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Biology Module 2 > 2.2 Biological Molecules > Flashcards

2.2 Biological Molecules Flashcards

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1
Q

what are most carbohydrates

A

polymers

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2
Q

what are polymers

A

molecule made of many similar, smaller molecules called monomers bonded together

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3
Q

what monomers are carbohydrates made out of

A

monosaccharides

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4
Q

explain glucose

A

hexose monosaccharide with six carbon atoms

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5
Q

what are 2 forms of glucose

A

alpha and beta - both with ring structure

alpha - H-OH on both strands
beta - OH H on the second strand

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6
Q

how is glucoses structure related to its function

A
  • main energy source in plants and animals
  • structure makes it soluble, so it can be easily transported (due to H bonds between the OH group and water (both polar))
  • chemical bonds contain a lot of energy
  • small, so can be transported and diffused across cell membranes
    • easilky broken down to release energy and produce ATP - molecules can join to form polysacharides
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7
Q

ribose

A

pentose monosaccharide with 5 carbon atoms
(sugar component of RNA nucleotide)

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8
Q

what are all carbohydrates made of

A

carbon, hydrogen, oxygen
1:2:1

  • Cx(H2O)y
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9
Q

what joins monosaccharides together, and what are the 2 types

A

glycosidic bonds

  • 1-4: bond between Carbon 1 and Carbon 4 (carbons are numbered clockwise, starting from the one on the right)
  • 1-6: leads to branching
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10
Q

how do monosaccharides join together

A

condensation reaction:
-during synthesis, the two hydroxyl groups bond together, releasing water from the H of one and OH of another
-releases a molecule of water

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11
Q

what is reverse of condensation reaction

A

hydrolysis:
molecule of water reacts with the glycosidic bond, breaking it apart

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12
Q

what is disaccharide

A

two monosaccharides joined together

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13
Q

examples of disaccharides

A

-alpha glucose + alpha glucose = maltose
-alpha glucose + fructose = sucrose
-(either) glucose + galactose = lactose

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14
Q

what is polysaccharide

A

more than two monosaccharides joined together
(e.g. lots of alpha glucose = amylose)

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15
Q

what is starch

A

the main energy storage material in plants:
- calls get energy from glucose
- excess glucose is stored as starch
- when a plant needs more glucose for energy, it breaks down starch to release the glucose

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16
Q

structure and function of starch

A
  • insoluble in water, so doesn’t cause water to enter cells by osmosis (would make them swell), so good for storage (even though glucose itself is soluble)
  • mixture of 2 polysaccharides of alpha glucose
    1) amylose:
  • long, unbranched chain of A-glucose
  • angles of the glycosidic bonds give it a coiled, helix structure, almost like a cylinder
  • makes it compact, so good for storage as you can fit more in a small space (energy dense)
    • only 1,4 glycosidic bonds
      2) amylopectin:
  • long, branched chain of A-glucose
  • side branches allow the enzymes that break down the molecule to get at the glycosidic bonds quickly due to many free ends
  • so glucose can be easily released
    • 1,4 and 1,6 glycosidic bonds
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17
Q

what is glycogen

A

main energy storage material in animals:
-animal cells get energy from glucose
-store excess as glycogen

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18
Q

structure and function of glycogen

A
  • polysaccharide of alpha glucose
  • similar structure to amylopectin, but with many more side branches coming off
  • means stored glucose can be released quickly, important for energy release in animals as more active than plants, as many free ends available to remove and add glucose
  • very compact molecule, good for storage
  • also insoluble
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19
Q

what is cellulose

A

major component of cell walls in plants

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20
Q

structure and function of cellulose

A
  • made of long, unbranched chains of beta glucose
  • when beta glucose molecules bond, they form straight cellulose chains (alternating upside down)
  • cellulose chains are linked together by (weak) hydrogen bonds to form strong fibres called microfibrils
  • means cellulose can provide structural support to cells, and be insoluble
  • 1,4 glycosidic bonds
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21
Q

what are the 3 types of lipids

A

triglycerides, phospholipids and cholesterol

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22
Q

why are triglycerides considered macromolecules

A

they’re complex molecules with a relatively large molecular mass

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23
Q

what chemical elements do all lipids contain?

