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BIOLOGY A LEVEL > CHAPTER 3 - BIOLOGICAL MOLECULES > Flashcards

CHAPTER 3 - BIOLOGICAL MOLECULES Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What 6 elements are the most abundant in biological molecules?

A

Carbon

Hydrogen

Oxygen

Nitrogen

Phosphorus

Sulfur

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2
Q

Which other elements have important roles in biochemistry

A

Sodium
Potassium
Calcium

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3
Q

explain how atoms join together to form molecules

A

atoms form bonds by sharing pairs of electrons

according to the bonding rules

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4
Q

explain the difference between cations and anions

A

cations are ions that have lost one or more electrons

Has a net positive charge

anions are ions that have gained one more electrons

Has a net negative charge (1)

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5
Q

explain why cells are visible under a light microscope but electron microscopes are needed to see chromosomes

A

cells are larger than ribosomes

electron microscopes have a higher resolution

molecules are smaller that the resolution limit of light and molecules are larger than the resolution limit of electron beam

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6
Q

What are the chemical elements that make up Lipids

A

C, H and O

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7
Q

What are the chemical elements that make up Carbohydrates

A

C, H, O (usually in the ratio Cx(H2O)x )

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8
Q

What are the chemical elements that make up proteins

A

C, H, O, N, S

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9
Q

What are the chemical elements that make up Nucleic acids

A

C, H, O, N, P

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10
Q

What type of ion are Calcium ions, what is its chemical formula and what are they necessary for?

A

Cation

Ca 2+

Nerve impuse transmission

Muscle Contraction

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11
Q

What type of ion are Sodium ions, what is its chemical formula and what are they necessary for?

A

Cations

Na +

Nerve impulse transmission

Kidney function

Regulates water potential

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12
Q

What type of ion are Potassium ions, what is its chemical formula and what are they necessary for?

A

Cation

K+

Nerve impulse transmission

Stomatal Opening

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13
Q

What type of ion are Hydrogen ions, what is its chemical formula and what are they necessary for?

A

Cation

H+

Catalysis of reactions

pH Determination

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14
Q

What type of ion are Ammonium ions, what is its chemical formula and what are they necessary for?

A

Cation

NH4 +

Production of nitrate ions by bacteria

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15
Q

What charge are Cations?

A

Positive (it is positive if you iron a cat)

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16
Q

What charge are on Anions?

A

Negative

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17
Q

What type of ion are nitrate ions, what is its chemical formula and what are they necessary for?

A

Anion

NO3 -

Nitrogen supply to plant for amino acid and protein formation

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18
Q

What type of ion are Hydrogen Carbonate ions, what is its chemical formula and what are they necessary for?

A

Anion

HCO3 -

Maintenance of blood pH

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19
Q

What type of ion are Chloride ions, what is its chemical formula and what are they necessary for?

A

Anion

Cl-

Balance positive charge of sodium and potassium ions in cells

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20
Q

What type of ion are Phosphate ions, what is its chemical formula and what are they necessary for?

A

Anion

PO4 3-

Cell membrane formation

nucleic acid and ATP formation

Bone formation

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21
Q

What type of ion are Hydroxide ions, what is its chemical formula and what are they necessary for?

A

Anion

OH -

Catalysis of reactions

pH determination

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22
Q

What is a covalent bond?

A

A chemical bond formed when two or atoms share electrons.

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23
Q

What is ionic bonding?

A

Transfer of electrons. this forms positive and negative ions.

The oppositely charged ions are electrostatically attracted

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24
Q

state the ‘bonding rules’

A

carbon atoms form 4 bonds

nitrogen atoms form 3 bonds

oxygen atoms form 2 bonds

hydrogen atoms form 1 bond

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25
Q

explain why life is often referred as ‘carbon-based’

A

carbon forms the backbone of most biological molecules as it can form 4 bonds

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26
Q

What are polymers?

A

long chain molecules made up by linking multiple individual molecules called monomers in a repeating pattern

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27
Q

what is an inorganic ion

A

An ion that doesn’t contain carbon

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28
Q

Example of a Biological molecule that exists asa Polymer

A

Carbohydrates - monomers are sugars (saccharides)

Proteins - monomers are amino acids

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29
Q

what are the roles of water

A

solvent
transport medium
coolant
habitat

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30
Q

what is a polar molecule?

A

a molecule with an uneven distribution of charge

e.g. Water

Region of negative charge = oxygen

region of positive charge = hydrogen

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31
Q

explain how hydrogen bonds form

A

Oxygen and hydrogen share electrons unequally when they bond.

Oxygen is more negative

Hydrogen, has a smaller share/is more positive

The more negative oxygen atom is attracted to the more positive hydrogen atom

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32
Q

Explain why water is a polar molecule

A

Water is a molecule with an unequal distribution of charge,

the Oxygen side is (-) and the hydrogen side is (+) due to the sharing of electrons in the covalent bond

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33
Q

What are Intermolecular forces

A

forces of attraction between molecules

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34
Q

What are intramolecular forces

A

bonding forces that hold the atoms of a molecule together

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35
Q

What is a hydrolysis reaction

A

addition of water to break bonds

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36
Q

what is a condensation reaction

A

water is produced
bonds are made

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37
Q

What is Cohesion

A

Attraction between molecules of the same substance

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38
Q

What is an adhesive

A

a substance that unites or bonds surfaces together.

this is where water molecules are attracted to other materials like other polar molecules or charged ions

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39
Q

How strong are hydrogen bonds?

A

weak

which break and reform between constantly moving water molecules

but the intra-molecular forces are very strong

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40
Q

explain why water a liquid at room temperature? (or have a unusually high boiling point)?

