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MBChB Year 1 Principles Biochemistry > Intro to Biochemistry > Flashcards

Intro to Biochemistry Flashcards

Covers lectures I-IV

1
Q

What 3 components make up an atom?

A

Protons, neutrons and electrons

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2
Q

What is the mass and charge of a proton?

A

Mass of 1 and +ve

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3
Q

What is the mass and charge of a neutron?

A

Mass of 1 and no charge

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4
Q

What is the mass and charge of an electron?

A

Negligible mass and -ve

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5
Q

What are the main properties of carbon?

A

Can form covalent bonds with itself. Can form 4 covalent bonds total which leads to tetrahedral form. Has variability in the elements it can bond with eg H, N, O etc

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6
Q

What is phosphorylation?

A

Addition of PO4

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7
Q

What is acylation?

A

Addition of C(O)R

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8
Q

What is carboxylation?

A

Addition of C(O)OH

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9
Q

What is esterification?

A

Condensation of a carboxylic acid and alcohol to form an ester (C(O)O) bond

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10
Q

What is a redox reaction?

A

One where reduction (gain of electrons) and oxidation (loss of electrons) occurs at the same time

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11
Q

As more hydrogens bond with carbon is this reduction or oxidation (eg 1 bond with hydrogen to CH4)?

A

Reduction, as carbon’s electronegativity is higher than hydrogen’s

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12
Q

As more chlorines are added to carbon is this reduction or oxidation?

A

Oxidation as carbon’s electronegativity is lower than hydrogen’s

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13
Q

What are some functions of biomolecules?

A

Information storage (eg DNA, RNA), structural (teeth etc), energy generation (glycolysis, citric acid cycle etc), energy currency/storage (ATP), and recognition/ communication/ specificity (receptors, hormones, enzymes etc)

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14
Q

What are the 4 major classes of biomolecules?

A

Peptides and proteins, lipids, nucleic acids and carbohydrates

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15
Q

What are the 3 types of carbohydrates?

A

Monosaccharides (eg glucose) - cannot be hydrolysed. Disaccharides (eg lactose/ sucrose) - made of 2 monosaccharides, allow transport and exist to stop energy waste. Polysaccharides (eg cellulose and glycogen) - made of >2 monosaccharides and mainly used for storage and rapid energy conversion

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16
Q

What is thermodynamics?

A

The biophysical discipline that deals with processes and whether or not they are energetically favourable.

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17
Q

What is the first law of thermodynamics?

A

Energy is neither created nor destroyed (simply converted from one form to another)

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18
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another, some of that energy is unable to do work (no energy transformation is 100% efficient)

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19
Q

What 3 things does a reaction involve change in?

A

Enthalpy (heat), entropy (degree of disorder) and free energy (energy of products - energy of reactants)

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20
Q

What is an exergonic reaction?

A

A reaction in which the total free energy of the products is less than the total free energy of the reactant. ΔG is -ve, so the reaction is spontaneous

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21
Q

What is an endergonic reaction?

A

A reaction in which the total free energy of the products is more than the total free energy of the reactants. ΔG is +ve and so the reaction cannot occur spontaneously (require an energy input)

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22
Q

How do we determine ΔG?

A

ΔG = ΔG’ (standard conditions) + RTln([C][D]/[A][B]) - units kJ/mol

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23
Q

What are standard conditions?

A

T = 298K, 1 atomosphere pressure, 1M (1mol/l) concentration of reactants (except H), pH = 7

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24
Q

Is ΔG related to the point of equilibrium? Why?

A

Yes as the further towards completion the point of equilibrium is, the more free energy is released. ΔG values close to 0 are usually readily reversible reactions

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25
Q

What happens if [C][D]/[A][B] becomes smaller than 1?

A

The ln of a number smaller than 1 is -ve

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26
Q

What type of cellular processes are unfavourable?

A

When they proceed in the direction of a +ve ΔG, transport against a gradient or synthesis of large molecules.

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27
Q

How to you drive an unfavourable process to become favourable?

A

Couple it with a highly favourable process

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28
Q

Why is ATP used as a universal energy currency?

