Biological Molecules Flashcards
1
Q
What makes water a polar molecule?
A
The shared negative hydrogen electrons are pulled towards the oxygen atom, so the other side of each hydrogen atom gets a slight positive charge. The unshared negative electrons on the oxygen atom give it a slight negative charge. This makes water a polar molecule as it has partial charges on each side.
2
Q
What are hydrogen bonds?
A
Hydrogen bonds are weak bonds between a slightly positively charged hydrogen atom in one molecule and a slightly negatively charged atom in another molecule (usually oxygen).
3
Q
What type of bonds form between water molecules?
A
Hydrogen bonds
4
Q
Why do water molecules form hydrogen bonds between them?
A
The slightly negatively charged oxygen atoms of water attract the slightly positively charged hydrogen atoms of other water molecules.
5
Q
What are the key properties of water?
A
- important metabolite
- good solvent
- large latent heat of vaporisation
- high specific heat capacity
- very cohesive
- high surface tension
- transparent
6
Q
How does water contribute to metabolic reactions?
A
Many metabolic reactions involve condensation or hydrolysis reactions. Hydrolysis reactions require a molecule of water to break a bond. Condensation reactions release a molecule of water for every bond they form.
7
Q
Why can water be described as a metabolite?
A
Water is a metabolite because it is a substance which is involved in metabolic reactions (chemical reactions which occur in living organisms to keep the organism alive).
8
Q
Why is water a good solvent?
A
Because water is polar, the slightly positively charged end of the molecule is attracted to a negative ion and vice versa. This means that ions get completely surrounded by water molecules, so they will dissolve.
9
Q
Why is it important that water is a good solvent?
A
Many metabolic reactions take place in solution (e.g. in the cytoplasm of cells), so water is important to allow this. Water also dissolves mineral ions and other substances to be transported in the blood plasma or around a plant.
10
Q
Why does water have a large latent heat of vaporisation?
A
Water can only evaporate when the hydrogen bonds between molecules are broken. It takes a lot of energy to break the hydrogen bonds, so it takes lots of energy to change the state of 1g of water. This means that water has a large latent heat of vaporisation.
11
Q
Why is water’s large latent heat of vaporisation useful for organisms?
A
They can use water loss through evaporation to cool down without using too much water. When water evaporates it carries away heat energy from a surface, which cools down the surface and helps to lower the temperature (e.g. sweating in humans).
12
Q
What is specific heat capacity?
A
The amount of energy needed to raise the temperature of 1g of a substance by 1 degrees C.
13
Q
Why does water have a high specific heat capacity?
A
It takes lots of energy to break the hydrogen bonds between water molecules, so there is less energy remaining to heat the water. It therefore takes lots of energy to heat up water.
14
Q
Why is it important that water has a high specific heat capacity?
A
Water’s high specific heat capacity means it can buffer (resist) changes in temperature. Because so much energy is needed to heat water, large bodies of water, like lakes, ponds or oceans, have a fairly stable temperature which rarely changes more than a few degrees, even if the air temperature is changing rapidly. This produces a stable environment for marine life. This is significant in organisms which use enzyme-controlled reactions, as these are heavily affected by temperature.
15
Q
Why is water very cohesive?
A
Water molecules a cohesive because they are polar. The slightly positively charged hydrogen atoms are attracted to the slightly negatively charged oxygen atoms of other water molecules. This causes water to ‘stick’ together and flow.
16
Q
What is cohesion?
A
Cohesion is the attraction between molecules of the same type.
17
Q
What is the importance of water’s strong cohesion?
A
It allows water to travel in columns, for example, through the xylem vessels of plants. It is key that water can move through the xylem vessels as it is needed for photosynthesis. Water’s cohesion also means that it has high surface tension. This allows pond skaters to move across the surface of a lake without drowning.
18
Q
What causes water’s high surface tension?
A
The water molecules are more attracted to each other than they are to the air around them, meaning objects can float on the surface of water without falling in.
19
Q
Why is it important that water is transparent?
A
The fact that water is transparent means that light can get to plants beneath the surface of ponds. This is crucial to these plants’ survival as they need light to carry out photosynthesis.
20
Q
What is an inorganic ion?
A
An atom or group of atoms with an electric charge which does not contain carbon.
21
Q
Where are inorganic ions found in the body?
A
Inorganic ions occur in solution in the cytoplasm and body fluids of organisms, some in high concentrations and others in very low concentrations.
