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Biochemical Structures > Proteins > Flashcards

Proteins Flashcards

1
Q

4 functional types of protein

A

structural proteins, enzymes, transporters and regulatory proteins

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2
Q

Amino acid definition

A

Zwitterionic monomers with a carboxyl and amino group and R group that undergo condensation reactions to form polypeptides.

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3
Q

What charge do amino acids have at pH 7?

A

0

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4
Q

5 functional types of amino acid side groups

A

Acidic, basic, hydrophobic, hydrophilic and structural

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5
Q

Basic amino acids

A

Arginine, lysine, histidine

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6
Q

Acidic amino acids

A

aspartate and glutamate

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7
Q

Hydrophobic amino acids

A

valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan and tyrosine

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8
Q

Which hydrophobic amino acid is the odd one out and why?

A

Tyrosine, as it is uncharged but still hydrophobic

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9
Q

Hydrophilic amino acids

A

cysteine, asparagine, glutamine, serine and threonine

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10
Q

Structural amino acid + what happens

A

Proline, produces kinks in chains due to its distinctive cyclic structure

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11
Q

Type of bond between two amino acids

A

Peptide bond

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12
Q

Properties of the peptide bond

A

Electrons are shared along the CO-NH system, resulting in partial charges on the oxygen and hydrogen.

The sharing of electrons means no rotation around the peptide bond, creating a rigid planar structure called the amide plane.

C-N bond has characteristics of a double bond, decreasing the length of time required for the proteins to fold.

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13
Q

What rotation occurs within amino acids?

A

Between C alpha - C and C alpha- N bonds , represented by phi and psi angles, which give proteins their 3D shape and flexibility

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14
Q

Why does stereoisomerism take place?

A

alpha carbon is chiral, as there are 4 groups attached, thus two isomers exist.

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15
Q

What isomer are human proteins made from?

A

L-type amino acids

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16
Q

What isomers do bacteria use + drug development?

A

D- type, thus when creating antibiotics, proteins are produced that mimic D-isomers to target bacteria

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17
Q

Significance of peptide bond in secondary structure

A

Carboxyl oxygen and amino hydrogen have partial charges, enabling them to hydrogen bond, producing a helix.

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18
Q

Levels of organisation of protein structure

A

Primary, secondary, tertiary and quaternary

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19
Q

Primary structure definition

A

The order and number of amino acids

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20
Q

Secondary structure definition

A

Three dimensional form of local segments of protein, containing hydrogen bonds.

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21
Q

Two main types of secondary structure

A

Alpha helix and beta pleated sheet

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22
Q

Alpha helix structure

A

Single polypeptide chain that twists around itself to form a rigid cylinder. Hydrogen bonds, running parallel to the helical axis, form every fourth peptide bond, linking the C=O and N-H. Helix twists every 3.6 amino acids.

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23
Q

Are alpha helices left or right hand and why?

A

Right hand, due to the L-type amino acids

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24
Q

Do R groups affect the alpha helix structure + why?

A

No, as the side chains project outwards

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25
Q

What are termed helix breakers + why?

A

Proline amino acids, as they do not have a primary amine group, thus cannot hydrogen bond as effectively.

26
Q

What other intermolecular force is present in secondary protein structures?

A

Van der Waals

27
Q

What are Van Der Waals and what is their function?

A

Weak attractive forces of attraction formed due to the instantaneous dipoles that arise as a result of the random movement of electrons in the protein. Are stronger over a shorter distance, which is the case in alpha helices.

28
Q

Alpha helix advantages

A

Structural stability and optimised H bonding. Atoms touching so strong van der Waals, little steric clashing as side chains are outside the helix. Rigid, useful as transmembrane receptors.

29
Q

Beta pleated sheet structure

A

Several beta strands, with 5-10 residues each align into sheets so that adjacent strands form hydrogen bonds.

30
Q

How are steric clashes minimised in a beta pleated sheet?