A

The breakdown of ATP to ADP and Pi has a very -ve ΔG and so can be used as a driving force for the processes in the body that are extremely unfavourable.

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29
Q

Why does ATP constantly have to be regenerated?

A

Cells do not store large amounts of ATP, and active muscle cells (eg) use it at a very high rate.

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30
Q

What are the special characteristics of water?

A

It is bent so forms a dipole (and has a tetrahedral shape), and is polar (unequal sharing of electrons).

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31
Q

What are the solvent properties of water?

A

Ionic and polar substances can dissolve in water (hydrophilic)

32
Q

What is a hydrogen bond?

A

A covalent bond between hydrogen and a more electronegative atom (NOF) creates a polarised bond - HB. Hydrogen has a partial positive charge so can interact with unshared electrons from another electronegative atom. THESE ARE STRAIGHT BONDS!!!

33
Q

Are hydrogen bonds strong?

A

Individually they are much weaker than covalent bonds but collectively they are very strong.

34
Q

What is the hydrophobic effect?

A

Non-polar substances are insoluble in water (hydrophobic) and instead form a two-layer system with water

35
Q

What are amphipathic molecules?

A

Have a polar (hydrophilic) heat at one end and a non-polar (hydrophobic) tail at the other. They form micelles in water as head bonds with water whilst the tails are sequestered from the water.

36
Q

What is the importance of cell membranes?

A

They are a selective and controllable barrier to the outside world and aid compartmentalisation by isolating organelles.

37
Q

What are the 2 main components of cell membrane and how do they work?

A

Lipids (structural and precursors of signalling molecules) and proteins (confer selectivity, involved in recognition etc). To interact with interior AND exterior of phospholipid bilayer proteins must have amphipathic properties.

38
Q

What are proteins and polypeptides made from?

A

20 different L-amino acids (L are the biologically active amino acids)

39
Q

What are D amino acids?

A

The stereoisomers of L amino acids

40
Q

All amino acids contain an a-carbon bonded to what 4 subgroups?

A

An amino acid (NH2), a carboxyl group (COOH), a hydrogen (H), and a side chain (R)

41
Q

What are stereoisomers?

A

Non-superimposable mirror image structures

42
Q

What are the characteristics of non-polar, hydrophobic amino acids?

A

Don’t dissolve in water, will interact with lipid or other non-polar structures and there is no charge difference between amino and carboxyl ends of molecule - mainly just hydrocarbon groups

43
Q

What are the characteristics of polar, weakly charged amino acids?

A

Dissolve in water, variable solubility contributes to amphipathic nature of some proteins and no charge difference between amino and carboxyl ends of molecule but possibility for hydrogen bonds with water

44
Q

What are the characteristics of acidic amino acids?

A

Have a COOH group and can be useful as a buffer or for pH sensitive function

45
Q

What are the characteristics of basic amino acids?

A

Have many NH(s) and can be used as a buffer or for pH sensitive functions

46
Q

What enzyme catalyses peptide bond formations?

A

Peptidyl transferase

47
Q

What direction do peptide chains move in?

A

N-terminus to their C-terminus

48
Q

What are some characteristics of peptide bonds?

A

Have partial double bond character (electrons from N and C contribute to strength but aren’t part of covalent bond). Bonds are planar and strong and rigid (important for protein folding)

49
Q

What is the strength of an acid dependent on?

A

How readily it donates a proton to a base - measured by Ka

50
Q

What is pH?

A

-log[H], one change is pH = tenfold change on proton concentration

51
Q

What is pKa?

A

-log[Ka]

52
Q

What equation related pH to pKa?

A

Henderson-Hasselbalch. pH = pKa + log([A]/[HA]), where A is the (conjugate) base and HA is the acid

53
Q

What is a buffer?

A

A solution to control the pH of a reaction mixture

54
Q

What is the pH = when the concentration of the acid = the concentration of the conjugate base?

A

pKA

55
Q

What occurs close to a buffers pKa?

A

The pH remains relatively unchanged in response to the addition of a base to an acid

56
Q

In neutral solutions, what do amino acids without side ions exist as?

