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year 1 flash cards > TOPIC 3 - proteins > Flashcards

TOPIC 3 - proteins Flashcards

1
Q

is the proteome the same as the no of genes in an organism?

A

no

proteonome is the full set of proteins encoded by the human genome

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2
Q

why is the proteome not equal to the no. of genes in an organism?

A

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
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3
Q

what is phenylketonuria and what happens in it

A
  • 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
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4
Q

what is ferritin

A

protein involved in transporting iron around the body

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5
Q

what do motion- muscle proteins do

A

important in movement of food around the gut and muscles

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6
Q

what is Duchenne muscle dystrophy

A
  • protein dystrophin absent/ineffective
  • patients lose ability to use muscles
  • wheelchair bound
  • dont sure past teens
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7
Q

what protein defect is CF due to

A

CFTR gene
Cl- channel protein
- this one gene mutation causes all the symptoms associated- lungs, digestive system, fertility

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8
Q

what happens in myasthenia gravis?

A

body creates antibodies to NT receptor at neuromuscular junction- therefore people have problems getting muscles to respond to neurological signals

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9
Q

what is the basic structure of an AA

A
  • central C
  • amino group
  • hydroxyl group
  • R group
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10
Q

what group on the AA structure is the most important and why

A

R group

  • AA named according to R group
  • Differences in AA due to different chemical groups of R group
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11
Q

with what categories due we categorise R groups ?

A
  • 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
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12
Q

Name the AA with non polar side chains

A
  • Glycine : Gly
  • Alanine : Ala
  • Valine: Val
  • Leucine: Leu
  • Isoleucine: Ile
  • Methionine: Met
  • Phenylalanine : Phe
  • Tryptophan: Trp
  • Proline: Pro
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13
Q

Name the AA with polar side chains

A
  • Serine: Ser
  • Threonine: Thr
  • Cysteine : Cys
  • Tyrosine: Tyr
  • Asparagine: Asn
  • Glutamine: Gln
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14
Q

Name the acidic AA- electrically charged

A
  • Aspartate : Asp

- Glutamate: Glu

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15
Q

Name the basic AA- electrically charged

A
  • Lysine : Lys
  • Arginine: Arg
  • Histidine: His
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16
Q

why is Proline not an AA and and Imino acid

A

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

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17
Q

what are the optical isomers AA produce

A

L isomer
D isomer
only L isomers found in proteins- due to specifity of enzymic reactions

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18
Q

what are electrically charged AA

A

weak acids or bases

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19
Q

what determines ionisation of weak acids or bases (electrically charged AA)

A
  • pH that surrounds them

- pKa will tell you what pH they are 50% ionised

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20
Q

what is the pKa for CA groups

A

1.8-2.5 – almost always -ve charged at like pH 7 in body

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21
Q

what is the pKa for Amino groups

A

9-10- almost always positively charged in body

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22
Q

what is the pKa for Histidine and why is this important

A
  • 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
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23
Q

if the pH is below pKa value what happens to the groups on weak acids/bases

A

group will have H attached

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24
Q

if the pH is above pKa value what happens to the groups on weak acids/bases

A

group will lose H+

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25
Q

what is the 1’ structure of proteins

A

AA sequence- defined by genes

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26
Q

what is the 2’ structure of proteins

A

local spatial arrangements of AA in peptide chain

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27
Q

what is the 3’ structure of proteins

A

organisation of 1’ and 2’ structure into 3D protein shape

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28
Q

what is the 4’ structure of proteins

A
  • arrangement of different subunits of proteins/ the arrangement of chains in relation to one another
  • addition of prosthetic groups
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29
Q

what is the name for AA chain

A

backbone

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30
Q

what is the name for AA in polypeptide chain

A

residues

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31
Q

what is the name for R groups

A

side chains

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32
Q

what bond joins AA

A
  • peptide bonds (amide bonds) to form proteins in condensation reaction
  • between double bond between C-O or between C-N
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33
Q

what kind of bond are peptide bonds?