A

R groups are found above and below the beta plane

31
Q

Two types of beta pleated sheet

A

parallel and antiparallel

32
Q

Difference between parallel and antiparallel beta pleated sheets

A

Parallel has the polypeptides running in the same direction, forming weaker hydrogen bonds at an angle, and greater distance, due to the incomplete sharing of the oxygen electron pair. Anti-parallel has the chains running in opposite directions, forming strong perfectly aligned hydrogen bonds.

33
Q

Beta pleated sheet eventual structures

A

Globular proteins

34
Q

What is a loop/turn?

A

Polypeptide chain makes a 180 degree change in direction- a dihedral angle

35
Q

What forms a loop?

A

Carbon atoms of two residues are close, separated by 1-5 peptide bonds, forming an inter main chain hydrogen bond which causes a turn.

36
Q

Example of a loop

A

Beta hairpin, two antiparallel strands linked by a loop

37
Q

What amino acids often involved + why?

A

Glycine and proline, as they often produce a dihedral angle

38
Q

Tertiary structure definition

A

Organisation of the secondary structure into a defined 3D shape, with interaction between R groups

39
Q

Interactions in tertiary structures

A

Van der Waals, disulfide bridges, hydrophobic interaction, ionic bonds and hydrogen bonds

40
Q

Explain ionic bonds

A

Charge-charge or charge-dipole. Longer distance interactions.

41
Q

Explain hydrophobic interactions

A

Polar, hydrophobic side chains tend to be forced together when in water and hydrophilic ones face the water to produce a more stable molecule. Present in globular proteins and transmembrane proteins.

42
Q

Explain disulfide bridges

A

Covalent bonds that form between two cysteine amino acids, stabilising the protein.

43
Q

Examples of domains and functions

A

Beta domain- barrels and saddles, such as immunoglobulin

Alpha domains- helix-loop-helix structures

ABC membrane domain- alpha helical, such as the CFTR transmembrane protein.

44
Q

What is a domain?

A

unit of organisation where the motifs appear to be structurally stable. Part of a protein that can fold independently from the rest of the protein into a compact and stable structure, often associated with different functions.

45
Q

What is the quaternary structure?

A

Interactions between many polypeptide chains and/or prosthetic groups to form a complex 3D structure- a complete functional protein unit.

46
Q

Oligomeric protein definition

A

A protein complex made of two or more subunits

47
Q

Two types of oligomeric protein

A

Homo-oligomeric and hetero-oligomeric

48
Q

Homo-oligomeric definition

A

protein formed of the same subunits- dimers, trimers etc.

49
Q

Hetero-oligermeric definition

A

Protein formed of different subunits- e.g Haemoglobin formed of two alpha globin and two beta globin subunits

50
Q

Myoglobin versus haemoglobin

A

Myoglobin consists of eight alpha helices connected by loops- single polypeptide chain with one haem group. Haemoglobin formed of 4 polypeptide chains each with a ham group

51
Q

Post translational modifications examples

A

disulfide bonding, cross linking and peptidolysis

52
Q

Crosslinking explained

A

covalent bond formed between adjacent amino acids in the same protein, or in different proteins forming a sub unit

53
Q

Peptidolysis explained

A

enzymic removal of part of a protein after synthesis. Often unassembled protein units or misfolded proteins removed

54
Q

Non-peptide attachments examples

A

Glycosylation, phosphorylation, adenylation and farnesylation

55
Q

Glycosylation explained. 3 amino acids involved

A

Addition of oligosaccarides to form glycoproteins. Attach to NH on asparagine and OH on serine and threonine

56
Q

Adenylation explained. 3 amino acids involved

A

addition of AMP group to protein, often to tyrosine, threonine or serine

57
Q

Phosphorylation explained. 3 amino acids involved

A

Addition of phosphate via kinases. Threonine, serine and tyrosine

58
Q

Farnesylation explained. Amino acid involved

A

Farnesyl (hydrocarbon) anchor which inserts into plasma membrane. Added to cysteine.

59
Q

functions of post translational modifications

A

regulation, targeting, inducing turnover, improve structure

60
Q

two different types of domains

A

structural and functional

Biochemical Structures (9 decks)

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