Biochemistry I-IV Flashcards

Question

Major Classes of Biomolecules

Answer 1

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

Answer 2

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

Answer 3

Change in enthalpy (H)

Answer 4

Randomness, Disorder (S)

Answer 5

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

Answer 6

Total free energy of product less than total free energy of reactant NEGATIVE Such reactions can occur spontaneously

Answer 7

Total free energy of product more than total free energy of reactant POSITIVE Such reactions cannot occur spontenously Need energy input

Answer 8

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

Answer 9

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.

Answer 10

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

Answer 11

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

Answer 12

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

Answer 13

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

Answer 14

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)

Answer 15

Synthesis of complex molecules from smaller molecules Consumes energy I.e. Gluconeogenesis - Non-carbohydrate precursors luke pyruvate

Answer 16

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

Answer 17

Polar - electrons shared unequally (electronegativity) Dipole - bent Ionic and polar substances dissolve in water - hydrophilic Dipole interactions - ions and dipoles

Answer 18

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

Answer 19

Hydrophobic Powerful attraction between water molecules I.e. Hydrocarbons - non-polar/hydrophobic Water tends to exclude hydrocarbons - oil

Answer 20

Both hydrophilic and hydrophobic Hydrophilic head Hydrophobic tail Micelles Sodium palmitate

Answer 21

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

Answer 22

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

Answer 23

No charge Found on interior of protein Leucine Proline Alanine Valine Methionine Tryptophan Phenylalanine Isoleucine

Answer 24

These side chains can form multiple hydrogen bonds, so they prefer to project into the aqueous phase Glycine Serine Asparagine Glutamate Threonine Cysteine Tyrosine

Answer 25

Acidic side chains at neutral pH Aspartic acid Glutamic acid

Answer 26

Basic side chains at neutral pH Lysine Arginine Histidine

Answer 27

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

Answer 28

Chain of amino acids N-terminal - amino group C-terminal - carboxyl group

Answer 29

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

Answer 30

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)

Answer 31

pH = pKa + log[A-]/[HA] Allows calculation of properties of buffer solutions

Answer 32

Solution to control pH of a reaction mixture Concentration of acid = Concentration of Conjugate Base pH = pKa - Resist change of pH

Answer 33

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

Answer 34

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

Answer 35

pH at which a particular molecule carries no net electrical charge

Answer 36

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

Answer 37

Sequence of amino acid sequence

Answer 38

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

Answer 39

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

Answer 40

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)

Answer 41

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

Answer 42

- Influences strength of CT - Weakened collagen results in bleeding gums - Covalent crosslinking increases with age

Answer 43

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

Answer 44

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

Answer 45

Sulphur containing side chains

Answer 46

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

Answer 47

- 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

Answer 48

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

Answer 49

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

Answer 50

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

Biochemistry I-IV Flashcards

(76 cards)