atom - binds to oxygen for transport to tissues. These are held in place by hydrogen bonds from histidine F8 and the bound oxygen molecule is stabilsed by histidine E7
What happens to the histidine that H bonds to the haem group in F8
this changes position causing major structural changes in the globin subunit
biological significance
- Relatively small changes in oxygen concentration result in large changes in the interaction of haemoglobin with oxygen
- This equates to tight oxygen binding in the lungs and subsequent release in tissues where oxygen concentration is lower
What is sickle cell anaemia
This is caused by a single amino acid change at position 6 in the beta chain of heamoglobin
•Hydrophilic glutamic acid to hydrophobic valine
This causes sickling of erythrocytes due to aggregation of mutated haemoglobin that forms stiff fibres (change in surface chemistry of the protein)
SHRIVELED NOT CONCAVE
What is the Bohr effect
The pH of the blood influences O2 binding to haemoglobin
What is the pH and oxygen trend
O2 binding occurs with higher affinity at high pH (lung) and lower affinity at low pH (peripheral tissues)
What happens during excerise
CO2 (acidic) builds up during exercise, which lowers blood pH facilitating faster oxygen delivery
Tell me about foetal haemoglobin
This is comprised instead of two alpha and two GAMMA subunits
Low O2% by the time blood reaches placenta so needs to bind with greater affinity than maternal haemoglobin
Due to absence of the beta chains foetal red blood cells are unaffected by sickle cell disease
Tell me about the structure of collagen
Tropocollagen is building block of the collagen fibre and consists of 3 polypeptide chains with a left handed twist wound together in a right handed supercoil
Tell me more about tropocollagen
GLYCINE is vital in the formation of tropocollagen triple helic as it has a small side chain that allows for tight turns (three amino acid residues per turn)
What is Proline
Another vital structure in tropocollagen as it imposes the left handed twist that provides the main stabilisng force
These can become hydroxylated to form hydroxyproline that forms strong hydrogen bonds that again hekp to stabilise the helix
How are collagen fibres held together
covalent crosslinks involving Lysine-derived aldehydes stabilise tropocollagen and the collagen fibre
The gaps provide access sites for lysyl oxidase
What causes osteogenisis imperfecta
a mutation in the gene coding for one of the collagen subunits leading to a Glycine being replaced by a Cysteine residue at one point in the chain
What are the symptoms and cause of ehlers-danloss syndrome
Loose skin and hypermobile joints
Lack of procollagen peptidase or lysyl oxidase
What does each strnegth building factor mean
Close packing of subunits = Glycine every 3rd residue
Opposing twists of subunits = High Proline content
and superhelix
Hydrogen Bonding = Hydroxyproline
Cross-linking = Lysine-derived aldehydes
