TOPIC 3 - proteins Flashcards
is the proteome the same as the no of genes in an organism?
no
proteonome is the full set of proteins encoded by the human genome
why is the proteome not equal to the no. of genes in an organism?
because one gene doest equal one protein as:
- single nucleotide polymorphisms in single base = different proteins by one AA
- alternative splicing of mRNA = different proteins
- post translational modifications - addition sugars and phosphates
what is phenylketonuria and what happens in it
- disease due to lack of enzyme phenylalanine hydroxylase
- phenylalanine (AA in food) not broken down = food not broken down
- babies not diagnosed with this disease can end up with permanent brain damage
what is ferritin
protein involved in transporting iron around the body
what do motion- muscle proteins do
important in movement of food around the gut and muscles
what is Duchenne muscle dystrophy
- protein dystrophin absent/ineffective
- patients lose ability to use muscles
- wheelchair bound
- dont sure past teens
what protein defect is CF due to
CFTR gene
Cl- channel protein
- this one gene mutation causes all the symptoms associated- lungs, digestive system, fertility
what happens in myasthenia gravis?
body creates antibodies to NT receptor at neuromuscular junction- therefore people have problems getting muscles to respond to neurological signals
what is the basic structure of an AA
- central C
- amino group
- hydroxyl group
- R group
what group on the AA structure is the most important and why
R group
- AA named according to R group
- Differences in AA due to different chemical groups of R group
with what categories due we categorise R groups ?
- Size (large/small)
- Shape (aliphatic-chains/aromatic-benzene ring)
- Hydrophobicity (polar/nonpolar)
- Charge (acidic / basic)
- Sulphur containing (cysteine / methionine)
- Imino acid - proline not an AA
Name the AA with non polar side chains
- Glycine : Gly
- Alanine : Ala
- Valine: Val
- Leucine: Leu
- Isoleucine: Ile
- Methionine: Met
- Phenylalanine : Phe
- Tryptophan: Trp
- Proline: Pro
Name the AA with polar side chains
- Serine: Ser
- Threonine: Thr
- Cysteine : Cys
- Tyrosine: Tyr
- Asparagine: Asn
- Glutamine: Gln
Name the acidic AA- electrically charged
- Aspartate : Asp
- Glutamate: Glu
Name the basic AA- electrically charged
- Lysine : Lys
- Arginine: Arg
- Histidine: His
why is Proline not an AA and and Imino acid
alpha amino group is linked to side chain making it secondary amine- makes carbon-nitrogen bond inflexible= limiting conformations proline can take up in 3D shape
what are the optical isomers AA produce
L isomer
D isomer
only L isomers found in proteins- due to specifity of enzymic reactions
what are electrically charged AA
weak acids or bases
what determines ionisation of weak acids or bases (electrically charged AA)
- pH that surrounds them
- pKa will tell you what pH they are 50% ionised
what is the pKa for CA groups
1.8-2.5 – almost always -ve charged at like pH 7 in body
what is the pKa for Amino groups
9-10- almost always positively charged in body
what is the pKa for Histidine and why is this important
- around 6.0
- close to our body’s pH therefore can be found positive or negatively charged
- pH 7 the histidine sidechain will be mainly uncharged
if the pH is below pKa value what happens to the groups on weak acids/bases
group will have H attached
if the pH is above pKa value what happens to the groups on weak acids/bases
group will lose H+
what is the 1’ structure of proteins
AA sequence- defined by genes
what is the 2’ structure of proteins
local spatial arrangements of AA in peptide chain
what is the 3’ structure of proteins
organisation of 1’ and 2’ structure into 3D protein shape
what is the 4’ structure of proteins
- arrangement of different subunits of proteins/ the arrangement of chains in relation to one another
- addition of prosthetic groups
what is the name for AA chain
backbone
what is the name for AA in polypeptide chain
residues
what is the name for R groups
side chains
what bond joins AA
- peptide bonds (amide bonds) to form proteins in condensation reaction
- between double bond between C-O or between C-N
what kind of bond are peptide bonds?