22
Q
What determines an ion’s role?
A
Each type of ion has a specific role, depending on its properties. An ion’s role determines whether it is in high or low concentrations.
23
Q
What is the role of iron ions in the body?
A
Iron ions are found in the Haemoglobin of red blood cells (Haemoglobin is a large protein that carries oxygen around the body, in RBC). Haemoglobin is made up of four polypeptide chains, each with an iron ion (Fe2+) in the centre. The Fe2+ ion binds to the oxygen in Haemoglobin. When the oxygen is bound, the Fe2+ ion becomes an Fe3+ ion, until the oxygen is released.
24
Q
What is the role of hydrogen ions?
A
The concentration of H+ ions determines the pH of an environment. The more H+ present, the lower the pH. Enzyme-controlled reactions are affected by pH. H+ ions are also involved in the buffering of solutions.
25
What is the role of sodium ions?
Glucose and amino acids can’t travel across cell membranes on their own. A molecule of glucose or an amino acid can be transported into a cell alongside sodium ions (co-transport).
26
What is the role of phosphate ions?
When a phosphate ion is attached to another molecule, it’s known as a phosphate group. DNA, RNA, and ATP all contain phosphate groups. The bonds between phosphate groups in ATP store energy. The phosphate groups in DNA and RNA allow nucleotides to join up to form polynucleotides. Phosphate ions are involved in the synthesis of ATP and the production of phospholipids.
27
What is the role of calcium ions?
Calcium ions are involved in the ossification of bones and teeth. They are also involved in synaptic transmission (the release of the neurotransmitter across the synaptic cleft).
28
What is the role of magnesium ions?
Magnesium is a major component of chlorophyll, so without magnesium ions, plants wouldn’t be able to photosynthesise.
29
What are monosaccharides?
The monomers from which larger carbohydrates are made.
30
What are disaccharides?
Disaccharides are formed by the condensation of two monosaccharides.
31
What type of bond is formed by the condensation of two monosaccharides?
Glycosidic bond
32
How is maltose formed?
By the condensation of two glucose molecules
33
How is sucrose formed?
By the condensation of a glucose molecule and a fructose molecule.
34
How is lactose formed?
By the condensation of a glucose molecule and a galactose molecule.
35
What type of sugar is sucrose?
Non-reducing sugar
36
What type of sugar are maltose and lactose?
Reducing sugars
37
What is an isomer?
Isomers are chemical compounds which have the same chemical formula but a different structural formula.
38
What are the two isomers of glucose?
Alpha and beta glucose
39
What is the difference between alpha and beta glucose?
In alpha glucose, the hydrogen on C1 is above C1 and the hydroxide is below C1. Whereas, in beta glucose, the hydrogen on C1 is below C1 and the hydroxide is above C1.
40
Describe the structure of glucose.
- 6 carbon atoms in a hexagonal ring
- the vertex of the hexagon between C1 and C5 is an oxygen atom
- the sixth carbon atom is bonded to the 5th carbon atom
- for C1, H above, OH below (beta glucose is opposite)
- for C2, H above, OH below
- for C3, OH above, H below
- for C4, H above, OH below
- for C5, CH2OH above, H below
41
How do you draw the simplified form of the glucose molecule?
You do not need to draw any of the hydrogen or carbon atoms on C2, C3, C5 or C6. You do need to draw the oxygen atom between C5 and C1 and the hydrogen and hydroxide ions on C1 and C4.
42
What type of bond is formed when two glucose molecules condense into a maltose molecule?
1 to 4 alpha glycosidic bond
43
What is the test for reducing sugars?
Add Benedict’s solution to the solution you are testing. Place in a heated water bath. If reducing sugars (monosaccharides and some disaccharides) are present, then a coloured precipitate will form (green, yellow, orange or brick red depending on amount of reducing sugar). If the solution remains blue, there is no reducing sugars.
44
How do you test for non-reducing sugars?
Heat a sample of the solution you are testing with dilute hydrochloric acid (breaks glycosidic bonds) in a water bath. Neutralise it with sodium hydrogencarbonate. Add Benedict’s solution and warm in a water bath. If the colour changes from blue to green/yellow/orange/brick red, non-reducing sugars are present.
45
What are polysaccharides?
Polysaccharides are large polymers of saccharides formed by the linkage of many (over 10) monosaccharides.
46
How are polysaccharides formed?
