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a-level biology > 2.1.2 Biological molecules > Flashcards

2.1.2 Biological molecules Flashcards

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1
Q

how polarity in water is formed (biology)

A

O pulls pair of electrons in covalent bond closer to it and further from H as has more protons
O has partially negative charge
H has partially positive charge

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2
Q

properties of water

A 
polar
liquid at room temperature 
high specific heat capacity (SHC)
high latent heat of vaporisation (LHV)
high cohesion/adhesion 
high surface tension 
water is denser than ice
not compressible (liquid)
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3
Q

roles of water for living organisms

A

site of chemical reactions (solvent)
stable enzyme-controlled reactions (high SHC)
allows molecules and ions to be transported easier in living things (solvent)
stable environment of aquatic organisms (high SHC and LHV)
columns of water pulled up by xylem vessels (adhesion due to hydrogen bonding)
important metabolite (photosynthesis, hydrolysis)

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4
Q

monosaccharide definition

A

sugar monomer

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5
Q

carbohydrate uses

A

source of energy (glucose)
store of energy (starch, glycogen)
structural unit (cellulose cell wall, chitin cell wall of fungi)

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6
Q

monosaccharide properties

A

sugars (sweet)
soluble in water
insoluble in non-polar solvents

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7
Q

reducing sugars examples

A

maltose
lactose
all monosaccharides

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8
Q

non-reducing sugars

A

most disaccharides (e.g. sucrose)

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9
Q

how disaccharides are formed

A

condensation reaction to form glycosidic bond between two monosaccharides

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10
Q

monosaccharides of maltose

A

alpha-glucose + alpha-glucose

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11
Q

monosaccharides of sucrose

A

alpha-glucose + fructose

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12
Q

monosaccharides of lactose

A

beta-galactose + beta-glucose

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13
Q

monosaccharides of cellobiose

A

beta-glucose + beta-glucose

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14
Q

how polymers are formed and broken down

A 
condensation reaction (release water molecule)
hydrolysis reaction (requires water molecule)
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15
Q

starch structure

A

only alpha-glucose

amylose + amylopectin

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16
Q

amylose structure

A

long
coiled (hydroxyl bonds create hydrogen bonds to maintain structure)
unbranched (1-4 glycosidic bonds only)
good for storage (compact)

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17
Q

amylopectin structure

A

long
also coil due to hydrogen bonds
branched due to 1,6-glycosidic bonds
more accessible ends for enzymes for faster hydrolysis into alpha-glucose

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18
Q

properties and function of starch

A

major carbohydrate storage molecule in plants
stored as intracellular starch grains (plastids)
produced from glucose made in photosynthesis
broken down during respiration for energy
insoluble so doesn’t affect water potential

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19
Q

glycogen structure

A

long
highly-branched (many 1,6 glycosidic bonds)
more accessible ends to enzymes (more than amylopectin) so faster hydrolysis into alpha-glucose

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20
Q

glycogen function and properties

A

main energy storage in animals
more glucose residue branches so energy is released quickly (animals have higher metabolism than plants)
stored in liver and muscles
less soluble, more compact than starch (animals have higher metabolism than plants)

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21
Q

cellulose structure

A

beta-glucose orientated 180° to form straight chains (prevent coiling)
1-4 glycosidic bonds
hydrogen bonding between adjacent chains to form microfibrils (more tensile strength)
bundles to form macrofibrils that criss-cross (more tensile strength)

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22
Q

cellulose cell wall features and role

A

tough, insoluble
hard to digest (strong glycosidic bonds, most animals lack necessary enzymes)
high tensile strength (glycosidic bonds, hydrogen bonds between chains) so doesn’t burst when turgid, support whole plant
permeable (gaps between macrofibrils)
can be reinforced (e.g. lignin, cutin)

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23
Q

other structural polysaccharides

A

peptidoglycan (bacterial cell wall, arranged similarly to cellulose)
chitin (exoskeleton of insects and crustaceans, fungi cell wall, arranged similarly to cellulose)

