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OCR Biology A level New Spec > 2.1.2 Biological molecules > Flashcards

2.1.2 Biological molecules Flashcards

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1
Q

what is the structure of water (draw and explain)

A

diagram of water molecule here

  • water is a polar molecule consisting of two slightly positively charged hydrogen atoms covalently bonded to 1 slightly negatively charged oxygen atom
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2
Q

what is a polar molecule

A

it has a partial negative charge on one side and a partial pos on the other

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3
Q

what is a hydrogen bond

A

it is a weak interaction when a slightly positively charged hydrogen atom is bonded to a slightly negatively charged atom
- hydrogen bonds hold water together and therefore give it useful properties

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4
Q

what are the properties of water

A
  1. high specific heat capacity (energy needed to raise 1 gram of a substance by 1 degree)
    - hydrogen bonds between water absorb a lot of energy
    - therefore the temp of water is stable and does not cool down or heat up easily
  2. high latent heat of evaporation
    - a lot of energy is needed to heat water up so it vaporises into a gas (bc of hydrogen bonds)
  3. it is cohesive
    - cohesion is the attraction between molecules of the same type
    - water is v cohesive bc of the polarity
  4. lower density when solid
    - when water freezes into ice it is less dense than water
    - the water molecules r held further apart in ice in a lattice shape
  5. acts as solvent
    - water is polar and therefore can dissolve ionic substances (slight pos and neg regions of water is attracted to pos and neg regions of ion)
    - they surround the ions and dissolve them
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5
Q

can you relate their properties to their function

A
  1. high specific heat capacity
    - makes good habitat since water temp is stable for aquatic organisms
    - living things need stable temps for enzyme reactions to take place
  2. high latent heat of vaporisation
    - can help cool down organisms to keep their temp stable (e,g, skin)
  3. cohesive
    - gr8 for transporting subs
    - helps transport up plant stems in transpiration stream
  4. lower density
    - ice can act as habitats for polar bears
    - it can help insulate ponds and bodies of water from extreme cold so aquatic organisms dont freeze
  5. solvent
    - helps transports subs e.g. important ions can dissolve in blood
    - ions and molecules can react in water
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6
Q

what do elements do carbohydrates contain +ratios

A

Carbon (C), Hydrogen (H), and Oxygen (O)

in the form: CxH2xOx for every carbon and oxy there r two hydros

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7
Q

define macromolecules

A
  • complex molecules w large molecular mass
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8
Q

define polymers and monomers

A

monomer: small molecule that binds together to form a dimer or polymer e.g. amino acids and monosaccharides
polymer: large molecule made up of many monomers -e.g. protein and starch

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9
Q

define hydrolysis and draw it

A

hydrolysis the the breakdown of one molecule into two molecules by the addition of a molecule of water

diagram here

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10
Q

define condensation and draw it

A

condensation is the joining of two molecules by the removal of a molecule of water

diagram here

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11
Q

the monomers that make up carbs are….

A

monosaccharides

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12
Q

describe and draw the structure of glucose (number carbons)

A
  • is a monosaccharide w 6 carbons (its hexose monosacc)
  • there are two forms of glucose (alpha (α) beta (β)) both w ring struc

diagrams here

difference between alpha and beta is that the H and OH groups are opposite: alpha H is top and beta OH is top

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13
Q

describe and draw structure of ribose (numbered carbons)

A

is a monosaccharide w five carbons (pentose sugar)

- it is the sugar component of RNA nucleotides (NOT DNA)

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14
Q

why are polysaccharides important for living things

A

-glucose is a reactant in respiration and energy released is used to ATP
- polysaccharides contain many glu molecules and hence it is a good store of energy to b released when ATP is needed
(monosacchrides - they have many C-H bonds to release energy
- they are soluble in water)

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15
Q

how are disaccharides formed and what r they (also give examples)