Polysaccharides are formed by the condensation of many glucose units.
47
What are the properties of polysaccharides?
Insoluble/colloidal, osmotically inactive, not sweet tasting, may be linear or branched
48
What are the functions of polysaccharides?
The specific function depends on which polysaccharide it is, but generally, polysaccharides are used for energy storage or for structural functions.
49
What are the properties of disaccharides?
Sweet tasting, soluble in water, osmotically active
50
What is the function of sucrose?
Energy transport and storage in plants
51
What is the function of lactose?
Energy transport and storage in mammal milk
52
What is the function of maltose?
Intermediate in starch digestion
53
What is the monomer for starch?
Alpha glucose
54
What are the two polysaccharides which make up starch?
- amylose
- amylopectin
55
What is the structure of amylose?
Amylose is a long, unbranched chain of alpha glucose. It is coiled into a helix and is very compact.
56
Why is amylose unbranched?
Amylose is unbranched because it only contains 1-4 alpha glycosidic bonds, so forms one long chain. There are no 1-6 alpha glycosidic bonds, so branches can’t form.
57
Why does amylose form a helix?
Amylose forms a helix because the angles of the glycosidic bonds make it coiled. There is also hydrogen bonding between glucose molecules, which makes it compact and coiled.
58
What is the structure of amylopectin?
Amylopectin is a long, branched chain of alpha glucose.
59
What is the importance of amylopectin being branched?
The side branches allow the enzymes that break down amylopectin to get to the glycosidic bonds easily. This means that the glucose can be released quickly, which means energy can be released through respiration.
60
What allows amylopectin to be branched?
Amylopectin has both 1-4 alpha glycosidic bonds, which hold together the molecules in the main chain, but also 1-6 alpha glycosidic bonds, which connect branch chains to the main chain. This allows for branching.
61
Where is starch stored?
Starch is only stored in plants, not in animals.
62
Why is starch good for storage?
Starch is insoluble in water and doesn’t affect water potential, so it doesn’t cause water to enter cells by osmosis, which would make them swell. Therefore, starch is good for storage. Starch also has a helical structure, so is compact, meaning lots of it can fit in a small space. Starch is a large molecule, so cannot leave cells.
63
What is the monomer for glycogen?
Alpha glucose
64
What is the function of starch?
Starch is used to store excess glucose in plants. When plants need energy, they hydrolyse starch to release glucose for respiration, releasing energy.
65
What is the function of glycogen?
Glycogen acts as an energy store in animals (excess glucose is stored as glycogen). This energy can be released when glycogen is broken down into glucose and used in respiration.
66
What is the structure of glycogen?
Glycogen is a long chain of alpha glucose molecules, with many branches. Glycogen is a compact molecule.
67
Why is it important that glycogen is very branched?
The fact that there is lots of branching in glycogen means that hydrolysis reactions can happen more quickly to break down the glycogen into starch (as enzymes can reach the glycosidic bonds more easily). This means that energy can be released from glycogen quickly as the glucose released is used in respiration.
68
Why is glycogen more branched than amylopectin?
The more branched the polysaccharides are, the more quickly their stored energy can be released. Since animals are more metabolically active than plants, glycogen is more branched than amylopectin, as glycogen is stored in animals, whereas amylopectin makes up starch, which is stored in plants.
69
Where is glycogen stored?
Glycogen is stored in animals, not in plants, in the liver and muscle cells
70
What is the test for starch?
Add the test solution to a test tube then add iodine in potassium iodide solution. If starch is present, the colour will change from brown/orange to black.
71
What is the monomer for cellulose?
Beta glucose
72
What type of bonds are formed between beta glucose molecules in cellulose molecules?
1-4 beta glycosidic bonds
73
What type of bonding is there between cellulose chains in cellulose?
Hydrogen bonding
74
What structure is formed by multiple chains of cellulose?
Microfibrils
75
What is the function of cellulose?
Cellulose provides structural support for plants (plant cell walls are made of cellulose), and give rigidity.
76
What makes cellulose strong?
The chains within the microfibrils are staggered to strengthen cellulose.
77
How are glycosidic bonds formed between beta glucose molecules in cellulose?
Alternate molecules have to be flipped 180 degrees so that there are two OH groups together in order to form the glycosidic bonds.
78
Describe the structure of cellulose
Cellulose is made up of microfibrils, which are made up of long, unbranched chains of beta-glucose. The chains are held together by hydrogen bonding.
