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Proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

Why do structures have flexibility?

A

Rotation about covalent bonds

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2
Q

Which are directional: covalent or ionic bonds?

A

Covalent

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3
Q

As pH of an ionic solution changes, what happens to the biological molecule?

A

Change in charge can lead to change in physical properties e.g. Colour (changes in light absorption) and solubility (charged groups react more favourably with water than uncharged). Can also change functional properties e.g. Catalysis or binding resulting from electrostatic interactions with pH, changing the space of the molecule

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4
Q

Stereoisomers name

A

L- (proteins) and D- (bacterial cell walls) alpha amino acids - non-super imposable mirror images

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5
Q

Side chains can be…

A

Hydrophobic/hydrophilic; acidic/basic; have aromatic ring structures or be reactive (cysteine)

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6
Q

Peptide bond

A

Amide bond formed from a condensation reaction (requires energy input), planar due to partial double bond, kinetically stable to hydrolysis. Amino acids always added at carboxylic acid group in vivo

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7
Q

Which way is a polypeptide read?

A

N-terminal to C-terminal

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8
Q

When CAN disulphides bonds form?

A

In an oxidation reaction with cysteine residues with -SH functional groups in their side chains

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9
Q

Primary structure

A

Peptide sequence plus location of any disulphides bonds (1-D)

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10
Q

How can protein sequences be compared for similarity of function?

A

Using statistical tests

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11
Q

Homologue

A

Proteins of similar sequence derived from a common ancestor

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12
Q

Ortholgue

A

Proteins with similar sequences and functions

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13
Q

Paralogue

A

Proteins with similar sequences and differing functions

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14
Q

Divergent evolution

A

Similar and evolved from a common ancestor

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15
Q

Convergent evolution

A

Similar function but from different ancestors

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16
Q

What allows the linear peptide to fold up into a 3D shape?

A

Rotation about bonds to alpha-carbon atoms in amino acid residues and folding is contained by steric hinderance

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17
Q

Steric hindrance

A

Only certain orientations of adjacent peptide bond “tiles” rotating about a central alpha carbon atom lead to structures where all the atoms are accommodated without clashes

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18
Q

Ramachandran diagram

A

Shows the limited set of combinations of rotational angles possible - steric exclusion e.g. Trans/cis clash of side chains

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19
Q

Secondary structure

A

Regular local folding patterns

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20
Q

Constants on shape

A

Orientation and rotation, electrostatic interactions between ionised groups carrying charges between or within biological molecules

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21
Q

Polarised covalent bonds

A

Bonds between elements of unequal electronegativity - separation of electrical charge

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22
Q

Why can molecules change shape when they dissolve?

A

Internal non-covalent interactions are replaced by interactions with water molecules (generally peripheral)

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23
Q

Hydrophobic effect

A

Leads to biological shapes in solution adopting a shape where polar and charged groups which can interact favourably are on the outside and non-polar regions are on the inside.

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24
Q

Amphipathic molecule

A

Has both hydrophobic and hydrophilic parts

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25
Q

What is secondary structure formation driven by?

A

Formation of hydrogen bonds between functional groups within peptide “backbone” (N-H…O=C)

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26
Q

Alpha helix

A

Formed from a single continuous peptide chain: H bonds run nearly parallel to axis of helix; side chains of amino acids residues project outward from helix. May have hydrophobic or hydrophilic surfaces of have charges or hydrophobic regions distributed over the surface

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27
Q

Beta sheets

A

Formed from adjacent parallel or antiparallel peptide chains. Chains can be parts of a continuous peptide if joined by loops; H bonds between backbone groups run nearly perpendicular to peptide backbones; multiple chains form a corrugated sheet, twisted in 3D; side chains project alternately above and below the sheet

28
Q

Beta turns

A

Used to join adjacent peptide strands in antiparallel beta sheets - proline and glycine usually present as residues in turns due to steric considerations

29
Q

Coils

A

Regions of irregular secondary structure

30
Q

How is tertiary structure formed?

A

Folding regions of assembled secondary structure in a polypeptide chain into a specific, defined, 3D shape

31
Q

Domain

A

A region of tertiary structure which can be recognised as an independent entity. It will fold by itself and may have its own functional role

32
Q

Motifs

A

Amino acid sequence signatures associated with specific functions which do not form a continuous region of sequence and do not or respond to a folding unit

33
Q

How is tertian structure maintained?

A

Non-covalent interactions involving H bonds from backbone and side chain functional groups, electrostatic interactions involving side chain groups and hydrophobic effects (maintains shape of globular proteins)

34
Q

How can regions of protein on the outside of inside of a protein be predicted?

A

From primary structure using hydrophobicity plots

35
Q

Inside out regions of proteins embedded in membranes

A

Hydrophobic regions exposed on the surface to interact with hydrophobic membrane lipids

36
Q

Why does tertiary structure allow flexibility?

A

Both side chains and backbone move within constraints set by steric exclusion and the interactions which maintain the structure

37
Q

How is quaternary structure formed?