A

carbon, hydrogen and oxygen

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24
Q

explain the basic structure of a triglyceride

A
  • one molecule of glycerol
  • three fatty acids attached on
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25
Q

explain the fatty acid chains on triglycerides

A
  • fatty acid molecules have long ‘tails’ made of hydrocarbons (compound containing only hydrogen and carbon)
  • the tails are hydrophobic (repel water molecules), meaning that lipids are insoluble in water
  • they are also non-polar, as have a more even distribution of electrons (charge)
  • all fatty acids have basic structure, but it is the hydrocarbon tail that varies
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26
Q

explain basic structure of fatty acids and glycerol

A

O =
C - R
OH -
(R= the variable hydrocarbon tail)

3 Cs attached to one OH and rest are just Hs

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27
Q

how are triglycerides made and broken down

A
  • synthesised by the formation of an ester bond between each fatty acid and the glycerol molecule
    ( ester bond forms between hydroxyl groups, and come together to form the O-C=O ester bond)
  • formed via a condensation reaction where water molecules is released, and is specifically called esterification
  • breaks down when each ester bond is broken in hydrolysis reaction where water is used up (3 water molecules for each ester bond)
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28
Q

what are the two types of fatty acids and explain the difference

A

saturated= don’t have any double bonds between the carbon atoms in the hydrocarbon chain, so is “saturated” with hydrogen - such as fats in animals
(CnH2n+1COOH)

unsaturated= have at least one double bond between carbons in hydrocarbon chain, which causes the chain to kink - means that molecules can’t pack close as easily, so liquid at room temp, such as oils in plants

  • use prefixes poly/mono as well to describe how many C=C
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29
Q

explain the basic structure of phospholipids

A
  • also macromolecules
  • similar to triglycerides, but one fatty acid chain is replaced with a phosphate group
  • phosphate group is hydrophilic ( attracts water molecules) and the fatty acid chains are still hydrophobic
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30
Q

properties and functions of triglycerides

A
  • in plants and animals, mainly used as energy storage molecules
  • in some bacteria (mycobacterium tuberculosis), used to store both energy and carbon
  • good for storage because:
    1) the long hydrocarbon tails of the fatty acids contain lots of chemical energy (lots of energy is released when they’re broken down). as a result, they contain about twice as much energy per gram as carbohydrates
    2) they’re insoluble, so don’t cause water to enter the cells via osmosis, which would make them well. the triglycerides bundle together as insoluble droplets in cells as the fatty acid tails are hydrophobic, so they face inwards, shielding themselves from the water with the glycerol heads
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31
Q

explain function and properties of phospholipids

A
  • found in the cell membranes (controls what enter and leaves cells) of all eukaryotes and prokaryotes, making up the phospholipid bilayer

1)phospholipid heads are hydrophilic (due to phosphate group) and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on either side
2) the centre of the bilayer is hydrophobic, so water soluble substances cannot easily pass through it - and membranes act as a barrier to those substances

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32
Q

explain function and structure of cholesterol

A
  • has a hydrocarbon ring structure attached to a hydrocarbon tail
  • ring structure has a polar hydroxyl (OH) group attached to it
  • in eukaryotic cells, cholesterol molecules help to regulate the fluidity of the cell membrane by interacting with the phospholipid bilayer

1) small size and flattened shape to fit in between the phospholipid molecules in the membrane
2) at higher temperatures, they bind to the hydrophobic tails of the phospholipids, causing them to pack more closely together, so the membrane is less fluid and more rigid
2) in lower temperatures, the cholesterol prevents the phospholipids from packing too closely together, and so increasing the membrane fluidity