79
What are two groups of lipid?
Triglycerides and phospholipids.
80
How are triglycerides formed?
Triglycerides are formed by the condensation of one molecule of glycerol and three molecules of fatty acid.
81
What type of bond is formed between glycerol and a fatty acid?
Ester bond
82
How many molecules of water are removed per triglyceride molecule formed?
3 (3 ester bonds are formed when 3 fatty acids bond to glycerol).
83
What is the difference between saturated and unsaturated fatty acids?
Saturated fatty acids contain only C-C single bonds, whereas unsaturated fatty acids contain C-C single bonds and C=C double bonds. This means that saturated fats are often solids as they can pack together closely, whereas unsaturated fats are often liquids, as the C=C double bonds cause the chain of hydrocarbons to ‘kink’, and so they cannot be compacted as easily, lowering the melting point.
84
What is the structure of a fatty acid?
Fatty acids consist of a carboxyl group and an R group. The R group represents (CH2)nCH3. The carboxyl group bonds to both the glycerol and the R group.
85
How does a fatty acid bond to glycerol?
The carboxyl group of the fatty acid bonds to the hydroxyl group of glycerol, with the elimination of a water molecule
86
How many hydroxyl groups does glycerol have?
3
87
What is the structure of phospholipids?
Phospholipids consist of a molecule of glycerol, 2 fatty acid molecules and a phosphate group.
88
What are the differences between triglycerides and phospholipids?
- triglycerides have 3 fatty acid tails, whereas phospholipids have 2 fatty acid tails
- phospholipids have a phosphate group, whereas triglycerides don’t
- triglycerides are mainly used as storage molecules, whereas phospholipids make up the bilayer of cell membranes
89
Why are triglycerides suited to their function?
Triglycerides function as storage molecules for energy. Their long fatty acid tails contain lots of chemical energy, so lots of energy is released when they are broken down. Therefore, lipids contain about twice as much energy per gram as carbohydrates. Triglycerides are also insoluble in water, so don’t affect water potential (which would cause water to enter the cells and make them swell. Also, if they were soluble, they would be broken down every time they contact water). The reason they are insoluble is that they bundle together as droplets because their fatty acid tails are hydrophobic, so the tails face inwards while the glycerol shields them form water.
90
What is the function of phospholipids and how are they suited to it?
Phospholipids are used in the bilayer of cell membranes, which control what enters and leaves a cell. This works because phosphate groups are hydrophilic, while the fatty acid tails are hydrophobic, so they form a double layer with the glycerol and phosphate pointing outwards. The centre of the bilayer is hydrophobic, so water-soluble substances can’t easily pass through it, making the membrane a barrier to these substances.
91
What is the biochemical test for lipids?
The emulsion test for lipids - shake the test substance with ethanol then pour the solution into water. Any lipid will show up as a milky emulsion. The more lipid there is, the more noticeable the milky colour is.
92
What is the monomer for proteins?
Amino acids
93
What is a dipeptide?
A dipepetide is a molecule formed by the condensation of two amino acids.
94
What is a polypeptide?
A polypeptide is a polymer formed when more than two (>10) amino acids undergo condensation reactions to join together.
95
What is the general structure of an amino acid?
R
I
H2N — C — COOH
I
H
96
What are the different chemical groups in an amino acid molecule?
- NH2 is the amine group
- COOH is the carboxyl group
- R is the variable ‘R’ group (side chain)
97
What is the difference between each of the twenty amino acids common to all organisms?
All amino acids have an identical structure except for the R group (side group), which is what makes different amino acids different.
98
What type of bond is formed between two amino acids?
Peptide bond
99
What do functional proteins consist of?
One or more polypeptides.
100
Which atoms does a peptide bond form between?
Peptide bonds form between the carbon of one amino acid’s carboxyl group, and the nitrogen of another amino acid’s amine group.
101
What is the primary structure of a protein?
The type, number and sequence of amino acids, linked by peptide bonds in a polypeptide.
102
What is the secondary structure of a protein?
The folding shape that the polypeptide chain forms as a result of hydrogen bonding (it will either coil into an alpha helix or fold into a beta pleated sheet).
103
What is the tertiary structure of a protein?
The overall specific 3D shape of the polypeptide chain. This forms when more bonds are formed between amino acids, causing the polypeptide to coil or fold further.
104
What are the two main groups of proteins based on their tertiary structure?