A

not like normal single covalent bond -have partial double bond characteristics

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34
Q

what is the significance of O and N being on opposite sides of the peptide bond

A

trans position

-maintains max distance between them = limited orientation around the bond = making the bond rigid

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35
Q

wha is an intrachain H bond

A

H-bonds between N-H and C=O of main chain stabilise the helix

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36
Q

what are the 2 types of 2’ structure

A
  • alpha helix

- B-pleated sheet

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37
Q

describe the features of an alpha helix

A
  • 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
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38
Q

describe the features of a B-pleated sheet

A
  • 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
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39
Q

protein activity changes which structure of the protein?

A

3’ and 4’

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40
Q

what’s the structure of membrane proteins

A
  • 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
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41
Q

which proteins is the 3’ structure vital?

A

enzymes

  • 3’ important in active and binding sites
  • Each of AA residue in AS interact with substrate to position and catalyse
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42
Q

in general what forces stabilise the 3’ and 4’ structure

A

sidechain interactions

- can be covalent or weak

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43
Q

name the side chain interactions involved in 3’ and 4’

A
  • disulphide bonds
  • electrostatic interactions
  • VDW
  • H Bonds
  • hydrophobic effect
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44
Q

what kind if bond are disulphide bonds and how are they formed

A
  • 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
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45
Q

how are electrostatic interactions formed?

A
  • 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
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46
Q

how are H-bonds formed?

A
  • 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)

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47
Q

how are VDW formed

A

a range of weak forces that occur in electrically neutral molecules and involves dipole
-Temporary/induced dipoles

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48
Q

how does the hydrophobic effect work?

A
  • 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
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49
Q

at physiological pH what does the overall charge of the protein depend on

A

-PI of the protein

isoelectric point- where protein has no overall charge

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50
Q

what 2 factors that affect AA chain folding

A
  • Rigidity of the peptide bond limits flexibility of chain

- Physical and chemical properties of side chains restrict the no. of stable options

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51
Q

at what point is a protein at its highest energy level?

A 
unfolded form
(fully folded form= lowest energy level)
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52
Q

what 2 families of proteins support effe time protein folding

A
  • 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
53
Q

what problems can protein misfolding lead to?

A
  • 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)
54
Q

give the biochemical features of Alzheimers disease

A
  • 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
55
Q

symptoms of Alzheimers

A

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

56
Q

what is and happens CJ disease

A
  • 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
57
Q

what are globular proteins?

A
  • 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
58
Q

what are fibrous proteins?

A

keratin (hair/nails), collagen

-elongated, often have repeating amino acid sequences, insoluble due to high hydrophobic amino acid content

59
Q

what are most Haemoglobinopathies due to

A

single amino acid change- haemoglobins differ by single AA

60
Q

are all Haemoglobinopathies fatal?

A

-Some fatal
–Some advantageous
–Some no clinical effect

61
Q

why are people with Thalassaemia and sickle cell trait protected against Plasmodium falciparum

A
  • 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.
62
Q

what is the role of myoglobin

A

oxygen store in tissues

63
Q

what is the role of Hb

A

Oxygen ( and CO2) transport

64
Q

where is Mb conc highest?

A

skeletal

cardiac muscle - not totally reliant on circulatory system

65
Q

features of Mb molecule

A
  • very compact
  • Contains haem prosthetic group
  • A typical globular protein
  • Mostly a -helical
  • Hydrophobic residues on inside, polar ones on surface
66
Q

what does the Haem prosthetic group made of

A

Fe 2+ + protoporphyrin IX ring ( iron on the middle of the ring )

67
Q

where and how is Haem bound

A

Non covantley bound to hydrophobic crevice in protein

68
Q

with what and how many coordinate bonds does Fe2+ make?

