Biochemistry I-IV Flashcards
Atoms
Protons - mass of 1, +ve
Neutrons - mass of 1, no charge
Electrons - negligible mass, -ve
Groups & Periods
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
Reactivity of Elements
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
Number of Electrons (Orbitals)
Outermost orbital unfilled –> REACTIVE
Outermost orbital filled –> STABLE
Covalent bonds
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
Ionic Bonds
Attraction of opposite charge
Low bond energy
Hydrogen bonds
Sharing of H atom
- H-O, H-N, H-F
Low bond energy
Hydrophobic Interaction
Interavtion of non-polar substance in the presence of polar substances (i.e. water)
Low bond energy
Van der Waals interaction
Interaction of electrons of non-polar substances
Low bond energy
Carbon
Form covalent bonds with itself
Can form 4 covalent bonds (tetrahedral)
Can from bonds with Hydrogen, Nitrogen and Oxygen
Electronegativity
Attractive force that an atomic nucleus exerts on electrons
- O2 has the highest whereas Potassium has the lowest
Phosphorylation & De-phosphorylation
Addition or removal of a phosphate groups
Contains 2 negative charges
Acylation
Addition of a acyl group
Carboxylation
Addition of a carboxyl group
Esterification
Carboxylic Acid + Alcohol –> Ester + H2O
Condensation
Monomers combine to form a polymer
Water is a by-product
Hydrolysis
Polymer broken up into monomers (smaller units)
Water is used in this reaction
Oxidation
Loss of Electrons
AH –> A
AH = Reducing Agent/ Electron donor
Reduction
Gain of Electrons
B –> BH
B = Oxidising Agent/ Electron Acceptor
Redox Reactions
Electrons transferred from one molecule to another
Oxidation & Reduction
Oxidation States of Carbon
Alkane > Alcohol > Aldehyde > Carboxylic Acid > Carbon dioxide
Losing an electron in each state
Functional Groups
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-)
BREAK
Biomolecule Functions
Information storage - DNA
Structural - Teeth/bones/cartilage
Energy Generation - glycolysis, TCA cycle, ETC
Energy Currency - ATP
Communication - receptors, hormones, enzymes
Major Classes of Biomolecules
Peptides and Proteins - made of amino acids
Lipids - Triglycerides, phospholipids, steroids
Nucleic Acids - DNA/RNA
Carbohydrates - mono/di/polysaccharides
Thermodynamics
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
Enthalpy
Change in enthalpy (H)
Entropy
Randomness, Disorder
(S)
Free Energy (G)
ΔG = ΔH – TΔS
ΔG = (energy of products) - (energy of reactants)
Exergonic Reactions
Total free energy of product less than total free energy of reactant
NEGATIVE
Such reactions can occur spontaneously
Endergonic Reactions
Total free energy of product more than total free energy of reactant
POSITIVE
Such reactions cannot occur spontenously
Need energy input
How to determine ΔG for a given reaction
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
Chemical Reactions run to equilibrium
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.
Equilibrium Constant (Keq)
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
Combining Exergonic and Endergonic Reactions
One process will be negative (favourable reaction) and the other positive (unfavourable reaction)
ATP
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
Metabolism
All reactions taking place in the body
Catabolism + Anabolism = Metabolsim
Catabolism
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)
Anabolism
Synthesis of complex molecules from smaller molecules
Consumes energy
I.e. Gluconeogenesis
- Non-carbohydrate precursors luke pyruvate
Control Points in Metabolism
Reactions close to equilibirum (ΔG = 0) not used as control points
Large negative ΔG = useful control points
BREAK
Water
Polar - electrons shared unequally (electronegativity)
Dipole - bent
Ionic and polar substances dissolve in water - hydrophilic
Dipole interactions - ions and dipoles
Hydrogen bonding
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
Non-Polar Substances
Hydrophobic
Powerful attraction between water molecules
I.e. Hydrocarbons - non-polar/hydrophobic
Water tends to exclude hydrocarbons - oil
Amphipathic Molecules
Both hydrophilic and hydrophobic
Hydrophilic head
Hydrophobic tail
Micelles
Sodium palmitate
Cell Membranes - Components and Importance
Selective barrier
Lipid - structural (bilayer), precursors of signalling molecules (DAG, IP3)
Proteins - confer selectivity, involved in recognition
Amino Acids
20 different L-amino acids
a-carbon bonded to an amino group (NH2), carboxyl group (COOH), hydrogen (H), side chain (-R)
Non-polar hydrophobic amino acids
No charge
Found on interior of protein
Leucine
Proline
Alanine
Valine
Methionine
Tryptophan
Phenylalanine
Isoleucine
Polar, uncharged amino acids
These side chains can form multiple hydrogen bonds, so they prefer to project into the aqueous phase
Glycine
Serine
Asparagine
Glutamate
Threonine
Cysteine
Tyrosine
Acidic Amino Acids
Acidic side chains at neutral pH
Aspartic acid
Glutamic acid
Basic Amino Acids
Basic side chains at neutral pH
Lysine
Arginine
Histidine
Peptide Bond
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
Peptides
Chain of amino acids
N-terminal - amino group
C-terminal - carboxyl group
Acids and Bases
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
pH
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)
Henderson-Hasselbalch Equation
pH = pKa + log[A-]/[HA]
Allows calculation of properties of buffer solutions
Buffer
Solution to control pH of a reaction mixture
Concentration of acid = Concentration of Conjugate Base
pH = pKa
- Resist change of pH
Titration curves
pH as a function of base added to an acid
Close to pKa, the pH remains relatively unchanged in response to base addition
Amino acid acid-base properties
Zwitterions
- Amino acids without charged side group in neutral solution
- Contain two titratable groups
Isoelectric pH
pH at which a particular molecule carries no net electrical charge
Acid-base properties of proteins
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
BREAK
Primary Structure
Sequence of amino acid sequence
Secondary structure
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
Tertiary structure
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
Quaternary structure
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)
Rotational Angles in Polypeptides
Polypeptides can rotate around the angles between the alpha carbon and the amino groups, and, the alpha carbon and the carboxyl group
Collagen
- Influences strength of CT
- Weakened collagen results in bleeding gums
- Covalent crosslinking increases with age
Fibrous Proteins
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
Globular proteins
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
Disulphide bonds
Sulphur containing side chains
Electrostatic interactions in proteins
Positive charges attract negative charges
Salt bridges
Repulsion between similar charges
Charged polar side groups are normally located on outside of protein
Hydrophobic interactions in proteins
- 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
Amino acid substitution and protein structure
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
Folding polypeptide chains
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
Disrupting protein structure
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
