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HLTH2210 > Macromolecules, Water, Acids and Bases > Flashcards

Macromolecules, Water, Acids and Bases Flashcards

1
Q

Describe the molecular hierarchy of the 4 main macromolecules

A
  • 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)
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2
Q

Name and describe key functional groups

A
  • 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
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3
Q

What is the relationship between structure and function of molecules

A
  • Structure determines function and can influence how receptors interact with cells
  • Interaction between molecules is specific
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4
Q

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

A
  • 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)
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5
Q

What is biochemistry

A
  • 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
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6
Q

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

A
  • 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
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7
Q

What is the biological importance and relevance of H bonds

A
  • 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
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8
Q

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

A
  • 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
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9
Q

What is ionisation

A
  • Ionisation is when an atom or molecule gains either a positive or negative charge
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10
Q

What is equilibrium, pH and associated constants

A
  • 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)
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11
Q

What is the importance of buffers (pH)

A
  • 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
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12
Q

What are biological buffer systems

A
  • 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
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13
Q

What is the structure and function of fats / FA

A
  • 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 containing4-36 C, saturated, monounsaturated, polyunsaturated
  • Undergo oxidation to produce energy / ATP
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14
Q

What is the structure and function of proteins / peptides

A
  • 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)
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15
Q

What is the basic structure of an amino acid

A
  • 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)
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16
Q

How do amino acids act as buffers

A
  • 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
Q

What are the 4 levels of protein structure

A
  • 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
Q

How can proteins be separated / purified

A
  • 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
Q

What are the key principles of protein folding / denaturation

A
  • 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
Q

How does proteolysis result in irreversible degradation of a protein

A
  • Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids
  • Hydrolysis of peptide bonds
  • Irreversible post translational modification
21
Q

What is the structure and function of carbohydrates and common ones

A
  • 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
Q

How are carbohydrates stored in humans

A
  • Glycogen
  • Branched homo-polysaccharide of glucose
  • Compact, more complex
23
Q

What are the properties of water

A
  • 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
Q

What is entropy and when does it change

A
  • 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
Q

What is a zwitterion

A
  • 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

HLTH2210 (9 decks)

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