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Biological Molecules Flashcards

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1
Q

What is the biological test for a lipid?

A

Add 2cm^3 of test solution into a test tube.
Add 5cm3 of alcohol and mix carefully.
Pour solution into a test tube containing water.

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2
Q

What is the positive test result for the biochemical test of a lipid?

A

A positive test = a white emulsion is formed (white/milky colour).

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3
Q

What is the negative result for the biochemical test of a lipid?

A

A negative test = solution remains clear.

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4
Q

What is a phospholipid?

A

A phospholipid = one fatty acid can be replaced by a polar phosphate group.

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5
Q

What are the factors of a hydrophilic phosphate?

A

Water loving/will dissolve in water (soluble).

A polar molecule (has a charge to it).

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6
Q

What are the factors of a hydrophobic fatty acid?

A

Water hating/insoluble in water.

Uncharged/Non-polar molecule (has no charge to it).

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7
Q

What is a triglyceride molecule?

A

Esterification happens 3 times so you need three fatty acids for 1 glycerol molecule.
1 fatty acid joins to 1 of the 3 oxygen molecules on the glycerol molecule, and the 2 other fatty acids join the other 2 oxygen molecules, so a condensation reaction has to happen 3 times for there to be 3 free oxygen molecules and 3 free carbon molecules and 3 molecules of water from the condensation reaction x 3.

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8
Q

What is an ester bond?

A

An ester bond is between the carbon (with the double oxygen bond) on the fatty acid and the oxygen of the glycerol which is found to bound a lipid together.

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9
Q

What are the properties of a lipid?

A 
Made of C, H and O. 
Can exist as fats, oils and waxes. 
They are insoluble in water. 
They are a good source of energy (38kJ/g). 
They are poor conductors of heat. 
Most fats & oils are triglycerides.
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10
Q

What roles do lipids have?

A
  1. Source of energy - when oxidised provide more than twice the energy as same mass of carbohydrate + release valuable water.
  2. Waterproofing - insoluble in water. Plants have waxy lipid cuticle to conserve water + mammals produce oily secretion from sebaceous gland in skin.
  3. Insulation - fats - slows conduction of heat .: stored beneath body surface to retain body heat.
  4. Protection - stored around delicate organs.
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11
Q

What is a monounsaturated fat?

A

One double bond between the carbon elements.

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12
Q

What is a polyunsaturated fat?

A

More than one double bond between the carbon elements.

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13
Q

What are the types of bonds in carbohydrates?

A

Glycosidic bonds in carbohydrates.

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14
Q

What are the types of bonds found in lipide?

A

Ester bonds are found in lipids.

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15
Q

What are lipids broken down by?

A

Lipids are broken down by the enzyme lipase into glycerol and fatty acids.

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16
Q

What are the 3 elements found in lipids?

A

Carbon, Hydrogen and Oxygen = the elements found in lipids.

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17
Q

What is a fatty acid made up of?

A

Made up of a carboxyl group (-COOH) attached to a hydrocarbon chain of any length - (hydrophobic).

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18
Q

What is the test for starch?

A
  1. Place 2cm3 of sample into test tube/
  2. Add two drops of iodine solution and shake.
  3. Starch present = blue/black. No starch = yellow/orange (stays same colour).
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19
Q

What is the definition for the activation energy?

A

The minimum amount of energy needed to activate the energy.

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20
Q

What type of proteins are enzymes?

A

Enzymes are globular proteins with a specific tertiary shape making them specific to only one reaction.

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21
Q

What are enzymes?

A

They are biological catalysts which can be used repeatedly, so are therefore effective in small amounts ( small amounts can go a long way).

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22
Q

How do enzymes work in the human body?

A

Lower the activation energy for a reaction - reactions can take place at lower temperatures - less energy needed from heat. This allows metabolic processes to happen rapidly at human body temperature. Without enzymes = too slow to sustain life.

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23
Q

What is the active site of an enzyme made of?

A

It is a specific region if the enzyme which is functional and made up of only a small number of amino acids.

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24
Q

What is the substrate?

A

The substrate is a molecule which acts on the enzyme.

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25
Q

What is an enzyme-substrate complex?

A

It is when the substrate fits neatly into the depression of the enzyme to form an enzyme-substrate complex.

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26
Q

What is the induced fit model of enzyme activity?