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24
Q

lipid general features

A

non-polar
insoluble in water, dissolve in alcohol
less dense than water
soluble in non-polar solvents

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25
Q

glycerol structure

A 
3 carbon molecules
3 hydroxyl (-OH groups) attached to carbons
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26
Q

fatty acid structure

A

carboxyl group (-COOH)
attached to hydrocarbon tail (2-20 carbons long)
acid as can dissociate H+ ions
can have saturated or unsaturated hydrocarbon tail

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27
Q

effect of double bond on hydrocarbon tail

A

creates “kink” at double bond
pushes molecule slightly apart
reduces intermolecular interactions between molecules so more fluid, lower MP

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28
Q

triglyceride structure

A

1 glycerol bonded to 3 fatty acids

by ester bonds formed in condensation reactions

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29
Q

ester bond

A

bond formed between fatty acids (or phosphate group) and triglyceride
formed between carboxyl group (-COOH) of fatty acid and hydroxyl group
between hydroxyl groups for phosphate
released water molecule per bond
esterification reaction

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30
Q

functions of triglycerides

A

energy source (broken down in respiration to provide ATP, releases around double energy than carbohydrates)
energy store (insoluble so doesn’t affect water potential of adipose tissue)
insulation (heat insulator e.g. blubber, electrical insulator on nerve cells)
buoyancy (less dense than water)
protection (can absorb shock when surrounds organs)

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31
Q

phospholipid structure

A

1 glycerol bound to 2 fatty acids, 1 phosphate group by ester bonds
hydrophilic phosphate head (as negative charge)
hydrophobic fatty acid tails
amphiphatic

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32
Q

behaviour of phospholipids in watee

A

hydrophilic phosphate heads face towards regions of water
hydrophobic fatty acid tails turn away from regions of water
forms bilayer or micelles

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33
Q

micelle definition

A

hydrophobic tails inside structure

hydrophilic heads facing outwards towards regions of water

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34
Q

sterols definition

A

complex alcohol molecules based on 4 carbon ring structure with hydroxyl group at one end (-OH) e.g. cholesterol

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35
Q

cholesterol structure

A

steroid nucleus (4 carbon rings)
hydroxyl group at one end
hydrocarbon side chain at other end

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36
Q

cholesterol functions

A

manufacture in liver and intestine
formation + stability of plasma membrane
synthesis of steroid hormone
can pass through plasma membrane because small + hydrophobic

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37
Q

amino acid definition

A

monomers of all proteins

all have same basic structure

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38
Q

protein functions

A

structural: muscles add of protein, whore
catalytic: form enzymes
carriers and pores: carrier and channel proteins of plasma membrane

39
Q

amino acid general structure

A

carboxyl group
amino group
central hydrogen
varying R group

40
Q

buffer definition

A

substance that helps to resist large changes in pH

41
Q

how amino acids join and break up

A

condensation reaction
forms peptide bond (OCHN) between amino group of one amino acid and carboxyl group of another amino acid
release water

hydrolysis reaction
breaks peptide bond
requires water
forms 2 amino acids

42
Q

primary structure definition

A

sequence of amino acids in a polypeptide chain

43
Q

secondary structure definition

A

coiling or folding of peptide chain to form alpha-helices or beta-pleated sheets due to hydrogen bonding

44
Q

why primary structure is important

A

determines shape of molecule (determines secondary, tertiary, quaternary structure)
many possible sequences so gives each enzyme a unique shape and specific function

45
Q

how alpha-helices form

A

peptide chain coils

held by hydrogen bonds that form between -NH group and -CO group of different amino acids

46
Q

how beta-pleated sheets form

A

chains fold over on itself slightly to form zig-zag structure
hydrogen bonds form between -NH and -CO groups of different amino acids

47
Q

tertiary structure definition

A

overall 3D shape of protein molecule due to hydrogen bonding, disulphides bridges, ionic bonds and hydrophobic interactions
between R groups of amino acids