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33
Q

explain proteins being polymers

A
  • made of the monomers amino acids
  • dipeptide is formed when 2 amino acids join together
  • polypeptide is formed when more then 2 amino acids join together
  • proteins are made of one or more polypeptides
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34
Q

explain the general structure of amino acids

A
  • made of a carboxyl group ( -COOH) and an amino group ( -NH2) attached to a carbon atom
  • difference between amino acids is the variable R group they contain
  • all amino acids contain carbon, oxygen, hydrogen, nitrogen, and may also contain sulfur

e.g glycine: H
H2N- C -COOH (H= R group)
H

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35
Q

how are amino acids joined and broken down

A
  • linked together by peptide bonds to form di and polypeptides
  • molecule of water is released during reaction ( bonding between the OH of COOH and the H of NH2), so is a condensation reaction
  • reverse is just adding water molecule to break peptide bond (hydrolysis reaction)
  • C-N bond is the peptide bond
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36
Q

primary structure of proteins

A
  • sequence of amino acids in a polypeptide chain
  • different proteins have a different sequence of amino acids in their chain
  • change in just one amino acid may change the structure of the whole protein
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37
Q

secondary structure of protein

A
  • hydrogen bonds form between the nearby amino acids in the chain, so the polypeptide chain does not remain straight and flat
  • coils into alpha helix or folds into a beta pleated sheet
38
Q

tertiary structure of protein

A
  • the coiled or folded chain of amino acids is often coiled or folded further
  • more bonds form between different parts of the polypeptide chain
  • the final 3D structure of proteins made of a single polypeptide chain
39
Q

quaternary structure of proteins

A
  • the way in polypeptide chains are assembled together in proteins made of several polypeptide chains held together by bonds (e.g haemoglobin made of 4 polypeptide chains)
  • final 3D structure
40
Q

how can you visualise protein structure

A
  • computer modelling can create 3D interactive images of proteins
  • useful for investigating the different levels of structure in a protein molecules
41
Q

explain the different types of bonding present in each level of protein structure

A

1) primary = peptide bonds between amino acids
2) secondary= hydrogen bonds
3) tertiary= several:
- ionic bonds due to attraction between negative R groups and positive R groups on different parts of the molecule
- disulfide bonds when two molecules of amino acid cysteine come close together, sulfur atom in one cysteine bonds to sulfur atom on another cysteine
- hydrophobic and hydrophilic interactions ( when hydrophobic R-groups come close together in protein, they clump together, meaning that hydrophilic R-groups are more likely to be pushed to the outside, affecting the way the protein folds
- weak hydrogen bonds that form between slightly positive hydrogen atoms in some R groups and slightly negative hydrogen atoms in other R groups
4) quaternary- influenced by all the bonds mentioned as it is dependent of the tertiary structure of the individual polypeptide chains being bonded together

42
Q

how will heating a protein affect its shape

A
  • break up the ionic and hydrogen bonds, and the hydrophobic and hydrophilic reactions, so shape changes
43
Q

explain globular proteins

A
  • in globular proteins, the hydrophilic R-groups on the amino acids are pushed to the outside of the molecule, due to the H+H interactions in the tertiary structure
  • so they are soluble, so easily transported in fluids
  • are round and compact
44
Q

examples of globular proteins

A

1) HAEMOGLOBIN - carries oxygen around the body in red blood cells
- is a conjugated protein (protein with a non- protein group (known as a prosthetic group) attached to it)
- each of the 4 polypeptide chains have the prosthetic group haem attached to them, which contains iron which the oxygen can bind to
2) INSULIN- hormone secreted by the pancreas to regulate the blood glucose level
- solubility is important, which means that it can be transported in the blood to the tissues where it acts
- consists of 2 polypeptide chains, which are held together by disulfide bond
3) AMYLASE - enzyme that catalyses the breakdown of starch in the digestive system (most enzymes are globular)
- made of a single chain of amino acids
- secondary structure contains both alpha helix and beta pleated sheets

