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A Level Biology > 2.2 Biological Molecules > Flashcards

2.2 Biological Molecules Flashcards

1
Q

Properties of water

A

Medium in which all metabolic reactions take place (70%-95% of the mass of a cell is water)
Major habitat for organisms
Composed of hydrogen and oxygen, 1 oxygen atom combines with two atoms of hydrogen by covalent bonding
Water as a whole is electrically neutral but sharing of atoms is uneven
Polar molecule

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2
Q

Polar molecule in water

A

sharing of electrons is uneven and oxygen attracts electrons more strongly than hydrogen atoms resulting in a weak negatively charge region on the oxygen atom and a weak positively charged region on the hydrogen atoms, resulting is asymmetrical shape

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3
Q

Polar molecule

A

When one molecule has one end that is negatively charged and one end is positively charged

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4
Q

Dipole

A

Separation of charge due to electrons in the covalent bonds being unevenly shared

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5
Q

Why are Hydrogen bonds formed in water

A

A result of polarity of water hydrogen bonds form between positive and negatively charged regions of adjacent water molecules

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6
Q

Hydrogen bond strength

A

When there are few they are weak so they are constantly breaking and reforming
When there are a large numbers present they form a strong molecule

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7
Q

What properties do hydrogen bonds contribute to water

A

Excellent solvent
Relatively high specific heat capacity
Relatively high latent heat of vaporisation
Water is less dense when a solid
Water has high surface tension and cohesion
It’s acts as a reagent

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8
Q

Water as a solvent

A

As its a polar molecules many ions and covalently bonded polar substances (eg glucose) will dissolve in it.

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9
Q

What does water being a good solvent lead to

A

Allows chemical reactions to occur within cells (as dissolved solutes are more chemically reactive when they are free to move about)
Metabolites can be transported efficiently (except non polar molecules which are hydrophobic)

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10
Q

Specific heat capacity

A

Amount of thermal energy required to raise the temperature of 1kg of a substance by 1’c

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11
Q

Water specific heat capacity

A

4200j/kg’C

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12
Q

Why does water have high specific heat capacity

A

Due to many hydrogen bonds present in water, its takes a lot of energy to break these bonds and a lot of energy to build them, thus them temperature of water does not fluctuate greatly

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13
Q

What are the advantages of water’s high specific heat capacity for living organisms

A

Provides suitable habitats
Able to contain constant temperature as water is able to absorb a lot of heat without big temperature fluctuations which is vital in maintain temperatures that are optimal for enzyme activity

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14
Q

Water in blood plasma

A

Vital in transferring heat around the body, helping to maintain a fairly constant temperature
As blood passes through more active (warmer) regions of the body, heat energy is absorbed but the temperature remains firmly constant

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15
Q

Water in tissue fluid

A

Plays an important role in maintaining a constant body temperature

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16
Q

High latent heat of vaporisation

A

In order to change state from liquid to gas a large amount of thermal energy must be absorbed by water to break the hydrogen bonds and evaporate

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17
Q

How does high latent heat of vaporisation benefit animals

A

Only a little water is required to evaporate for the organism to lose a great amount of heat, this provides a cooling effect for living organisms, (eg transpiration from leaves or evaporation of water in sweat)

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18
Q

Cohesion in water

A

Hydrogen bonds between water molecules allow for strong cohesion between water molecules

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19
Q

What does cohesion between water molecules allow

A

Columns of water to move through xylem of plants through blood vessels in animals
Enables surface tension where a body of water meets the air, these hydrogen bonds occur between the top layer of water molecules to create a sort of film on the body of water (this allows insects such as pond skaters to float)

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20
Q

Adhesion is water molecules

A

When water is able to hydrogen bond to other molecules which enables water to move up xylem due to transpiration

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21
Q

Key molecules that are required to bold structures that enable organisms to function

A

Carbohydrates, proteins, lipids, nucleic acids, water

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22
Q

Monomers

A

Smaller units from which larger molecules are made

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23
Q

Polymers

A

Molecules made from a large number of monomers joined together in a chain

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24
Q

Polymerisation

A

Carbon compounds can form small single subunits (monomers) that bond with many repeating subunits to form large molecules (polymers)

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25
Q

Macromolecules

A

Very large molecules
Contain 1000 or more atoms so high high molecular mass
Polymers can be macromolecules however not all macromolecules are polymers as the subunits of polymers have to be repeating units

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26
Q

Covalent bonds

A

Sharing of two or more electrons between two atoms
Can be formed equally forming a non polar covalent bond
Can be formed unequally forming a polar covalent bonding

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27
Q

Properties of covalent bonds

A

Very stable as high energy required to break bonds
Multiple pairs of electrons can be shared forming double or triple bonds

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28
Q

Covalent bonds in monomers

A

When two monomers are close enough that their outer orbitals overlap which results in their electrons being shared and a covalent bond forming. If more monomers are added then polymerisation occurs and/or a macromolecule forms