48
Q

quaternary structure definition

A

how multiple polypeptide chain subunits come together

only in complex proteins e.g. haemoglobin, insulin

49
Q

hydrogen bonds in tertiary structure

A

between carboxyl, hydroxyl and amino groups

between R groups of amino acids

50
Q

ionic bonds in tertiary structure

A

carboxyl and amino groups in R group ionise into COO- and NH3+ respectively
oppositely charged ions strongly attracted to each other to form ionic bond

51
Q

disulfide bridges in tertiary structure

A

R group of cysteine has sulfur

strong covalent bonds form between sulfur on R groups of 2 cysteine amino acids

52
Q

hydrophobic/philic interactions in tertiary structure

A

hydrophobic parts tend to associate together at centre of polypeptide to avoid water
hydrophilic parts found at edge of polypeptides close to water
both causes twisting and changing of polypeptide chain’s shape

53
Q

fibrous proteins features

A

regular, repetitive sequence of small range of amino acids
insoluble in water
long chain
thin structure
has structural function (e.g. collagen, elastin)
little/no tertiary structure

54
Q

globular protein features

A

relatively spherical shape
soluble in water
have very specific shape
often have metabolic roles (enzymes, hormones, haemoglobin)

55
Q

collagen properties and functions

A

mechanical strength (lots of hydrogen bonds)
collagen around arteries to prevent from bursting
tendons, cartilage and connective tissue made out of collagen
bones made out of collagen then reinforced with calcium phosphate

56
Q

keratin properties and functions

A

lots of cysteine so more disulfide bonds
makes it strong
provides mechanical protection, impermeable barrier to infection, waterproof
found in nails, hair, claws, hooves, forms, scales, fur, feather (anywhere hard)

57
Q

elastin properties and features

A

cross-linking + coiling so strong and extensible

found in skin, lungs, blood vessels (anything that needs to change its shape and stretch)

58
Q

haemoglobin structure, properties and functions

A

two alpha and 2 beta globin chains
each chain holds a prosthetic haem group (Fe2+)
conjugated protein
oxygen molecule binds to iron ions in haem groups and gets released at tissues

59
Q

insulin structure, properties and functions

A

2 polypeptide chains (A and B) joined by disulfide bridges
A chain begins with alpha helix
B chain ends with beta pleated sheet
hydrophilic R groups on outside of molecule so is soluble
binds to glycoprotein receptors (muscle, fat cells) to increase intake and consumption of glucose from blood

60
Q

pepsin structure, properties and functions

A

single polypeptide chain folded into symmetrical tertiary structure held by hydrogen bonds and disulfide bridges
made up of 43 AA with acidic R groups
few basic groups to accept hydrogen ions
so low pH has little effect on structure

61
Q

Ab initio (in italics) protein modelling

A

protein model is built based on physical and electrical properties of atoms in each amino acid in sequence
multiple solutions can be made
other methods required to deduce real structure of protein

62
Q

comparative protein modelling

A 
protein threading (scans a amino acid sequence against related proteins with known structures)
produces set of possible models
63
Q

Ca 2+ functions

A 
involved in 
transmission of nervous impulses
regulating of protein channels 
muscle contractions
hardening of teeth and bones
64
Q

Na + functions

A

involved in
transmission of nervous impulses
active transport Na+ pump
co-transport of glucose and amino acids across membranes

65
Q

K + functions

A

Involved in
transmission of nervous impulses
active transport
plant cell turgidity

66
Q

H + functions

A

The higher the concentration, the lower the pH of bodily fluids

67
Q

NH4 + functions

A

Source of nitrogen used to make organic molecules

68
Q

NO3 - functions

A

Source of nitrogen used to make organic molecules

69
Q

HCO3 - functions

A

Involved in the regulation of blood pH and transport of carbon dioxide in the blood

70
Q

Cl - functions

A

involved in
transport of carbon dioxide in the blood through the chloride shift
production of hydrochloric acid

71
Q

allosteric effect

A

binding of ligand to one site of protein molecule so properties of another sire on same protein molecule are affected