45
Q

explain fibrous proteins

A
  • insoluble, strong and rope shaped
  • structural proteins that are fairly unreactive (unlike many globular proteins)
46
Q

examples of fibrous proteins

A

1) COLLAGEN - found in animal connective tissues, such as bone, skin and ,muscle
- very strong molecule
- minerals can bind to collagen to increase its rigidity, for example in the bone
2) KERATIN - found in many external structures of animals, such as skin, hair, feathers, horns, nails
- can be flexible (skin) or tough (nails) - dependent on degree of disulfide bonds
3) ELASTIN- found in elastic connective tissue ( skin, large blood vessels and some ligaments)
- is elastic, so allows tissues to return to their original shape after they have been stretched

47
Q

what is an ion

A

an atom with an electric charge

48
Q

what are positive and negative ions called

A

positive: cations
negative: anion

49
Q

what is an inorganic ion

A
  • ion which does not contain carbon
  • important to biological processes
50
Q

calcium ion

A

Ca2+
- involved in transmission of nerve impulses
- release of insulin from the pancreas
-act as cofactor for many enzymes, e.g. those involved in blood clotting, important for bone formation

51
Q

sodium ion

A

Na+
- important in generating nerve impulses, for muscle contraction and regulating fluid balance in body

52
Q

potassium ion

A

K+
- generating nerve impulses
- muscle contraction
- regulating fluid balance in body
- activates essential enzymes for photosynthesis

53
Q

Hydrogen ion

A

H+
-affect pH of substances (H+>OH- means acid)
- important for photosynthesis reactions occuring in thylakoid membrane in chloroplasts

54
Q

Ammonium ion

A

NH4+
- absorbed by plants from soil and an important source of nitrogen
(used to make amino and nucleic acids)

55
Q

Nitrate ion

A

NO3-
- absorbed from soil by plants and an important source of nitrogen
(amino and nucleic acids made with)

56
Q

Hydrogencarbonate

A

HCO3-
- act as buffer, to maintain pH of blood

57
Q

Chloride

A

Cl-
- involved in chloride shift (help maintain pH of blood during gas exchange
-act as cofactor in amylase enzyme
- some nerve impulses

58
Q

Phosphate

A

PO4(3-)
- photosynthesis and respiration reactions
-needed for synthesis of biological molecules such as nucleotides (ATP), phospholipids and calcium phosphate (strengthen bones)

59
Q

Hydroxide ion

A

OH-
- affects pH of substance (OH->H+ means alkali)

60
Q

what functions does water have?

A

1) REACTANT for loads of important chemical reactions, e.g. hydrolysis
2) SOLVENT, means substances can dissolve in it - most biological reactions take place in solutions, e.g. in cytoplasm
3) TRANSPORTS substances, easily as is a liquid and a solvent
4) TEMPERATURE CONTROL as high specific heat capacity and high latent heat, so acts as a coolant
5) HABITAT, means organisms can survive and reproduce in it as it helps with temperature control, is solvent and is less dense when freezes

61
Q

how is water bonded together

A
  • one atom of oxygen joined to two atoms of hydrogen by shared electrons
62
Q

why is water polar

A
  • the shared negative electrons from hydrogen are pulled towards the oxygen atom, meaning the other side of hydrogen atoms have a slightly positive charge
  • unshared electrons of oxygen give it a slight negative charge
  • so polar, partially + and - sides
63
Q

how does water do hydrogen bonding

A
  • slightly negative oxygen atoms attract the slightly positive hydrogen atoms on other molecules
64
Q

explain water’s high specific heat capacity

A
  • SHC = energy needed to raise the temperature of 1g of substance by 1 degree
  • hydrogen bonds between water molecules absorb a lot of energy, takes lot of energy to heat up
  • doesn’t experience rapid temperature change, so good habitat as temperature under water is more likely to be more stable than on land
65
Q

explain high latent heat of evaporation of water

A

-takes a lot of energy to break hydrogen bonds between water molecules
- so high LHOE, lots of energy used up when evaporates
- good for cooling things - some mammals sweat when too hot as when it evaporates, cools the surface of skin