A

it can form hydrogen bonds between individual molecules
hydrogen bonds absorb a lot of energy

so water has a high specific heat capacity, taking lao too energy to break hydrogen bonds

so it doesn’t experience a rapid temperature change

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41
Q

explain why water having a high specific heat capacity is important for the survival of organisms

A

the temperature of water is likely to be more stable than it Is on land
as it takes a lot of energy to increase the temperature.

this makes a good habitat METABOLIC reactions can occur in the same rate and GASES remain SOLUBLE

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42
Q

Define specific heat capacity

A

the energy needed to raise the temperature of 1 gram a substance by one degree Celsius

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43
Q

explain why hydrogen bonds have a high latent heat of evaporation

A

takes a lot of energy to break hydrogen bonds between water molecules

so a lot of energy is used to break these bonds for water to evaporate

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44
Q

explain how high later heat of evaporation of water is important for the survival of organisms

A

used as a cooling technique
for instance mammals can sweat

this is because it takes energy from mammals to break hydrogen bonds that hold water molecules together
in order for water to evaporate
cooling down organisms

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45
Q

explain why the cohesive retry of water is important for the survival or organisms

A

its good for the transportation fo substances

water being cohesive helps create a flow

eg in plant stems In the transpiration stream

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46
Q

Explain why ice floats in reference to the properties of water

A

hydrogen bonds fix the positions of the polar molecules slightly further apart than in liquid state

producing a giant, rigid but open structure

so water becomes less dense

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47
Q

what causes a ‘skin’ of surface tension

A

The water molecules are more strongly cohesive to each other than they are to air

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48
Q

explain why a pond skater can ‘walk’ on water

A

the water molecules are more strongly cohesive to each other
than they are to air

resulting in a ‘skin’ of surface tension

that is strong enough to supports the pond skater (and other small insects)

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49
Q

explain how water acts as a POLAR solvent

A

water is polar

biological molecules such as amnio acids are also polar molecules
and charged ions

both attract to water

molecules in forces of attraction
the molecules then breakdown and are able to dissolve
surrounded by water molecules

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50
Q

explain why water makes up most cytosol (cytoplasm) of most prokaryotic and Eukaryotes

A

water is a liquid

water allows the movement of substrates and enzymes
necessary for reactions to take place

water is a substrate for some reaction

water is a polar solvent and most biological molecules are polar solvents and charged ions both dissolve in the water for a chemical reaction to take place

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51
Q

explain why water makes a good transportation medium

A

cohesion between water molecules (molecules stick together)
and adhesion between water molecules and other polar molecules

result in water exhibiting a capillary action

so water can rise up a narrow tube against the force of gravity

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52
Q

explain why xylem can draw up water

A

water has cohesive properties
this means it moves as one mass as the molecules are attracted to each other

so when water is drawn up the molecules don’t separate

and adhesion between water molecules and other polar molecules

result in water exhibiting a capillary action

so water can rise up a narrow tube against the force of gravity

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53
Q

What is capillary action?

A

the attraction of the surface of a liquid to the surface of a solid

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54
Q

explain why water acts as a coolant during chemical reactions in prokaryotic and Eukarytic cells

A

due to the large amounts of energy required to overcome hydrogen bonding
maintaining constant temperatures in cellular environments is really important as enzymes are only active in narrow temperature ranges

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55
Q

What is a coolant?

A

helping to buffer temperature changes during chemical reactions

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56
Q

explain why water can provide a constant environment for aquatic organisms

A

it does not change temperature easily

Floating ice can insulate water belowwhat

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57
Q

What are the different properties of water

A
  • thermal stability
  • forms a liquid
  • Higher density than ice
  • surface tension
  • cohesion
  • solvent
  • metabolic
  • transparency
  • high specific heat capacity
  • high specific latent heat of vaporisation
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58
Q

What is the benefit of thermal stability of water to an organism

A

Stable enviroment for aquatic organisms

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59
Q

What is the benefit to an organism of water as a liquid

A

Transport medium in animals and plants

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60
Q

What is the benefit to an organism of the low density of ice

A

Ice floats on water and insulates the water below

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61
Q

What is the benefit to an organism of the surface tension of water

A

Small animals can move across the surface of the water

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62
Q

What so teh benefit to an organism of water being cohesive

A

Water molecules form a strong water column that moves up the xylem of plants

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63
Q

What is the benefit to an organism of water being transparent

A

Water allows light to move through it so aquatic plants can photosynthesise

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64
Q

What is the benefit to an organism of water being metabolic

A

Water is used to break bonds in hydrolysis and make bonds in condensation reactions

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65
Q

Suggest with reasons which properties of water make it such an important component of blood

A

Liquid so transport medium

Polar solvent

Biological molecules are polar

Ions are charged

Coolant so resistant to temp change

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66
Q

Water forms the basis of the storma in chloroplasts and the matrix in mitochondria.
Describe which properties of water make it such an important component of these particular organelles

A

Water as a POLAR solvent

Biological molecules that are polar and charged ions would dissolves

Water is a liquid

Allows movement of substance AND enzymes

Necessary for reaction to take place

Water is a sub star ate fro some reactions

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67
Q

How is water important for aquatic life

A

Water provides stable environment due to high specific heat capacity

It is a liquid between 0 and 100 degrees so it can be used as a transport medium in a aquatic plants and animals

Ice has a lower density than water so it floats on top of the water insulating the water below

Water is transparent so it allows light through to reach aquatic plants form phtotsynthesis

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68
Q

How does the structure of water contribute to its function as a transport medium

A

Water is a polar solvent (1)

liquid

Cohesion between water molecules and solute due to hydrogen bonds forming (1)

Adhesive between water molecules and wall / xylem/ blood vessel due to hydrogen bonds forming

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69
Q

explain how water is used as a coolant in maulticellular organisms

A

Water has a high latent heat of vaporisation

Water evaporates from surfaces taking heat with it

For example sweating /panting

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70
Q

What is the difference between specific heat capacity and latent heat capacity

A

Specific heat capacity is a measure of how much energy is needed to warm up a substance

Specific latent heat capacity is a measure of how much energy is needed to convert a substance from one stage to another - energy needed in breaking bonds that hold molecules together

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71
Q

explain why ice floating is essential for aquatic organisms

A

insulating layer on top of water

water below doesn’t freeze
fish don’t freeze and can still move around

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72
Q

explain why elephants spray themselves with water to cool down

A

water evaporates on the surface of elephant body

hydrogen bonds that hold water molecules together
need a lot energy to be broken from elephant

this cools surface of elephant body

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73
Q

What are Carbohydrates?

