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Foundation of Medicine 1 > Biochemistry I-IV > Flashcards

Biochemistry I-IV Flashcards

1
Q

Atoms

A

Protons - mass of 1, +ve
Neutrons - mass of 1, no charge
Electrons - negligible mass, -ve

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2
Q

Groups & Periods

A

Groups = Down
- Shared chemical properties
- Increasing electron orbitals
- Increasing electrons that can be lost/gained/shared

Periods = Along
- Same number of electron shells
- 1-7, increase in electron shells

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3
Q

Reactivity of Elements

A

Ionisation Energy - energy input needed to discharge an electron
- Increases from Left to Right
- Increases from periods 7 to 1

Electron affinity - energy released when electron is attached to neutral atom
- Same as ionisation energy trends

Atomic radius - distance from nucleus to outer orbital

Metal Character - malieable, conduct heat, electricity
- More metal at bottom left of transition metals and less metal at helium

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4
Q

Number of Electrons (Orbitals)

A

Outermost orbital unfilled –> REACTIVE
Outermost orbital filled –> STABLE

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5
Q

Covalent bonds

A

E.g. H2
- Sharing electron pairs to fill each others orbitals

High bond energy
DIfferent number of bonds due to number of reactive electrons in outer shell

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6
Q

Ionic Bonds

A

Attraction of opposite charge
Low bond energy

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7
Q

Hydrogen bonds

A

Sharing of H atom
- H-O, H-N, H-F
Low bond energy

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8
Q

Hydrophobic Interaction

A

Interavtion of non-polar substance in the presence of polar substances (i.e. water)
Low bond energy

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9
Q

Van der Waals interaction

A

Interaction of electrons of non-polar substances
Low bond energy

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10
Q

Carbon

A

Form covalent bonds with itself
Can form 4 covalent bonds (tetrahedral)
Can from bonds with Hydrogen, Nitrogen and Oxygen

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11
Q

Electronegativity

A

Attractive force that an atomic nucleus exerts on electrons
- O2 has the highest whereas Potassium has the lowest

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12
Q

Phosphorylation & De-phosphorylation

A

Addition or removal of a phosphate groups
Contains 2 negative charges

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13
Q

Acylation

A

Addition of a acyl group

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14
Q

Carboxylation

A

Addition of a carboxyl group

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15
Q

Esterification

A

Carboxylic Acid + Alcohol –> Ester + H2O

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16
Q

Condensation

A

Monomers combine to form a polymer
Water is a by-product

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17
Q

Hydrolysis

A

Polymer broken up into monomers (smaller units)
Water is used in this reaction

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18
Q

Oxidation

A

Loss of Electrons

AH –> A
AH = Reducing Agent/ Electron donor

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19
Q

Reduction

A

Gain of Electrons

B –> BH
B = Oxidising Agent/ Electron Acceptor

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20
Q

Redox Reactions

A

Electrons transferred from one molecule to another
Oxidation & Reduction

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21
Q

Oxidation States of Carbon

A

Alkane > Alcohol > Aldehyde > Carboxylic Acid > Carbon dioxide

Losing an electron in each state

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22
Q

Functional Groups

A

Methyl groups –> CH3
Methylene groups –> CH2
Amino Group and Amides –> NH2 & O=C-NH2
Carboxyl groups and Esters –> COOH & COO
Carbonyl groups and aldehydes –> C=O
Phosphates –> PO4(3-)

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23
Q

BREAK

A
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24
Q

Biomolecule Functions

A

Information storage - DNA
Structural - Teeth/bones/cartilage
Energy Generation - glycolysis, TCA cycle, ETC
Energy Currency - ATP
Communication - receptors, hormones, enzymes

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25
Q

Major Classes of Biomolecules

A

Peptides and Proteins - made of amino acids
Lipids - Triglycerides, phospholipids, steroids
Nucleic Acids - DNA/RNA
Carbohydrates - mono/di/polysaccharides

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26
Q

Thermodynamics

A

First Law - Energy is neither created nor destroyed
Second Law - Energy converted from one form to another, some of that energy becomes unavailable to do work

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27
Q

Enthalpy

A

Change in enthalpy (H)

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28
Q

Entropy

A

Randomness, Disorder
(S)

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29
Q

Free Energy (G)

A

ΔG = ΔH – TΔS
ΔG = (energy of products) - (energy of reactants)

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30
Q

Exergonic Reactions

A

Total free energy of product less than total free energy of reactant

NEGATIVE

Such reactions can occur spontaneously

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31
Q

Endergonic Reactions

A

Total free energy of product more than total free energy of reactant

POSITIVE

Such reactions cannot occur spontenously

Need energy input

32
Q

How to determine ΔG for a given reaction

A

ΔG = ΔGo’ + RTln([C][D]/[A][B])

R = 8.3 jK-1mol-1
T = Absolute Temp
Unit = kJ/mol

ΔGo’ = change in free energy under standard conditions

33
Q

Chemical Reactions run to equilibrium

A

ΔG is related to the point of equilibrium: The further towards completion the point of equilibrium is, the more free energy is released
ΔG values near zero are characteristic of readily reversible reactions.