A

Active site and enzyme are not complementary.
Active site changes shape (is flexible) to become exactly complementary to substrate shape.
Allows substrate to fit active site so enzyme-substrate complexes can be formed.

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27
Q

What is the word used to describe an enzymes shape?

A

COMPLIMENTARY shape to the active site.

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28
Q

What is the lock and key model of enzyme activity?

A

Similar to a key as a key operates a lock, and each key has a specific shape that fits and operates only one lock. Similarly, a substrate only fits active site of one particular enzyme. Model is supported by the observation that enzymes are specific in reactions they catalyse. The shape of the substrate (key) exactly fits the active site of the enzyme (lock) which is why it’s known as the lock and key method.

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29
Q

What is a limitation of the lock and key model of enzyme activity?

A

Enzymes have a specific active site shape which doesn’t change. This shape is exactly complementary to only one substrate’s shape. so a substrate con only fit one enzyme’s active site.

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30
Q

Are all proteins enzymes?

A

No.
Enzymes have an active site.
Not all proteins are enzymes. Many proteins have binding sites/receptor sites which are not reception sites.
Some hormones are proteins and these have receptor sores but they are not receptor sites.

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31
Q

What are the types of bonds found in enzymes?

A

Hydrogen, covalent, ionic and disulphides bonds.

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32
Q

What are the different factors which affect enzyme activity?

A

Temperature
pH
Enzyme concentration
Substrate concentration.

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33
Q

For an enzyme to work, what must happen?

A

Must come into physical contact with its substrate.

Have an active site which fits/is complimentary to its substrate.

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34
Q

How do you measure enzyme-catalysed reactions?

A

Usually measure it’s time course. The two measurements that are changed most frequently are:
Formation of products, e.g. Volume of oxygen produced when enzyme catalyses hydrogen peroxide.
Disappearance of the substrate, e.g. The reduction in concentration of starch with presence of amylase enzyme.

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35
Q

How do you measure the rate of change?

A

To measure rate of reaction = measure gradient at certain point.
Rate = always expressed as per unit time.
If measuring the effect of one variable on something, all the other variables must be kept constant + all possible inhibitors should be kept absent.

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36
Q

How does an increase in temperature have an effect on enzyme action?

A

Temperature rise = molecules have more kinetic energy - move more rapidly so collide with each other more often.
In enzyme catalysed reaction enzyme + substrate will come together more often in a set time, so therefore there will be more effective collisions = more enzyme substrate complexes formed = rate of reaction increases.
Temperature rise = hydrogen bonds in enzyme to break = enzyme + active site changing shape, = substrate fits less easily into active site of enzyme which slows the rate of reaction.
Past a certain temperature, ( normally 60degrees) enzyme is denatured = permanent change + enzyme doesn’t function after.
On graph, is indicated by a falling curve.
Optimum working temperature differs from enzyme to enzyme.

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37
Q

How does a decrease in temperature affect enzyme activity?

A

Decrease in temperature = molecules are given less kinetic energy from heat, so molecules move around slower + therefore collide less often. Means substrate molecules will collide with enzymes less often so less enzyme substrate complexes are produced, so rate of reaction slows. Shown on graph by a low rate of reaction point at the beginning.

38
Q

What is the optimum temperature of an enzyme in the human body?

A

40degrees.

39
Q

What is the temperature where enzymes in the human body start to denature/the hydrogen bonds holding the enzyme break causing enzyme + active site change shape?

A

About 45 degrees.

40
Q

What is the temperature when an enzyme is disrupted hindering it from working any more/denatured?

A

60 degrees.

41
Q

How has the human body evolved to be 37 degrees?

A

Although higher body temperatures = increase in metabolic energy but more energy in form of food = needed to maintain high temperature.
Other proteins, apart from enzymes in the human body, may be denatured at higher temperatures.
At higher temperatures, any further rise in temperature, for example, during illness, may cause the enzymes to denature.

42
Q

What is the pH measuring?

A

The pH is a measure of its hydrogen ion concentration.

43
Q

How does the pH affect enzyme activity?

