Topic 1 - Biological Molecules Flashcards
(104 cards)
1
Q
What is a monomer?
A
A small unit from which larger molecules are made.
2
Q
What is a polymer?
A
A molecule made from a large number of monomers bonded together.
3
Q
What are 3 examples of monosaccharides?
A
Glucose, Fructose, Galactose
4
Q
What are 3 examples of monomers?
A
Monosaccharides, amino acids, nucleotides.
5
Q
What is a condensation reaction?
A
A reaction that joins two molecules together with the formation of a chemical bond and involves the removal of a water molecule.
6
Q
What is a hydrolysis reaction?
A
A reaction that breaks the chemical bond between two molecules and involves the use of a water molecule.
7
Q
What bond is formed from a condensation reaction between two monosaccharides?
A
A glycosidic bond.
8
Q
What are monosaccharides?
A
The monomers from which larger carbohydrates (contain C, H, O) are made.
9
Q
How are the disaccharides maltose, sucrose and lactose created?
A
Maltose - Formed by the condensation of two alpha glucose molecules.
Sucrose - Formed by the condensation of a fructose molecule and a glucose molecule.
Lactose - Formed by the condensation of a glucose and a galactose molecule.
10
Q
Describe the structure of alpha glucose:
A
Hydroxyl groups below.
11
Q
Describe the structure of beta glucose:
A
Hydroxyl group below on the left, hydroxyl group above on the right.
12
Q
How are polysaccharides formed?
A
By the condensation of many glucose units.
13
Q
How is starched formed?
A
By two polymers of alpha glucose: amylose and amylopectin.
14
Q
Where is starch found?
A
In starch grains inside plant cells, e.g. inside chloroplasts.
15
Q
What is the function of starch?
A
An insoluble store of glucose.
16
Q
Describe the structure of amylose:
A
A long, straight chain of alpha glucose, each glucose unit forms a 1-4 glycosidic bond. The unbranched chain of amylose coils up to form a helix.
17
Q
Describe the structure of amylopectin:
A
Contains 1-4 glycosidic bonds, and 1-6 glycosidic bonds that create a branch.
18
Q
Where is glycogen found?
A
In the liver and muscle cells of animals.
19
Q
What is the function of glycogen?
A
An insoluble store of glucose.
20
Q
Describe the structure of glycogen:
A
Many 1-4 glycosidic bonds, but also has multiple 1-6 glycosidic bonds to create a highly branched polymer.
21
Q
What is the difference between glycogen and amylopectin?
A
Glycogen has more 1-6 glycosidic bonds to create a highly branched polymer.
22
Q
How is cellulose formed?
A
By beta glucose.
23
Q
Where is cellulose found?
A
The cell walls of plant cells.
24
Q
What is the function of cellulose?
A
To provide structural strength to the plant cell wall, this prevents the cell from bursting when it becomes turgid with water.
25
Describe the structure of cellulose.
Contains long, straight chains of beta glucose with 1-4 glycosidic bonds. The chains line up parallel to each other and are held together by hydrogen bonds. This structure forms a fibrin.
26
What is an inorganic ion?
An ion that doesn’t contain carbon, hydrogen or oxygen.
27
Where do inorganic ions occur?
In solution in the cytoplasm and bodily fluids of organisms (some in high concentrations, some in low concentrations).
28
What is the role of the hydrogen ion?
Determines pH. The higher the concentration of hydrogen ions - the lower the pH. This is important because pH affects enzyme function.
29
What is the role of iron ions?
A key component of haemoglobin in red blood cells. The iron ion binds to the oxygen - allowing haemoglobin to associate with oxygen and transport is around the body.
30
What is the role of sodium ions?
Responsible for co-transport - the process of transporting glucose and amino acids into cells across a cell-surface membrane.
31
What is the role of phosphate ions?
1. To join the nucleotides in DNA and RNA together to form sugar-phosphate backbone.
2. Used to produce ATP.
3. Phosphate groups can be added to molecules to make them more reactive via a process called phosphorylation.
32
Describe the simple structure of a triglyceride:
A glycerol molecule joined up with 3 fatty acid chains via a condensation reaction forming 3 ester bonds.
33
Describe the simple structure of a phospholipid:
A glycerol molecule and a phosphate group join up with 2 fatty acid chains via a condensation reaction forming 2 ester bonds.
34
What is a saturated fatty acid?
A fatty acid that only consists of single bonds between the carbons.
35
What is an unsaturated fatty acid?
A fatty acid that consists of at least one double bond between the carbons.
36
Name 4 ways the triglyceride structure results in its properties:
1. Storing energy - Due to the large ratio of energy-storing hydrogen-carbon bonds compared to the amount of carbon atoms, a lot of energy is stored in the molecule.
2. Water source - Due to the large ratio of hydrogen to oxygen atoms, they act as a metabolic water source. Triglycerides release water when they are oxidised, which is essential for animals that live in the desert e.g. camels.
3. Don’t affect water potential or osmosis - Triglycerides are large and hydrophobic, so are insoluble in water.
4. Relatively low mass - meaning a lot can be stored without increasing the mass and preventing movement.
37
How do you use the emulsion test to test for lipids?
1. Dissolve sample in ethanol and shake.
2. Add distilled water and shake.
If a white emulsion appears, lipids are present.
38
Describe the head and tails of lipids:
Hydrophilic head - Can attract with water as it is charged. Due to the phosphate being charged, it repels other fats.