A

Molecules that only contain elements C, H, O

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74
Q

What does Carbohydrate mean and what ration are the elements in?

A

Hydrated carbon

Ratio Cx(H2O)y

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75
Q

Other names for carbohydrates?

A

Sugar or saccharides

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76
Q

Example of a monosaccharide

A

Glucose, Fructose and ribose

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77
Q

What is formed when 2 monosaccharides are joined together

A

Disaccharides

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78
Q

Example of Disaccharides

A

Lactose and Sucrose

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79
Q

What forms when a chain of monosaccharides join together?

A

Polysaccharide

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80
Q

Example of Polysaccharide

A

Glycogen, Cellulose, Starch

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81
Q

Formula for glucose

A

C6 H12 O6

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82
Q

What type of monosaccharide is glucose?

A

Hexose monosaccharide

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83
Q

What direction are carbons numbered on glucose?

A

Clockwise, Starting from Far Right

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84
Q

What are there 2 structural variations in Glucose?

A

Alpha and beta

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85
Q

What is the difference between the two glucose structures (alpha and beta)

A

The OH (hydroxyl) group on Carbon 1 is flipped

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86
Q

Properties of glucose

A

Polar

Soluble in water

can form H bonds

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87
Q

Where is dissolved glucose found in the cell

A

Cytosol

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88
Q

What is formed when 2 glucose molecules are next to each other

A

They react

Forms maltose and Water

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89
Q

What is the covalent bond formed in the condensation reaction of 2 glucose molecules?

A

Glycosidic

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90
Q

Sources of Monosaccharides

A

Fructose - Fruit

Galactose - Milk/Milk Products

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91
Q

Sweetness of monosaccharides

A

Fructose

Glucose

Galactose

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92
Q

Where are ribose sugars present?

A

RNA nucleotides

DNA nucleotides

Other Biological molecules

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93
Q

What type of Sugar is ribose

A

Pentose

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94
Q

What is formed when many Glucose molecules are formed?

A

Starch

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95
Q

Name one of the polysaccharides in starch

A

Amylose

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96
Q

What shape does Amylose form?

A

helix, stabilised by Hydrogen bonds

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97
Q

Why is amylose’s structure suited to its function

A

More compact - more can be stored

Compact - Less Soluble

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98
Q

Why is amylopectin branched?

A

it has both 1,4 and 1,6 glycosidic bonds

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99
Q

What is the equivalent of starch in animals and fungi?

A

Glycogen

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100
Q

What is one advantage of Glycogen?

A

Forms more branches (than eg amylopectin) so it is more compact and needs less space for storage

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101
Q

Advantages of branching

A

Compact

Easy to add to (eg more glucose molecules to free ends)

Speeds up releasing of molecules

Insoluble

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102
Q

What is starch (in plants) and Glycogen (in animals and fungi) needed for?

A

Respiration

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103
Q

What type of reaction is undergone to release glucose from starch/glycogen

A

Hydrolysis - catalysed by enzymes

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104
Q

What is cellulose comprised of?

A

beta-glucose molecules

Alternately turned upside down

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105
Q

Cellulose make what bonds forming what?

A

Hydrogen bonds

Microfibrils

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106
Q

What do many microfibrils combine to create?

A

Macrofibrils

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107
Q

What do many macrofibrils join together to create?

A

Cellulose fibres

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108
Q

What quality of cellulose fibres make a good cell wall?

A

Insoluble

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109
Q

Explain how the structure of cellulose is related to its function

A

Cellulose makes cell walls strong

Can resist turgor pressure

Bonds difficult to break;

Resists action of enzymes/hydrolysis

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110
Q

Explain why beta glucose, when polymerised, leads to the production of cellulose instead of starch

A

In beta glucose the hydroxyl group at carbon 1 is above the ring

so alternate glucose molecules must rotate 180 degrees

so the hydroxyl groups on carbon 1 and carbon 4 are close enough to react.

Condensation reaction forming a glycosidic bond.

The rotation of molecules produces a straight chain molecules- cellulose.

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111
Q

How do reducing sugars act?

A

Donate electrons or reduce another molecule/chemical

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112
Q

What is the chemical test for a reducing?

A

Benedicts reagent

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113
Q

How is the Test for carbohydrates carried out?

A

Place sample in boiling tube (if solid, grind up or blend in water)

Add equal volume of Benedict’s reagent

Heat mixture in water bath for 5 minutes

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114
Q

What will happen if a reducing sugar is precent?

A

Reducing sugars will react with the copper ions in the copper sulphate (Benedict’s reagent)

Results in addition of electrons to blue Cu2+ ions and turns them to red Cu+ ions

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115
Q

What is Benedict’s Reagent also known as?

A

Copper (II) Sulfate

Cu(SO4)

116
Q

What are the positive tests for carbohydrate

A

(None - Blue)

Low conc - Green

Medium conc - Orange/yellow

High conc - Red

117
Q

Test for non-reducing sugars

A

Negative result for Benedict’s

Boil with dilute HCl

Positive result for Benedict’s as the sugar has been hydrolysed

118
Q

Acronym for Tests

A

CB SI PB LE

Carbohydrates - Benedict

Starch - Iodine

Proteins - Biuret

Lipids - emulsion

119
Q

What is the iodine test method?

A

Add a few drops of potassium iodide solution to sample

If solution changes from yellow/brown to purple/black, starch is present

120
Q

Name another method that can be used to test the presence of reducing sugars and one advantage

A

Reagent Strips

Shows concentration of the sugar

121
Q

How is colorimetry of Benedict’s test conducted?

A

Filter placed in colorimeter

Colorimeter calibrated using distilled water

Benedicts test performed on range of known concentrations of glucose

resulting solutions filtered to remove the precipitate

% transmission of each of the solutions measured

Calibration curve plotted

122
Q

Example of a non-reducing sugar

A

Sucrose

123
Q

Example of a reducing sugar

A

Glucose

124
Q

What do biosensors do?