34
Q

Equilibrium Constant (Keq)

A

The ratio between the amount of reactant and the amount of product which is used to determine chemical behaviour

> 1 = More products
<1 = More reactants

At equilibrium –> ΔG = 0

35
Q

Combining Exergonic and Endergonic Reactions

A

One process will be negative (favourable reaction) and the other positive (unfavourable reaction)

36
Q

ATP

A

ATP production is negative (-30 kJ/mol)

Structure
- ATP less stable than ADP due to electrostatic repulsion
- Repulsion relieved by removing phosphate groups

ATP constantly regenerated - i.e. creatine phosphate, 2ADP

37
Q

Metabolism

A

All reactions taking place in the body
Catabolism + Anabolism = Metabolsim

38
Q

Catabolism

A

Breaking down complex molecules into smaller molecules
Releases energy

Some process that are energy consuming are catabolic - i.e. glycolysis (uses 2 ATP to break down glucose to produce 4 ATP)

39
Q

Anabolism

A

Synthesis of complex molecules from smaller molecules
Consumes energy

I.e. Gluconeogenesis
- Non-carbohydrate precursors luke pyruvate

40
Q

Control Points in Metabolism

A

Reactions close to equilibirum (ΔG = 0) not used as control points

Large negative ΔG = useful control points

41
Q

BREAK

A
42
Q

Water

A

Polar - electrons shared unequally (electronegativity)
Dipole - bent

Ionic and polar substances dissolve in water - hydrophilic
Dipole interactions - ions and dipoles

43
Q

Hydrogen bonding

A

Covalent bond between H and more electronegative atom (i.e. O, F, N)
Interact with unshared electrons from another electronegative atom
Bonds tend to be linear

44
Q

Non-Polar Substances

A

Hydrophobic
Powerful attraction between water molecules
I.e. Hydrocarbons - non-polar/hydrophobic

Water tends to exclude hydrocarbons - oil

45
Q

Amphipathic Molecules

A

Both hydrophilic and hydrophobic
Hydrophilic head
Hydrophobic tail

Micelles
Sodium palmitate

46
Q

Cell Membranes - Components and Importance

A

Selective barrier
Lipid - structural (bilayer), precursors of signalling molecules (DAG, IP3)
Proteins - confer selectivity, involved in recognition

47
Q

Amino Acids

A

20 different L-amino acids

a-carbon bonded to an amino group (NH2), carboxyl group (COOH), hydrogen (H), side chain (-R)

48
Q

Non-polar hydrophobic amino acids

A

No charge
Found on interior of protein

Leucine
Proline
Alanine
Valine
Methionine
Tryptophan
Phenylalanine
Isoleucine

49
Q

Polar, uncharged amino acids

A

These side chains can form multiple hydrogen bonds, so they prefer to project into the aqueous phase

Glycine
Serine
Asparagine
Glutamate
Threonine
Cysteine
Tyrosine

50
Q

Acidic Amino Acids

A

Acidic side chains at neutral pH

Aspartic acid
Glutamic acid

51
Q

Basic Amino Acids

A

Basic side chains at neutral pH

Lysine
Arginine
Histidine

52
Q

Peptide Bond

A

Carboxyl group of one amino acid and the amino group of another amino acid
Removal of H2O
CO-NH

Resonance structures
- Partial double bond character
- The stability of the peptide bond is due to the resonance of amides. With resonance, the nitrogen is able to donate its lone pair of electrons to the carboxyl carbon and push electrons from the carboxyl double bond towards the oxygen, forming the oxygen anion
- Planar
- Strong and rigid

53
Q

Peptides

A

Chain of amino acids

N-terminal - amino group
C-terminal - carboxyl group

54
Q

Acids and Bases

A

Acids = proton donors
Conjugate Acid = formed when a proton is added to a base

Bases = proton acceptors
Conjugate Base = formed when a proton is removed from an acid

Dissociation constant Ka = a measure of the extent to which an acid dissociates in solution and therefore its strength

Ka = [H+][A-]/[HA]

Strong acid = High Ka, Low pKa
Weak acid = Low Ka, High pKa

55
Q

pH

A

Concentration of protons in a solution (H+)
pH = -log10[H+]
pKa = -log10[Ka]

Water
- [H+] = 10-7 mol/L = pH 7

pH = 7 (neutral)
pH < 7 (acidic)
pH >7 (base)

56
Q

Henderson-Hasselbalch Equation

A

pH = pKa + log[A-]/[HA]