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29
Q

Condensation reaction

A

Occurs when monomers combine together by covalent bonds to form polymers or macromolecules and water is removed

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30
Q

Hydrolysis

A

Breaking down a chemical bond between two molecules and involves the use of a water molecule

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31
Q

Hydrolysis of polymers

A

Covalent bonds are broken when water is added

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32
Q

Type of Covalent bonds in carbohydrates

A

Glycosidic

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33
Q

Type of covalent bond in proteins

A

Peptide

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34
Q

Type of covalent bond in lipids

A

Ester

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35
Q

Types of covalent bond in nucleic acids

A

Phosphodiester

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36
Q

Why are Carbon atoms key to organic compounds

A

Each carbon atom can form 4 covalent bonds making the compound very stable
Carbon atoms can form covalent bonds with oxygen, nitrogen and sulfur
Carbon atoms can form straight chains, branched chains or rings

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37
Q

What do carbohydrates, proteins, lipids and nucleic acids contain making them organic compounds

A

Carbon and hydrogen

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38
Q

Function of carbohydrates

A

Source of energy e.g. glucose is used for energy-release during cellular respiration
Store of energy e.g. glycogen is stored in the muscles and liver of animals
Structurally important e.g. cellulose in the cell walls of plants

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39
Q

3 types of carbohydrates

A

monosaccharides, disaccharides and polysaccharides

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40
Q

Monosaccharide

A

Single sugar monomer, all are reducing sugars

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41
Q

Examples of monosaccharide

A

Glyceraldehyde (3c), ribose (5c), glucose (6c)

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42
Q

Function of monosaccharide

A

Source of energy in respiration, building blocks for polymers

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43
Q

Disaccharide

A

A sugar formed two monosaccharides joined by a glycosidic bond in a condensation reaction

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44
Q

Examples of disaccharides

A

Maltose-(glucose+glucose)
Sucrose-(glucose+fructose)
Lactose-(glucose+galactose)

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45
Q

Function of disaccharide

A

Sugar fund in germinating seeds (maltose)
Mammal milk sugar (lactose)
Sugar stored in sugar cane (sucrose)

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46
Q

What makes up maltose

A

Glucose+glucose

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47
Q

What makes up sucrose

A

Glucose+fructose

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48
Q

What makes up lactose

A

Glucose+galactose

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49
Q

Polysaccharide

A

A polymer formed by many monosaccharides joined by glycosidic bonds in a condensation reaction

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50
Q

Examples of polysaccharide

A

Cellulose (glucose)
Starch (glucose in the form of amylose and amylopectin)
Glycogen (glucose)

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51
Q

What makes up cellulose

A

Glucose

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52
Q

What makes up starch

A

Glucose in the form of amylose and amylopectin

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53
Q

What makes up glycogen

A

Glucose

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54
Q

Function of polysaccharides

A

Energy storage- (plants-starch, animals-glycogen)
Structural- cellulose cell wall

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55
Q

Types of lipids

A

triglycerides (fats and oils), phospholipids, waxes, and steroids (such as cholesterol)

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56
Q

Functions of lipids

A

Source of energy
Store of energy
Insulating layer

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57
Q

Lipids as a source of energy

A

Source of energy that can be respired (lipids have a high energy yield)

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58
Q

Lipids as a store of energy

A

lipids are stored in animals as fats in adipose tissue and in plants as lipid droplets

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59
Q

Lipids as an insulating layer

A

thermal insulation under the skin of mammals and electrical insulation around nerve cells

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60
Q

Eg of carbohydrate as source of energy

A

glucose is used for energy-release during cellular respiration

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61
Q

Carbohydrates as store of energy

A

glycogen is stored in the muscles and liver of animals

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62
Q

Eg of carbohydrates being structurally important

A

cellulose in the cell walls of plants

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63
Q

Functions of proteins

A

Required for cell growth
Structurally important
Can act as carrier molecules in cell membrane

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64
Q

Eg of proteins being structurally important

A

in muscles, collagen and elastin in the skin, collagen in bone and keratin in hair

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65
Q

Eg of nucleic acids

A

DNA and rna

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66
Q

Function of nucleic acids (dna and rna)

A

Carrying the genetic code in all living organisms
Nucleic acids are essential in the control of all cellular processes including protein synthesis

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67
Q

Reducing sugars

A

Can donate electrons and the sugars become the reducing agent

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68
Q

Examples of reducing sugars

A

glucose, fructose and galactose

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69
Q

Non-reducing sugars

A

cannot donate electrons, therefore they cannot be oxidised

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70
Q

Example of non reducing sugar

A

Sucrose

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71
Q

Glucose molecular formula

A

C6H12O6

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72
Q

Why is glucose so important

A

The main function of glucose is as an energy source
It is the main substrate used in respiration, releasing energy for the production of ATP
Glucose is soluble and so can be transported in water

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73
Q

Penrose sugars

A

Sugars that contain five carbon molecules

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74
Q

Learn how to draw alpha and beta glucose

A

Type?

