Topic 3 - Proteins Flashcards
Which amino acids have non-polar side chains?
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Phenylalanine
- Tryptophan
- Proline
Which amino acids have polar side chains?
- Serine
- Threonine
- Cysteine
- Tyrosine
- Asparagine
- Glutamine
Which amino acids have electrically charged side chains?
ACIDIC - Aspartate, Glutamate
BASIC - Lysine, Arginine, Histidine
Which amino acids are acidic?
Aspartate
Glutamate
Which amino acids are basic?
Lysine
Arginine
Histidine
What is the charge of a histidine molecule at pH 7?
Mainly uncharged
What is the pKa?
the pH at which a group is 50% ionised
What happens to histidines group when pH is below pKa?
Group will have H attached
What happens to histidines group when pH is above pKa?
Group will lose H+
What are the levels of structure in a polypeptide chain?
- Amino acid sequence (primary)
- Local spatial arrangements of amino acids in the peptide chain (secondary)
- Organisation of the primary and secondary structures into the 3D protein shape (tertiary)
- Arrangement of different subunits in a protein (quaternary)
What is the primary structure of a ppt chain?
Amino acid sequence as coded my mRNA
What is the secondary structure of a ppt chain?
Local spatial arrangements of amino acids in the peptide chain
(Alpha helix or beta pleated sheet)
What is the tertiary structure of a ppt chain?
Organisation of the primary and secondary structures into the 3D protein shape
(Di-sulfide bridges, Hydrophobic interactions, Hydrogen bonding, Ionic bonding)
What is the quaternary structure of a ppt chain?
Arrangement of different subunits in a protein (2+ ppt chains in one protein)
What is an alpha helix?
In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact.
What is a beta pleated sheet?
In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions.
Which forces stabilise tertiary and quaternary protein structure?
- Electrostatic interactions
- Van der Waals forces (dipoles)
- H-bonds
- Burial of hydrophobic residues (hydrophobic interactions)
- Disulphide bonds
What does the charge of a protein depend on?
pI and pH
What is pI?
The isoelectric point (pI) is the pH of a solution at which the net charge of a protein becomes zero. At solution pH that is above the pI, the surface of the protein is predominantly negatively charged, and therefore like-charged molecules will exhibit repulsive forces.
Low pH?
High H+ (as acidic), positive overall charge
High pH?
Low H+ (basic), negative overall charge
Physiological pH?
Overall charge of ppt chain depends on pI of protein
What is tetany?
A condition marked by intermittent muscular spasms, caused by malfunction of the parathyroid glands and a consequent deficiency of calcium
Which equilibrium controls blood pH?
CO2 + H2O <> H2CO3 <> H+ + HCO3-
How is calcium transported in the blood?
Ca2+
Half in solution half bound to proteins
What is alkalosis?
High pH.
Increased calcium binding to protein – decreased availability of free calcium.
What is Acidosis?
Low pH.
Decreased calcium binding to protein – increased availability of free calcium.
Why would an increase in blood pH reduce the availability of free Ca++?
- Hyperventilation leads to increased CO2 loss.
- This causes plasma pH to rise as H+ is combined with bicarbonate to create additional CO2 to help maintain equilibrium.
- As plasma pH rises, proteins become more negatively charged, as they release H+ from ionisable groups such as COOH and NH3+.
- Calcium ions, being positively charged, bind more effectively to the negatively charged proteins, decreasing the availability of free calcium.
- Decreased free calcium in extracellular fluid causes increased excitability of sensory nerves (causing numbness/pins and needles) and motor nerves (causing prolonged muscular contraction).
What are two examples of globular proteins?
Enzymes
Haemoglobin
What are the features of globular proteins?
- Compact
- Soluble
- Hydrophobic residues on the inside
What are two examples of fibrous proteins?
Keratin
Collagen
What are the features of fibrous proteins?
- Elongated
- Often have repeating amino acid sequences
- Insoluble
- Hydrophobic residues on the outside
What are the 3 types of proteins?
Globular
Fibrous
Membrane
How many mutant Hb are there?
> 400 known
95% due to single amino acid change
Why do we need oxygen binding proteins (Hb)?
- Cells require O2 for oxidation of foodstuffs.
- O2 only sparingly soluble in blood, therefore we need a transport and storage system.
What is the function of Hb?
