Macromolecules, Water, Acids and Bases Flashcards Preview

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Flashcards in Macromolecules, Water, Acids and Bases Deck (25)
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1

Describe the molecular hierarchy of the 4 main macromolecules

- Macromolecules have three levels, monomer, polymer and cell structure
- AA - polypeptide - protein filament - membrane (peptide)
- Nucleotide - DNA - chromatin / chromosome
- Monosaccharide - starch - starch granules (glycosidic)
- Fatty acid - triacly-glycerol - fat (ester)

2

Name and describe key functional groups

- Part of the structure of molecule however the structure of the group provide various functional properties
- Hydroxyl (OH)
- Amino (NH3)
- Acetyl (COO) - middle
- Carboxyl (COO) - end
- Methyl (CH3)
- Ketone (CO) - middle
- Aldehydes (CO) - end

3

What is the relationship between structure and function of molecules

- Structure determines function and can influence how receptors interact with cells
- Interaction between molecules is specific

4

What is the difference between stereo and geometric (cis / trans) isomers

- Stereo: Different chemical structure, different physical properties
- Geometric: Same chemical structure, different physical and chemical properties, cis (same side, kink) and trans (different sides, straight)

5

What is biochemistry

- Chemistry of living matter
- Basis of all life is chemical reactions that take place within the cell
- Initiation and acceleration of reactions
- Organisation and specificity of metabolism
- Signalling, storage and transfer of information / energy

6

What is the role of water and H bonds in human systems

- Water can serve as both H donor and acceptor
- H bonds give water anomalously high BP and MP
- Large surface tension
- Source of unique properties

7

What is the biological importance and relevance of H bonds

- Strong dipole-dipole interactions
- Arise between a covalently bound H and lone pair of e
- Involve two electronegative atoms
- Strongest when bonded molecules allow for linear bonding patterns
- Source of unique properties of water, S / F of proteins, DNA and polysaccharides
- Binding of hormones to receptors and substrates to enzymes
- Matching of mRNA and tRNA

8

List and describe the 4 main non-covalent bonds and their role in biological systems

- Non-Covalent: No sharing electrons, exchange
- Ionic: Electrostatic attraction between charged ions or ion and dipole, ataractic / repulsive
- H: Electrostatic attraction between uncharged polar or neutral groups
- Van der Waals: Weak but complementary interaction between all atoms, attractive (longer) and repulsive (shorter),
- Hydrophobic: Non-polar molecules in aqueous solution (polar), avoidance

9

What is ionisation

- Ionisation is when an atom or molecule gains either a positive or negative charge

10

What is equilibrium, pH and associated constants

- Equilibrium: Relationship between concentrations of participating species in an equilibrium process
- pH: The negative logarithm of the hydrogen ion concentration (pH = -log[H+])
- Ka: Determines the extent of dissociation of weak electrolytes, we can calculate the pH if the Ka is known
- pKa: Measures acidity (-log Ka), low (strong, fully dissociates) and high (weak)

11

What is the importance of buffers (pH)

- Buffers: Resist change in pH, at pH = pKa, there is a 50:50 mixture of acid and anion forms of compound
- Buffering Capacity: Of an acid/anion system is greatest at pH = pKa, capacity is lost when the pH differs from pKa by more than 1 pH unit

12

What are biological buffer systems

- Intracellular pH: Enzyme-catalysed reactions have optimal pH, solubility of polar molecules depends on H-bond donors and acceptors, equilibrium between CO2 gas and dissolved HCO3– depends on pH
- Blood Buffer: Resists decreasing pH (high H) through carbonic anhydrase, facilitates production of H2O and CO2 from HCO3 + H

13

What is the structure and function of fats / FA

- Structurally diverse, organic
- Low solubility in water (hydrophobic), glycerol or sphingosine backbone, ester linkages (glycerol and FA)
- Storage of energy, insulation, water repellent
- Either contain (complex) or don't contain FA
- Fatty Acids: Carboxylic acids with hydrocarbon chains containing 4-36 C, saturated, monounsaturated, polyunsaturated
- Undergo oxidation to produce energy / ATP