A

Zwitterions (with no net charge) - that contain two titratable groups

57
Q

What is the pH at which a molecule has no net charge?

A

Isoelectric point

58
Q

Why can proteins act in different ways as pH varies?

A

Uncharged amino acids have 2 titratable groups = 2 pKa values.

59
Q

What is a protein’s primary structure?

A

The sequence of amino acids

60
Q

What is a protein’s secondary structure?

A

The localised shape of the polypeptide

61
Q

What is a protein’s tertiary structure?

A

The 3D structure of the entire polypeptide, including all of its side chains

62
Q

What is a protein’s quaternary structure?

A

Multiple subunits of polypeptide chains all joined together

63
Q

Where do polypeptide chains rotate between?

A

The a carbon and the amino group AND the a carbon and the carboxyl group

64
Q

What are the 3 types of bonding in the backbone of a polypeptide chain? (Hint; secondary structure)

A

Alpha helix, beta strands and sheets, and triple helix

65
Q

What are alpha helices’ main characteristics?

A

Rod-like, one polypeptide chain, mostly right handed, the CO of one amino acid forms an H bond with the NH of an amino acid 4 residues away. (proline residues break a helices)

66
Q

What are beta sheets’ main characteristics?

A

Almost complete extension of the backbone (no folding), H bonds between CO and NH of neighbouring carbons. Amino acid side chains have little influence. Can be parallel or antiparallel, with turns between strands (glycine and proline). Have a repeated zigzag structure (beta pleated sheet)

67
Q

What tissues does collagen make up?

A

Bone and connective tissue - most abundant protein in vertebrates

68
Q

What are the main characteristics of the collagen triple helix?

A

Extremely strong, water-insoluble, three left handed chains twisted to form a right handed superhelix (tropocollagen), repeating X-Y-Gly in all strands where X=amino acid, Y=proline/ hydroxyproline, interchain H bonds (hydroxylysine and hydroxyproline), covalent inter and intra molecular bonds.

69
Q

Why is collagen important?

A

Influences the strength of connective tissue, and weakened collagen results in bleeding gums

70
Q

What are the 2 types of tertiary proteins?

A

Fibrous and globular

71
Q

What is the composition of fibrous proteins?

A

Contain polypeptide chains organised parallel along a single axis. Consist of long fibres (or large sheets), mechanically strong, insoluble in water and dilute salt solutions and are very structurally important. Eg keratin and collagen

72
Q

What is the composition of globular proteins?

A

Folded more or less in a spherical shape. Soluble in water and salt solution, most of their polar side chains face out and interact with aq environment through H bonds and ion dipole interactions. Non-polar side chains are buried inside and nearly all have large sections of alpha helices and beta sheets. Eg myoglobin and haemoglobin

73
Q

What different bond types are involved in tertiary protein structures?

A

Covalent disulphide bridges, salt bridges (electrostatic), hydrophobic interactions, hydrogen bonds (backbone and side chains), and complexes with metal ions

74
Q

How do disulphide bonds work?

A

They can be reduced (lose H) or oxidised (gain H) and so often act as redox centres. They can cause reversible changes in protein shape and so have reversible function

75
Q

How do electrostatic interactions work?

A

The +ve charges attract -ve charges, whilst similar charges repulse each other. Charged side groups (polar) are usually on the outside of proteins

76
Q

How do hydrophobic interactions work?

A

Water forms H bonds with other water molecules, weaker attraction between water and hydrocarbon, weaker attraction again between hydrocarbon and hydrocarbon which causes a strong organising influence - the Hydrophobic Effect. Amino acids with hydrophobic side chains tend to be found at the centre of globular proteins.

77
Q

What physical conditions/ chemical agents will cause protein denaturation?

A

Heat (more vibrations), extremes of pH (electrostatic interactions interrupted), detergents/ urea/ guanidine hydrochloride (disrupt hydrophobic interactions) or thiol/ reducing agents (disrupt disulphide bonds)

MBChB Year 1 Principles Biochemistry (4 decks)

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