Allows calculation of properties of buffer solutions

57
Q

Buffer

A

Solution to control pH of a reaction mixture

Concentration of acid = Concentration of Conjugate Base

pH = pKa
- Resist change of pH

58
Q

Titration curves

A

pH as a function of base added to an acid
Close to pKa, the pH remains relatively unchanged in response to base addition

59
Q

Amino acid acid-base properties

A

Zwitterions
- Amino acids without charged side group in neutral solution
- Contain two titratable groups

60
Q

Isoelectric pH

A

pH at which a particular molecule carries no net electrical charge

61
Q

Acid-base properties of proteins

A

Ends of proteins can be ionised
Several amino acid side chains can be ionised
Proteins can act as buffers
A change in pH can change ionisation of a protein

62
Q

BREAK

A
63
Q

Primary Structure

A

Sequence of amino acid sequence

64
Q

Secondary structure

A

Localised conformation of the polypeptide backbone

Hydrogen-bonded 3D arrangements of a polypeptide chain

Alpha Helix - rod-like, one polypeptide chain, mostly right-handed, -C-O of one amino acid forms a hydrogen bond with the N-H group of an amino acid 4 residues away
Proline - amino group has no free hydrogen to bond with a carbonyl because of the imino ring

Beta strands
- Polypeptide backbone almost completely extended
- More than 1 chain
- Parallel & Antiparallel
- Turns between strands (Gly, Pro)
Beta sheets
- Repeated zigzag structures - beta pleated sheet

Triple Helix
- Collagen triple helix
- Water-soluble fibres
- 3 LHS helical chains twist around to form a RHS helix
- Tropocollagen- repeating X-Y-Gly in all strands
- Inter-chain H-bonds
- Covalent inter- and intra-molecular bonds

65
Q

Tertiary structure

A

3D structure of an entire polypeptide including side chains

Arrangement of all atoms of a polypeptide in space
Consists of local regions with distinct secondary structure

Forces stabilising tertiary structures
- Covalent disulphide bonds
Electrostatic interactions
Hydrophobic interactions
Hydrogen bonds (backbone, side chain)
Complex formation with metal ion

66
Q

Quaternary structure

A

Spatial arrangement of polypeptide chains in a protein with multiple subunits

E.g. Haemoglobin (Hb)
- 4 subunits (2 alpha, 2 beta)
- Each subunit bind one oxygen molecule (binding of one oxygen changes affinity of other subunits)

67
Q

Rotational Angles in Polypeptides

A

Polypeptides can rotate around the angles between the alpha carbon and the amino groups, and, the alpha carbon and the carboxyl group

68
Q

Collagen

A
  • Influences strength of CT
  • Weakened collagen results in bleeding gums
  • Covalent crosslinking increases with age
69
Q

Fibrous Proteins

A

Contain polypeptide chains organised approximately parallel along a single axis
- Consist long fibers or large sheets
- Mechanically strong
- Insoluble in water and dilute salt solutions
- Important structural roles

70
Q

Globular proteins

A

Proteins which are folded to a more or less spherical shape
- Soluble in water and salt solution
- Most polar side chains outside and interact with aqueous environment by hydrogen bonding and ion-dipole interactions
- Most non-polar side chains are inside
- Nearly all have substantial sections of alpha-helix and beta-sheet

71
Q

Disulphide bonds

A

Sulphur containing side chains

72
Q

Electrostatic interactions in proteins

A

Positive charges attract negative charges
Salt bridges
Repulsion between similar charges
Charged polar side groups are normally located on outside of protein

73
Q

Hydrophobic interactions in proteins

A
  • Water forms H-bonds with other water molecules
  • Weaker attraction between water and hydrocarbon
  • Weaker attraction between hydrocarbon and hydrocarbon (Van der Waals)
  • Hydrophobic effect
  • Amino acids with hydrophobic side-chains tend to cluster in centre of globular proteins
74
Q

Amino acid substitution and protein structure

A

Glutamic acid to Valine
- Negatively charged (can form ionic bonds/hydrogen bonds with water or other amino acid side chains)
- Hydrophobic (interacts with other hydrophobic amino acids)

Functional changes

E.g. Sickle Cell Anaemia

75
Q

Folding polypeptide chains

A

Primary structure of a protein contains all the info needed for its 3D shape
Proteins may fold spontaneously into their correct shape
Can be slow and erroneous - may begin to fold incorrectly before completely synthesised, may associate with other proteins before its fold properly)
Sometimes folding process is aided by other specialised proteins -chaperones

76
Q

Disrupting protein structure

A

Denaturation
Heat - increase in vibrations ina protein
Extremes of pH - electrostatic interactions interrupted
Detergents, urea, guanidine hydrochloride - disrupt hydrophobic interactions
Thiol agents, reducing agents - reduce and thereby disrupt disulphide bonds

Foundation of Medicine 1 (39 decks)

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