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IMS 1 > S3- Proteins > Flashcards

S3- Proteins Flashcards

1
Q

What is collagen?

A

Major structural protein (25% of total body’s protein) in the extra cellular matrix, resilient sheets to support skin and internal organs, molecular cables for tendons, bones and teeth

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2
Q

Bones and teeth are made by adding….to collagen

A

Hydroxy-apatite crystals (dash for pronunciation)

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3
Q

What is the primary structure of collagen protein?

A

Repeated sequence of 3 amino acids: Glycine-X-Y-Gly-X-Y
Forming a secondary alpha chain

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4
Q

The X and Y amino acids in the collagen primary structure are frequently…..

A

Proline and it’s modified version hyrdoxyproline

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5
Q

The 3 levels of collagen structure are…

A

Triple helix= 3 alpha chains
Collagen fibrils= cross-linking
Collagen fibre= packing

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6
Q

There are at least…types of collagen and have different…and different alpha chains combinations therefore…

A

12
Functions
Quaternary structure

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7
Q

The most common types of collagen are….and they form long….

(Fibril-forming collagen)

A

I, II, III
long fibrils (fibril-forming)

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8
Q

Type I collagen is..% of total collagen and is the main component of….

It is found in….,…,…but not in….

It is used in….

A

90%
Bone
Skin, hair, tissue
Cartilage
Tissue repair

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9
Q

Type II collagen is the main component of….and is found in the…..and…

A

Cartilage
Cornea
Vitreous humour

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10
Q

Type III collagen combines with type….and it’s found in…with…properties/ hollow organs such as…..

A

Type I
Tissues
Elastic
Skin, arteries, muscle, lungs, intestine (organs that stretch)

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11
Q

(Network forming collagen)
Type IV and VI collagen form a….which is important in the…..

A

2-dimensional matrix
Basal lamina (epithelial cells)

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12
Q

The specialised cells that make collagen (according to their location in the body) are called….

A

Fibroblasts = encode different alpha chains that will form different collagen molecules

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13
Q

Collagen mRNA goes from nucleus to RER, then Golgi then exocytosis to leave cell, what are the 6 steps of collagen production?

A

In RER = preprocollagen
1. Pro alpha chain backbone (Gly-X-Y)
2. Hydroxylation of proline and lysine (requires vitamin C)
3. Glycosylation
Procollagen (triple helix structure)
4. Exocytosis
Outside cell (the ends of the chains are still not wrapped around each other- so they just get cut later)
5. Cleavage of procollagen C and N terminals = form tropocollagen
6. Formation of cross-links (stabilised by lysyl oxidase)- copper dependent

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14
Q

Hydroxylation of proline and lysine forms…and the enzymes….are used

The reaction requires….to assist addition of oxygen from our diet

A

Hydroxyproline and hydroxylysine
Prolyl hydroylase and lysyl hydroxylase

Vitamin C

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15
Q

Proline hydroxy: stability of….due to extra…

Lysine hydroxy: stability of the…due to extra….

A

Triple helix, H bonds
Fibrils, cross linking

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16
Q

The cross linking of collagen uses the enzyme….which uses….as a cofactor

A

Lysyl oxidase
Copper

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17
Q

Extracellular matrix collagen have no….in fibril but rather very…layers to allow soft tissues (unlike bones and teeth)

A

Crosslink
Loose

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18
Q

What happens to collagen in old age?

A
  • more cross0linking= more brittle and less elastic
  • synthesis decreases
  • bones more easily broken (brittle)
  • arteries and skin less elastic
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19
Q

Aging or disease causes….which harms the damages the tissues and its functions

A

Fibrosis (thick/ stiff tissue scarring/ over-growth/ hardening and is attributed to excess deposition of extracellular matrix components like collagen)

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20
Q

Collagen is one of the….in fibrotic tissues

A

Upregulated genes (increased rate)

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21
Q

4 pathologies of collagen are:

A
  1. Osteogenesis imperfecta= mutations in collagen chains
  2. Scurvy= lack of vitamin c in diet= less hydrocylation
  3. Menke’s disease= copper deficiency
  4. Ehlers-Danlos syndrome type VI= lysyl oxidation deficiency
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22
Q

Osteogenesis imperfecta in known as….
It is caused by….(no family history/ genetic disorder)
Its severity increases with ….
Sometimes it is mistaken for….

A

Brittle bone disease
Spontaneous mutation
Substitution by large and charged amino acids (they prevent triple helix forming tight/ stable/ sturdy structure= loose= bones easily broken)
Child abuse

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23
Q

Osteogenesis imperfecta types, protein, defect, phenotype, sclera, life-expectancy

A

Type I= alpha 1 collagen/ collagen quantity/ mild non-deforming/ blue/ normal age
Type II= alpha1 and 2/ collagen structure/ perinatal lethal/ blue/ perinatal
Type III= 1and2/ collagen structure/ progressively deforming/ blue than normal/ childhood
Type IV= 1and2/ collagen structure/ moderately deforming/ normal eyes/ slight reduction in age

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24
Q

Scurvy is triggered by lack of…(vit C) which prevents….
Therefore collagen is not stabalised (less H bonds between alpha chains and less cross-linking)

A

Ascorbic acid
The enzyme activity of proline and lysyl hydroxylases

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25
Q

The main symptoms of scurvy are….
Around 200 cases of death in UK in 2022 due to….