66
Q

explain water being cohesive

A
  • cohesion = attraction between molecules of the same type
  • water molecules are very cohesive, tend to stick together, because they are polar
  • helps water flow, so good for transporting substances
  • helps water to be transported up plant stems in the transpiration stream
67
Q

explain water as a solvent

A
  • a lot of important biological reactions are ionic, e.g. salt ( one positively charged and one negatively charged atom or molecules)
  • water is polar, so slightly negative and slightly positive sides will be attracted to opposite charges ion
  • results in ion getting completely surrounded by water molecules, so dissolved
  • useful solvent for living organisms, e.g. in humans important ions dissolve in blood to be transported around body
68
Q

explain water’s density as a solid

A
  • at low temperature, water freezes and turns into a solid
  • water molecules are held further apart in ice than in liquid because water molecules form 4 hydrogen bonds to other molecules
  • this makes lattice shape, so less dense, and reason to float
  • ice forms insulating layer in cold temperatures, and water below doesn’t freeze
  • fish don’t freeze and can move around
69
Q

how to test for glucose

A
  • test strip coated in a reagent
  • dipped in test solution
  • change colour if glucose present
  • colour can be compared to chart to give concentration of clucose
  • useful for testing urine
70
Q

how to test for starch

A
  • iodine test
  • add iodine dissolved in potassium iodide solution
  • browney/orange to bluey/black
71
Q

how to test for proteins

A
  • biuret test
  • add drops of sodium hydroxide solution (needs to be alkaline)
  • add copper(II) sulfate solution
  • blue to purple
72
Q

how to test for lipids

A
  • emulsion test
  • add ethanol
  • shake for one minute
  • pour solution into water
  • clear to milky/ cloudy (NOT precipitate)
73
Q

what is sugar

A
  • general term for monosaccharides and polysaccharides
74
Q

test for reducing sugars

A
  • monosaccharides and some disaccharides (maltose and lactose)
    add benedict’s reagent to sample and heat in water bath to bring to boil (above 70 degrees)
  • blue to: green, yellow, orange, brick red
  • colour of precipitate changes
  • more accurate = filter and weigh precipitate
75
Q

test for non-reducing sugars

A

disaccharides (sucrose)
- need to be broken down into monosaccharide
- add dilute HCL and heat in water bath to be brought to a boil
- neutralise with sodium hydrogencarbonate
- carry out normal Benedict’s test

76
Q

how can u find concentration of glucose

A
  • benedict’s reagent
  • colorimeter
  • gives a quantitative estimate of how much glucose/ reducing sugar present in a solution
77
Q

what is a colorimeter

A
  • device that measures the strength of a coloured solution by seeing how much light passes through
  • measures absorbance ( amount of light absorbed by the solution)
  • more concentrated the colour = higher absorbance
78
Q

what would you expect in using a colorimeter for glucose

A
  • measure the blue Benedict’s solution left after the test
  • paler the solution, more concentrated the glucose
  • so higher the absorbance, lower the concentration of glucose
79
Q

how would you make up the glucose solutions for the test

A

serial dilution

1) Line up five test tubes in a rack.
2) Add 10 cm* of the initial 40 mM glucose solution to the first test tube and 5 cm° of distilled water to the other four test tubes.
3) Then, using a pipette, draw 5 cm° of the solution from the first test tube, add it to the distilled water in the second test tube and mix the solution thoroughly. You now have 10 cm of solution that’s half as concentrated as the solution in the first test tube (it’s 20 mM).
4) Repeat this process three more times to create solutions of 10 mM, 5 mM and 2.5 mM.

