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proteins > proteins 1 > Flashcards

proteins 1 Flashcards

1
Q

what is an example of proteins providing structure in the body?

A

collagen - most abundant protein in mammals, main component of connective tissue, found in skin, tendons, organs, bone.

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2
Q

what is an example of proteins providing a transport function in the body?

A

haemoglobin carries oxygen around the body

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3
Q

what are the structural features of haemoglobin?

A

4 protein subunits per molecule; each subunit contains a haem group that can bind one oxygen molecule; harm is a prosthetic group; once one oxygen molecule has minded to a ham group there is a conformational change which increases the affinity for oxygen, same in reverse (i.e. losing oxygen)

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4
Q

what is LDL and an LDL receptor and what are their functions?

A

LDL is composed of a polar phospholipid shell AND A SINGLE MOLECULE OF apolipoprotein B. carries cholesterol to cells in the circulatory system. LDL receptors mediate and facilitate the uptake of LDL into cells.

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5
Q

antibody structure

A

two heavy and two light chains linked by disulphide bonds. highly specific antigen recognition site which tightly binds the complementary antigen allowing recognition of foreign proteins by the immune system,

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6
Q

what does lysozyme do?

A

an enzyme which catalyses the breakdown of polysaccharide chains.

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7
Q

what does the lac repressor do?

A

the lac repressor binds to DNA and prevents expression of the gene in the absence of lactose. lactose is produced in bacteria cells.

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8
Q

proteins functions and activity essentially comes down to binding. what influences and controls the binding of proteins.

A

the specific conformation of proteins. Change the conformation of proteins, change the function.

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9
Q

describe the general structure of amino acids

A

central chiral carbon surrounded by 4 different groups: side chain (R group); amino group NH3+; carboxylate group (COO-); and -H.

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10
Q

how many different amino acids are used to build proteins in the body?

A

20, 8 of which are essential (cannot be synthesised and must be obtained from diet)

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11
Q

name the basic (therefore hydrophilic) amino acids (3)

A

lysine (Lys), Arginine (Arg), and histidine (His)

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12
Q

name the two acidic (and therefore hydrophilic) amino acids

A

Aspartate (Asp) and Glutamate (Glu)

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13
Q

Name the 4 polar amino acids (and hydrophilic)

A

Serine (Ser), Threonine (Thr), Asparagine (Asn) and Glutamine (Gln)

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14
Q

Name the 8 hydrophobic amino acids

A

Alanine (Als), Valine (Val), Isoleucine (Ile), Leucine (Leu), Methionine (Met), phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp)

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15
Q

what are the special properties of the amino acid Cysteine?

A

It can form disulphide bonds with other cysteine residues

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16
Q

what are the special properties of the amino acid Glycine?

A

Glycine has the smallest R group (H) and so fits in small spaces and can lead to tight loops forming in the secondary structure of proteins

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17
Q

What are the special properties of the amino acid Proline?

A

The side chain of Proline bends around to form a covalent bond with the nitrogen atom of the amino group. Proline therefore creates a kink in the secondary structure of proteins.

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18
Q

what is an acid and what range of pH do they usually have?

A

an acid is a molecule that readily releases a hydrogen ion and has a pH below 7

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19
Q

what is a base and what range of pH do they have?

A

a molecule that readily accepts a hydrogen ion and has a high pH from 7 to 14.

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20
Q

what is the pKa?

A

the pH at which dissociation is 50% complete

21
Q

over how many units does dissociation largely occur over, centring on the pKa?

A

2

22
Q

receptor mediated endocytosis in the uptake of LDL

A

reduced pH in the endosome (pH5) causes a conformational change in the LDL receptor due to histidine residues within the protein . LDL can no longer bind and is released into the lysosome to be broken down.

23
Q

what do patients with familial hypercholesterolemia frequently have?

A

mutations in the histidine residues of the LDL receptor

24
Q

what does the peptide bond consist of?