A

disaccharides r two monosaccharides that are bonded together with glycosidic bonds formed by condensation reactions (they r broken down by hydrolysis)

e.g. alpha glucose + alpha glucose = maltose
beta glucose + fructose = sucrose
beta glucose + beta glucose = cellobiose

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16
Q

what is a polysaccharide (and examples)

A

when more than two monosaccharides r bonded together w glycosidic bonds
e.g starch

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17
Q

draw a diagram of hydrolysis and condensation reaction of 2 alpha glucose molecules

A

pic here

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18
Q

what is the function and structure of starch

A
  • main energy storage material in plants
  • plants store excess glucose as starch
  • insoluble in water therefore does not affect osmotic balance - good for storage
  • is a mixture of: 1. amylose, 2. amylopectin
  • amylose: made of long unbranched chains of alpha glucose and angle of bonds make it coil (Hbonds), hence compact and good 4 storage (1,4 glycosidic bond)
  • amylopectin: made of long branched chain of alpha glucose, side branches allow enzymes to break down faster and glucose can b released fast (1,4 glycosidic bond), also branches formed by (1,6 glycosidic bonds)
    it also coiled (Hbonds) so is compact
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19
Q

what is the structure of glycogen and its function

A
  • main energy storage material in animals
  • animals store excess glucose as glycogen
  • similar to amylopectin but it is even more branched (alpha glucose, long, branched)
  • (1,4 glycosidic bond), also branches formed by (1,6 glycosidic bonds)
  • enzymes can break down the glycosidic bonds faster due to the branches so glucose can be released faster
  • also compact structure so good for storage
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20
Q

what is the structure and function of cellulose

A
  • major component of cell walls in plants
  • tough, insoluble and fibrous
  • long, unbranched chains of beta glucose
  • they bond to form straight cellulose chains that lay side by side
  • every other b glucose is rotated 180 so they can bond (1,4 glycosidic)
  • H bonds form within chains (this stops it spiralling) and join other chains
  • when many chains bond (60/70) this forms microfibrils
  • when 400 microfibrils bond it forms macrofibrils which r embedded in pectins to form plant cell walls
  • strong fibres means structural support for plant cells
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21
Q

draw a cellulose chain + condensation reaction of 2 beta glucose

A

diagram

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22
Q

relating structure to function in cellulose

A

microfibrils and macrofibrils have high tensile strength - bc of glycosidic bonds n H bonds

  • macrofibrils criss cross the wall for more strength
  • difficult to digest cellulose (glycosidic bonds)
  • important bc plants do not have skeleton but rely on cell wall for structural support
  • space inbetween macrofibrils for water/mineral ions to pass on their way out (cell wall is permeable)
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23
Q

what r lipids and what do they consist of

A

macromolecules NOT polymers

contain Carbon, Hydrogen, and Oxygen

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24
Q

what 3 types of lipids r there

A

triglycerides
phospholipids
cholesterol

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25
Q

explain structure of a triglyceride and draw it

A
  • 1 molecule of glycerol and 3 fatty acid chains linked by 3 ester bonds between each fatty acid and the glycerol

trigly diagram here

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26
Q

draw a diagram of condensation and hydrolysis of a triglyceride

A

diagram here

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27
Q

what is the name for when triglycerides r synthesised

A

esterification

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28
Q

draw and explain structure of fatty acid

A
  • contains a variable R group (hydrocarbon tail) which is hydrophobic
  • the tail makes lipids insoluble in water

draw here

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29
Q

what r the two types of fatty acids and what differentiates them

A
  1. saturated fatty acid
    - no double bonds between carbon atoms in the tail
    -most animal fats r saturated
  2. unsaturated fatty acid
    - here are double bonds between carbon atoms in the tail
    causing chain to kink
    - kinks make the melting point lower
    - most plants have unsaturated fats
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30
Q

