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2 - foundations in bio > 2.1.2 - biological molecules > Flashcards

2.1.2 - biological molecules Flashcards

1
Q

how do hydrogen bonds form between water molecules?

A
  • oxygen is more electron-negative than hydrogen, so attracts electron density in covalent bonds more strongly
  • water is polar: O is 𝛿- and H is 𝛿+ (slightly charged)
  • there are intermolecular forces of attraction between a lone pair on O 𝛿- of one molecule of H 𝛿+ on an adjacent molecule
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2
Q

state 7 biologically important properties of water

A
  • reaches maximum density at 4°C
  • high surface tension
  • incompressible
  • metabolite/solvent for chemical reactions in the body
  • high specific heat capacity
  • high latent heat of vaporisation
  • cohesion between molecules
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3
Q

why is the incompressible nature of water important for organisms?

A
  • provides turgidity to plant cells
  • provides hydrostatic skeleton (supported by fluid pressure) for some small animals e.g. earthworms
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4
Q

explain why ice floats on water, why is this important for organisms?

A
  • ice is less dense than water because H-bonds hold molecules in fixed positions further away from each other
  • insulates water in arctic climates so aquatic organisms can survive; water can act as a habitat
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5
Q

why is the high surface tension of water important for organisms?

A
  • slows water loss due to transpiration in plants
  • water rises unusually high in narrow tubes, lowering demand on root pressure
  • some insects can ‘skim’ across the surface of water
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6
Q

why is water an important solvent for organisms? give an example

A
  • polar universal solvent dissolves and transports charged particles involved in intra and extracellular reactions
  • e.g. PO4^3- for DNA synthesis
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7
Q

why are the high specific heat capacity and latent of vapourisation of water important for organisms?

A
  • acts as a temperature buffer which enables endotherms (animals reliant on/capable of internal generation of heat) to resist fluctuations in core temperature to maintain optimum enzyme activity
  • cooling effect when water evaporates from skin surface as sweat/from mouth when panting
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8
Q

define ‘monomer’ and give examples

A
  • smaller units that can join together to form larger molecules
  • monosaccharides: e.g. glucose, fructose, galactose, ribose
  • amino acids
  • nucleotides
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9
Q

define ‘polymer’ and give some examples

A
  • molecules formed when many monomers join together
  • polysaccharides: starch, glycogen, cellulose
  • proteins
  • DNA/RNA
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10
Q

what happens in condensation reactions?

A

chemical bond forms between 2 molecules and a molecule of water is produced

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11
Q

what happens in hydrolysis reactions?

A

a water molecule is used to break a chemical bond between 2 molecules, e.g peptide bonds in proteins or glycerol in lipids

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12
Q

name the elements found in carbohydrates and lipids

A

C, H, O

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13
Q

name the elements found in proteins

A

C, H, O, N, S

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14
Q

name the elements found in nucleic acids

A

C, H, O, N, P

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15
Q

draw the structure of a-glucose and b-glucose

A
  • (refer to flashcard drawing)
  • both hexose monosaccharides (6C) with ring structure
  • H above and OH below on alpha, opposite on beta
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16
Q

describe and explain the properties of a-glucose

A
  • small and water soluble = easily transported in bloodstream
  • complementary shape to antiport (intrinsic protein that transports substances in opposite direction to concentration gradient) for co-transport = for absorption in the gut
  • complementary shape to enzymes for glycolysis = respiratory substrate
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17
Q

draw the structure of ribose

A
  • (refer to flashcard drawing)
  • pentose monosaccharide (5C)
  • ring structure
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18
Q

what type of bond forms when monosaccharides react?

A
  • 1,4 or 1,6 glycosidic bond
  • 2 monomers = 1 chemical bond = disaccharide
  • multiple monomers = many chemical bonds = polysaccharide
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19
Q

name 3 disaccharides and describe how they form

A
  • maltose: glucose + glucose
  • sucrose: glucose + fructose
  • lactose: glucose + galactose
    ^ all have molecular formula C12H22O11
    ^ condensation reaction forms glycosidic bond between 2 monosaccharides
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20
Q

describe the structure and functions of starch

A
  • storage polymer of a-glucose in plant cells: large so does not diffuse out of cells, insoluble so no osmotic effect
  • made from amylose: 1,4 glycosidic bonds, helix with intermolecular H-bonds = compact
  • also made from amylopectin: 1,4 and 1,6 glycosidic bonds, branched = many terminal ends for hydrolysis into glucose
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21
Q