A

They use biological components to determine the presence and concentration of molecules such as glucose

125
Q

what are the Components of a biosensor

A

Molecular recognition - A protein or single strand of DNA is immobilised to a surface eg. a glucose test strip, which will bind to the molecule under investigation

Transduction - Cause a change in a transducer. A transducer detects changes, eg pH, and produces a response, eg release of a dye or electric current

Display - This then produces a visible, qualitative or quantitative signal such as a particular colour on a test strip or reading on machine

126
Q

Describe the feature of enzymes essential to their role as components in a biosensor

A

enzymes have active site

active site is specific to a molecule

127
Q

Why does Benedicts reagent turn red when warmed with a reducing sugar?

A

Reducing sugars react with copper ions in Benedict’s reagent

resulting in the addition of electrons to blue Cu2+ ions

Reducing them to brick red Cu+ ions

128
Q

Explain why an iodine test is used in experiments to show that plants require light for photosynthesis

A

Iodine test produces a purple/black colour indicating the presence of starch

Starch is a product of photosynthesis

The test shows that starch is produced when light is available to the plant

but not when the plant is kept in the dark

129
Q

Suggest how reagent strips might be useful in the management of the medial condition diabetes, where a person’s blood sugar level can become too high

A

Reagent strips are quantitative

They can be used to estimate the concentration

of glucose in the blood.

They are simple to use and interpret

130
Q

What is the difference between a fat and an oil?

A

Fats are lipids that are solid at room temp

Oils are lipids that are liquid at room temp

131
Q

Why are Lipids non-polar?

A

The electrons in the outer orbitals are more evenly distributed than in polar molecules

No positive or negative areas within molecule

Not soluble in water

132
Q

Why are Lipids macromolecules?

A

Large and Complex

Built from monomers

133
Q

How is a triglyceride formed?

A

Combining a glycerol (alcohol) with 3 fatty acids (Carboxylic acids with hydrocarbon chain attached)

134
Q

How do Glycerol and Fatty acids react?

A

Glycerol is a triol

each OH group on alcohol reacts with OH of each COOH on fatty acid

Forms 3 ester bonds (esterification) and 3 water molecules

135
Q

What is needed to reverse the triglyceride formation reaction

A

Water

Hydrolysis reaction

Forms glycerol and 3 fatty acids

136
Q

What is the difference between saturated vs unsaturated fatty acids

A

Saturated chains have no double bonds present between carbon atoms - maximum amount of Hydrogens

Unsaturated chains have double bonds present, can be called mono- or polyunsaturated

137
Q

What are Phospholipids?

A

Modified triglycerides that contain Phosphorus as well as C,H,O

One of the fatty acid chains on a triglyceride is replaced by a phosphate group

138
Q

What charge are on Phosphate ions and what property does this give them?

A

negative (3-)

contains extra electrons

Soluble in water

139
Q

What are the charges on a phospholipid

A

Hydrophilic, polar, charged (phosphate) Head

Hydrophobic, non-polar, uncharged (fatty acid) tails

140
Q

What occurs when a phospholipid is in the presence of water?

A

Hydrophilic phosphate head will stick head on water

Hydrophobic Fatty acid tails stick out of water

Forms layer on top of water

141
Q

What are Phospholipids also called?

A

Surface active agents or surfactants

142
Q

What arrangement of phospholipids are present in membranes

A

Bilayer

143
Q

What are sterols also known as?

A

Steroid Alcohols

144
Q

What is an example of a sterol?

A

Cholesterol

145
Q

What are sterols based on?

A

4 carbon ring structure with OH group at one end

Has hydrophilic and Phobic sides (OH is phillic, rest of molecule is phobic)

146
Q

Where is cholesterol manufactured in the body?

A

Liver and Intestines

147
Q

What role does cholesterol play in membranes

A

Adds stability and regulates fluidity

148
Q

What are the roles of lipids?

A

membrane formation (creation of hydrophobic barriers)

Hormone Production

Electrical Insulation for impulse transmission

Waterproofing (eg birds feathers, plant leaves)

149
Q

What role do lipids play under the skin and around vital organs?

A

Thermal Insulation to reduce heat loss (eg penguins)

Cushioning to protect vital organs (eg heart and kidneys)

Buoyancy for aquatic animals (eg whales)

150
Q

How can lipids be identified?

A

Emulsion Test

151
Q

Describe the method for the emulsion test?

A

Mix sample with ethanol

Add water and Shake

If a white emulsion forms as a top layer, lipid is present

152
Q

Explain how hardening vegetable oils produces solid fats

A

hydrogenation

removes double bonds in fatty acids

closer packing of molecules

153
Q

Explain why it is considered more healthy to have a low overall fat content as well as a low saturated fat content in a spread

A

unsaturated and saturated fat have high energy content

excess energy intake leads to obesity

154
Q

Using your knowledge of the structure of fatty acids describe why oils are liquid and fats are solid at room temperature

A

Oils are unsaturated

unsaturated fatty acids contain double bonds

molecules cannot pack closely

Fats are usually saturated so fatty acids have no double bonds

155
Q

Describe the formation and the hydrolysis of an ester bond

A

Hydroxyl group from glycerol

Hydroxyl group from fatty acid

Condensation reaction (forms ester bond)

Hydrolysis is reverse of the process above

156
Q

Some bacteria are extremophiles meaning they live in extreme environments that are very high acidic or have very high temperatures. The phospholipids present in other bacteria or eukaryotic cells would be broken down in such extreme conditions. Extremophiles have membranes composed of modified phospholipids.