- globular proteins - soluble e.g. enzymes, haemoglobin
- fibrous proteins - insoluble e.g. collagen
105
What is the quaternary structure of a protein?
The quaternary structure is the way in which multiple polypeptides combine together, forming the final 3D structure of some proteins (for proteins with only one polypeptide, the tertiary structure is its final 3D structure).
106
What are the 3 main types of bonding that determine the tertiary structure of a protein?
- hydrogen bonding
- disulphide bonds (also called disulphide bridges)
- ionic bonds
107
Where do hydrogen bonds form in proteins?
Hydrogen bonds form between strongly polar groups. They often form between the hydrogen of one amino acid’s amine group, and the oxygen of another amino acid’s carboxyl group.
108
How can hydrogen bonds be broken in proteins?
They can be broken by high temperatures or pH changes.
109
Where do ionic bonds form in proteins?
Ionic bonds form between ionised amine and carboxyl groups of different amino acids (on the side chains)
110
How can ionic bonds be broken in proteins?
They can be broken by pH changes.
111
Where do disulphide bonds form in proteins?
Disulphide bonds form between cysteine molecules (the sulphur of one cysteine molecule bonds to the sulphur atom of another cysteine molecule).
112
How can disulphide bonds in proteins be broken?
They can be broken by reducing agents.
113
Where do hydrophobic interactions occur in proteins?
Hydrophobic interactions occur between non-polar side chains.
114
Describe the structure of haemoglobin.
Haemoglobin is made up of four polypeptide chains (two alpha chains and two beta chains), each one surrounding a haem molecule that holds a single iron atom.
115
What bonds hold the polypeptide chains together in haemoglobin?
Disulphide bonds
116
What is the prosthetic group in haemoglobin and what does this mean?
The prosthetic group in haemoglobin is the haem group. This means that it is not made of protein.
117
What is the significance of haemoglobin being a globular protein?
The fact that haemoglobin is a globular protein means that it is soluble, which makes it ideal for transporting oxygen around the body,
118
Describe the structure of collagen.
Every third molecule in collagen is glycine. The polypeptide chains coil into alpha helices. Three polypeptide chains are tightly coiled together to form collagen, which makes it strong, and therefore ideal for supportive tissue in animals.
119
How does the structure of enzymes relate to their function?
Enzymes are usually roughly spherical in shape due to the tight folding of polypeptide chains. They’re soluble and have roles in metabolism.
120
How does the structure of antibodies relate to their function?
Antibodies are involved in the immune response and are found in the blood. They’re made up of two light (short) polypeptide chains and two heavy (long) polypeptide chains bonded together. Antibodies have variable regions - the amino acid sequences in these regions vary greatly between antibodies.
121
How does the structure of transport proteins relate to their function?
Channel proteins are present in cell membranes. They contain hydrophobic and hydrophilic amino acids, which cause the protein to fold up and form a channel. These proteins transport molecules and ions across membranes.
122
How does the structure of structural proteins relate to their function?
Structural proteins are physically strong. They consist of long polypeptide chains lying parallel to each other with cross-links between them. Structural proteins include keratin and collagen.
123
What is the biochemical test for proteins?
The Biuret test:
- add a few drops of sodium hydroxide (buiret solution 1) to the test solution (as the solution must be alkaline for the test to work)
- then, add copper (II) sulfate solution (biuret solution 2) down the side of the test tube
- if protein is present, the solution will turn from blue to purple
124
What are enzymes?
Enzymes are a type of protein which act as a biological catalyst.
125
What does biological catalyst mean?
It means that enzymes speed up the rate of metabolic reactions without being used up themselves.
126
What makes an enzyme specific to its substrate?
The shape of the active site means it can only bind to a certain substrate. The shape of the active site is determined by the tertiary structure of the active site.
127
How do enzymes catalyse reactions?
Enzymes catalyse reactions by lowering their activation energy. It does this because when an enzyme-substrate complex forms, this stresses (distorts) the bonds in the substrate, making it easier to break up. If the substrates are being combined into one product, then being attached to the enzyme hold them closer together, reducing repulsion between the molecules, which makes them bond together more easily.
128
What is the lock and key model of enzyme action?
The lock and key model states that the enzyme and the substrate have a complementary shape, so the two can fit together to form an enzyme-substrate complex. The products are formed and released.
129
What is the induced fit model of enzyme action?