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75
Q

What Penrose sugar makes up rna and dna

A

Ribose-rna
Deoxyribose-dna

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76
Q

What does a glycosidic bond result in

A

one water molecule being removed, thus glycosidic bonds are formed by condensation

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77
Q

Example of Penrose and heroes monosaccharide

A

Pentose-ribose
Hexose-glucose

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78
Q

Difference between heroes and Penrose monosaccharide

A

Pentose- five carbon atoms
Hexose- six carbon atoms

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79
Q

How is a glycosidic bond formed

A

A condensation reaction between two monosaccharides forming disaccharides and polysaccharides

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80
Q

How are glycosidic bonds broken down

A

Water is added in hydrolysis, disaccharides and polysaccharides are broken dow in hydrolysis reaction

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81
Q

What happens when you heart sucrose

A

When sucrose is heated with hydrochloric acid this provides the water that hydrolyses the glycosidic bond resulting in two monosaccharides that will produce a positive Benedict’s test

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82
Q

What result does sucrose give in Benedict test when not heated

A

Sucrose is a non-reducing sugar which gives a negative result

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83
Q

Condensation reaction

A

two molecules join together via the formation of a new chemical bond (glycosidic bond), with a molecule of water being released in the process

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84
Q

How to calculate chemical formula of disaccharide

A

you add all the carbons, hydrogens and oxygens in both monomers then subtract 2x H and 1x O (for the water molecule lost)

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85
Q

Examples of disaccharides

A

Maltose, sucrose and lactose

All three of the common examples above have the formula C12H22O11

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86
Q

Maltose

A

The sugar formed in the production and breakdown of starch

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87
Q

Sucrose

A

The main sugar produced in plants

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88
Q

Lactose

A

A sugar found only in milk

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89
Q

Monosaccharide components of maltose

A

Glucose + glucose

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90
Q

Monosaccharide components of sucrose

A

Glucose + fructose

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91
Q

Monosaccharide components of lactose

A

Glucose + galactose

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92
Q

What are Starch, glycogen and cellulose

A

Polysaccharides

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93
Q

What are polysaccharides

A

macromolecules (polymers) that are formed by many monosaccharides joined by glycosidic bonds in a condensation reaction to form chains

These chains may be:
Branched or unbranched
Folded (making the molecule compact which is ideal for storage eg. starch and glycogen)
Straight (making the molecules suitable to construct cellular structures e.g. cellulose) or coiled

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94
Q

What two polysaccharides construct starch

A

Amylose
Amylopectin

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95
Q

Amylose in starch

A

(10 - 30% of starch)
Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
The helix shape enables it to be more compact and thus it is more resistant to digestion

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96
Q

Amylopectin in starch

A

(70 - 90% of starch)
1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between glucose molecules creating a branched molecule

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97
Q

What makes up glycogen

A

It is made up of α-glucose molecules
There are 1,4 glycosidic bonds between α-glucose molecules and also 1,6 glycosidic bonds between glucose molecules creating a branched molecule

Glycogen has a similar structure to amylopectin but it has more branches

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98
Q

Monomer in amylose, amylopectin and glycogen

A

Glucose for all of them

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99
Q

Branched feature in amylose, amylopectin and glycogen

A

Amylose- no
Amylopectin- yes (every 20 monomers)
Glycogen-yes (every 10 monomers)

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100
Q

Do amylose, amylopectin and glycogen have a helix (coiled) shape

A

Amylose- yes
Amylopectin- no
Glycogen- no

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101
Q

Glycosidic bonds present in amylose, amylopectin and glycogen

A

Amylose- 1,4
Amylopectin- 1,4 and 1,6
Glycogen- 1,4 and 1,6

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102
Q

Cellulose

A

polysaccharide found in plants

It consists of long chains of β-glucose joined together by 1,4 glycosidic bonds

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103
Q

Why is cellulose strong

A

β-glucose is an isomer of α-glucose, so in order to form the 1,4 glycosidic bonds consecutive β-glucose molecules must be rotated 180° to each other

Due to the inversion of the β-glucose molecules, many hydrogen bonds form between the long chains giving cellulose its strength

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104
Q

Why are starch and glycogen storage polysaccharides

A

they are:
Compact
So large quantities can be stored
Insoluble
So they will have no osmotic effect, unlike glucose which would lower the water potential of a cell causing water to move into cells

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105
Q

What is starch stored as in plants

A

It is stored as granules in plastids such as amyloplasts and chloroplasts

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106
Q

Plastids

A

Plastids are membrane-bound organelles that can be found in plant cells. They have a specialised function eg. amyloplasts store starch grains