what is the general formula for a fatty acid

A

CnH(2n+1)COOH

31
Q

what is the structure of a phospholipid and draw it

A
  • contains a glycerol molecule, 2 fatty acid chains, and a phosphate group joined by 3 ester bonds and a bond to the phosphate group
  • phosphate group is hydrophilic since it is negatively charged
  • is amphipathic (has hydrophilic and hydrophobic qualities)
  • dra here
32
Q

how may phospholipids arrange themselves

A
  • might form a layer on the surface of water w heads in water and tails sticking up out of water
  • form micelles (small balls w tails tucked inside) w head pointing at surrounding water
33
Q

what is the structure of cholesterol and draw

A

it has a hydrocarbon ring structure and attached to a hydrocarbon tail

  • ring structure has polar hydroxyl (OH) group attached to it
  • steroid alcohol
  • hydrophobic
  • draw
34
Q

what is the function of triglycerides

A
  • energy source, can be broken down in respiration to release energy for making ATP
  • energy store, bc it is insoluble and does not affect osmotic balance of cells
  • insulation, acts as a heat insulator e.g. blubber in whales
  • buoyancy, fat is less dense than water - helps to float aquatic mammals
  • protection, humans have fat around delicate organs acting as a shock absorber
35
Q

what is the function of phospholipids

A
  • forms membranes around cells and organelles
  • they form a bilayer w two rows of phospholipids
  • tails pointing inwards n head pointing outwards
  • gives flexibility and stability in membranes
36
Q

what is the function of cholesterol

A
  • sits in the middle of phospholipid bilayer to provide stability to the membrane ( it is hydrophobic)
  • regulates fluidity of membrane
37
Q

what does a protein consist of and what is it

A
  • it is a polymer consisting of monomers called amino acids and is made up of Carbon, Hydrogen, Oxygen, Nitrogen and sometimes Sulfur
  • amino acids make up dipeptides and polypeptides and proteins usually consist of one or more polypeptides
38
Q

what r the properties of proteins

A
  • forms structural components of animals e.g. muscles

- adopting specific shapes e.g enzymes/hormones

39
Q

what is the structure of an amino acid and draw

A
  • each aa has an amino group at one end and a carboxyl group on the other
  • also has an R variable group (in glycine it is H, and alanine is CH3)
    draw
40
Q

how are amino acids linked and draw

A
  • they are linked thru condensation reactions and bonded by peptide bonds
  • draw
41
Q

what is the primary structure of a protein

A
  • the sequence of amino acids in the polypeptide chain
  • if the sequences changes the structure of the protein can change
  • held together by peptide bonds
  • function of a protein is determined by its structure
42
Q

whats the secondary structure of a protein

A
  • this is the shape of the polypeptide: it either coiled into an alpha α helix or betaβ pleated sheet
  • this is held together by hydrogen bonds forming between the amino and carboxyl groups of the amino acids in the chain
43
Q

whats the tertiary structure of a protein

A
  • after the polypeptide folds/coils it coils and folds further, in the tertiary structure these bonds are involved:
    1. ionic bonds - attractions between negatively charged R groups and pos charged R groups in diff parts of molecule
    2. disulfide bridges - this is a bond between two sulfur molecules, when two molecules of cysteine come together the Sulfurs bond together for form a bond
    3. hydrophobic and hydrophilic interactions - when hydrophobic R groups r close they clump together so hydrophilic R groups get pushed to the outside which affetcs final shape
    4. hydrogen bonding- weak bonds form between slightly pos charged H atoms and sligh neg charged atoms between diff R groups

for proteins made of 1 polypeptide its 3D structure is the final structure

44
Q

what is the quaternary structure of a protein

A
  • this is determined by how multiple polypeptide chains bond together - can be influenced by all the bonds mentioned in teritary
  • this is usually the final struc
    e. .g haemoglobin is made of 4 polypeptide chains
45
Q

what r the features of a globular protein + name examples

A
  • it is round and compact
  • due to hydrophilic and hydrophobic interactions the molecule is usually soluble and easily transported in fluids
  • usually involved in metabolic roles
    e. .g haemoglobin, insulin, pepsin
46
Q