O2 transport and CO2 transport
What is the function of myoglobin?
O2 storage in tissues
Where are the highest concentrations of myoglobin?
Skeletal and cardiac muscle
What are the features of myoglobin?
- Small protein
- Very compact
- Contains haem prosthetic group
- 8 alpha-helices
- Hydrophobic residues on the inside, hence soluble
What is the haem prosthetic group?
- Haem - Fe2+ + protoporphyrin IX
- Tightly bound, nonpolypeptide unit essential for biological activity of protein
- Non-covalently bound in a hydrophobic crevice in protein
How many ligands can Fe2+ coordinate with?
6 ligands:
- 4N from porphyrin ring
- N from proximal His (F8)
- Oxygen atom
What is the effect of O2 binding?
First O2 to bind to Fe changes the position Distal His (E7) also involved in O2 binding
What are the advantages of associating haem unit with a protein molecule?
- Fe atoms are kept in Fe2+ form
- Binding of other small molecules e.g. carbon monoxide is inhibited
What are the symptoms of CO poisoning?
Dizziness
Nausea
Confusion
What is the structure of haemoglobin?
- Four polypeptide chains held together by non-covalent interactions
- Adult haemoglobin has 2 alpha, 2β chains
- Each chain contains a haem group, therefore Hb can bind four O2
- Four chains packed tightly together in a tetrahedral array with overall spherical shape.
- Hb tetramer may be considered as 2 pairs of subunits - a1β1, a2β2
How is Hb an allosteric protein?
The binding of O2 to one subunit affects interactions with the other subunits
What type of binding between O2 and Hb?
Cooperative and therefore binding curve is sigmoidal
Mb non cooperative
What is Hb O2 affinity dependent on?
pH and CO2
Mb is independent
What is Hb regulated by?
BPG
Mb not regulated by this
What does a sigmoidal binding curve mean for Hb?
Cooperative binding between O2 and Hb
Binding of one O2 makes binding of next easier
What does cooperative binding mean for Hb?
The change in shape caused by the first O2 binding also causes a change in affinity to oxygen; the more oxygen is bound, the higher the molecule’s affinity for oxygen becomes.
What are the exact effects of an O2 binding to one Hb subunit?
- Proximal His F8 is pulled in
- Shifts helix F, EF and FG corners
- Altered shape transmitted to subunit surfaces
- Some interchain salt bridges rupture
- These structural changes increase the affinity of the remaining subunits for O2
What is the T state of Hb?
- ‘Tense state’ – more salt bridges between subunits
- Low affinity for O2
What is the R state of Hb?
- ‘Relaxed state’ – fewer salt bridges
- High affinity for O2
What is the Bohr effect?
- Increase in [H+] (lowering of pH) decreases affinity of Hb for O2
- Increased CO2 in blood or increased lactic acid will lower pH
- Increased release of O2 to respiring rapidly tissues or muscle releasing lactic acid
How so H+ ions affect O2 binding?
- pH affects protonation state of amino acid residues
- When H+ is high, additional residues are protonated (esp Histidine residues)
- Additional positively charged residues can form new salt bridges – these stabilise the T-state and decrease affinity for O2
What can cause BPG levels to increase?
- High altitude
- Hypoxia
What is hypoxia?
poor oxygenation of peripheral tissues
What does BPG do?
Decreases affinity of Hb for O2 so causing more oxygen release under certain conditions
Where does BPG bind?
The space between the β subunits – in the T-state only
How does BPG decrease Hb affinity for O2?
- Negative charges on BPG interact with positive amino acid residues lining the space between β subunits
- CO2 binds to amino groups on the globin protein, forming carbaminohaemoglobin
- H+, CO2 and BPG interact at different sites, therefore their effects are additive
How does foetal Hb have a higher affinity for O2?
It binds BPG less effectively
Allows efficient transfer of O2 across placenta
What can mutations in Hb affect?
- Amount of Hb synthesised
- Structure, e.g. subunit interfaces
- Stability of Hb – leading to haemolytic anaemia
- Affinity for O2
- Affinity for regulators e.g. BPG
What is a conservative substitution in Hb mutations?
- Maintains hydrophobic interior of molecule
- Interior of Hb often see change of one non-polar residue for another, e.g.Ala → Ile
What is a non-conservative substitution in Hb mutations?
e.g. Leu → Lys
will have a major effect on protein structure and function.