The active site of an enzyme is not complementary to the substrate initially. When the substrate binds to the active site, the active site changes so that it is complementary to the substrate (an enzyme-substrate complex forms). The E-S complex causes the stressing and distortion of bonds in the substrate, which causes the bonds to break. This forms the products, which are no longer complementary to the active site, so are released. This is the currently accepted model.
130
What affects the tertiary structure of an enzyme’s active site?
The primary structure determines where the hydrogen, ionic and disulphide bonds form in the tertiary structure, which affects the shape of the active site. If there is a mutation in a gene, the primary structure of the protein may change, which may change the tertiary structure and thus the shape of the active site. Temperature and pH changes also alter the tertiary structure of the active site, which means the enzyme cannot catalyse the reaction anymore as the substrate no longer fits into the active site (denaturation).
131
How can the rate of enzyme activity be measured?
- by measuring how fast the product is made
- by measuring how fast the substrate is broken down
132
How does temperature affect the rate of enzyme-controlled reactions?
When the temperature is increased, the rate of reaction increases initially, as the molecules gain more kinetic energy, so they move more quickly. The substrates are more likely to collide with the enzymes’ active sites, and each collision is more likely to result on a reaction as the energy is higher. However, once the enzyme’s optimum temperature is exceeded, increasing temperature beyond this will slow the rate of reaction as the enzymes become denatured. This will eventually cause the reaction to stop. This is because the rise in temperature makes the enzyme’s molecules vibrate more. If the temperature goes above a certain level, the vibration breaks some of the bonds that hold the enzyme in shape. The shape of the active site changes as a result, so the active site is no longer complementary to the substrate.
133
How does pH affect the rate of enzyme-controlled reactions?
All enzymes have an optimum pH. Above and below this optimum pH, the H+ and OH- ions found in acids and alkalis can disrupt the ionic and hydrogen bonds that holds the enzyme’s tertiary structure in place. The enzyme becomes denatured, and the active site changes shape so the enzyme’s active site is no longer complementary to the substrate. So, too low or too high a pH decreases the rate of reaction.
134
How does substrate concentration affect the rate of enzyme-controlled reactions?
Initially, the rate of reaction increases with increasing substrate concentration, as the more substrate molecules there are, the more successful collisions there are between the substrate and the enzyme’s active site, so more E-S complexes are formed. However, once the saturation point is reached (the point where all of the active sites are occupied), increasing the substrate concentration will have no effect on the rate of reaction as the reaction cannot go any faster (the substrates have to wait unit an active site is available).
135
How does enzyme concentration affect the rate of enzyme-controlled reactions?
Initially, increasing the enzyme concentration increases the rate of reaction as there are more enzymes available, so collisions between enzymes and substrates are more likely to occur. Therefore, more E-S complexes are formed and so the reaction goes faster. However, if the amount of substrate is limited, the rate will plateau (level off) as all of the substrates are already being broken down or synthesised by enzymes, so adding more enzymes after this point makes no difference.
136
How do competitive inhibitors work?
Competitive inhibitor molecules have a similar shape to that of the substrate, so are able to bind to the active site of the enzyme. When an inhibitor occupies the active site, a substrate molecule cannot, so competitive inhibitors prevent the formation of enzyme-substrate complexes and thus reduce the rate of reaction.
137
How does increasing the substrate concentration affect the rate of an enzyme-controlled reaction with a competitive inhibitor?
Increasing the substrate concentration increases the rate of reaction as the substrate molecules can out-compete the inhibitor molecules, and so enzyme-substrate complexes form more frequently, increasing the rate of reaction.
138
How do non-competitive inhibitors work?
Non-competitive inhibitors bind the enzyme away from the active site (allosteric site). This breaks some of the hydrogen/ionic/disulphide bonds in the tertiary structure of the active site, changing the shape of the active site, meaning the substrate can no longer fit into the active site of the enzyme (prevents E-S complexes forming).
139
How does increasing the substrate concentration affect the rate of an enzyme-controlled reaction with a non-competitive inhibitor?
Increasing the substrate concentration has very little effect on the rate of a reaction with a non-competitive inhibitor, as once the non-competitive inhibitor has bonded to the allosteric site, the shape of the active site is altered, and substrate molecules can no longer bind to it. Therefore, the concentration of the substrate has little effect on rate as the substrate can’t bind to the active site.