A

Loss of teeth and easy bruising (lack of collagen to repair wear and tear by everyday activities)

Malnourishment

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26
Q

Menke’s disease are….and…
They are caused due to mutation in a….
Without treatment, life expectancy is…

A

Rare and X-linked
Copper transporter
3 years

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27
Q

Ehlers-Danlos has more than…types due to mutations in at least 20 genes found

Many of these genes are responsible for making collagen, others make….

A

20
Proteins that process, fold, or interact with collagen

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28
Q

Collagen has 3…handed helix chains that have…residues per turn
These combine to form…handed triple helix

A

Left
3.3
Right

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29
Q

In collagen helix structure, proline and hydroxyproline are on the….to max….
Small…residues are packed into the…

A

Outside, hydrogen bonds
Glycine, centre

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30
Q

Collagen 1 is made of 2….chains and 1….chain

A

Alpha 1
Alpha 2

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31
Q

Oxygen is….in blood and needs a transport system

….is for O2 and CO2 transport
….is for O2 storage

A

Sparingly soluble in blood

Haemoglobin
Myoglobin

32
Q

Haemoglobin is the…that makes blood red
Its composed of 4….and 2…and 2…
Oxygen binds….

A

Protein
Protein chains
Alpha and beta (each has haem group with iron atom)
Reversibly

33
Q

Haem is male of…

A

Fe2+ and proto-porphyrin IX

34
Q

Hb chain has very similar….to Mb but differs at…of amino acid residues

A

3D structure
83%

35
Q

Oxygen binding…tertiary and quaternary structure of Hb because binding to one subunit affects…with other subunits, which makes binding of next O2….

A

Alters
Interactions
Easier

36
Q

Mb has greater…for O2 than Hb, so its good for….

A

Affinity (binding)
Storage function

37
Q

Binding of O2 to Hb is….and the binding curve is…

A

Co-operative
Sigmoidal (s shaped)

38
Q

Haem enables transport of other molecules like:…

A

Nitric oxide, carbon monoxide

39
Q

Nitric oxide affects…which…
It binds to specific…and…

A

Walls of blood vessels= relax/ vasodilation= reduce blood pressure

Cysteine residues in Hb and Fe in haem group

40
Q

Carbon monoxide is a…which binds…to haem
It causes…deaths each year
Symptoms include:…

A

Toxic gas
Irreversibly (better than O2)
60
Nausea, dizziness, confusion

41
Q

Structure of amino acid?
Basic amino acid has….
Acidic amino acid has….
At neutral pH they exist as…
The nature of amino acid side chain/ R group determines…

A

Amine/ amino group NH2- carbon+H+R group- carboxyl group COOH
NH3+ (accepts H+= basic)
O- (donates H+= acidic)
Zwitterion
Its properties

42
Q

The 4 types of amino acid groups are…

A
  1. Electrically charged side chains (acidic and basic)
  2. Polar uncharged side chains
    3.special cases
  3. Hydrophobic side chains
43
Q

Peptide is….linked by…
The bond is…

A

1+ amino acids
Peptide bond/ amide bond
Very chemically stable/ planar (between HN and O)

44
Q

Each amino acid unit on polypeptide is called…

A

Residue

45
Q

Primary structure is…
It defines how the protein will…
Single change in amino acid structure can cause…

A

Linear sequence of amino acids
Fold and function
Disease

46
Q

Secondary structure of protein has…and forms….such as….and…

A

H bonds
Stable structural elements
Alpha helix
Beta sheets

47
Q

What determines the possible confirmations/ shapes/ structure of polypeptides?

A

Bond length and bond angle

48
Q

Alpha helix has a…structure with….bonds
…residues per turn

A

Coiled
Intrachain H bonds (within a chain)
3.6

49
Q

Beta sheets are stabilised by….
The chains can…by making…

A

Hydrogen binds between strands
Change direction
Reverse turns and loops

50
Q

To function, proteins….to form a…structure
They create a…or…to hold a substrate
Two or more chains bind to give a….and form a….structure

A

Fold into compact, globular shape
Tertiary structure
Pocket or active site
Functional molecule, quaternary structure

51
Q

The 5 interactions/ bonding that is holding the tertiary and quaternary proteins together are…

A
  1. H bonds= (between H atoms) covalently bound to proton donor and acceptor
  2. Ionic= charged amino acids, often surface exposed on outside
  3. Disulfide= between cysteine residues
  4. Van der waals= weak electrostatic forces of attraction
  5. Hydrophobic interactions= between hydrophobic residues often on the inside of proteins
52
Q

5 types of protein functions:

A
  1. Structural= cytoskeletal
  2. Regulatory= chaperones
  3. Carriers= membrane transporters
  4. Catalytic= enzymes
  5. Sensory= receptors
53
Q

Protein misfolding results in….and it can be driven by…

A

Disease
Change in primary sequence or escape from negative folding pathway

54
Q

Prion diseases are….
Can originate through…or…
Caused by accumulation of…

A

Fatal neurodegenerative diseases
Transmission or inheritance
Prion protein aggregates

55
Q

Misfolding of amyloid protein results in…with…

A

Formation of fibrils
Cross-beta structure that cannot be degraded

56
Q

Amyloid beta are associated with….