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107
Q

Why does starch take longer to digest than glucose

A

Due to the many monomers in a starch molecule

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108
Q

How can amylopectin in starch help the plant

A

has branches that result in many terminal glucose molecules that can be easily hydrolysed for use during cellular respiration or added for storage

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109
Q

Glycogen

A

the storage polysaccharide of animals and fungi, it is highly branched and not coiled

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110
Q

Glycogen in liver and muscles cells

A

have a high concentration of glycogen, present as visible granules, as the cellular respiration rate is high in these cells (due to animals being mobile)

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111
Q

Benefits of glycogen being more branched than amylopectin

A

Makes it more compact which animals store more

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112
Q

Branching in glycogen

A

The branching enables more free ends where glucose molecules can either be added or removed allowing for condensation and hydrolysis reactions to occur more rapidly – thus the storage or release of glucose can suit the demands of the cell

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113
Q

Cellulose

A

main structural component of cell walls due to its strength which is a result of the many hydrogen bonds found between the parallel chains of microfibrils

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114
Q

What does the high tensile strength of cellulose allow

A

it to be stretched without breaking which makes it possible for cell walls to withstand turgor pressure

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115
Q

How does cellulose increase strength of the cell walls

A

The cellulose fibres and other molecules (eg. lignin) found in the cell wall forms a matrix

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116
Q

What do cell walls do

A

The strengthened cell walls provide support to the plant

117
Q

Permeability of cellulose fibres

A

Cellulose fibres are freely permeable which allows water and solutes to leave or reach the cell surface membrane

118
Q

Benedict’s test for reducing sugars method

A

Add Benedict’s reagent (which is blue as it contains copper (II) sulfate ions) to a sample solution in a test tube
Heat the test tube in a water bath or beaker of water that has been brought to a boil for a few minutes
If a reducing sugar is present, a coloured precipitate will form as copper (II) sulfate is reduced to copper (I) oxide which is insoluble in water

119
Q

Why is it important there is an excess of Benedict’s solution

A

so that there is more than enough copper (II) sulfate present to react with any sugar present

120
Q

Benedict’s reagent

A

Benedict’s reagent is a blue solution that contains copper (II) sulfate ions (CuSO4 ); in the presence of a reducing sugar copper (I) oxide forms
Copper (I) oxide is not soluble in water, so it forms a precipitate

121
Q

Colour change in Benedict’s test for reducing sugars

A

A positive test result is a colour change somewhere along a colour scale from blue (no reducing sugar), through green, yellow and orange (low to medium concentration of reducing sugar) to brown/brick-red (a high concentration of reducing sugar)

122
Q

Examples of reducing sugars

A

Galactose, glucose, fructose and maltose

123
Q

Example of non-reducing sugars

A

Sucrose (only one need to know)

124
Q

Test for non-reducing sugars

A

Add dilute hydrochloric acid to the sample and heat in a water bath that has been brought to the boil
Neutralise the solution with sodium hydrogencarbonate
Use a suitable indicator (such as red litmus paper) to identify when the solution has been neutralised, and then add a little more sodium hydrogencarbonate as the conditions need to be slightly alkaline for the Benedict’s test to work
Then carry out Benedict’s test as normal
Add Benedict’s reagent to the sample and heat in a water bath that has been boiled – if a colour change occurs, a reducing sugar is present

125
Q

Why do we add hydrochloride acid to test non-reducing sugars

A

The addition of acid will hydrolyse any glycosidic bonds present in any carbohydrate molecules
The resulting monosaccharides left will have an aldehyde or ketone functional group that can donate electrons to copper (II) sulfate (reducing the copper), allowing a precipitate to form

126
Q

Iodine test for starch

A

Iodine- orange/black

If starch is present, iodide ions in the solution interact with the centre of starch molecules, producing a complex with a distinctive blue-black colour

127
Q

Why do iodine test

A

To show starch in a sample has been digested by enzymes

128
Q

Lipids

A

macromolecules that contain carbon, hydrogen and oxygen atoms. Unlike carbohydrates, lipids contain a lower proportion of oxygen
Lipids are non-polar and hydrophobic (insoluble in water)

129
Q

2 groups of lipids

A

Triglycerides (the main component of fats and oils)
Phospholipids

130
Q

What do lipids pay a role in

A

Lipids play an important role in energy yield, energy storage, insulation and hormonal communication

131
Q

Triglycerides

A

Triglycerides are non-polar, hydrophobic molecules

132
Q

What monomers make up tryglycerides

A

Glycerol and fatty acids

133
Q

How can fatty acids vary

A

Length of the hydrocarbon chain (R group)
The fatty acid chain (R group) may be saturated (mainly in animal fat) or unsaturated (mainly vegetable oils, although there are exceptions e.g. coconut and palm oil)

134
Q

Phospholipids

A

a type of lipid, therefore they are formed from the monomers glycerol and fatty acids
Unlike triglycerides, there are only two fatty acids bonded to a glycerol molecule in a phospholipid as one has been replaced by a phosphate ion (PO43-)