not like normal single covalent bond -have partial double bond characteristics
what is the significance of O and N being on opposite sides of the peptide bond
trans position
-maintains max distance between them = limited orientation around the bond = making the bond rigid
wha is an intrachain H bond
H-bonds between N-H and C=O of main chain stabilise the helix
what are the 2 types of 2’ structure
- alpha helix
- B-pleated sheet
describe the features of an alpha helix
- Helix formed by backbone of chain and side chains extend out of helix
- Right-handed helix
- 2 types of H bonding in 2’ structure: intrachain and interchain
- Rod like structure- H-bonds parallel to helix axis= elasticity in helix
- Each C=O oxygen is hydrogen bonded to NH of AA 4 residues ahead in the linear sequence
- Eg: Residue 1 to residue 5
describe the features of a B-pleated sheet
- Polypeptide chains run alongside one another-
- Stabilised by H-bonding between adjacent strands- may be between 2 parts of same chain (intrachain) or between different AA (interchain)
- Side chains lie above or below plane of sheet
- Fully extended polypeptide chain/backbone
- No elasticity – rigid
- Zigzag/pleated shape –
- The strand be run parallel or anti parallel
- Loops and turns between strands allow for change in direction of chain
protein activity changes which structure of the protein?
3’ and 4’
what’s the structure of membrane proteins
- Soluble proteins fold so that interior of soluble proteins is hydrophobic
- exterior of soluble proteins is mostly hydrophilic
- as membrane proteins have to interact with hydrophilic environment
which proteins is the 3’ structure vital?
enzymes
- 3’ important in active and binding sites
- Each of AA residue in AS interact with substrate to position and catalyse
in general what forces stabilise the 3’ and 4’ structure
sidechain interactions
- can be covalent or weak
name the side chain interactions involved in 3’ and 4’
- disulphide bonds
- electrostatic interactions
- VDW
- H Bonds
- hydrophobic effect
what kind if bond are disulphide bonds and how are they formed
- covalent
- oxidation between pairs of Cys
- Cys = sulphur containing AA has thiol group (SH)
- 2 cys residues close= 2 SH groups = disulphide bond
- may bring two polypeptide chains together
how are electrostatic interactions formed?
- stabilise tertiary and 4’ interaction by electrostatic interactions between oppositely charged chains
- this is called an ion pair. Interaction known as salt bridges
- 2 similar charges however repel one another = ruin structure
how are H-bonds formed?
- Created as a result of dipole formation
- Attraction between an H atom of a donor group (e.g. -OH and =NH) and non-bonding electrons on an acceptor group (O=C)
how are VDW formed
a range of weak forces that occur in electrically neutral molecules and involves dipole
-Temporary/induced dipoles
how does the hydrophobic effect work?
- Most important in stabilising proteins
- Non-polar AA try to minimise contacts with water and are buried in the core of proteins in aqueous solution - to not affect H -bonding in water = drives hydrophobic molecules together to minimise their interaction with water
- drives protein so hydrophilic residues on outside and hydrophobic residues on inside
at physiological pH what does the overall charge of the protein depend on
-PI of the protein
isoelectric point- where protein has no overall charge
what 2 factors that affect AA chain folding
- Rigidity of the peptide bond limits flexibility of chain
- Physical and chemical properties of side chains restrict the no. of stable options
at what point is a protein at its highest energy level?
unfolded form (fully folded form= lowest energy level)
what 2 families of proteins support effe time protein folding
- Molecular chaperones- bind to short segments of a protein to facilitate correct folding in that particular area
- chaperonins- form folding chambers which provide a stable environment to encourage correct folding
what problems can protein misfolding lead to?