A

Change in pH = more extreme, beyond a certain pH, enzyme becomes denatured (only small changes though). PH affects enzymes in the following ways:
Change in pH alters charges on amino acids making up active site of an enzyme, so the substrate can no longer be attached to active site + enzyme-substrate complexes can no longer be formed.
May cause bonds holding protein’s tertiary structure to break, causing active site to therefore break = no more substrate can fit into substrate. No longer complimentary to active site’s shape.
Arrangement of active site = down to ionic + hydrogen bonds between -NH2 and -COOH groups of polypeptides that make up an enzyme. Change in H+ ions affects this bonding, causing active site to change.

44
Q

What term is used to say an enzyme stops working?

A

Denaturation.

Enzymes = not living organisms/not alive, so cannot be ‘killed’ and the correct term is therefore denatured.

45
Q

What is the effect of enzyme concentration on rate of reaction?

A

As long as there’s an excess of substrate, an increase in enzyme concentration leads to a proportional increase in rate of reaction.
Proportional increase at first - more substrates than enzyme’s active sites can cope with. Intermediate enzyme concentration = maximum rate of reaction - all substrate molecules can occupy active site at same time.
However once it reaches a certain point, the substrate concentration becomes limiting, as there are not enough active sites to accommodate all available substrate molecules. So addition of further enzyme molecules = no effect, so no increase in rate of reaction so rate of reaction will stabilise at constant level, indicated by a graph levelling off after a certain point.

46
Q

What is a key fact about enzymes?

A

Remember enzymes are not used up, can be used repeatedly. Once an enzymes active site has acted on its substrate it is free to repeat procedure on another substrate molecule. Enzymes work efficiently in very low concentrations.

47
Q

How does the substrate concentration have an effect on enzyme action?

A

Means the enzyme concentration has to be fixed + substrate concentration = slowly increased so rate of reaction increases proportionally to substrate conc. Enzyme molecules have limited number of substrate molecules to collide with - therefore there are too few substrate molecules to occupy all active sites.
More substrate = added, active sites become filled until point where enzyme’ active sites are all occupied at one time, so ror = at maximum.
After this point, addition/increase of substrate concentration has no effect on ror as all active sites = occupied at one time. There is no increase in the ror. Excess of substrate = ror levels off.

48
Q

What are thermophilic bacteria?

A

They are bacterium that live in very high temperatures, e.g. bacteria that live in hot springs function faster at 95 degrees + to continue to operate effectively at 100 degrees.

49
Q

What are the two type of inhibitors?

A

Competitive inhibitors - bind to active site of enzyme.

Non-competitive inhibitors - bind to enzyme at a position other than active site - allosteric site.

50
Q

What are competitive inhibitors?

A

They have a molecular shape similar to substrate - can occupy active site of enzyme so therefore compete against substrate for available active site.
If enzyme activity = increased, effect of inhibitor decreases.
Inhibitor molecule is not permanently bound to the active site of the enzyme, can leave + another molecule can take its place - molecule = substrate or inhibitor, depends on how much is present.
Soon all substrates will occupy an active site of an enzyme.
However, greater the concentration of inhibitor the longer it takes for that to happen.

51
Q

What is a non-competitive inhibitor and how does it work?

A

They attach themselves to binding site (allosteric site) - not the active site.
When attached to enzyme, inhibitor changes shape of enzyme + its active site so substrate molecules can no longer occupy it + enzyme can no longer function.
As substrate + inhibitor = not competing for same site, increase in substrate concentration does not decrease effect of inhibitor.

52
Q

What does ATP stand for?

A

Adenosine triphosphate.

53
Q

What is an ATP molecule made out of?

A

ATP molecule = a phosphorylase macromolecule made of following parts:
Adenine - nitrogen-containing organic base (nitrogenous base).
Ribose - a sugar molecule with a 5-carbon ring structure (pentose sugar) that acts as the backbone to which the other arts are attached.
Phosphates - chain of three phosphate groups.

54
Q

How does ATP store energy?

A 
Adenosine triphosphate (ATP), as name suggests has three phosphate groups. 
Bonds between phosphate groups = unstable + have a low activation energy, so are easily broken. 
When they break they release a considerable amount of energy. 
Usually in living cells = only terminal phosphate that = removed.
55
Q

What is the equation (symbol and word) of ATP being hydrolysed to ADP and what is the enzyme that catalyses this reaction?

A

ATP + (H2O) –> ADP + Pi + E.
Adenosine triphosphate + water –> adenosine diphosphate + inorganic phosphate + energy.
Water = used to convert ATP to ADP, = known as a hydrolysis reaction (water = added to break down a molecule. And reaction is catalysed by the enzyme ATP hydrolyse (ATPase).