135
Q

Polarity of phospholipids

A

As the phosphate is polar it is soluble in water (hydrophilic)
The fatty acid ‘tails’ are non-polar and therefore insoluble in water (hydrophobic)

136
Q

Amphipathic

A

Eg. Phospholipids
Have both hydrophobic and hydrophilic parted

137
Q

What do phospholipids having hydrophobic and hydrophilic parts lead to

A

phospholipid molecules form monolayers or bilayers in water

138
Q

Function of phospholipids

A

Cell membrane component

139
Q

Function of triglycerides

A

Energy storage

140
Q

How are triglycerides formed

A

Esterification

141
Q

How do ester bonds form

A

when a hydroxyl (-OH) group from the glycerol bonds with the carboxyl (-COOH) group of the fatty acid

142
Q

Process of esterification

A

An H from glycerol combines with an OH from the fatty acid to make water
The formation of an ester bond is a condensation reaction
For each ester bond formed a water molecule is released
Three fatty acids join to one glycerol molecule to form a triglyceride

143
Q

How many water molecules are released when one triglyceride is formed

A

3

144
Q

What makes up tryglycerides

A

Fatty acid and glycerol molecules

145
Q

What are tryglycerides

A

Fats and oils

146
Q

Functions of fats and oils (tryglycerides)

A

energy storage, insulation, buoyancy, and protection

147
Q

Why do tryglycerides store more energy per gram than carbs and proteins

A

The long hydrocarbon chains in triglycerides contain many carbon-hydrogen bonds with little oxygen (triglycerides are highly reduced)
So when triglycerides are oxidised during cellular respiration this causes these bonds to break releasing energy used to produce ATP

148
Q

Why can tryglycerides store more

A

As triglycerides are hydrophobic they do not cause osmotic water uptake in cells so more can be stored

149
Q

Why would mammals store tryglycerides

A

Mammals store triglycerides as oil droplets in adipose tissue to help them survive when food is scarce (e.g. hibernating bears)

150
Q

How do triglycerides link to water

A

The oxidation of the carbon-hydrogen bonds releases large numbers of water molecules (metabolic water) during cellular respiration
Desert animals retain this water if there is no liquid water to drink
Bird and reptile embryos in their shells also use this water

151
Q

How do triglycerides act as an insulator

A

Triglycerides compose part of the adipose tissue layer below the skin which acts as insulation against heat loss (eg. blubber of whales)

Triglycerides are part of the composition of the myelin sheath that surrounds nerve fibres

152
Q

How do triglycerides lead to buoyancy

A

The low density of fat tissue increases the ability of animals to float more easily

153
Q

How do triglycerides protect mammals

A

The adipose tissue in mammals contains stored triglycerides and this tissue helps protect organs from the risk of damage

154
Q

What forms phospholipids

A

they are formed from the monomer glycerol and fatty acids

155
Q

How do phospholipids create a barrier to water soluble molecules

A

Due to the presence of hydrophobic fatty acid tails, a hydrophobic core is created when a phospholipid bilayer forms

156
Q

Compartmentalisation in cells

A

Compartmentalisation enables cells to organise specific roles into organelles, helping with efficiency

157
Q

How do phospholipids link to cell membranes

A

Phospholipids are the main component (building block) of cell membranes

158
Q

How do phospholipids allow the cell membrane to be used to compartmentalise

A

The hydrophilic phosphate heads form H-bonds with water allowing the cell membrane to be used to compartmentalise

159
Q

How does the composition of phospholipids contribute to the fluidity of the cell membrane

A

If there are mainly saturated fatty acid tails then the membrane will be less fluid
If there are mainly unsaturated fatty acid tails then the membrane will be more fluid

160
Q

How do phospholipids control protein orientation

A

Weak hydrophobic interactions between the phospholipids and membrane proteins hold the proteins within the membrane but still allow movement within the layer

161
Q

Cholesterol molecules

A

cholesterol molecules have hydrophobic and hydrophilic regions
Their chemical structure allows them to exist in the bilayer of the membrane

162
Q

Where of molecules of cholesterol synthesised

A

Molecules of cholesterol are synthesised in the liver and transported via the blood

163
Q

How does cholesterol affect the fluidity and permeability of the cell membrane

A

It disrupts the close-packing of phospholipids, increasing the rigidity of the membrane (makes the membrane less flexible)
It acts as a barrier, fitting in the spaces between phospholipids. This prevents water-soluble substances from diffusing across the membrane

164
Q

What are molecules of cholesterol used to produce

A

steroid-based hormones such as oestrogen, testosterone and progesterone

165
Q

Lipid test method

A

Add ethanol to the sample to be tested
Shake to mix
Add the mixture to a test tube of water

166
Q

Lipid test results

A

If lipids are present, a milky emulsion will form (the solution appears ‘cloudy’); the more lipid present, the more obvious the milky colour of the solution
If no lipid is present, the solution remains clear