- discontinuation of cellular process
- accumulate and hinder normal cellular processes (e.g., Alzheimer’s)
- conformational changes in other proteins = damaging accumulations of aggravated proteins (e.g., Creutzfeldt-Jakob disease)
give the biochemical features of Alzheimers disease
- amyloid disease
- APP ( membrane protein) cleaved by proteases = amyloid B protein in brain ( contains large amount of b sheet stricture accumulates and aggregates forming insoluble fibrils)
- The fibrils aggregate to form plaques
- These plaques damage and destroy neurons
- Cerebral cortex = loss of neurones
- no cure
- progressive dementia
symptoms of Alzheimers
Devastating mental deterioration- memory loss, loss of language ability, loss of the ability to mentally manipulate visual info, poor judgment, confusion, restlessness, mood swings) and eventual death
what is and happens CJ disease
- Prion disease
- vacuoles in brain- resemblance of a sponge
- Prion proteins are normally water soluble and can be broken down by proteases
- Contact of normal soluble PrPc protein (mostly a- helical) with abnormal form PrPsc (mostly B-pleated sheet ) causes the PrPc protein to acquire the abnormal PrPsc structure
- PrPsc- insoluble and resistant to breakdown by proteases
- contact of these 2 = forming insoluble aggregates
what are globular proteins?
- soluble enzymes, haemoglobin
- compact, soluble, spheroidal.
- hydrophilic (polar) residues outside so can interact with aqueous environment
- hydrophobic residues (non polar)hidden in centre
- Contain α-helices and/or β-sheets in varying proportions
what are fibrous proteins?
keratin (hair/nails), collagen
-elongated, often have repeating amino acid sequences, insoluble due to high hydrophobic amino acid content
what are most Haemoglobinopathies due to
single amino acid change- haemoglobins differ by single AA
are all Haemoglobinopathies fatal?
-Some fatal
–Some advantageous
–Some no clinical effect
why are people with Thalassaemia and sickle cell trait protected against Plasmodium falciparum
- Thalassaemia carriers are protected = their red cells are smaller and contain less haemoglobin = the parasite uses up all the haemoglobin before it has finished growing = cannot spread to neighbouring cells.
- Sickle cell carriers = their red cells respond to the presence of the parasite by sickling. The sickle cell becomes trapped in the spleen and the parasite is killed.
what is the role of myoglobin
oxygen store in tissues
what is the role of Hb
Oxygen ( and CO2) transport
where is Mb conc highest?
skeletal
cardiac muscle - not totally reliant on circulatory system
features of Mb molecule
- very compact
- Contains haem prosthetic group
- A typical globular protein
- Mostly a -helical
- Hydrophobic residues on inside, polar ones on surface
what does the Haem prosthetic group made of
Fe 2+ + protoporphyrin IX ring ( iron on the middle of the ring )
where and how is Haem bound
Non covantley bound to hydrophobic crevice in protein
with what and how many coordinate bonds does Fe2+ make?
6 ligands:
- 4 N from porphyrin ring
- 1 N proximal His
- 1 oxygen molecule
why is It important to associated haem molecule with protein
- keeps Fe in Fe2+ form
- binding more oxygen specific ( CO binding inhibited)
does oxygen or CO have a higher affinity to Hb
- CO binds to haem with 250-fold greater affinity than O2 so prevents O2 binding- even when oxygen bonded the affinity for CO still higher
- Symptoms include nausea, dizziness and confusion- symptoms can be mistaken for flu symptoms
describe the structure of Hb
- 4 polypeptide ca=hains
- non- covalent interactions
- 2a and 2 B chains
- 4 chains packed together tightly in spherical shape = 4’
- can bind 4 oxygens
compare Hb and Mb in binding, affinity and BPG dependence
- Hb co-operative, Mb not
- Hb affected by pH and CO2
- Hb regulated by BPG, mb not
Hb is an allosteric protein, what does this mean?
the binding of O2 to one subunit affects interactions with the other subunits
does Mb or Hb have a higher affinity for O2
Mb
even though Hb has more binding sites, Mb doesn’t have subunits which are affected by Oxygen binding
describe the tense state
- low affinity for O2
- position of a residue’s oxygen binding site less accessible
- more salt bridges between sub units
describe the relaxed state
- high affinity for O2
- Fewer salt bridges
- O2 binding site more accessible
how does pH affect O2 binding
- affects protonation of AA residues
- high [H+] = more AA protonated = postive charged = more salt bridges
= stabilse T state = decease affinity for O2
-In case of lactic acid/ CO2 production = more oxygen to tissues
where is BPG found and what does it do?