56
Q

How is the synthesis of ATP carried out?

A

Conversion of ATP to ADP = a reversible reaction + therefore energy can be used to add an inorganic phosphate to reform ATP according to the equation for ATP –> ADP.
This reaction = catalysed by enzyme called ATP synthase.
Water = removed in this process, so therefore reaction = known as a condensation reaction (as water is removed in order to join two molecules together).

57
Q

When does the synthesis of ATP take place?

A

In chlorophyll-containing plant cells during photosynthesis (photophosphorylation).
In plant + animal cells during respiration (oxidative phosphorylation).
In plant + animal cells when phosphate groups = transferred from donor group to ADP (substrate-level phosphorylation).

58
Q

What is the synthesis of ATP from ADP called?

A

Phosphorylation, there are different types of this (photophosphorylation, oxidative phosphorylation and substrate-level phosphorylation = the only ones I know so far).

59
Q

What is the role of ATP?

A

To provide an immediate energy source to a cell. So cells do not store large quantities of ATP, instead a few seconds’ supply = Not a problem as ATP can be rapidly reformed from ADP and inorganic phosphate (Pi) + so a little goes a long way.

60
Q

Why is ATP a better immediate energy source than glucose?

A

ATP = better immediate energy source than glucose for following reasons.
Each ATP molecule releases less energy than each glucose molecule. Energy = released in smaller, more manageable quantities, instead of much greater and therefore less manageable release of energy from a glucose molecule.
Hydrolysis of ATP to ADP = a single reaction that release immediate energy. Breakdown of glucose = long series of reactions + therefore energy release takes longer than it would from an ATP molecule.

61
Q

Why does ATP have to be continuously made within the mitochondria of the cell?

A

ATP cannot be stored + has to be made continuously within mitochondria of cells that need ATP. Cells such as muscle fibres + epithelium of small intestine - require energy for movement + active transport respectively, so therefore, these cells posses many large mitochondria.

62
Q

How is ATP used in energy-requiring processes?

A 
Metabolic processes. 
Movement. 
Active transport. 
Secretion. 
Activation of cell molecules.
63
Q

How is ATP used in metabolic processes?

A

In metabolic processes, ATP provides energy needed to build up macromolecules from their basic units. For example, making starch from glucose, or polypeptides from amino acids.

64
Q

How is ATP used in movement?

A

ATP provides energy for muscle contraction. In muscle contraction, ATP provides energy for muscle filaments of muscle to slide past one another + therefore shorten overall length of a muscle fibre.

65
Q

How is ATP used in active transport?

A

ATP provides energy to change shape of carrier proteins in plasma membranes. Allows molecules/ions to be moved against concentration gradient.

66
Q

How is ATP used in secretion?

A

ATP = needed to form lysosomes, which are necessary for secretion of cell products.

67
Q

How is ATP used in the activation of cell molecules?

A

An inorganic phosphate is released during the hydrolysis of ATP and can be used to phosphorylase other compounds in order to make them more reactive, therefore lowering the activation energy in enzyme-catalysed reactions. For example, the addition of phosphate to glucose molecules at the starts of glycolysis.

68
Q

What is ATP not?

A

ATP = not a ‘high energy’ substance. ATP = an ‘intermediate energy’ substance that is used to transfer energy.

69
Q

What are most polymers made out of?

A

Carbon, Hydrogen, oxygen and nitrogen.

70
Q

What is the general formula for monosaccharides?

A

(CH2O)2 or C2H2nO2.

71
Q

What are three examples of monosaccharides?

A

Glucose, Galactose and Fructose.

72
Q

What is the test for a reducing sugar?

A

Benedict’s Raegent test.

  1. Add 2cm3 of food sample to test tube (Grind with water if not in liquid form.
  2. Add equal volume of Benedict’s Raegent.
  3. Heat gently in water bath for 5 mins.
  4. Will go any colour apart from blue if is a reducing sugar (red precipitate is strongest).
73
Q

What type of bond is formed between two monosaccharides?

A

Glycosidic bond.

74
Q

What is maltose made of?

A

Glucose + Glucose. Both alpha.

75
Q

What is sucrose made of?