167
Q

What are proteins

A

Proteins are polypeptides (and macromolecules) made up of monomers called amino acids

168
Q

What are proteins important for

A

cell growth, cell repair and structure

169
Q

What do proteins form

A

Enzymes
Cell membrane proteins (eg. carrier)
Hormones
Immunoproteins (eg. immunoglobulins)
Transport proteins (eg. haemoglobin)
Structural proteins (eg. keratin, collagen)
Contractile proteins (eg. myosin)

170
Q

Amino acids

A

Monomers of polypeptides

171
Q

Bonds between amino acids

A

Peptide

172
Q

What type of bond are peptide bonds

A

Covalent bonds

173
Q

How is a peptide bond formed

A

a hydroxyl (-OH) is lost from the carboxylic group of one amino acid and a hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid
This is a condensation reaction so water is released

174
Q

Dipeptides

A

formed by the condensation of two amino acids

175
Q

Polypeptides

A

formed by the condensation of many (3 or more) amino acids

176
Q

What happens during hydrolysis reaction of polypeptides

A

During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids

177
Q

4 levels of protein structure

A

Primary, secondary, tertiary, quaternary

178
Q

Primary protein structure

A

The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein

179
Q

How is primary structure of a protein determined

A

The DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence. This affects the shape and therefore the function of the protein

180
Q

Specificity of primary structure

A

The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

181
Q

Secondary structure of a protein

A

The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

182
Q

What two shapes can form within proteins due to hydrogen bongs

A

Helix
Pleated sheet

183
Q

When does a helix shape occur

A

when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)

184
Q

When does a pleated sheet shape occur

A

The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

185
Q

What does secondary structure only relate to

A

The secondary structure only relates to hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)

186
Q

How can hydrogen bonds be broken

A

High temperatures and pH changes

187
Q

Tertiary structure

A

Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)

188
Q

Additional bonds (tertiary structure)

A

Hydrogen (these are between R groups)
Disulphide (only occurs between cysteine amino acids)
Ionic (occurs between charged R groups)
Weak hydrophobic interactions (between non-polar R groups)

189
Q

Disulphide bonds

A

strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with a sulphur atom)

190
Q

Disulphide bonds strength

A

These bonds are the strongest within a protein but occur less frequently, and help stabilise the proteins

191
Q

How can disulphide bonds be broken

A

Oxidation

192
Q

Where are Disulphide bonds common

A

This type of bond is common in proteins secreted from cells eg. insulin

193
Q

Ionic bonds

A

Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups

194
Q

Ionic bond strength

A

Ionic bonds are stronger than hydrogen bonds but they are not common

195
Q

How can ionic bonds be broken

A

By ph changes

196
Q

Hydrogen bongs

A

Hydrogen bonds form between strongly polar R groups. These are the weakest bonds that form but the most common as they form between a wide variety of R groups

197
Q

Hydrophobic interactions

A

Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins

198
Q

Why will polypeptide chain fold differently

A

A polypeptide chain will fold differently due to the interactions (and hence the bonds that form) between R groups

199
Q

Why is there a vast range of protein configurations and therefore functions

A

Each of the twenty amino acids that make up proteins has a unique R group and therefore many different interactions can occur creating a vast range of protein configurations and therefore functions

200
Q

Quaternary structure

A

Quarternary structure exists in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin

201
Q

What is each polypeptide chain in a quaternary structure referred to as

A

A subunit of a protein

202
Q

Bonds in primary structure

A

Peptide

203
Q

Bonds in secondary structure

A

Peptide and hydrogen

204
Q

Bonds in tertiary structure

A

Peptide, hydrogen, disulphide, ionic, hydrophobic interactions

205
Q

Features of globular proteins

A

Globular proteins are compact, roughly spherical (circular) in shape and soluble in water

206
Q

Why do globular proteins form spherical shape when folding into their tertiary structure

A

their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings and
their polar hydrophilic R groups orientate themselves on the outside of the protein

207
Q

How does orientation of globular proteins enable them to be generally soluble in water

A

the water molecules can surround the polar hydrophilic R groups

208
Q

What does solubility in globular proteins mean

A

they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions

209
Q

How do globular proteins have specific shapes

A

The folding of the protein due to the interactions between the R groups results in globular proteins having specific shapes

210
Q

What does globular proteins having specific shape enable

A

enables globular proteins to play physiological roles, for example, enzymes can catalyse specific reactions and immunoglobulins (antibodies) can respond to specific antigens

211
Q

Conjugated protein

A

A protein that contains a non-protein chemical group such as a prosthetic group or cofactor.