describe the structure and functions of glycogen

A
  • main storage polymer of a-glucose in animal cells (but also found in plant)
  • 1,4 and 1,6 glycosidic bonds
  • branched = many terminal ends for hydrolysis
  • insoluble = no osmotic effect and does not diffuse out of cells
  • compact
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22
Q

describe the structure and functions of cellulose

A
  • polymer of b-glucose gives rigidity to plant cell walls (prevents bursting under turgor pressure, holds stem up)
  • 1,4 glycosidic bonds
  • straight chain, unbranched molecule
  • alternate glucose molecules are rotated 180°
  • H-bond crosslinks between parallel strands form microfibrils = high tensile strength (maximum stress that a material can handle before breaking)
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23
Q

how do triglycerides form? draw and explain

A
  • (refer to flashcard drawing)
  • condensation reaction between 1 molecule of glycerol and 3 fatty acids which forms ester bonds
24
Q

compare saturated and unsaturated fatty acids

A

saturated:
- contain only single bonds
- straight chain molecules: many contact points
- higher melting point = solid at room temp.
- found in animal fats
unsaturated:
- contain C=C double bonds
- ‘kinked’/bent chain molecules: fewer contact points
- lower melting point = liquid at room temp.
- found in plant oils

25
Q

relate the structure of triglycerides to their function

A
  • insoluble hydrocarbon chain = no effect on water potential of cells + can be used for waterproofing
  • less dense than water = buoyancy of aquatic animals
  • slow conductor of heat = thermal insulation (e.g. adipose tissue)
  • high energy:mass ratio = high calorific value from oxidation (energy storage)
26
Q

describe the structure and function of phospholipids

A
  • amphipathic: glycerol backbone attached to 2 hydrophobic non-polar fatty acid tails + 1 hydrophilic polar phosphate head
  • forms phospholipid bilayer in water = component of membranes
    -tails can splay outwards = waterproofing (e.g. for skin)
27
Q

are phospholipids and triglycerides polymers?

A

no: they are not made from a small repeating unit, they instead are macromolecules

28
Q

describe the structure and function of cholesterol

A
  • steroid structure of 4 hydrocarbon rings
  • hydrocarbon tail on one side, hydroxyl group (-OH) on the other side
  • adds stability to cell surface phospholipid bilayer by connecting molecules and reducing fluidity
29
Q

what is the general structure of an amino acid? draw and explain

A
  • (refer to flashcard drawing)
  • COOH carboxyl/carboxylic acid group
  • ‘R’ variable side group consists of carbon chain and may include other functional groups
  • NH2 amine/amino group
30
Q

how do polypeptides form? draw this

A
  • (refer to flashcard drawing
  • condensation reactions between amino acids form peptide bonds
  • there are 4 levels of protein structure that can be formed
31
Q

describe ‘primary structure’ of a protein

A

sequence, number and type of amino acids in the polypeptide, determined by sequence of codons on mRNA

32
Q

describe ‘secondary structure’ of a protein

A
  • hydrogen bonds form between O 𝛿- attached to -C=O and H 𝛿+ attached to -NH
  • a-helix: spiral shape, H-bonds parallel to helical axis, all N-H bonds on same side of protein chain
  • b-pleated sheet: N-H and C=O groups alternate from one side to the other
33
Q

describe tertiary structure of a protein, and describe the bonds present

A
  • 3D structure formed by further folding
  • disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cysteine
  • ionic bonds: relatively strong bonds between charged R groups (pH changes cause these bonds to break)
  • hydrogen bonds: numerous and easily broken
34
Q

describe ‘quaternary structure’ of a protein

A
  • functional proteins may consist of more than one polypeptide
  • precise 3D structure held together by the same types of bonds as tertiary structure
  • may involve addition of prosthetic groups e.g. metal ions or phosphate groups
35
Q

describe the structure and function of globular proteins

A
  • spherical and compact
  • hydrophilic R groups face outwards and hydrophobic R groups face inwards = usually water-soluble
  • involved in metabolic processes e.g. enzymes such as amylase, insulin (2 polypeptide chains linked by 2 sulfide bonds), haemoglobin
36
Q

describe the structure of haemoglobin

A
  • globular conjugated protein with prosthetic group
  • 2 a-chains, 2 B-chains, 4 prosthetic haem groups
  • water soluble so dissolves in plasma
  • Fe2+ haem group forms coordinate bond with O2
  • tertiary structure changes so it is easier for subsequent O2 molecules to bind (cooperative binding)
37
Q

describe the structure and function of fibrous proteins

A
  • can form long chains or fibres
  • insoluble in water
  • useful for structure and support e.g. collagen in skin
38
Q

give the function of collagen

A

component of bones, cartilage, connective tissue and tendons

39
Q

give the function of elastin

A

provides elasticity to connective tissue, arteries, skin, lungs, cartilage and ligaments