72
Q

ligand meaning

A

ion or molecule that binds to another (usually larger) molecule

73
Q

PO4 3- functions

A

Component of biological molecules such as nucleotides, ATP and the formation of the phospholipid bilayer

74
Q

OH - functions

A

The higher the concentration, the higher the pH of bodily fluids

75
Q

deficiency definition

A

when organism doesn’t have enough of a particular inorganic ion

76
Q

test for starch

A

add iodine dissolved in potassium iodide to sample
positive if yellow-brown turns blue black
triiodide ions slips into middle of amylose helix, causes colour change

77
Q

test for reducing sugars

A

add Benedict’s solution in excess (alkaline copper (II) sulfate)
heat in water bath (80°C, 3 minutes)
positive if colour change from blue to brick-red and anything in between
blue Cu 2+ ions turn into brick red Cu + ions as are donated electrons from reducing sugars

78
Q

test for non-reducing sugars

A

test for reducing sugars first
take separate sample and boil with hydrochloric acid (hydrolyse to form monosaccharides)
cool solution, neutralise using hydrogencarbonate solution
test for reducing sugars again
positive if only second test has colour change

79
Q

test for lipids

A

mix sample throughout with ethanol
filter and pour solution into water in clean test tube
positive if cloudy white emulsion forms
tiny lipid droplets come out of ethanol solution when mixed with water

80
Q

test for proteins

A

add biuret A (sodium hydroxide)
add biuret B (copper sulfate)
positive if lilac-colour formed
complex formed between Cu 2+ and nitrogen atom in peptide chain

81
Q

quantitative test for reducing sugar

A

conduct reducing sugar test with excess Benedict’s solution
separate unreacted Benedict’s solution using centrifuge
collect supernatant using pipette and place into cuvette
place (red) colour filter into colorimeter
calibrate colorimeter using distilled water
test supernatant with colorimeter
less transmission / more absorption = more unreacted copper sulfate solution = less reducing sugar
more transmission / less absorption = less copper dilate solution = more reducing sugar

82
Q

creating calibration curve

A

carry out Benedict’s test on samples of known concentrations of reducing sugar
separate Benedict’s solution from each sample with centrifuge
use colorimeter and record percentage transmission of light through each supernatant
plot graph (transmission of light against glucose concentration) and draw line of best fit
can estimate glucose concentration of unknown samples with transmission readings

83
Q

biosensor definition

A

takes biological or chemical variable hard to measure and converts it into electrical signal

84
Q

biosensors general mechanism

A

molecules to be measured bind to biological layer via receptors
transducer surface creates electronic signal
signal conditioner creates an output

85
Q

stationary phases

A

chromatography paper (made of cellulose) or thin-layer chromatography plate (sheet of plastic coated with thin layer of silica gel or aluminium hydroxide)

86
Q

mobile phase

A

solvent that carries biological molecules

flows through and across stationary phase

87
Q

how chromatography works

A

solvent moves up stationary phase, carrying soluble pigments with it
pigments move at different speeds (due to polarity, size, solubility in solvent)
more polar = stick to the stationary phase more = slowly and vice versa

88
Q

relative distance (chromatography) formula

A 
Rf = x/y
Rf = relative distance travelled by a pigment
x = distance between CENTRE of spot of pigment and pencil line
y = distance between solvent and pencil line
89
Q

how to spot colourless molecules in chromatography with UV light

A

TLC plates have chemical that fluoresces under UV light, colourless pigment will mask plate from UV light so no glowing

90
Q

how to spot colourless molecules in chromatography with ninhydrin

A

allow plate to dry
spray with ninhydrin
binds to amino acids, become visible as brown or purple spots

91
Q

how to spot colourless molecules in chromatography with iodine

A

allow plate to dry
place in enclosed space with few iodine crystals
gas formed from iodine binds to molecules in each spot

92
Q

uses of chromatography

A

monitor progress of reactions (as it is quick)

analyse for illegal drugs in urine of athletes, purity of components of drugs, contaminants in food

93
Q

reducing sugar disaccharides

A

lactose
maltose
cellobiose

a-level biology (24 decks)

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