A

Alzheimer’s disease

57
Q

Hb vs Mb

A

Hb= allosteric, co-operative, affinity changes by pH and CO2, regulated by biphosphateglycerate

Mb= non co-op, not affected by pH, CO2 or BPG

58
Q

The 2 states of Hb

A

R state= relaxed= less salt bridges between units= high affinity of O2

T state= tense= more salt bridges= low affinity of O2 (de-oxy state since no O2 is bound)

59
Q

Hb in lungs vs tissue

Loading and unloading

A

Lungs= lots of O2= high affinity so more O2 bind to Hb
Tissue= less O2= low affinity so more O2 released

When one O2 release= protein changes shape promoting the 3 other to quickly release/ when one O2 binds (hardest to bind)= protein changes shape so its easier for the rest to bind

60
Q

Bohr effect= Hb has less affinity for O2 when:

A

PH is lower/ more H+/ due to increased CO2 or lactic acid in blood (to promote fast release of O2 to tissue and muscle quickly)

61
Q

Why do H+affect O2 binding

A

PH affects protonation state of amino acid residues (particularly histidine)= H+ conc is high= residues protonated= more positively charged

Form new salt bridges= stabilise T state (more tense due to increases salt bridges= decrease affinity for O2)

62
Q

2,3- BPG is…and is found at high conc in…
The structure of BPG is..charged
It…affinity of O2
BPG levels are…at high altitude and under…conditions
This means Hb releases…O2 in these 2 situations

A

2,3- Biphosphateglycerate
RBC
Negatively (phosphate groups are negative)
Decreases
Increased, hypoxic (lack of O2 in tissue)
More

63
Q

BPG binds in the space between…so HbF…
Negative charges of BPG interact with..

A

Beta chains
Is not affected by BPG
Positive amino acid residues

64
Q

H+, CO2 and BPG interact at….sites
So their effects can be…

A

Different
Additive

65
Q

HbF has…than HbA
It pro-dominates during last 2….and by end of fist year our body makes entirely…

A

Higher affinity to O2
Trimesters of gestation
HbA

66
Q

HbA vs HbF

A
  1. Both have 4 subunits
  2. 2 identical alpha subunits
  3. HbF= 2 gamma subunits (instead of beta)
  4. Gamma increases affinity for O2
    5.no beta chains= no 2,3-BPG binding
  5. BPG reduces affinity in HbA= so under same conditions, HbA will release O2 and HbF will capture it
67
Q

How do mutations affect haemoglobin:

A
  1. Amount of Hb synthesised
  2. Structure (ie subunit interfaces)
  3. Stability of Hb= leading to haemolytic anaemia
  4. Affinity for O2
  5. Affinity for regulators (ie BPG)
68
Q

Types of position mutations in Hb:

A

Position (mutations in critical residues will affect function ie: promoter region/ exon splice site/ protein structure)

Types: 1. Conservative= maintains properties (non-polar replaced with non-polar residue)
2. Non-conservative= changes properties

69
Q

2 haemoglobinopathies (opathies= disease suffix)

A
  1. Sickly cell anaemia (affects Hb structure)
  2. Beta-thalassaemia (affects Hb production)
70
Q

Sickly cell heamoglobin=…
Is caused by…

A

HbS
Mutation in beta-globin chain (beta chain subunit)= (B6 Glu is replaced by Val)

71
Q

HbS makes…patches in subunit surface and it…
They stick together to form…that distort shape of RBC= sickle

A

Sticky hydrophobic
Sticks to another hydrophobic patch
Long fibres

72
Q

Sickly cell crisis occurs when…
It lasts for…
Other symptoms are…
Its treated by…

A

Sicked RBC becomes trapped within small blood vessels and block them= damage organs
7 days
Tiredness, headaches, dizziness, increased infection risks
Fluids, painkiller, antibiotics, transfusions (no cure)

73
Q

Sickle cell anaemia is an…
Sickle cell trait=…
It occurs more in geographical areas with…as it gives a…against malaria

A

Autosomal recessive disease
Carrier= one copy of mutated beta globin
High incidence of malaria
Protective effect

74
Q

HbF can be a…to sickle cell because it…
As…% of HbF in blood reduces the symptoms
…therapy is researched to increase level of HbF
…anticancer drug that is shown to be effective as it increased HbF levels

A

Solution
Lacks beta chains
20
Gene therapy (surpresses a silencer of HbF gene= more is expressed)
Hydroxyurea

75
Q

Thalassaemia effects…and its caused by…
The severity depends on…
Less Hb=…

A

Production of haemoglobin
Reduction or absence of alpha or beta chains
Type
Less HbS= less sickling

IMS 1 (14 decks)

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