80
Q

how would you perform colorimetry on your solutions

A

1) Do a Benedict’s test on each solution (plus a negative control of pure water, and when in colorimeter, set to 0 after).
Use the same amount of Benedict’s solution in each case.
2) Remove any precipitate — either leave for 24 hours (so that the precipitate settles out) or centrifuge them.
3) Use a colorimeter (with a red filter) to measure the absorbance of the Benedict’s solution remaining in each tube.
4) Use the results to make the calibration curve, showing absorbance against glucose concentration.

Then you can test the unknown solution in the same way as the known concentrations and use the calibration curve to find its concentration.

81
Q

what are biosensors

A

a device that uses a biological molecule (e.g. enzyme) to detect a chemical
- the biological molecule produces a signal (e.g chemical) which is converted to an electrical signal by a transducer
- the electrical signal is then processed and used to work out other information

82
Q

explain glucose biosensors

A
  • used to determine the concentration of glucose in a solution
  • uses enzyme glucose oxidase and electrodes
  • enzyme catalyses the oxidation of glucose at the electrodes, which creates a charge and can be converted to an electrical signal by the electrodes
  • the signal is processed to work out the initial glucose concentration
83
Q

what is chromatography used for

A
  • separating mixtures and identifying the components
  • components such as amino acids, carbohydrates, vitamins and nucleic acids
84
Q

what are the two types of chromatography

A
  • paper
  • thin-layer: uae a layer of thin silica-gel on a rigid surface, such as glass or metal sheet
85
Q

what are the two phases of chromatography

A
  • mobile phase
  • stationary phase
86
Q

what is the mobile phase

A
  • where the molecules can move
  • the liquid solvent (ethanol and water)
87
Q

what is the stationary phase

A
  • where the molecules can’t move
  • paper: chromatography paper
  • thin layer: silica gel, glass, plastic plate (0.1 to 0.3mm)
88
Q

what is the basic concept of chromatography

A
  • mobile phase moves through or over the stationary phase
  • the components in the mixture spend different amounts of time in the phases:
    1) longer in mobile = move faster and further
  • it is time spent in different phases that separates out the components
  • end up with chromatograph
89
Q

PAG: explain how you would complete paper chromatography to identify an unknown amino acid

A

1) Draw a pencil line near the bottom of a piece of chromatography paper and put a concentrated spot of the mixture of amino acids on it. It’s best to carefully roll the paper into a cylinder with the spot on the outside so it’ll stand up.

2) Add a small amount of prepared organic solvent (a mixture of butan-1-ol, glacial ethanoic acid and water is usually used for amino acids) to a beaker and dip the bottom of the paper into it (not the spot).
This should be done in a fume cupboard. Cover with a lid to stop the solvent evaporating.

3) As the solvent spreads up the paper, the different amino acids (solutes) move with it, but at different rates, so they separate out. (this is due to difference in interactions with stationary phase and solubility in mobile phase of each amino acid)

4) When the solvent’s nearly reached the top, take the paper out and mark the solvent front with pencil. Then you can leave the paper to dry out before you analyse it (see below).

5) Amino acids aren’t coloured, which means you won’t be able to see them on the paper. So before you can analyse them, you have to spray the paper with ninhydrin solution to turn the amino acids purple.
This should also be done in a fume cupboard and gloves should be worn. (Note: you can’t use ninhydrin to detect all biological molecules, only proteins and amino acids.)

6) You can then use R, values to identify the separated molecules:

90
Q

what is Rf value and how do you measure it

A
  • ratio of the distance travelled by the solute to the distance travelled by the solvent
  • always less than 1
    -(DISTANCE TRAVELLED BY SOLUTE/DISTANCE TRAVELLED BY SOLVENT)
  • measure from point of origin to the vertical centre of the spot
  • look up Rf values in a database or table of known values

Biology Module 2 (6 decks)

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