- found at high concentration in erythrocytes
- increase at high altitude and in hypoxia (poor oxygenation)
- BPG decreases affinity of Hb for O2
where does BPG bind?
- in the space between the β subunits – in the T-state only
- Negative charges on BPG interact with positive amino acid residues lining the space- stabilise deoxygenated state so easier release of oxygen
how does CO2 affect Hb
- binds to amino groups on the globin protein- N terminal amine and , forming carbaminohaemoglobin
- releases further H+
- stabilises the T state
what are the chains in HbF
2 alpha chains
2 gamma chains
doesBPG affect HbF
binds less effectively as space between alpha and gamma subunits in molecules doesn’t work as well for BPG
- higher affinity for O2
- survive if mother slightly oxygen deficient
- Allows efficient transfer of O2 across the placenta
what is the mutation in sickle cell anemaia ?
Mutation in one of Hb chains which then allow aggravation of Hb chains = sickle shape
what is the mutation in B-thalassemia ?
lack of synthesis of beta chain so person doesn’t have suffient Hb
why do not all mutations in Hb cause disease?
- depends on:
- position of mutation-mutations in critical residues will affect function
- and type: conservative or non conservative
what is a conservative mutation?
AA replaced have same property = affects not bad
- eg. maintains hydrophobic interior of molecule
what is a non conservative mutation?
will have a major effect on protein structure and function.
- eg. negative charged leu subbed by positive charged lys
what’s the most abundant protein in mammals?
collagen
how many polypeptide chins is collagen made from?
3 (all alpha chains )
what are types 1,2,3 of collagen called and what are they involved in
- fibril forming collagens ( as form long fibrils)
- involved in bone, cartilagge and skin
- most common types
what are types 4,7 of collagen called and what are they involved in
network forming collagens
( as form grid like structures/sheets)
-Important in basal lamina
what are types 5,9,12 of collagen called and what are they involved in
fibril associated collagens
mainly associated with main types and may be used in cross linking
what are basal lamina
- extracellular structures found close to the plasma membrane on the basal surface of epithelial and endothelial cells
- surround muscle and fat tissues
- Role in tissue support
highlight the steps in the biosynthesis of collagen
- polypeptide synthesis
- post translational modifications
- pro-collagen triple helix assembled in fibroblasts
- pro collagen moves into golgi which forms vesicles of pro-collagen
- secretion into extraceullar spaces of connective tissue
- removal of extension peptides
- tropocollagen formation
- spontaneous aggression into microfibril
- cross linking to form collagen fibre
what are fibroblasts
-cell that synthesises extracellular collagen
•Different types of fibroblasts depending on part of body- eg. Osteoblasts
what is procollagen?
all 3 pro alpha chains of collagen together
what is the 1’ repeating sequence of collagen?
Glycine -Proline -Hydroxyproline (usually)
why are gly residues always repeated as the 3rd residue in collagen 1’ sequnce?
- smallest AA so only one that fits in the centre of the procollagen = allows helixes to interact with each other
what are the 3 covalently modified AA in collagen
- 4-Hydroxyproline (Hyp)
- 5-hydroxylysine (HyL)
- Allysine
what process occurs before the polypeptide chain synthesis of collagen but after the chain formation ?
hydroxylation of proline and lysine residues
what enzymes are involved in the hydroxylation of proline and lysine residues and what co factor do they both require?