140
Core practical 1 - measuring the effect of a named variable on the rate of an enzyme-controlled reaction
Catalase catalyses the breakdown of hydrogen peroxide into water and oxygen. Set up a boiling tube containing hydrogen peroxide and hydrogen peroxide solution. Add a bung connected to a delivery tube. Put the delivery tube underneath an upturned measuring cylinder full of water within a water trough. Measure the volume of oxygen collected. Repeat for different concentrations of hydrogen peroxide.
141
Describe control variables for core practical 1 (rate of enzyme controlled reaction affected by substrate concentration)
- pH - use a buffer solution to keep the pH constant across all trials of the experiment
- temperature - conduct the experiment in a water bath at a constant temperature
- enzyme concentration - use catalase from the same stock solution each trial, stir the solution with a glass stirring rod to ensure the concentration is the same throughout
- volume of enzyme and substrate solutions - use a graduated pipette to get accurate volumes of each solution (use the same volume each time) - measure at eye level from the bottom of the meniscus
142
Describe a suitable control for core practical 1 (enzymes)
Repeat the experiment in the exact same way as previously described, but use boiled catalase (it will be denatured, so shouldn’t speed up the rate of reaction). This will confirm that the catalase enzymes are what is causing the increase in rate in the experimental trials.
143
How do you measure the initial rate of reaction from a product/time graph?
Draw a tangent to the graph at its steepest point (this should be where the reaction starts. Calculate the gradient of the line to get the initial rate of reaction.
144
What is the role of DNA and RNA?
DNA and RNA are nucleic acids which are important information-carrying molecules. In all living cells, DNA holds genetic information and RNA transfers genetic information from DNA to ribosomes.
145
What are ribosomes made from?
Ribosomes are made from RNA and proteins
146
What are the monomers of DNA and RNA?
Nucleotides
147
What are nucleotides made of?
All nucleotides consist of a phosphate group, a pentose sugar and a nitrogenous base.
148
What is the structure of a DNA nucleotide?
DNA nucleotides consist of a phosphate group, a deoxyribose sugar and a nitrogenous base (adenine, thymine, cytosine or guanine).
149
What is the structure of an RNA nucleotide?
RNA nucleotides consist of a phosphate group, a ribose sugar molecule and a nitrogenous base (adenine, uracil, cystosine or guanine).
150
What are the complementary base pairs in DNA?
Adenine - thymine (2 hydrogen bonds)
Cytosine - guanine (3 hydrogen bonds)
151
What is the difference between purines and pyrimidines?
Purines have a 2-ring structure while pyrimidines have a 1-ring structure
152
Which of the bases are purines?
Adenine and guanine are purines (2-ring structure)
153
Which of the bases are pyrimidines?
Thymine, cytosine and uracil are pyrimidines (1-ring structure)
154
What is the name of the bond which joins nucleotides?
Phosphodiester bond
155
How are polynucleotides formed?
They are formed by the condensation of many nucleotides, and the formation of many phosphodiester bonds. Water is also released.
156
What is the overall structure of DNA?
DNA molecules have a double helix structure with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs. The two polynucleotide strands run anti parallel to each other, with the chain of phosphate groups and deoxyribose molecules being known as the sugar-phosphate backbone.
157
How does the structure of DNA relate to its function?
- sugar-phosphate backbone protects bases
- large molecule so can store lots of information
- helix so compact
- base sequence allows information to be stored
- double-stranded so replication can occur semi-conservatively
- weak hydrogen bonds so strands can be separated for replication
158
What are the differences between DNA and RNA structure?
DNA:
- deoxyribose sugar
- adenine, thymine, cytosine and guanine are the bases
- double stranded (helix)
- DNA is more stable and longer lasting
- found in the nucleus
- there is only one form of DNA
RNA:
- ribose sugar
- adenine, uracil, cytosine and guanine are the bases
- single stranded (chain)
- less stable and breaks up more quickly than DNA
- found in the nucleus and cytoplasm
- varieties are mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosomal RNA)
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Why did scientists initially doubt that DNA carried the genetic code?
When DNA was first discovered, many believed that it didn’t contain the genetic code because of its relatively simple chemical composition. Some believed that proteins carried the genetic code because they were much more varied.
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Why does DNA replicate?
DNA copies itself before cell division so that each new cell has the full amount of DNA. This is called semi-conservative replication because half of the strands in each new DNA molecule are from the original DNA molecule. This ensures genetic continuity between generations.
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What is the role of DNA helicase in DNA replication?