A) identify which of the phospholipids in the diagram is present in the cell membrane of extremophiles (pg58)
B) outline the similarities and differences between the two types of phospholipid
C) Suggest why the phospholipids oil the membranes of extremophiles can withstand extremes of temperature and pH

A

A) A

B) Both have phosphate group attached to glycerol
Both have fatty acid (tail)

Cross links between fatty acid tails in A
Ester bond not present (on A)

C) Cross links stabilise the membrane

157
Q

Read the following statements

Lipids are not soluble in water

Lipids and ethanol are soluble in water

Water is more soluble than lipids in ethanol

use the information to explain how the emulsion test for lipids woks

A

procedure for emulsion test statement 2, sample / lipid, dissolved in ethanol

water is mixed with ethanol (and lipid) solution

statement 3, idea that water displaces lipid from ethanol forming suspension

statement 1, (suspension forms because) lipids not soluble in water

158
Q

What are peptides?

A

Polymers made up of amino acid molecules

159
Q

What is a protein

A

One or more polypeptides arranged as a complex macromolecule

160
Q

What elements are proteins made from?

A

C, H, O, N

161
Q

What is the structure of an amino acid?

A

Amine group (-NH2)

Carboxylic acid group (-COOH)

Central Carbon w/ a hydrogen and an R (variable group) attached

162
Q

How is a peptide bond formed?

A

H on NH2 and OH in COOH group of 2 amino acids form water

Nitrogen then bonds to the carbon

163
Q

Structural formula for Amino Acid and a dipeptide

A

NH2 CHR COOH

NH2 CHR CONH CHR COOH

164
Q

What type of reaction forms a dipeptide?

A

Condensation

165
Q

What is the name given to many amino acids joined together?

A

polypeptide

166
Q

What is the enzyme which catalyses the reaction for peptide bond formation and where is it found?

A

Peptidyl Transferase

Ribosomes - sites of protein synthesis

167
Q

What happens when Various R groups interact with each other?

A

Leads to long chains of amino acids (polypeptides) folding into complex precise 3D shapes (proteins)

168
Q

What method is used to separate individual components of a mixture?

A

Thin Layer Chromatography

169
Q

What are the 2 phases in chromatography?

A

Mobile phase (Organic Solvent)

Stationary Phase (Silica Gel)

170
Q

How are amino acids separated in TLC?

A

Solubility in mobile phase

If they are more soluble, they will be higher up the plate

if they are less soluble, they will be lower down the plate

171
Q

Describe the method for TLC

A

Draw line 2cm up from the bottom of the plate using pencil

Mark point(s) (equally spaced if multiple)

Spot Amino acid solution onto base line using capillary tube, let dry, then spot again

Place plate into a closed jar of solvent, no more than 1 cm deep

Leave plate until solvent has reached 2cm from top, mark solvent front with pencil

Spray plate with Ninhydrin in fume cupboard, Mark each spot with pencil

Analyse results

172
Q

Suggest why gloves were worn by the student and the plate was only handled by the edges (TLC)

A

Prevent contaminating stationary phase

Biological material on skin

173
Q

A mixture of solvents (such as hexane, water, acetic acid and butanol) is usually used as the mobile phase when separating an unknown mixture of amino acids. Suggest Why (TLC)

A

testing unknown compounds

not known whether substance is polar or non-polar

Different solvents will dissolve both polar and non-polar compounds

174
Q

Explain why the solvent was no more than 1 cm deep (TLC)

A

so the concentrated spots were not covered

175
Q

Suggest why the jar was sealed (TLC)

A

Air inside jar is saturated with solvent

prevents evaporation of solvents

176
Q

What is Primary structure of a protein?

A

The sequence in which he amino acids are joined together

Directed by information in DNA

Particular amino acids in the sequence will fold to give its shape

177
Q

What bonds are involved in primary protein structure?

A

Peptide bonds only

178
Q

What is the secondary structure of a protein

A

Alpha Helix or Beta pleated sheet

Hydrogen bonds form, coiling it into shape

179
Q

What bonds are in secondary structure of a protein?

A

Peptide and Hydrogen

(R groups are not involved in this stage)

180
Q

What determines if a secondary protein is an alpha helix or a beta pleated sheet?

A

Hydrogen bonds that form due to the sequence of amino acids

181
Q

What is Tertiary protein structure

A

Folding of a protein into its final shape, often including sections of secondary structure

Interaction of R groups

182
Q

What bonds are in tertiary protein structure

A

Hydrophobic and Hydrophilic interactions (R-groups)

Hydrogen Bonds

Ionic bonds (R-groups)

Disulphide bridges (R-groups)

Peptide Bonds

183
Q

What is quaternary protein structure?

A

The association of 2 or more individual proteins called subunits

Same interactions in tertiary structure, but are between proteins rather than within a molecule

184
Q

Can protein sub units be different?

A

Protein subunits can be identical or different

Enzymes often consist of 2 identical subunits

Hormones can consist of 2 different subunits eg insulin

185
Q

Name an example of a quaternary structured protein

A

Haemoglobin

Found in Blood

Two sets of 2 identical sub units (2 alpha chains, 2 beta chains)

186
Q

What determines if the protein is hydrophobic or hydrophilic, and the way it folds?

A

R-Groups

187
Q

What enzyme is used to catalyse the breakdown of peptides?

A

Proteases

188
Q

What test is used to identify proteins?

A

Biuret test

189
Q

Describe the procedure of a biuret test

A

Add 10% Sodium Hydroxide solution to equal volume of liquid sample

Then add 1% Copper sulphate solution dropwise until blue

Mix Solution and leave to stand for 5 minutes

If violet coloured, proteins are present

190
Q

State the colour you would expect to see on addition of the copper sulfate solution if protein is present in the sample?

A

Purple

191
Q

State the colour you would expect to see if the sample contains amino acids instead of proteins

A

No peptide bonds present as no protein

Test is negative

Solution remains blue

As Copper sulfate solution is blue

192
Q

Suggest why the Biuret test is not used quantitatively

A

Biuret test identifies peptide bonds

Degree of colour change dependent on number of peptide bonds

Different proteins have different numbers of peptide bonds

Different degrees of colour change could indicate different proteins not different quantities of protein

193
Q

Describe the formation of a peptide bond

A

Condensation reaction

between amine group of one amino acid

and carboxylic acid group of another

forming a water molecule.

