Biochemistry Flashcards
Features of Protons
Positive charge
Mass of +1
Features of Electrons
Negative charge
Negligible mass
Features of Neutrons:
No charge
Mass of 1
Covelant bond:
Formed when unpaired electrons are shared
Strongest type
Ionic bonds
Attraction to opposite charges
Hydrogen bonds:
Sharing of H atoms
Hydrophobic interaction
Interaction of non-polar substances in the presence of polar substances (e.g. water)
Van der waals interaction
Interaction of electrons of non-polar substances
Electronegativity:
Attractive force that an atomic nucleus exerts on electrons within a bond
Phosphorylation and de-phosphorylation:
addition or removal of a phosphoryl group
Acylation reaction:
Addition of an acyl group
Relatively stable, useful for joining molecules
Carboxylation
Addition of a carboxyl group
Usually occurs at the end of a molecule
What is the end of a molecule referred to as?
Reaction centre
Esterification
Occurs between acid and alcohol group, producing an ester bond
Water is released
Condensation reaction:
Water is removed
Molecules polymerize
Hydrolysis:
Water is added, molecules depolymerize
Oxidation-reduction reactions (redox):
Electrons transferred from one molecule to another
As one molecule is oxidised, another is reduced
Oxidation and reduction:
Oxidation: Loss of electrons
Reduction: Gain of electrons
Oxidation and reduction:
Oxidation: Loss of electrons
Reduction: Gain of electrons
Oxidation states of carbon:
Vary depending on structure of molecule and electronegativity differences
Charge imbalances help form reactive groups on biological molecules
Monosaccharides:
Carbohydrates with a single ring structure
Disaccharides
Carbohydrates with a double ring structure
Polysaccharides:
Long chains of monosaccharides, storage carbohydrates
E.g. Branching of glycogen enables fast metabolism of glucose
1st law of thermodynamics:
Energy is neither created or deystroyed
2nd law of thermodynamics:
When energy is converted from one form to another, some of that energy becomes unavailable to do work
No energy transformation is 100% efficient
Thermodynamics reactions are reactions involved in change in:
Enthalpy (heat content)
Entropy (randomness/disorder)
Change in free energy:
(energy of products) – (energy of reactants)
𝝙G = 𝝙H - T 𝝙S
What does 𝝙G near 0 mean?
Reaction is readily reversible
Exergonic
Total free energy of products is less than total free energy of reactants
Reactions can occur spontaneously
Endergonic reactions
Total free energy of products is more than total free energy of reactants
Reactions require input of energy
Coupling of reactions:
Many reactions within the body occur by coupling an unfavorable reaction (positive 𝝙G) with a favorable reaction
e.g. ATP + H2O → ADP + Pi + H+
Therefore, ATP is widely used as energy for many cellular processes
Metabolism
All reactions taking place in the body
Catabolism:
Breaking down complex molecules into smaller ones and releasing energy
Yields energy - exergonic and oxidative
Anabolism
Synthesizing complex molecules out of smaller ones in energy-consuming reactions
Requires energy - endergonic and reductive
Polar property of water:
Electrons shared unequally causing a difference in change from one side of the molecule to the other
Enables water to act as a universal solvent
Shape of water:
Tetrahedral
Molecules form a dipole
How are water molecules held together?
H bonds
Hydrophobic effect:
When non-polar substances aggregate in aqueous solution and exclude water molecules
E.g. micelles, lipid bilayer, ‘oil slick’
Amphipathic molecules:
Moelcules with a polar (hydrophilic) ‘head’ and a non-polar (hydrophobic) tail
Form micelles and lipid bilayer of membranes
What is a side chain represented by?
-R
What is an amino group represented by?
-NH2
Classifications of amino acids:
- Non-polar, hydrophobic
- Polar, hydrophilic
- Acidic
- Basic
Peptide bonds:
Join amino acids
Produced by condensation reaction
Important for folding proteins
What is a base?
Proton acceptor
What is an acid?
Proton donator
Strength depends on how readily it donates proton to base
How is acid strength measured?
By the acid dissociation constant Ka:
- Ka = [H+][A-]/[HA]
- pKa = -log10[Ka]
What is pH and its equation?
The measurement of the number of protons in a solution
pH = -log10[H+]
What is the Henderson-Hasselbalch equation?
Connects the Ka of a weak acid with the pH of a solution containing this acid
pH = pKa + log[A]/[HA]
What is a buffer?
A solution used to control the pH of a reaction mixture
When does pH=pKa?
When the concentration of acid is equal to the concentration of the conjugate base
Buffer at pKa value…
Resist a change in pH on addition of moderate amounts of acid or base
How can change in pH affect proteins?
Change the ionisation of protein, therefore change its structure and function
Primary protein structure:
The sequence of amino acid residues
Secondary protein structure:
Localised conformation of the polypeptide backbone
Hydrogen bonded
What are the 3 types of secondary protein structure?
- ⍺ helix
- β sheet
- Triple helix
Tertiary protein structure:
3D structure of entire polypeptide
Structure and solubility of tertiary fibrous proteins:
- Mechanically strong e.g. collagen
- Polypeptide chains are parallel and single axis
- Insoluble in water
Shape and solubility of tertiary globular proteins:
- Spherical e.g. haemoglobin
- Soluble in water and salt solutions
Quaternary protein structure:
The spatial arrangement of polypeptide chains in a protein with multiple subunits
E.g. haemoglobin and tropocollagen
Haemoglobin structure and function:
4 subunits - 2 ⍺ and 2 β chains
Each subunit contains 1 haem group - binds to oxygen
Binding of 1 oxygen changes the affinity of other subunits
Tropocollagen structure and function:
Structural unit of a collagen fibre
Three helical chains twisted around each other to form a right-handed superhelix
Contains interchain H-bonds and intermolecular covalent bonds