212
Q

Simple proteins

A

Proteins that just contain amino acids

213
Q

Prosthetic group

A

A permanent, non protein part of a protein molecule eg. A haem group in haemoglobin

214
Q

Example Globular proteins as conjugated proteins

A

haemoglobin which contains the prosthetic group called haem

215
Q

Haemoglobin

A

a globular protein which is an oxygen-carrying pigment found in vast quantities in red blood cells

216
Q

Structure of haemoglobin

A

It has a quaternary structure as there are four polypeptide chains. These chains or subunits are globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group

217
Q

What bonds the 4 globin subunits

A

Disulphide bonds

218
Q

How are the 4 globin subunits arranged

A

arranged so that their hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape) and the hydrophilic R groups are facing outwards (helping maintain its solubility)

219
Q

Why is the arrangement of the R groups important to the functioning of haemoglobin

A

If changes occur to the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing

220
Q

Example of sequence of amino acids in subunits of haemoglobin changin

A

This is what happens to cause sickle cell anaemia (where base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble)

221
Q

How is oxyhaemoglobin formed

A

The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule

Therefore Each haemoglobin with the four haem groups can carry four oxygen molecules (eight oxygen atoms)

222
Q

What is haemoglobin responsible for

A

binding oxygen in the lung and transporting the oxygen to tissue to be used in aerobic metabolic pathways

223
Q

How does haemoglobin lead to oxygen being carried around the body more efficiently

A

As oxygen is not very soluble in water and haemoglobin is, oxygen can be carried more efficiently around the body when bound to the haemoglobin

224
Q

How does structure change in haemoglobin affect its affinity for oxygen

A

The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more easily because as each oxygen molecule binds it alters the quaternary structure (due to alterations in the tertiary structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent oxygen molecules and they bind more easily

225
Q

How is oxygen allowed to reversible bind

A

The existence of the iron II ion (Fe2+) in the prosthetic haem group also allows oxygen to reversibly bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to binding with oxygen

226
Q

How are enzymes biological catalysts

A

Biological’ because they function in living systems
‘Catalysts’ because they speed up the rate of chemical reactions without being used up or changed

227
Q

What type of proteins are enzymes

A

Globular

228
Q

Insulin

A

globular protein produced in the pancreas. It plays an important role in the control of blood glucose concentration

229
Q

How many polypeptide chains in insulin

A

It consists of two polypeptide chains
Polypeptide A has 21 amino acid residues
Polypeptide B has 30 amino acid residues

230
Q

what are the polypeptide chains in insulin held together by

A

The two polypeptide chains are held together by three disulfide bridges

231
Q

Fibrous proteins

A

long strands of polypeptide chains that have cross-linkages due to hydrogen bonds

These proteins have little or no tertiary structure

232
Q

Solubility of fibrous proteins

A

Due to a large number of hydrophobic R groups, fibrous proteins are insoluble in water

233
Q

Why is the sequence of fibrous proteins highly repetitive

A

Fibrous proteins have a limited number of amino acids

234
Q

What does the highly repetitive sequence in fibrous proteins mean

A

creates very organised structures that are strong and this along with their insolubility property, makes fibrous proteins very suitable for structural roles

235
Q

Examples of fibrous proteins

A

Keratin, elastin, collagen

236
Q

Keratin

A

makes up hair, nails, horns and feathers (it is a very tough fibrous protein)

237
Q

Elastin

A

is found in connective tissue, tendons, skin and bone (it can stretch and then return to its original shape)

238
Q

Collagen

A

is a connective tissue found in skin, tendons and ligaments

239
Q

Shape of globular and fibrous proteins

A

Globular- roughly circular
Fibrous- long strands

240
Q

Amino acid sequence of globular and fibrous proteins

A

Globular- irregular ad wide range of R groups
Fibrous- repetitive with a limited range of R groups

241
Q

Function of globular and fibrous proteins

A

Globular- physiological/functional
Fibrous- structural

242
Q

Examples of globular and fibrous proteins

A

Globular- haemoglobin, enzymes, insulin, immunoglobulin
Fibrous- collagen, keratin, myosin, actin, fibrin

243
Q

Solubility of globular and fibrous proteins

A

Globular- generally soluble in water
Fibrous- generally insoluble in water

244
Q

Collagen

A

most common structural protein found in vertebrates
It provides structural support
It’s an insoluble fibrous protein

245
Q

Function a collagen

A

flexible structural protein forming connective tissues

great tensile strength. This enables collagen to be able to withstand large pulling forces without stretching or breaking

246
Q

Solubility of collagen

A

The length of collagen molecules means they take too long to dissolve in water (making it insoluble in water)

247
Q

Number of polypeptide chains in collagen and haemoglobin

A

Collagen-3
Haemoglobin- 4

248
Q

Shape of collagen and haemoglobin

A

Collagen-long,thin
Haemoglobin-spherical,round

249
Q

What type of protein is collagen and haemoglobin

A

Collagen-fibrous
Haemoglobin-globular

250
Q

Main function of collagen and haemoglobin

A

Collagen- structural (connective tissue eg. Tendons, skins)
Haemoglobin- functional (transport of oxygen)