- propyl hydroxylase
- lysyl hydroxylase
- vitamin C/ascorbic acid as cofactor
what is hydroxyproline used for
- involved in additional H: maximising H bonding taking place
- stabilises and allows triple helix to form
what is hydroxylysine used for
- attachment sites for sugar residues glucose and galactose
- involved in cross-linking between collagen chains
is collagen glycosylated?
yes- heavily glycosylated
- amount of glycosylation varies between different collagen types
what type of helix is each polypeptide chain in collagen
LEFT handed : rope like structure
v tightly wound
what type of helix is the tropocollagen molecule
RIGHT handed helix
where do the residues of collagen sit in tropocollagen
- Gly packed in centre
- Pro and Hydroxyproline on outside
why are Proline and Hydroxyproline situated on outside of tropocollagen?
allow cross linkage between collagen molecules
what are extension peptides and why are they important?
- additional amino acids (N and C terminus) at each end
- facilitate formation of tropocollagen: as disulphide bond formation between C-terminal extensions help the chains align correctly and hold them together to form the triple helix
at what point are peptidase enzymes used in the assembly of collagen and what do they do?
remove extension peptides after secretion into extracellular space= get tropocollagen
what is the function of Lysyl oxidase
deaminates some lysine and hydroxylysine residues to form allysine
what do allysine do and what do they react with
Allysine has a reactive aldehyde group which then reacts spontaneously with the amino group on other lysine or allysine molecules, forming cross-links between adjacent chains
why are corsslinkages important in collagen
give strength and rigidity
highlight how bone is formed within collagen fibrils
Holes between tropocollagen fibres are nucleation sites for calcium deposition to create bone
why are evenly spaced gaps between tropocollagen important ?
even deposition of calcium phosphate = strong bone
what breaks down collagen and why is this important?
- Collagenase– a family of metalloproteinases
- necessary for growth, tissue remodelling (e.g. pregnancy/ after birth) tissue repair
why are collagenases important in cancer ?
important in tumour invasion and metastasis (spreading) – often produced at high levels by tumour cells- breaks collagen and allows it to spread and metastasis as gets through basement membrane
what is Dupuytren’s contracture?
disabling condition caused by excess collagen production affecting the connective tissue of the hand, causing it to thicken
- lead to impaired hand function as hand contracts to point its unusable
what can we use to treat Dupuytren’s contracture?
- injection of collagenase
- or surgical
name 3 diseases that are caused when collagen structure or synthesis is abnormal
- Osteogenesis Imperfecta
- Ehlers-Danlos syndrome
- Scurvy
what is Scurcy due to?
lack of vitamin C
– vitamin C cofactor for prolyl hydorxylase to make hydroxy proline- without it destabilises structure of collagen
what are the symptoms of Scurvy
bleeding gums, tooth decay, rough skin
what is Ehlers-Danlos syndrome and what’s the cause
•Inherited disorders resulting from poorly formed/weak collagen in connective tissue (ligaments, tendons, blood vessels, internal organs)
- Lysyl oxidase deficiency
what can Ehlers-Danlos syndrome cause
- Joint hypermobility = regular dislocations
- Extreme fatigue
- Stretchy skin
- Joints far more mobile that they should be
- Digestive problems
- Organ prolapse/hernias- organs slip out normal place
- Postural hypotension (POTS)- blood vessels not respond properly to changes in posture - so can’t stand properly
- Fragile blood vessels
what is another name for Osteogenesis imperfecta
brittle bone disease
what is Osteogenesis imperfecta
•A range of inherited disorders characterised by increased risk of bone fractures
- Severity of symptoms/deformity depends on the nature of the mutation
what is the mildest type of Osteogenesis imperfecta and what happens
type 1 : bowing of long bones, and spine deformity
decreased production of alpha 1 and alpha 2 collagen chains
what is the fatal type of Osteogenesis imperfecta and why
Type 2
- damage to collagen so great so ribcage cannot protect heart and body cant survive
what are the severe types of Osteogenesis imperfecta and what is caused
Types 3 & 4
- multiple fractures- amputations? metal rods inserted to support leg bones?
- serious spinal deformity – - damage to joints- particularly in leg- legs are weight baring