14

What is the structure and function of proteins / peptides

- Linear hetero-polymers of alpha amino acids
- Involved in catalysis (polymerase), transport (Hg), structure (collagen) and motion (actin / myosin)
- 3D conformation, native fold = protein is functional
- AA polymerise to form peptides, condensation product
- Peptides consist of AA, cofactors (non AA), co enzymes (organic) and prosthetic groups (non protein)

15

What is the basic structure of an amino acid

- Linear hetero-polymers, a carbon has 4 substituents, tetrahedral, all chiral (except glycine)
- Peptide bonds
- All (except proline) have acidic carboxyl (COO), basic amino (NH3), alpha hydrogen and R substituent (unique)
- Well suited to carry out varies of functions
- 5 basic groups, non polar / aliphatic (7), aromatic (5), polar / uncharged (5), positively charged (3) and negatively charged (2)

16

How do amino acids act as buffers

- Ionisable Proteins: Amino acids contain at least two ionisable protons each with its own pKa
- COOH: Acidic pKa, protonated at low pH
- NH3: Basic pKa, protonated at high pH
- Low pH: Amino acid exists in positively charged form (cation), carboxyl / amino groups are protonated
- High pH: Amino acid exists in negatively charged form (anion), carboxyl / amino groups are deprotonated

17

What are the 4 levels of protein structure

- Primary: AA linked by peptide bonds, includes disulphide bonds, cannot rotate, resonance, less reactive, almost planar
- Secondary: Local spacial arrangement, a helices (H bonds of backbone and every 4th AA), b sheets (H bonds of backbone and amides in different strands, parallel / antiparallel)
- Tertiary: Overall spatial arrangement, weak interaction between side chains (hydrophobic / polar / disulphide)
- Quaternary: Assembly of individual polypeptides into a large functional cluster, ribbon / surface contour model

18

How can proteins be separated / purified

- Chromatography: Separation of solutions, mobile and stationary phase, separated based on charge, size, affinity
- SDS PAGE: Separates proteins by molecular weight, SDS = -ve detergent, thus proteins have a uniform -ve charge, native shape doesn't matter, unfolds

19

What are the key principles of protein folding / denaturation

- Folding: Function depends on primary, secondary, tertiary and quaternary folds
- Fold to lowest energy fold in u secs, direction toward native structure is thermodynamically favourable
- Denaturation: Loss of integrity / structure and thus activity, changes in temp, pH, presence of chaotropic agents (disrupts H bonds of H2O)
- Mis-Folding: Promotes aggregation, basis of human diseases

20

How does proteolysis result in irreversible degradation of a protein

- Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids
- Hydrolysis of peptide bonds
- Irreversible post translational modification

21

What is the structure and function of carbohydrates and common ones

- Sugar
- Energy source / storage, structural component (cell wall), cell-cell signalling
- Glycosidic bonds
- Ribose (5), glucose (6), galactose / mannose (epimers of glucose), fructose (ketose of glucose)
- Disaccharide, polysaccharide (linear or branched)

22

How are carbohydrates stored in humans

- Glycogen
- Branched homo-polysaccharide of glucose
- Compact, more complex

23

What are the properties of water

- Dipolar, tetrahedral arrangement, H have localised partial +ve charges and O has a partial -ve charge
- Good solvent for charged polar substances (AA)
- Poor solvent for non-polar substances
- Able to dissolve salts by hydrating component ions

24

What is entropy and when does it change

- Entropy: Thermodynamic quantity, degree of randomness
- Increases as temperature increases and as a substance changes from solid to liquid to gas
- High Entropy: Thermodynamically favourable, flickering clusters of H2O molecules in bulk phase
- Low Entropy: Thermodynamically unfavourable, highly ordered H2O form ‘cages’ around hydrophobic alkyl chains

25

What is a zwitterion

- Predominate between pKa values of COOH (pK1) and NH3 (pK2)
- Single molecule has both +ve and -ve charge
- Isoelectric point is (pK1pK2)/2
- Net charge is 0, not soluble in water, does not migrate in electric field