40
Q

give the function of keratin

A

structural component of hair, nails, hooves/claws, horns and epithelial cells of outer layer of skin

41
Q

describe how to test for proteins in a sample

A
  • biuret test confirms presence of peptide bond
    1. add equal volume of sodium hydroxide to sample at room temperature
    2. add drops of dilute copper (II) sulphate solution, swirl to mix
    (steps 1 and 2 make biuret reagent)
    3. positive result = colour change from blue to purple
    negative result = solution remains blue
42
Q

describe how to test for lipids in a sample

A
  1. dissolve solid samples in ethanol
  2. add an equal volume of water and shake
  3. positive result = milky white emulsion forms
43
Q

describe how to test for reducing sugars

A
  1. add an equal volume of Benedict’s reagent to a sample
  2. heat the mixture in an electric water bath at 100°C for 5 mins
  3. positive result = colour changes from blue to brick red
    (or use a test strip coated in a reagent that changes colour if reducing sugar is present)
44
Q

describe the Benedict’s test for non-reducing sugars

A
  1. repeat steps for reducing sugar: negative result = Benedict’s remain blue
  2. hydrolyses non reducing sugars into their monomers by adding 1cm3 of hydrochloric acid, then heat in a boiling water bath for 5 mins
  3. neutralise the mixture using sodium carbonate solution
  4. repeat Benedict’s test
45
Q

describe the test for starch

A
  1. add iodine solution to sample
  2. positive result = colour changes from orange to blue-black
46
Q

state the role and chemical symbol of nitrate

A
  • NO3-
  • used to make DNA, amino acids, NADP for photosynthesis and NAD for respiration
47
Q

state the role and chemical symbol for ammonium

A
  • NH4+
  • can be converted into nitrate by saprobionts (type of decomposer) during nitrogen cycle), produced by deamination (removal of amino group) of amino acids during ornithine cycle in the liver
48
Q

state the role and chemical symbol of hydroxide

A
  • OH-
  • ions that affect pH and can interact with bonds in the tertiary structure to cause denaturation
49
Q

state the role and chemical symbol of phosphate ions

A
  • PO4^3-
  • component of ATP/ADP for energy release and NADP
50
Q

state the roles and chemical symbols of sodium and potassium ions

A
  • Na+ and K+
  • involved in maintenance of resting potential of neurons/generation of action potentials
  • Na+ is also involved in co-transport mechanisms
51
Q

state the role and chemical symbol of chloride ions

A
  • Cl-
  • involved in inhibitory synapses to cause hyperpolarisation
52
Q

state the role and chemical symbol of hydrogen and hydrogencarbonate ions

A
  • H+ and HCO3-
  • both form in organisms where CO2 dissolves in water
  • H+ regulates pH and can interact with bonds in tertiary structure to cause denaturation. H+ pump is involved in chemiosmosis and active loading in translocation
53
Q

state the role and chemical symbol of calcium ions

A
  • Ca^2+
  • used to make calcium pectate to add stability to middle lamella of plant cell walls, regulates exocytosis of neurotransmitter and binds to troponin to stimulate muscle contraction
54
Q

how can the concentration of a solution be measured quantitatively

A
  • use colourimetry: to measure absorbance/% transmission. Refer to a calibration curve from solutions of known concentration
  • use biosensors: a bioreceptor detects the presence of a chemical, a transducer converts the response into a detectable electrical signal
55
Q

outline the principles and process of paper/thin-layer chromatography

A
  1. use capillary tube to spot solution onto pencil ‘start line’ (origin) 1cm above the bottom of paper
  2. place chromatography paper in solvent (origin should be above solvent level)
  3. allow solvent to run until it almost touches other end of the paper, molecules in mixture move different distances based on relative solubility in solvent/attraction to paper
56
Q

what are Rf values? how can they be calculated?

A
  • ratios that allow comparison of how far molecules have moved in chromatograms
  • Rf value = distance between origin and centre of pigment spot ÷ distance between origin and solvent front

2 - foundations in bio (6 decks)

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