251
Q

Elastin

A

allows tissues in your body to stretch out and shrink back

252
Q

Keratin

A

Protects epithelial cells, strengthens the skin, strengthens internal organs, controls the growth of epithelial cells, and maintains the elasticity in the skin

253
Q

Ion

A

An atom that has an electrical charge

254
Q

Cation

A

Ion with positive charge

255
Q

Anion

A

Ion that has negative charge

256
Q

Inorganic ion

A

Does not contain carbon

257
Q

Cofactors

A

Non- protein chemical compounds that are required for a protein to function

258
Q

Hydrogen ions

A

H+

259
Q

Calcium ions

A

CA2+

260
Q

Iron ions

A

Fe2+/Fe3+

261
Q

Sodium ions

A

Na+

262
Q

Potassium ions

A

K+

263
Q

Ammonium ions

A

NH4+ (4 belongs to H)

264
Q

Nitrate ions

A

NO3- (3 belongs to o)

265
Q

Hydrogen carbonate ions

A

HCO3- (3 belongs to o)

266
Q

Chloride ions

A

Cl-

267
Q

Phosphate ions

A

PO4 3- (4 belongs to o)

268
Q

Hydroxide ions

A

OH-

269
Q

What chemical is used to test proteins

A

Biuret

270
Q

Method biuret test

A

Add sodium hydroxide to the food solution sample to make the solution alkaline
Add few drops of Biuret ‘reagent’ contains an alkali and copper (II) sulfate
Repeat steps 1 and 2 using the control solution
Compare the colours of the control solution and the food sample solution

271
Q

Results biuret test

A

If a colour change is observed from blue to lilac/mauve, then protein is present.

If no colour change is observed, no protein is present

272
Q

What to do when colour change is very subtle

A

hold the test tubes up against a white tile when making observations

273
Q

Limitations of biuret tes

A

it does not give a quantitative value as to the amount of protein present in a sample

If the sample contains amino acids or dipeptides, the result will be negative (due to lack of peptide bonds)

274
Q

Colour change to represent sugar concentration

A

The intensity of any colour change seen relates to the concentration of reducing sugar present in the sample
A positive test is indicated along a spectrum of colour from green (low concentration) to brick-red (high concentration of reducing sugar present)

275
Q

Colorimeter

A

A colorimeter is an instrument that beams a specific wavelength (colour) of light through a sample and measures how much of this light is absorbed (arbitrary units)

276
Q

How do colorimeter work

A

They contain different wavelengths or colour filters (depends on the model of colorimeter), so that a suitable colour can be shone through the sample and will not get absorbed. This colour will be the contrasting colour (eg. a red sample should have green light shone through)

277
Q

What must be done when using colorimeter

A

Colorimeters must be calibrated before taking measurements
This is completed by placing a blank into the colorimeter and taking a reference, it should read 0 (that is, no light is being absorbed)
This step should be repeated periodically whilst taking measurements to ensure that the absorbance is still 0

278
Q

Chromatography

A

a technique that can be used to separate a mixture into its individual components

279
Q

Two phases of chromatography

A

All chromatography techniques use two phases:
The mobile phase
The stationary phase

280
Q

What does chromatography rely on

A

Chromatography relies on differences in the solubility of the different chemicals (called ‘solutes’) within a mixture

281
Q

How is the distance travelled different

A

Differences in the solubility of each component in the mobile phase affects how far each component can travel
Those components with higher solubility will travel further than the others

282
Q

Why do components with higher solubility travel further

A

they spend more time in the mobile phase and are thus carried further up the paper than the less soluble components

283
Q

The mobile phase in Paper chromatography

A

The mobile phase is the solvent in which the sample molecules can move, which in paper chromatography is a liquid e.g. water or ethanol

284
Q

The stationary phase in paper chromatography

A

The stationary phase in paper chromatography is the chromatography paper

285
Q

Paper chromatography method

A

A spot of the mixture (that you want to separate) is placed on chromatography paper and left to dry
The chromatography paper is then suspended in a solvent
As the solvent travels up through the chromatography paper, the different components within the mixture begin to move up the paper at different speeds
Larger molecules move slower than smaller ones
This causes the original mixture to separate out into different spots or bands on the chromatography paper

286
Q

Using chromatography to separate a mixture of monosaccharides methd

A

Use a stain if needed

Spots of solution of different monosaccharide placed on a line beside the sample spot

The chromatography paper is then suspended in a solvent

As the solvent travels up through the chromatography paper, the different monosaccharides within the mixture separate out at different distances from the line

287
Q

Rf equation

A

Rf = distance moved by solute ÷ distance moved by solvent

Always lower than one

288
Q

What does Rf Value demonstrates

A

The Rf value demonstrates how far a dissolved molecule travels during the mobile phase
A smaller Rf value indicates the molecule is less soluble and larger in size

A Level Biology (10 decks)

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