What is collagen?
- Family of fibrous proteins
- Forms insoluble fibres, high tensile strength
- Most abundant protein in mammals
- Major fibrous element of skin, bone, tendon, cartilage, blood vessels, teeth
- Present in most organs
- Holds cells together in discrete units – basement membranes
- Also a directive role in developing tissue
What are the fibril-forming collagens?
Type I, II, and III
Form long fibrils
What are the network-forming collagens?
Types IV and VII
Form a 2D matrix
Important in basal lamina
What are fibril-associated collagens?
eg. Types V, IX, XII
Mainly associated with major forms
May be involved in crosslinking
How many ppt chains do collagens consist of?
3
What are the steps to biosynthesis of collagen?
- Polypeptide synthesis
- Post-translational modifications
- Procollagen triple helical cable
- Secretion
- Removal of extension peptides
- Tropocollogen
- Aggregation into microfibril
- Cross-linking to form collagen fibre
What is the primary structure of collagen?
-Gly every third residue (33%)
-Covalently modified amino acids (4-Hydroxyproline (Hyp),
5-hydroxylysine (HyL),
Allysine)
When and what by does the hydroxylation of proline and lysine residues occur in collagen?
- Occurs before the ppt chain forms helix
- Enzymes involved: propyl hydroxylase and lysyl hydroxylase
What is the function of hydroxyproline in collagen?
It is involved in H-bond formation, which helps to stabilise the triple helix
What is the function of hydroxyplysine in collagen?
The residues are attachment sites for sugar residues, and are involved in cross-linking between collagen chains
What is the 2,3 and 4 structure of collagen?
-Each polypeptide chain forms LEFT handed helix, 3.3 residues per turn
-triple helix formed
(tropocollagen)
RIGHT handed twist
-Gly residues pack into centre
-Pro and Hyp residues on the outside
-The three ppt chains folded together form a triple-helical cable
What are the steps to assembly of collagen?
- Collagen chains are synthesised with additional amino acids at each end – extension peptides
- Assembly begins with disulphide bond formation between C-terminal extensions – facilitates triple helix assembly
- Peptidase enzymes remove extension peptides after secretion into extracellular space
- Tropocollagen spontaneously forms fibrils – stabilised by covalent cross-links
What gives tropocollagen its strength and rigidity?
-Covalent cross links
-Lysyl oxidase deaminates some lysine and hydroxylysine residues to form allysine
-Cross-links form between Lys and allysine
or allysine and allysine
How does collagen aid bone formation?
Holes between tropocollagen fibres are nucleation sites for calcium deposition.
What is the structure of a tendon?
Tendon ↓ Tertiary fibre bundle ↓ Secondary fibre bundle ↓ Primary fibre bundle ↓ Collagen fibre ↓ Collagen fibril -Endotenon is contiguous with epitenon, the fine layer of connective tissue that sheaths the tendon unit
When is collagen breakdown necessary?
- Growth/tissue remodeling (eg pregnancy/after birth)
- Tissue repair
Which family do collagenase enzymes belong to?
metalloproteinases
What is Dupuytren’s contracture?
A potentially disabling condition caused by excess collagen production affecting the connective tissue of the hand. Recent report from clinical usage study shows successful treatment by injection of collagenase.
What causes osteogenesis imperfecta?
Mutation in collagen chains - Type I collagen
What is osteogenesis imperfecta?
Brittle bone disease
What causes Ehlers-Danlos syndrome type VI?
Lysyl oxidase deficiency
What causes scurvy?
Vitamin C defiency.
Vitamin C is a cofactor required for the functioning of the enzymes prolyl hydroxylase and lysyl hydroxylase, so collagen synthesis is abnormal in patients with scurvy
What is Ehlers-Danlos syndrome?
Inherited disorders resulting from poorly formed/weak collagen in connective tissue
What can Ehlers-Danlos syndrome cause?
- Joint hypermobility/dislocations
- Extreme fatigue
- Stretchy skin
- Digestive problems
- Organ prolapse/hernias
- Postural hypotension (POTS)
- Fragile blood vessels
What are the symptoms associated with scurvy?
- fatigue
- joint pain
- muscle weakness
- poor healing
- skin hemorrhages
- gum disease
