Proteins

Question 1

Why do structures have flexibility?

Answer 1

Rotation about covalent bonds

Question 2

Which are directional: covalent or ionic bonds?

Answer 2

Covalent

Question 3

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

Answer 3

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

Question 4

Stereoisomers name

Answer 4

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

Question 5

Side chains can be…

Answer 5

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

Question 6

Peptide bond

Answer 6

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

Question 7

Which way is a polypeptide read?

Answer 7

N-terminal to C-terminal

Question 8

When CAN disulphides bonds form?

Answer 8

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

Question 9

Primary structure

Answer 9

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

Question 10

How can protein sequences be compared for similarity of function?

Answer 10

Using statistical tests

Question 11

Homologue

Answer 11

Proteins of similar sequence derived from a common ancestor

Question 12

Ortholgue

Answer 12

Proteins with similar sequences and functions

Question 13

Paralogue

Answer 13

Proteins with similar sequences and differing functions

Question 14

Divergent evolution

Answer 14

Similar and evolved from a common ancestor

Question 15

Convergent evolution

Answer 15

Similar function but from different ancestors

Question 16

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

Answer 16

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

Question 17

Steric hindrance

Answer 17

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

Question 18

Ramachandran diagram

Answer 18

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

Question 19

Secondary structure

Answer 19

Regular local folding patterns

Question 20

Constants on shape

Answer 20

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

Question 21

Polarised covalent bonds

Answer 21

Bonds between elements of unequal electronegativity - separation of electrical charge

Question 22

Why can molecules change shape when they dissolve?

Answer 22

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

Question 23

Hydrophobic effect

Answer 23

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.

Question 24

Amphipathic molecule

Answer 24

Has both hydrophobic and hydrophilic parts

Question 25

What is secondary structure formation driven by?

Answer 25

Formation of hydrogen bonds between functional groups within peptide "backbone" (N-H...O=C)

Question 26

Alpha helix

Answer 26

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

Question 27

Beta sheets

Answer 27

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

Question 28

Beta turns

Answer 28

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

Question 29

Coils

Answer 29

Regions of irregular secondary structure

Question 30

How is tertiary structure formed?

Answer 30

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

Question 31

Domain

Answer 31

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

Question 32

Motifs

Answer 32

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

Question 33

How is tertian structure maintained?

Answer 33

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)

Question 34

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

Answer 34

From primary structure using hydrophobicity plots

Question 35

Inside out regions of proteins embedded in membranes

Answer 35

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

Question 36

Why does tertiary structure allow flexibility?

Answer 36

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

Question 37

How is quaternary structure formed?

Answer 37

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

Question 38

Denaturation

Answer 38

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

Question 39

Folding is a balance between...

Answer 39

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

Question 40

Effect of a solvent on a protein

Answer 40

Increased entropy - oil drop effects and favour folding

Question 41

Disulphide bonds

Answer 41

Stabilise 3D structures but do not determine them

Question 42

Anfinsen experiments

Answer 42

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

Question 43

Levinthal's paradox

Answer 43

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

Question 44

Chaperonins

Answer 44

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

Question 45

Misfiled stages

Answer 45

Lead to formation of aggregates

Question 46

Fibrous protein

Answer 46

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

Question 47

Keratin

Answer 47

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

Question 48

Collagen

Answer 48

Triple helix structure - high proline and glycine

Question 49

Silk

Answer 49

Beta sheet structure - high gly, ser, ala

Question 50

Gliadins (globular) and glutenins (fibrous)

Answer 50

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

Question 51

Binding of oxygen (ligand) to myoglobin (receptor)

Answer 51

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

Question 52

Dissociation constant, Kd

Answer 52

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

Question 53

Y(L)

Answer 53

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

Question 54

Proteins acting as ligands

Answer 54

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

Question 55

Antibodies

Answer 55

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

Question 56

Haemoglobin

Answer 56

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.

Question 57

How do enzymes decrease Ea?

Answer 57

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

Question 58

How is catalysis carried out?

Answer 58

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

Question 59

V =

Answer 59

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

Question 60

Kcat

Answer 60

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

Question 61

Bohr effect

Answer 61

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

Question 62

Reversible inhibitors

Answer 62

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

Question 63

Irreversible inhibitors

Answer 63

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

Question 64

Competitive (reversible) inhibitor

Answer 64

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

Question 65

Non competitive (irreversible) inhibitor

Answer 65

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

Question 66

Ki

Answer 66

Lower = stronger binding between enzyme and inhibitor

Question 67

Strategies to regulate enzyme activity in vivo

Answer 67

Reversible covalent modification and irreversible proteolytic Activation