A

6 ligands:

  • 4 N from porphyrin ring
  • 1 N proximal His
  • 1 oxygen molecule
69
Q

why is It important to associated haem molecule with protein

A
  • keeps Fe in Fe2+ form

- binding more oxygen specific ( CO binding inhibited)

70
Q

does oxygen or CO have a higher affinity to Hb

A
  • 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
71
Q

describe the structure of Hb

A
  • 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
72
Q

compare Hb and Mb in binding, affinity and BPG dependence

A
  • Hb co-operative, Mb not
  • Hb affected by pH and CO2
  • Hb regulated by BPG, mb not
73
Q

Hb is an allosteric protein, what does this mean?

A

the binding of O2 to one subunit affects interactions with the other subunits

74
Q

does Mb or Hb have a higher affinity for O2

A

Mb

even though Hb has more binding sites, Mb doesn’t have subunits which are affected by Oxygen binding

75
Q

describe the tense state

A
  • low affinity for O2
  • position of a residue’s oxygen binding site less accessible
  • more salt bridges between sub units
76
Q

describe the relaxed state

A
  • high affinity for O2
  • Fewer salt bridges
  • O2 binding site more accessible
77
Q

how does pH affect O2 binding

A
  • 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
78
Q

where is BPG found and what does it do?

A
  • found at high concentration in erythrocytes
  • increase at high altitude and in hypoxia (poor oxygenation)
  • BPG decreases affinity of Hb for O2
79
Q

where does BPG bind?

A
  • 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
80
Q

how does CO2 affect Hb

A
  • binds to amino groups on the globin protein- N terminal amine and , forming carbaminohaemoglobin
  • releases further H+
  • stabilises the T state
81
Q

what are the chains in HbF

A

2 alpha chains

2 gamma chains

82
Q

doesBPG affect HbF

A

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
83
Q

what is the mutation in sickle cell anemaia ?

A

Mutation in one of Hb chains which then allow aggravation of Hb chains = sickle shape

84
Q

what is the mutation in B-thalassemia ?

A

lack of synthesis of beta chain so person doesn’t have suffient Hb

85
Q

why do not all mutations in Hb cause disease?

A
  • depends on:
  • position of mutation-mutations in critical residues will affect function
  • and type: conservative or non conservative
86
Q

what is a conservative mutation?

A

AA replaced have same property = affects not bad

- eg. maintains hydrophobic interior of molecule

87
Q

what is a non conservative mutation?

A

will have a major effect on protein structure and function.

- eg. negative charged leu subbed by positive charged lys

88
Q

what’s the most abundant protein in mammals?

A

collagen

89
Q

how many polypeptide chins is collagen made from?

A

3 (all alpha chains )

90
Q

what are types 1,2,3 of collagen called and what are they involved in

A
  • fibril forming collagens ( as form long fibrils)
  • involved in bone, cartilagge and skin
  • most common types
91
Q

what are types 4,7 of collagen called and what are they involved in

A

network forming collagens
( as form grid like structures/sheets)
-Important in basal lamina

92
Q

what are types 5,9,12 of collagen called and what are they involved in

A

fibril associated collagens

mainly associated with main types and may be used in cross linking

93
Q

what are basal lamina

A
  • 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
94
Q

highlight the steps in the biosynthesis of collagen

A
  • 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
95
Q

what are fibroblasts

A

-cell that synthesises extracellular collagen

•Different types of fibroblasts depending on part of body- eg. Osteoblasts

96
Q

what is procollagen?

A

all 3 pro alpha chains of collagen together

97
Q

what is the 1’ repeating sequence of collagen?

A

Glycine -Proline -Hydroxyproline (usually)

98
Q

why are gly residues always repeated as the 3rd residue in collagen 1’ sequnce?

A
  • smallest AA so only one that fits in the centre of the procollagen = allows helixes to interact with each other
99
Q

what are the 3 covalently modified AA in collagen

A
  • 4-Hydroxyproline (Hyp)
  • 5-hydroxylysine (HyL)
  • Allysine
100
Q

what process occurs before the polypeptide chain synthesis of collagen but after the chain formation ?