A

covalent bond forms when the carbon atom of the carboxylate group (negatively charged) shares an electron with the (positively charged) nitrogen atom of the amine group. condensation reaction as a molecule of water is lost.

25
Q

what is the primary structure of proteins?

A

the sequence and type of amino acids in a polypeptide chain.

26
Q

what is the secondary structure of proteins?

A

the secondary structure is the initial folding pattern of the polypeptide chains, stabilised by hydrogen bonds. The three main types of secondary structure are alpha-helix, beta sheet and bend/loop

27
Q

alpha helix structure

A

clockwise turns; all side chains face outwards; has turns every 3.6 residues; hydrogen bonds between the amino and carboxyl groups every 4th amino acid

28
Q

beta sheet

A

hydrogen bonds form between adjacent polypeptide chains; sometimes has a pleated appearance as the polypeptides lie above and below the plane

29
Q

parallel beta sheets

A

when adjacent polypeptide strands are orientated in the same direction.

30
Q

anti parallel beta sheets

A

when adjacent polypeptide strands are orientated in opposite directions

31
Q

bend/loop structure

A

the polypeptide chains fold back on themselves, usually 4 amino acids are required to form the turn. proline residues are frequently found in the bends/loops

32
Q

tertiary protein structure

A

3D/spatial arrangement of the secondary structure; interactions between amino acid side chains; hydrophobic residues are buried on the inside of the protein and hydrophilic residues are exposed to the outside of the protein. Many proteins are arranged into different domains which usually contribute a specific function to the overall protein.

33
Q

name the five different types of bonds that stabilise tertiary structure

A

hydrogen bonds, van der waals interactions, hydrophobic interactions, ionic interactions and disulphide bonds.

34
Q

which amino acid forms the disulphide bond

A

the cysteine residues

35
Q

what is the quaternary structure of proteins?

A

the association of more than one polypeptide. each polypeptide chain is called a subunit.

36
Q

what is an oligomeric protein?

A

a protein composed of more than one subunit

37
Q

what is the structural arrangement of haemoglobin?

A

haemoglobin consists of a symmetrical assembly of two different subunits (2 of each): alpha globin and beta globin. each of the four subunits contains a haem prosthetic group which binds oxygen.

38
Q

what is cooperative oxygen binding?

A

when the first oxygen molecule binds to haemoglobin the conformation of the other subunits change and the affinity for further oxygen molecules increases.

39
Q

how is sickle cell anaemia caused?

A

by the change of a single amino acid at position 6 in the beta chain of haemoglobin. hydrophilic glutamic acid is replaced with hydrophobic valine.

40
Q

what is tropocollagen?

A

a building block of the collagen fibre, consists of 3 polypeptide chains with a left handed twist wound together in a right handed supercoil. multiple microfibril makes up one fibril which makes up one fibre. makes these fibres extremely strong.

41
Q

why is glycine essential for the formation of tropocollagen?

A

it has a small side chain which allows tight turns; there are 3 residues per turn; allows close packing of subunits.

42
Q

why is proline also essential for the formation of tropocollagen?

A

proline imposes left hand twists which are important in the helix that provide the main stabilising force.

43
Q

what do some proline become hydroxylated to become?

A

hydroxyproline which forms strong hydrogen bonds to help stabilise the triple helix.

44
Q

how are collagen microfibrils joined together to form a fibril?

A

via cross linking by an aldehyde derivative. the spaces between the fibres allow access for lysol oxidase.

45
Q

what is osteogenesis imperfecta?

A

a brittle bone disease caused by a glycine amino acid being replaced by cysteine at one point in the chain. The tropocollagen subunits cannot pay closely enough together and therefore there is a knock-on effect.

46
Q

what causes scurvy?

A

lack of proline hydroxylation (Vit C), therefore no hydrogen bonding

47
Q

what causes ehlers-danloss syndrome?

A

lack of pro collagen peptidase or lysol oxidase.

48
Q

which amino acid is important in pH buffering resulting in a physiological pH?

A

histidine

proteins (1 decks)

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