A

Glucose(alpha) + Fructose.

76
Q

What is lactose made of?

A

Glucose (alpha) + Galactose.

77
Q

How are two monosaccharides joined together?

A

Condensation reaction (removal of water molecule) and a glycosidic bond between the two monomers.

78
Q

How is a disaccharide broken up?

A

Hydrolysis breaks the glycosidic bond between the two monomers. So the addition of water breaks them up.

79
Q

What is the test for non-reducing sugars?

A
  1. Grind with water if not in liquid form.
  2. Add 2cm3 of food sample to 2cm3 of Benedict’s raegent in a test tube.
  3. Heat gently for 5 mins. If solution doesn’t change colour from blue then a reducing sugar is not present.
  4. Add another 2cm3 food sample to 2cm3 of dilute hydrochloric acid in a test tube + heat for 5 mins. (HCl will hydrolyse disaccharides into constituent monosaccharides).
  5. Slowly add sodium hydrogencarbonate solution to neutralise HCL - Benedict’s raegent doesn’t work in acidic conditions.
  6. Retest resulting solution with 2cm3 Benedict’s raegent + heat gently for 5 mins.
  7. Will now go orangey-brown due to hydrolysis of non-reducing sugar producing reducing sugars.
80
Q

What is an advantageous property of polysaccharides?

A

Very large molecules, so they are insoluble - good for storage/ giving structure to molecules, e.g. cellulose provides strength structural support for plant cells.

81
Q

How is the lock and key model different to the induced fit model?

A

Active site doesn’t change.
Active site shape is fixed.
Active site shape is already complementary to substrate’s shape.

83
Q

How is starch’s structure adapted to its function?

A
  1. Insoluble - doesn’t affect water potential .: water = NOT drawn into cells by osmosis.
  2. Large + insoluble - doesn’t diffuse out of cells.
  3. Compact - lot stored in small space.
  4. Hydrolysed - forms alpha glucose - easily transported - used in respiration.
  5. Branched form = many ends - each acted on by enzyme at the same time .: glucose molecules released quickly.
84
Q

How is glycogen’s structure adapted to its function?

A
  1. Insoluble - doesn’t diffuse into/out cells by osmosis.
  2. Compact - lot stored in a small space.
  3. Highly branched (more than starch) = more ends for enzymes to work on = readily broken down to glucose molecules used in respiration. Important for animals with high metabolic + respiratory rates than plants as they’re more active.
85
Q

Where is glycogen found?

A

Animals + bacteria.

NEVER plants.

86
Q

Where is starch found?

A

Plants as small grains - seeds + storage organs, e.g. Potato tubers.

87
Q

How is cellulose’s structure adapted to its function?

A
  1. Made of beta-glucose - for, long, straight unbranched chains.
  2. Cellulose chains run antiparallel to one another + = cross linked by hydrogen bonds - add collective strength.
  3. Molecules form microfibrils = grouped to form fibrils - provide more strength.
88
Q

How is the structure of triglycerides adapted to its function?

A
  1. High ratio of energy storing carbon-hydrogen bonds to carbon atoms .: good source of energy.
  2. Low mass to energy ratio = good storage molecules. More energy stored in small volume - +ve for animals - reduces mass they carry as they move around.
  3. Large non-polar molecules. .: insoluble in water - storage doesn’t affect osmosis in cells/water potential of them.
  4. High ratio of hydrogen to oxygen atoms .: release water when oxidised - provides important source of water - vital for organisms living in dry deserts.
89
Q

What are the 4 chemical groups in a protein molecule?

A
  1. Amino Group (-NH2).
  2. Carboxyl Group (-COOH).
  3. Hydrogen atom (-H).
  4. R (side) group.
90
Q

What are the 2 stable groups in a protein?

A

Carboxyl + amino groups.

91
Q

What is the variable Group in the protein - one which changes depending on the type of protein formed?

A

The R (side) group.

92
Q

What does cellulose do?

A

Provide structure and rigidity to a plant with long, unbranched chains of beta glucose which run parallel to one another with hydrogen bonds between them to add to collective strength of the plant.
Prevent cells from bursting by osmosis by exerting an INWARD pressure - stops any influx of water. .: Living cells = turgid + push against one another making non-woody parts of plants semi-rigid - maximised surface area for photosynthesis.

Biology A Level (13 decks)

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