DNA helicase breaks the hydrogen bonds between bases on the two polynucleotide strands, separating the strands.
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What is the role of DNA polymerase in DNA replication?
DNA polymerase catalyses the condensation reaction which join the nucleotides of the new DNA strand together.
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What is the overall process of semi-conservative replication?
1. The enzyme DNA helicase breaks the hydrogen bonds between the bases on the two polynucleotide DNA strands. This makes the helix unwind to form two single strands.
2. Each original single strand acts as a template for a new strand. Complementary base pairing means that free-floating DNA nucleotides are attracted to their complementary exposed bases on each original template strand (A-T, C-G)
3. Condensation reactions join the nucleotides of the new strand together - catalysed by the enzyme DNA polymerase. Hydrogen bonds form between the bases on the original and new strands. Each new DNA molecule contains one strand from the original DNA molecule and one new strand.
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What is the difference between the 3’ (3 prime) and 5’ (5 prime) end of a DNA molecule?
At the 3’ end there is a hydroxyl group attached to the pentose sugar, while at the 5’ end, there is a phosphate group.
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Which direction does a DNA polymerase molecule work in and why?
DNA polymerase molecules always work from the 3’ to the 5’ end, as the active site is only complementary to the 3’ end. This means that nucleotides are added in a 5’ to 3’ direction, as the strands in DNA run anti-parallel.
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What was the method of Meselson and Stahl’s experiment?
1. Two samples of bacteria were grown for many generations - one in a nutrient broth containing light nitrogen, and one in a nutrient broth containing heavy nitrogen. As the bacteria reproduced, they took up nitrogen from the broth to help make nucleotides for new DNA. Over time, the nitrogen gradually became a part of the bacteria’s DNA
2. A sample of DNA was taken from each batch of bacteria, and spun in a centrifuge. The DNA from the heavy nitrogen bacteria settled lower in the centrifuge tube than the DNA from the light nitrogen bacteria because it’s heavier.
3. The bacteria grown in the heavy nitrogen broth were taken out and put in a broth containing only light nitrogen. The bacteria were left for one round of DNA replication, then another DNA sample was taken out and spun in the centrifuge.
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What were the results of Meselson and Stahl’s experiment?
The DNA settled out in the middle of the centrifuge tube because it contained a mixture of the light and heavy nitrogen. This proved that DNA replication was semi-conservative because otherwise, the DNA would have settled in two different places (one for the heavy DNA and one for light DNA).
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What does ATP stand for?
Adenosine triphosphate
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What are the components of ATP?
ATP exists as molecules containing a ribose molecule, an adenine base and 3 inorganic phosphate groups. It is therefore known as a nucleotide derivative because it is similar in structure to a DNA nucleotide.
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How is energy stored and released in ATP?
ATP stores energy in the high energy bonds between the phosphate groups and is released via hydrolysis reactions.
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Which compound is ATP hydrolysed into and by which enzyme?
ATP undergoes a hydrolysis reaction catalysed by the enzyme ATP hydrolase to produce ADP (adenosine diphosphate) and an inorganic phosphate group. Energy is also released, which can be used by the cell (as it cannot get energy directly from the glucose in respiration).
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What is ADP hydrolysed to?
ADP can be hydrolysed to AMP (adenosine monophosphate), which can further be hydrolysed into adenosine.
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What can the inorganic phosphate released in ATP hydrolysis be used for?
The inorganic phosphate groups can be used to resynthesise ATP or for phosphorylation (the addition of a phosphate group to a compound to make it more reactive).
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How can ATP be resynthesised?
A condensation reaction between ADP and Pi, catalysed by the enzyme ATP synthase, can form ATP (energy is used).
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What is the role of ATP in a cell?
ATP is an energy carrying molecule, which is synthesised when energy is released from a reaction, such as in photosynthesis or respiration. ATP then diffuses to the part of the cell which requires energy and is hydrolysed there to release energy, which is used by the cell.
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Why is ATP a particularly good energy source?
- ATP stores or releases only a small, manageable amount of energy at a time, so little energy is wasted as heat
- ATP is a small, soluble molecule, so it can be easily transported around the cell
- it’s easily broken down, so energy can be released instantaneously
- it can be quickly remade
- it can make other compounds more reactive by transferring a phosphate group to them (phosphorylation)
- ATP can’t pass out of the cell, so the cell always has an immediate supply of energy