194
Q

Describe how hydrogen bonds form within the secondary structure of proteins

A

Oxygen is relatively negative and hydrogen (attached to nitrogen) is relatively positive

Oxygen and hydrogen are attracted to each other, forming bonds

195
Q

Alpha Keratin, a protein found in sheep’s will, is primarily composed of alpha helices. Explain why alpha keratin has a more regular structure than the quaternary protein haemoglobin

A

Secondary structures are simple repeating structures

haemoglobin, has multiple tertiary structures

tertiary structure is formed from complex folding of secondary structure

196
Q

Compare and contrast the role of R-group interactions in the formation of the tertiary and quaternary proteins

A

R groups on amino acids interact

tertiary structure – interactions within a protein molecule

determines shape of molecule

quaternary structure – interactions between protein molecules

holds molecules together

Both involve the same interactions

i.e., hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic and hydrophilic interactions

197
Q

What are the two main groups of proteins?

A

Fibrous and Globular

198
Q

Describe Globular Proteins and their properties

A

Tertiary proteins

Water soluble

Compact

Roughly Spherical

199
Q

Example of a Globular protein

A

Insulin

200
Q

What does insulin do?

A

Regulates blood glucose

201
Q

Where are hormones transported?

A

Bloodstream

202
Q

How do hormones effect a target cell?

A

Hormones fit into specific receptors on cell-surface membranes therefore needing precise shapes

203
Q

What are conjugated proteins?

A

Globular proteins containing a non-protein prosthetic group

204
Q

What types of prosthetic groups are there

A

Lipids

Carbohydrates

Lipoproteins

Glycoproteins

Metal ions eg Iron ions

205
Q

Example of a conjugated protein?

A

Haemoglobin, contains harm group (iron ions) bound reversibly to each sub unit

Catalase, contains 4 haem groups

206
Q

What does catalase do?

A

Speeds up breakdown of harmful Hydrogen Peroxide into water and oxygen, due to its Iron II ions

207
Q

What are fibrous proteins

A

Long, insoluble molecules

high proportion of amino acids are hydrophobic

High repetition, organised structures

208
Q

Examples of Fibrous protein

A

Keratin, Elastin, Collagen

209
Q

What is Keratin, where is it found and what properties does it have?

A

A fibrous protein

Present in hair, skin and nails

Large proportion of sulfur containing amino acids, so they have lots of disulphide bridges

Strong, inflexible and insoluble

210
Q

What is elastin, where is it found and what properties does It have?

A

Elastin is a fibrous protein found in elastic fibres

Present in blood vessel walls and alveoli of the lungs

Gives flexibility

Quaternary protein Made from stretchy molecules called tropoelastin

211
Q

What is Collagen, where is it found and what properties does it have?

A

Fibrous protein

Connective tissue found in the skin, tendons, ligaments and the nervous system

made up of 3 polypeptides wound together in a long, rope-like structure

gives strength and flexibility

212
Q

Suggest what property the arrangement of collagen fibres into large bundles gives to tendons

A

strength or non-elastic

213
Q

As we age, the collagen in our skin starts to break down. This leads to the loss of Full of wrinkles. Many beauty products are available that contain collagen in the form of creams and capsules. Using your knowledge of the structure of collagen, suggest why these products are unlikely to have any beneficial effect in reducing or preventing wrinkles.

A

large molecule so unlikely to enter skin

has a complex structure,

Individual components arranged in hierarchical structure,

New molecules would not incorporate into existing collagen

214
Q

What is the order for increasing bond strength out of these three bonds, weakest-strongest,
ionic bonds, disulphide bonds, hydrogen bonds?

A

Hydrogen bonds

Ionic bonds

Disulfide bridges

215
Q

Explain the difference between a simple protein and a conjugated protein

A

Conjugated proteins contain a non-protein group

called a prosthetic group

simple proteins do not

216
Q

Describe the differences in properties and functions of insulin, a hormone, and keratin, present in nails and hair

A

Insulin globular protein

soluble (1)

specific shape (1)

binds to receptor (1);

chemical messenger

Keratin fibrous protein

strong

structural function (e.g. hair, nails)

217
Q

Describe why global proteins are soluble in water but fibrous proteins are not

A

Globular proteins hydrophobic R groups, in the centre (of the molecule) not in contact with water

hydrophilic R groups, on the outside (of the molecule) / in contact with water

Hydrophobic R groups are repelled by water / hydrophilic R groups are attracted to water

fibrous proteins have R groups on the outside of the molecule

218
Q

Myoglobin is an oxygen carrying molecule found primarily in muscle tissue. It is formed from a single polypeptide chain which is folded to form eight alpha helices. This chain is further folded around a central prosthetic group which binds reversibly with oxygen. The hydrophobic R groups of the amino acids are positioned towards the centre of the molecule.

Discuss the similarities and differences in the structures of haemoglobin and myoglobin.

A

similarities
globular (protein)

alpha helices

prosthetic group

hydrophobic R groups positioned towards the centre (of the molecule)

differences
single polypeptide not four

polypeptides / myoglobin tertiary not quaternary

no beta chains

219
Q

What are nucleic acids?

A

Large molecules discovered in the nucleus of cells

220
Q

What are the two types of nucleic acid?

A

DNA and RNA

221
Q

What elements comprise nucleic acids and nucleotides?

A

C, H, O, N, P

222
Q

What are the 3 components to a nucleotide monomer?

A

Pentose sugar (ribose)

Phosphate group -PO4 2-

Nitrogenous base

223
Q

What are phosphodiester bonds bonding

A

Phosphate at Fifth carbon pentose (ribose) sugar (5’) of one nucleotide bonds covalently to the OH group at carbon 3 (3’) of the next sugar

224
Q

What are phosphodiester bonds also known as?

A

Sugar Phosphate backbone

225
Q

What does DNA stand for and what is the difference from RNA (not asking bases)

A

Deoxyribonucleic acid

One fewer oxygen atom on the ribose sugar

226
Q

What 2 type of bases are there?

A

Pyrimidines (smaller) - C, T

Purines Bigger - A, G

GorillAs are BIGGER than CaTs (Egypt worshiped cats so CT are pyrimidines)

227
Q

What are the complementary base pairs in DNA?