A

By combining protein subunits containing a single polypeptide chain in a complete tertiary structure, into a single molecule. Held together by multiple weak interactions across the faces of individual subunits - easy to dissciate

38
Q

Denaturation

A

Loss of higher-order structure in proteins, which results in loss of function (function depends on 3D structure) as higher order structures are maintained by non-covalent interactions. The co-operative nature of interactions causes denaturation to occur over a relatively small range of conditions

39
Q

Folding is a balance between…

A

Energy of non-covalent interactions in protein (favourable), energy of non-covalent interaction in solvent, decreased entropy effects of folding protein (unfavourable), entropy effects in solvent = free energy

40
Q

Effect of a solvent on a protein

A

Increased entropy - oil drop effects and favour folding

41
Q

Disulphide bonds

A

Stabilise 3D structures but do not determine them

42
Q

Anfinsen experiments

A

Shows that disulphides bonds do not maintain structure when proteins refold but act as locks to help maintain folded conformations

43
Q

Levinthal’s paradox

A

Folding cannot occur via random expo,ration of all different conformations possible - progressive model of protein folding up a structure heirachy

44
Q

Chaperonins

A

Are cellular components that aid the folding process by allowing incorrectly folded regions to refold

45
Q

Misfiled stages

A

Lead to formation of aggregates

46
Q

Fibrous protein

A

Rod-like shape at the molecular level - often short sequences of AAs repeated

47
Q

Keratin

A

Helical structure with cross linking between molecules from cysteine aa residues (can be affected by reducing agents)

48
Q

Collagen

A

Triple helix structure - high proline and glycine

49
Q

Silk

A

Beta sheet structure - high gly, ser, ala

50
Q

Gliadins (globular) and glutenins (fibrous)

A

Wheat storage proteins; water insoluble, form a net like structure; elasticity makes an elastic dough

51
Q

Binding of oxygen (ligand) to myoglobin (receptor)

A

Involves a prosthetic haem group bound tightly to the protein, continuing an iron atom to which oxygen bunds weakly. Thus changes the absorption spectrum of the haem group. Gives a hyperbolic curve of proportion of myoglobin containing o vs o conc

52
Q

Dissociation constant, Kd

A

[R]/[L] / [RL] Kd = [L] when 50% receptor contains bound ligand

53
Q

Y(L)

A

Fraction of protein molecules containing bound ligand : [L] / Kd + [L]. When Y(L) = 0.5, Kd = [L]

54
Q

Proteins acting as ligands

A

Specific interaction can be determined by part of the molecule that interacts with the receptor (usually a loop)

55
Q

Antibodies

A

Binding sites on proteins can be selected to fit any given ligand

56
Q

Haemoglobin

A

Tetramer of similar subunits containing 4 oxygen binding sites; the binding curve of proportion of molecules containing bound o vs o conc is S-shaped (sigmoidal) which allows more efficient loading and unloading of Haemoglobin. Model suggests protein goes from a low affinity form (T-) to a high affinity (R-) when oxygen binds. This change can be visualised in a change in the 3D structure of the oxygen binding site.

57
Q

How do enzymes decrease Ea?

A

Rate constants increased, stabilise intermediate stage (transition state) through forming a complex with reacting molecules.

58
Q

How is catalysis carried out?

A

Enzyme forms favourable interactions with the intermediates state to stabilised it, decrease ea to affect rate increase. May also form temporary chemical bonds with reactants

59
Q

V =

A

Vmax x ([S] / ([S] + Km))

60
Q

Kcat

A

Vmax/[E] - max number of molecules of substrate reacted per molecule of enzyme per second

61
Q

Bohr effect

A

Binding of o affected by pH - bidding of o Dec pH from 7.6 to 6.8 to help unload in tissues (become acidic upon exercise - lactic acid). Affinity of Haemoglobin affected by conformational change mediated by a salt bridge interaction

62
Q

Reversible inhibitors

A

Bind to the enzyme by non-covalent interactions to form a complex and dissociate to restore enzyme activity

63
Q

Irreversible inhibitors

A

React with enzyme go form a covalent bond and cannot be removed. Often reactive chemicals - react non-specifically with functional groups on amino acid side chain. Can be made specific for enzyme by incorporating reactive groups into substrate analogues - affinity labels

64
Q

Competitive (reversible) inhibitor

A

Binds at the same site on the enzyme as the substrate. Can be removed by excess substrate. No effect on Vmax but increase apparent Km

65
Q

Non competitive (irreversible) inhibitor

A

Bind at the site on the enzyme distinct from the substrate binding site. Cannot be removed by excess substrate - no effect on Km but decrease apparent Vmax. Major regulators of metabolic pathways - feedback inhibition of first step

66
Q

Ki

A

Lower = stronger binding between enzyme and inhibitor

67
Q

Strategies to regulate enzyme activity in vivo

A

Reversible covalent modification and irreversible proteolytic Activation

Molecules and cells (6 decks)

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