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proteins Flashcards

1
Q

What kinds of proteins provide support?

A

Collagen (the protein of the bone), skin and tendon

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2
Q

Tell me about collagen fibres

A

These are the main component of connective tissue

Found in skin, tendons, organs and bone

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3
Q

What are erythrocytes

A

This is another name for a red blood cell

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4
Q

Tell me about haemoglobin

A

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

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5
Q

What are LDLs composed of?

A

a phospholipid shell and a single molecules of apolipoprotein

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6
Q

What are LDLs used for?

A

To transport cholesterol between cells via the circulatory system

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7
Q

What is the uptake of LDL particles mediated by

A

the LDL receptor that binds LDL and facilitates internalisation

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8
Q

What condition is associated with a mutation in the LDL receptor gene

A

Hypercholesterolemia

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9
Q

Describe the structure of antibodies

A

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

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10
Q

Lysozyme is an exmpale of a biological catalyst: describe it

A

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

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11
Q

What kind of protein regulates genes?

A

the lac repressor - helps controls gene expression

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12
Q

Describe the lac repressor

A 
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
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13
Q

what do the functions of protein come down to

A

SPECIFIC BINDING = CHANGE OF CONFORMATION = CHANGE OF ACTIVITY

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14
Q

What bonds are proteins joined by

A

peptide bonds

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15
Q

Whats the structure hierarchy of proteins

A

PRIMARY - SECONDARY - TERTIARY - QUATERNARY

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16
Q

What is the general structure of an amino acids

A

An amino group, a carboxylic acid and a unique side chain

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17
Q

What does the r-group determine

A

the structure and function of the protein

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18
Q

Name the hydrophilic amino acids

A

Lysine, arginine, histidine - basic
aspartate, glutamate - acidic
Serine, threonine, asparagine, glutamine - polar uncharged r-groups

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19
Q

Name the hydrophobic amino acids

A

alanine, valine, isoeucine, leucine, methionine, phenylalanine, tyrosine, tryptophan

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20
Q

Name the special amino acids

A

Cysteine, glycine, proline

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21
Q

what is special about cysteine

A

it can form covalent disulphide (-s-s-) bons with other cysteine residues

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22
Q

What is special about glycine

A

It is the smallest amino residue and can fit into tight spaces

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23
Q

Why is proline special

A

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

24
Q

What is an acid

A

any molecule that tends to release a hydrogen ion

25
What is a base
a base is a molecule that readily combines with a hydrogen ion
26
Whats the equilibrium constant:
Ka = [H+][A-] / [HA]
27
Whats the pH equation
pH = pKa + log [A-] | [HA]
28
What is the pKa rule
•The pKa of any acid is equal to the pH at which half the molecules are disassociated
29
What does the charge of an amino acid vary with
pH
30
What is pKa
pKa is the pH at which dissociation is 50% complete
31
What can influence pKa
Local enviroment
32
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.
33
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
34
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
35
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
36
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
37
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
38
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
39
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
40
What is amino acid resdue
When two or more amino acids combine to form a peptide
41
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.
42
What kind of bonds stabilise tertiary structure
``` Di-sulphide bonds H-bonds Ionic interactions Van der Waals interactions Hydrophobic interactions ```
43
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
44
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
45
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
46
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
47
What is the Bohr effect
The pH of the blood influences O2 binding to haemoglobin
48
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)
49
What happens during excerise
CO2 (acidic) builds up during exercise, which lowers blood pH facilitating faster oxygen delivery
50
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
51
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
52
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)
53
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
54
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
55
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
56
What are the symptoms and cause of ehlers-danloss syndrome
Loose skin and hypermobile joints Lack of procollagen peptidase or lysyl oxidase
57
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

Y1S1 (71 decks)

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