A

hydroxylation of proline and lysine residues

101
Q

what enzymes are involved in the hydroxylation of proline and lysine residues and what co factor do they both require?

A
  • propyl hydroxylase
  • lysyl hydroxylase
  • vitamin C/ascorbic acid as cofactor
102
Q

what is hydroxyproline used for

A
  • involved in additional H: maximising H bonding taking place
  • stabilises and allows triple helix to form
103
Q

what is hydroxylysine used for

A
  • attachment sites for sugar residues glucose and galactose

- involved in cross-linking between collagen chains

104
Q

is collagen glycosylated?

A

yes- heavily glycosylated

- amount of glycosylation varies between different collagen types

105
Q

what type of helix is each polypeptide chain in collagen

A

LEFT handed : rope like structure

v tightly wound

106
Q

what type of helix is the tropocollagen molecule

A

RIGHT handed helix

107
Q

where do the residues of collagen sit in tropocollagen

A
  • Gly packed in centre

- Pro and Hydroxyproline on outside

108
Q

why are Proline and Hydroxyproline situated on outside of tropocollagen?

A

allow cross linkage between collagen molecules

109
Q

what are extension peptides and why are they important?

A
  • 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
110
Q

at what point are peptidase enzymes used in the assembly of collagen and what do they do?

A

remove extension peptides after secretion into extracellular space= get tropocollagen

111
Q

what is the function of Lysyl oxidase

A

deaminates some lysine and hydroxylysine residues to form allysine

112
Q

what do allysine do and what do they react with

A

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

113
Q

why are corsslinkages important in collagen

A

give strength and rigidity

114
Q

highlight how bone is formed within collagen fibrils

A

Holes between tropocollagen fibres are nucleation sites for calcium deposition to create bone

115
Q

why are evenly spaced gaps between tropocollagen important ?

A

even deposition of calcium phosphate = strong bone

116
Q

what breaks down collagen and why is this important?

A
  • Collagenase– a family of metalloproteinases

- necessary for growth, tissue remodelling (e.g. pregnancy/ after birth) tissue repair

117
Q

why are collagenases important in cancer ?

A

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

118
Q

what is Dupuytren’s contracture?

A

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

119
Q

what can we use to treat Dupuytren’s contracture?

A
  • injection of collagenase

- or surgical

120
Q

name 3 diseases that are caused when collagen structure or synthesis is abnormal

A
  • Osteogenesis Imperfecta
  • Ehlers-Danlos syndrome
  • Scurvy
121
Q

what is Scurcy due to?

A

lack of vitamin C

– vitamin C cofactor for prolyl hydorxylase to make hydroxy proline- without it destabilises structure of collagen

122
Q

what are the symptoms of Scurvy

A

bleeding gums, tooth decay, rough skin

123
Q

what is Ehlers-Danlos syndrome and what’s the cause

A

•Inherited disorders resulting from poorly formed/weak collagen in connective tissue (ligaments, tendons, blood vessels, internal organs)
- Lysyl oxidase deficiency

124
Q

what can Ehlers-Danlos syndrome cause

A
  • 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
125
Q

what is another name for Osteogenesis imperfecta

A

brittle bone disease

126
Q

what is Osteogenesis imperfecta

A

•A range of inherited disorders characterised by increased risk of bone fractures
- Severity of symptoms/deformity depends on the nature of the mutation

127
Q

what is the mildest type of Osteogenesis imperfecta and what happens

A

type 1 : bowing of long bones, and spine deformity

decreased production of alpha 1 and alpha 2 collagen chains

128
Q

what is the fatal type of Osteogenesis imperfecta and why

A

Type 2

- damage to collagen so great so ribcage cannot protect heart and body cant survive

129
Q

what are the severe types of Osteogenesis imperfecta and what is caused

A

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

year 1 flash cards (23 decks)

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