what r the features of haemoglobin

A
  • globular protein + carries oxygen around body
  • the quaternary struc is made up of 4 polypeptides: 2 alpha -globin chains and two beta-globin chains
  • it is held together by all the bonds mentioned
  • is a conjugated protein
  • meaning it a protein w a prosthetic (non protein) group attached
  • each 4 polyp has a haem group attached to it
47
Q

what r the features of insulin

A
  • globular protein, hormone secreted by pancreas
  • made up of 2 polypeptide chains
  • one chain starts w an alpha helix and the other ends w a beta pleated sheet
  • in tertiary struc it is held in place by disulfide links
  • hydrophobic/philic interactions make it soluble
  • in pancreas 6 join to form a large globular struc
48
Q

what r the features of pepsin

A
  • is a globular protein and enzyme that digests protein in the stomach
  • made up of 1 single chain of polypeptide of 327 aas
  • folds into a symmetrical tertiary struc
  • it has many acidic R groups so it can b stable in stomach
  • tertiary struc held by H bonds and 2 disulfide bridges
49
Q

what r the 2 approaches to predicting the tertiary struc of a protein w computer modelling

A
  1. Ab initio protein modelling - model is built on physical and electrical properties of atoms in each amino acid in sequence, can be multiple solutions to same aa sequence
  2. Comparative protein modelling - 1 approach is protein threading, which scans aa sequence against a database of solved strucs to predict possible models that match
50
Q

what r inorganic ions

A

these r ions that do not contain carbon

51
Q

what are the 2 types of ions

A

cations - these are pos charged ions

anions - these r neg charged ions

52
Q

name all the cations u need to know and their chemical symbols and charges

A 
calcium - Ca2+
sodium - Na+
Potassium - K+
Hydrogen - H+
Ammonium - NH(4)+
53
Q

name all the anions u need to know and their chemical symbols and charges

A 
Nitrate - NO(3)-
Hydrogencarbonate - HCO(3)-
Chloride - Cl-
Phosphate - PO(4)3-
Hydroxide - OH-
54
Q

state the cations functions

A

Ca2+:
1. involved in transmission of nerve impulses
2. involved in release of insulin from pan
3. cofactor for enzymes
Na+:
1. important for generating nerve impulses
2.for muscle contraction
3. regulating body fluids
K+:
1. important for generating nerve impulses
2.muscle contraction
3.regulates body fluid
4.activates essential enzymes for photosynthesis in plantcells
H+:
1. involved in regulation of blood pH
2. important for photosynthesis reactions in thylakoid membranes
3. important for respiration reactions in inner membrane of mitochondria
NH(4)+:
1. important source of nitrogen for plants
2. used to make aa and nucleic acids in plants

55
Q

state the anions functions

A

NO(3)-:
1. important source of nitrogen for plants
2. used to make aa and nucleic acids in plants
HCO(3)-:
1. involved in regulation of blood pH
2. involved in transport of CO2 in and out of blood
Cl-:
1. helps production of urine in kidney and maintaining water balance
2. involved in transported CO2 in/out of blood
3. involved in regulation of blood pH
4. cofactor for amylase
PO(4)3-:
1. involved in regulation of blood pH
2. helps root growth in plants
3. needed for synthesis of nucleotides/phospholipids
OH-:
1. involved in regulation of blood pH

56
Q

what is the test for carbs (starch)

A
  1. add iodine solution (in potassium iodide) to sample

2. if starch is present colour changes from brown-orange to blue-black

57
Q

what is the test for reducing sugars

A
  1. add benedict’s reagent to a sample and heat it in a water bath that has been brought to boil
  2. if pos solution will form a coloured precipitate from blue to green to yellow to orange-red
  3. intensity of red is proportional to how much sugar there is
58
Q

test for non-reducing sugars?