A

Adenine - Thymine (2 Hydrogen Bonds)

Guanine - Cytosine (3 Hydrogen Bonds)

228
Q

What structure does a DNA molecule form? (2 strands)

A

Double Helix

229
Q

How is a double Helix held together?

A

Hydrogen bonds

230
Q

How are the two DNA strands orientated?

A

Antiparallel

3’-5’ one chain

5’-3’ opposite chain

231
Q

Why does complementary base paring help DNA structure?

A

maintains constant distance/ chain width between backbones

Equal Volumes of CG and equal volumes of AT

232
Q

function of DNA

A

stores genetic information that controls protein synthesis

233
Q

function of RNA

A

polynucleotide molecules that synthesise proteins from copying and transferring instructions in DNA

234
Q

What base is different in RNA?

A

Thymine is replaced by Uracil (bonds to adenine)

235
Q

Why is mRNA necessary to life?

A

DNA is to big to fit through nuclear pores

mRNA molecule transcribes information and leaves nucleus through pores

Much shorter than the whole chromosome

Travels to ribosomes

236
Q

What reaction creates phosphodiester bonds

A

Condensation

237
Q

What happens to RNA after protein synthesis?

A

Degrades in the cytoplasm

Phosphodiester bonds are hydrolysed

Nucleotides are released and reused

238
Q

Describe the method used to extract DNA from plant material?

A

Grind sample in mortar and pestle - breaks down cell walls

Mix sample with detergent - breaks down cell membrane, releasing cell contents into solution

Add salt - Breaks the hydrogen bonds between the DNA and water molecules

Add Protease - Breaks down proteins associated with DNA in the Nuclei

Add a layer of Ethanol on top of the sample - Alcohol causes the DNA to precipitate

The DNA will be seen as white strands forming between the layer of sample of alcohol

Can be picked up by spooling onto a glass rod

239
Q

The temperature should be kept low throughout this DNA extraction procedure. Suggest why.

A

Reduce activity of enzymes

Reduce breakdown of DNA

240
Q

Explain why detergent breaks down cell membranes

A

Disrupts membrane structure

Phospholipids form suspension in aqueous solution

241
Q

Describe the differences between DNA and RNA nucleotides

A

DNA nucleotide – deoxyribose sugar, thymine base

RNA nucleotide – ribose sugar, uracil base

242
Q

Explain the base pairing rule

A

A pyrimidine base always pairs with a purine base

Adenine and thymine/uracil always hydrogen bond together

Cytosine and guanine always hydrogen bond together

243
Q

Explain how the structure of DNA is ideally suited to its role

A

Polymer so contains a lot of information

Base sequence is used as a code

Double stranded so molecule is stable

Double stranded so accurate replication

244
Q

How does DNA replicate

A

Semi-conservatively

245
Q

Describe the process of Semi-conservative replication

A

Double helix unwinds into two strands, Hydrogen bonds between bases broken, Catalysed by DNA Helicase

Free nucleotides will pair with exposed bases of separated strands

Hydrogen bonds will form between them

New Nucleotides will join to their adjacent molecules with phosphodiester bonds, Catalysed by DNA Polymerase

2 molecules of DNA created - 4 strands, Each molecule consisting of 1 old strand and 1 new strand

246
Q

What enzymes are involved in DNA replication?

A

DNA Helicase

DNA Polymerase

DNA Ligase

247
Q

What direction does DNA polymerase move

A

Travels in direction 3’ to 5’ (known as leading strand)

248
Q

DNA polymerase has to replicate both of the strands, in opposite directions. Which side is continuously replicated and what side is discontinuously replicated?

A

Continuous: 3’ to 5’ (direction of movement of DNA polymerase)

Discontinuous: 5’ to 3’ (opposite to movement of DNA polymerase)

249
Q

What is Discontinuous Replication

A

Where the DNA polymerase has to go back after it has finished the Continuous strand

Adds DNA in sections (Okazaki fragments) then joined together, catalysed by DNA Ligase

Lagging strand

250
Q

Describe the difference between Continuous and Discontinuous replication

A

Continuous replication – DNA polymerase binds to the end of a strand, free DNA nucleotides added without any breaks;

discontinuous replication – DNA polymerase cannot bind to the end of a strand, free DNA nucleotides added in sections, sections then joined.

251
Q

Using your knowledge of enzymes, explain why DNA polymerase does not catalyse the joining of Okazaki fragments into a single strand but a different enzyme (DNA Ligase) is used

A

Enzymes are (substrate) specific

DNA polymerase catalyses the joining of nucleotides

Nucleotides have a different shape to Okazaki fragments

252
Q

What occurs as a result of a replication error

A

Mutation

253
Q

What is the Genetic code?

A

DNA code for sequences of Amino acids, that make up proteins that are the foundation to different physical and biochemical characteristics of living things

254
Q

What is a codon

A

A sequence of 3 bases, each codon codes for an amino acid

255
Q

What is a gene

A

A section of DNA that contains the complete sequence of bases to code for an entire protein

256
Q

What is Degenerate code

A

Many amino acids can be coded for by more than one codon

many codon options for most amino acids

(not necessary) eg. Argentine can be coded CGG, CGA, CGC, CGT, AGA, AGG,

257
Q

Explain why DNA replication is described as semi-conservative

A

Semi-conservative means ‘half the same’

When DNA replicates the double helix unwinds
into two separate strands

Free nucleotides pair with their complementary bases

Two new molecules of DNA are produced

Each with one old strand and one new strand

258
Q

Explain what is meant by the triplet code

A

The triplet code is a particular sequence of three bases

That codes for a specific amino acid

259
Q

Enzymes are cellular proteins that catalyse reactions, they have active sites in which specific substrates fit precisely. Suggest how a genetic mutation may result in an enzyme becoming non-functional.