A
  1. test sample for reducing sugars first
  2. separate sample and boil with hydrochloric acid to hydrolyse sucrose into glucose and fructose
  3. cool solution and use sodium hydrogencarbonate sol to neutralise it
  4. test for reducing sugars again
  5. pos result (green/yellow/orange/red) indicates non reducing sugar is present
59
Q

what does reducing mean

A

a reducing sugar is one that are all monosaccharides and some disaccharides - bc they can reduce or give electrons to other molecules

60
Q

what is the test for lipids (emulsion test)

A
  1. take sample and mix it well w ethanol
  2. filter it
  3. pour solution into water in clean test tube
  4. if solution turns into a cloudy white emulsion it indicates presence of lipids
61
Q

what is the test for proteins (biuret test)

A
  1. add sodium hydroxide to solution to make it alkaline
  2. add copper (II) sulfate solution
  3. if present it will turn from light blue to purple/lilac
62
Q

what is qualitative testing?

A

this determines if a sub is present in a sample or not

63
Q

what is quantitative testing

A

determines the concentration or how much of a sub is present in a sample

64
Q

what is colorimetry

A
  • helps to quantify the concentration of sugar in the original sample
65
Q

how to use a colorimeter

A
  1. switch it on and allow 5 mins for calibration - set it up so youre using the red filter
  2. add distilled water to a curvette and place into colorimeter to calibrate it - the absorbance measured should be 0
  3. using a pipette take the excess benedicts solution from ur sample (the supernatant) and put some in a curvette
  4. place this into a colorimeter
  5. do not stain the curvette or it will affect results
  6. measure absorbance
  7. repeat steps for other concentrations
66
Q

how do u create a calibration curve

A
  1. take known concs of reducing sugar
  2. using sample of each carry out benedicts test
  3. use colorimeter to record absorbance of each supernatant
  4. plot graph to show absorbance against conc of reducing sugar
    - this provides calibration curve and u can use it w other unknown samples to work out their conc
67
Q

what is a biosensor

A

u can also do colorimetry w a biosensor
- they take a bio/chemical variable which cannot be easily measured and convert it into an electrical signal
it first produces a signal (eg chemical), and then converted to an electrical signal by a transducer (another part of biosensor)
- the signal is then processed and can be used to work out other info

68
Q

give an example of how the biosensor works

A
  • a glucose biosensor determines the glucose conc in a solu
  • uses enzymes glucose oxidase and electrodes
  • enzymes catalyses oxidation of glucose at the electrodes
  • creating a charge which is covered into an electrical signal by the electrodes
  • the electrical sig is then processed to work out the initial glucose conc
69
Q

what is chromatography

A

it separates a mixture into its constituents - in this case bio molecules such as glucose/aa/vitamins and nucleic acids

70
Q

what r the phases of chromatography

A
  1. stationary phase
    - where the molecules cannot move
    - the S phase is a piece of chromatography paper or thin-layer chromatography (TLC) plate
    - paper is made of cellulose
    - TLC is made of a sheet of plastic coated w silica gel/aluminium hydroxide
  2. mobile phase
    - this is when molecules can move
    - in both P and TCL this is a liquid solvent e.g ethanol/water
71
Q

how do u calculate the Rf value?

A

Rf=x/y

x=dist from pencil line to the centre of a spot of pigment
y= dist from pencil line to the solvent front (dist travelled by the solvent up the paper)

72
Q

how can u see colourless molecules ?

A
  1. ultraviolet light - TLC plates have chemical which fluoresce under UV light , space where molecules r do not
  2. ninhydrin- all plate to dry and spray w ninhydrin - molecules will turn brown/purple
  3. iodine - allow plate to dry + place in enclosed container w iodine crystals will make them appear coloured
73
Q

how does chromatography work

A

the speed at which molecules move depends on their solubility to the solvent and their polarity
- the more polar the slower it will travel as it sticks to the paper or plate

74
Q

where is chromatography used

A
  • TLC is used to monitor progress of reactions
  • urine testing for atheles
  • analysing drug purity

OCR Biology A level New Spec (28 decks)

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