A

mutation in the DNA changes the triplet code

meaning different amino acids are incorporated into the protein/enzyme

that the DNA codes for. If such a change affects the precise structure of the active site

a substrate may not be able to bind

260
Q

The sequence of bases in specific sections of DNA and the sequences of amino acids in specific proteins are both used to compare how closely related different species are. The fewer differences in the sequences, the more closely related species. Explain why there are likely to be more differences, overall, between base sequences of DNA than between amino acid sequences of proteins.

A

The triplet code of DNA is degenerative

there are 64 different triplets/codons but only 20 amino acids

therefore an amino acid can be coded for by more than one codon

so more opportunity for differences in DNA sequence than amino acid sequence

261
Q

What are the two stages of Protein synthesis

A

Transcription and Translation

262
Q

Where is DNA contained in a Eukaryotic Cell

A

Nucleus (inside nuclear envelope)

263
Q

Where does protein synthesis occur?

A

Ribosomes in cytoplasm

264
Q

Why can’t DNA molecules leave the nucleus

A

too large to fit through the nuclear pore

265
Q

What does Transcription produce

A

Shorter molecules of RNA

266
Q

Which strand acts as the template strand?

A

Antisense (sense strand is desired code)

267
Q

Describe the process of Transcription

A

Section of DNA that contains gene for protein is unzipped, H bonds break, catalysed by DNA Helicase

Sense strand is 5’ to 3’ codes for protein

Antisense strand is 3’ to 5’ and is template, doesn’t code for a protein

Free RNA nucleotides will base pair with exposed antisense strand

Phosphodiester bonds form between RNA nucleotides, catalysed by RNA Polymerase

When Transcription stops, a molecule of Messenger RNA (mRNA) is formed

Same base sequence as sense strand (U instead of T)

mRNA Detaches and leaves through the Nuclear pore to go to ribosome in cytoplasm

Double helix reforms

268
Q

Describe Translation

A

mRNA binds to specific site on small subunit of ribosome, large subunit clamps on top

Transfer RNA (tRNA) contains complementary anticodons folded in a way so they are on end of molecule

tRNA anticodons bind to complementary codons, amino acid is created and primary structure is coded by the mRNA

Amino acids are added one at a time to form a polypeptide chain

Ribosomes catalyse assembly of protein (peptide transferase in rRNA component of ribosome)

Once completed, Polypeptide is released, and folds into secondary and tertiary structure and sent to the Golgi for further modification

Many ribosomes can join onto the mRNA molecule to synthesise protein, one after the other

269
Q

Describe the roles of mRNA, tRNA and rRNA in protein synthesis

A

mRNA –
copies gene from DNA

takes copy to ribosome

tRNA –
brings amino acid to ribosome

rRNA –
formation of ribosome

270
Q

An enzyme forms part of the structure of a ribosome. Suggest the role of this enzyme

A

catalyse the formation of bond between two amino acids

Peptide bond

Peptidyl Transferase

271
Q

rRNA also forms part of the structure of a ribosome. Suggest why RNA needs to be present in a ribosome

A

bind to tRNA

complementary base pairing

272
Q

Ribosomes are either free floating within the cytoplasm or bound to endoplasmic reticulum. Suggest a reason for the different ribosomal sites

A

Free floating ribosomes produce proteins for use in cell

RER bound ribosomes produce proteins for export from the cell

273
Q

Post transcriptional modification of mRNA is carried out before it can leave the nucleus. This involves capping each end to protect the mRNA from degradation in the cytoplasm and the removal of Introns. Introns are non-coding sections of DNA and have no role in the formation of proteins.

1) Explain why unnecessary base sequences must be removed before protein synthesis begins
2) suggest an advantage of being able to edit mRNA
3) Suggest a reason for the presence of Introns within Genes

A

1) role of protein dependent on structure

shape / 3D structure, dependent on primary structure / sequence of amino acids

base triplets / codons, on mRNA, code for amino acids

introns would code for, unnecessary amino acids / stop signal

codons could cause frameshift

2) different proteins produced from one gene

3)originally functional gene

could be mutated mutated

base sequence/s changed

no longer code for (useful) amino acid

274
Q

What processes do cells require energy for

A

Synthesis (eg proteins)

Transport (eg ions across membranes via active transport)

Movement (eg protein fibres that cause muscle contraction)

275
Q

What is the universal energy currency?

A

ATP

276
Q

What is an ATP molecule comprised of

A

3 Phosphate groups

Ribose sugar

Adenine base

277
Q

How does ATP release energy?

A

Small amount of energy is required to break the bond holding the last Phosphate group

Releases large amount of energy

Forms ADP + Pi + Energy

278
Q

Why is ATP not a good long-term energy store

A

Phosphate groups are too unstable

279
Q

How is ATP created?

A

Cellular respiration of Fats and Carbohydrates (better long term energy stores)

280
Q

How is ATP recycled?

A

Reattaching a Phosphate group group to an ADP molecule (Phosphorylation)

281
Q

Why do cells not store large amounts of ATP

A

Unstable

Good source of immediate energy

282
Q

Properties of ATP

A

Small - Can move easily in, out and within cells

Water soluble - energy requiring processes happen in aqueous environments

Contains Bonds between phosphates for immediate energy that is large enough for cellular reactions but not so large that energy Is wasted

Easily regenerated - can be recharged with energy (the addition of a phosphate)

283
Q

Describe the structure of ATP

A

sugar/ribose sugar

joined to a base/adenine

Three phosphates

284
Q

Describe why ATP is called the universal energy currency

A

Present in all cells (1)

It is present in all organisms

It releases energy in, small/ manageable quantities

285
Q

People and other animals store excess energy in the form of fat. Explain why fat is stored, not ATP

A

fat is long term energy store

Fat is stable molecule and ATP is unstable molecule

fat has other uses

e.g., insulation

286
Q

Outline how energy is transferred with reference to bond formation and cleavage

A

Bond formation releases energy

bond uses energy

287
Q

Discuss the validity of the statement: ATP is the universal energy currency

A

ATP provides energy for, reactions / processes

ATP is present in all living organisms

idea that there is no other equivalent molecule

therefore statement is valid

BIOLOGY A LEVEL (24 decks)

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