Hydrophobic tails - Not charged, so repels water. However they will mix with other fats.
39
Why are phospholipids polar molecules?
Because they have two charged regions.
40
Describe the phospholipid bilayer membrane structure:
• Two sides: Extracellular and intracellular
• Makes up the plasma membranes around cells.
In water they are positioned so that the heads are exposed to water and the tails are not.
41
Describe the role of calcium ions:
• Help insulin to be released from pancreas.
• Responsible for transmitting nerve impulses.
• Necessary for bone formation.
42
Describe the role of potassium ions:
• Responsible for nerve impulses and fluid balance.
• Help the contraction of muscle fibres.
• Responsible for the opening and closing of stomata in plants (so control the concentration of carbon dioxide taken in by plant).
43
Describe the role of magnesium ions:
• Cofactor for the enzymes amylase and lipase which break down glucose and fats.
• Necessary for the production of chloroplasts in plants.
44
Describe the role of chloride ions:
• Keep the pH level of blood constant during gas exchange.
• Responsible for transmitting certain nerve impulses.
• Cofactor the amylase enzyme.
45
What are some examples of reducing sugars?
All monosaccharides and some disaccharides e.g. maltose and lactose.
46
How do you carry out the reducing sugar test?
Benedicts test:
• Add Benedict’s reagent to the sample and heat it in a water bath that has been brought to boil.
• The test is positive is a coloured precipitate has been formed.
• The test is negative if the sample remains blue.
47
What is an accurate way of measuring and comparing the concentration of reducing sugars in different solutions?
• Filter the solution and weigh the precipitate.
• or… remove the precipitate and use a colorimeter to measure the absorbance of the remaining Benedict’s reagent.
48
What are the 4 different precipitates for the positive result of a Benedict test + state their concentrations:
Green -> Trace amount of reducing/non reducing sugar.
Yellow -> Low amount
Orange -> Medium amount
Brick Red -> Large amount
49
Give an example of a non-reducing sugar:
Sucrose.
50
How do you carry out the test for non-reducing sugars:
Non-reducing Benedict’s test:
• Break up the sample into monosaccharides: to do this, start by getting a new sample of the test solution (one you haven’t already added Benedict’s reagent to), and add dilute hydrochloric acid to it and carefully heat it in a water bath thats been brought to boil.
• Neutralise the sample using sodium hydrogen carbonate.
• Finally, carry out the Benedict’s test as you would for reducing sugars: add Benedict’s reagent to the sample and heat in a water bath thats been brought to boil.
51
How do you carry out the test for starch?
Iodine test:
• Add iodine dissolved potassium iodide solution to a sample.
Positive result = colour changes from browny-orange to blue-black.
Negative result = colour remains browny-orange.
52
How do you carry out the test for proteins?
Biuret test:
1. Test solution needs to be alkaline, so add a few drops of sodium hydroxide solution.
2. Add some copper (II) sulfate solution.
Positive result = colour changes from blue to purple.
Negative result = colour remains blue.
53
What are amino acids?
The monomers which proteins consist of.
54
What is a dipeptide?
Two amino acids joined together.
55
What is a polypeptide?
More than two amino acids joined together.
56
How do amino acids joined together via the condensation reaction?
• One amine group/NH3 joins to one carboxyl group/ COOH to form peptide bond.
• So at one end theres a free amine group, and the other end theres a free carboxyl group.
57
Describe the primary structure of a protein:
The sequence of amino acids in the polypeptide chain.
58
Describe the secondary structure of a protein:
• The polypeptide chain doesn’t remain flag and straight. Hydrogen bonds form between the amino acids in the chain, this automatically makes it coil into an alpha helix or a pleated beta sheet.
59
Describe the tertiary structure of a protein:
The coiled or folded chain is often coiled or foiled further. More bonds are formed between different parts of the polypeptide chain, including hydrogen bonds or ionic bonds. A disulfide bridge is also formed when two molecules of the amino acid cysteine come close to each other. The sulfur atom from one cysteine bonds with the sulfur atom in the other. For proteins that consist of only one polypeptide chain, the tertiary structure forms their final 3D structure.
60
Describe the quaternary structure of a protein:
• The polypeptide chains bond together.
• For proteins with more than one polypeptide chain, the quaternary structure forms their final 3D structure.
61
How does the enzyme shape determine its function (PROTEIN TOPIC)?
• They’re usually roughly spherical due to the tight folding of the polypeptide chain, they’re also soluble.
• This means they have roles in metabolism e.g. some enzymes break down large food molecules, others synthesise large molecules.
62
How does the shape of antibodies determine its function (PROTEIN TOPIC)?
• Antibodies are found in the blood and consist of two light (short) polypeptide chains and two heavy (long) polypeptide chains joined together.
• Antibodies also have variable regions; the amino acid sequences in these regions vary greatly.
• This means that antibodies are involved in the immune response.
63
How does the shape of transport proteins determine its function (PROTEIN TOPIC)?
For example: channel proteins.
• 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.
• This means they transport molecules and ions across membranes.
64
How does the shape of a structural protein determine its function (PROTEIN TOPIC)?
• They are physically strong, and contain long polypeptide chains that line up parallel to each other with cross-links between them.
• They include keratin (found in hair and nails) and collagen (found in connective tissue); collagen has three polypeptide chains tightly coiled together.
• This means they make great supportive tissues in animals.
65
What is an enzyme?
A tertiary structure protein that catalyses a reaction.
66
What is an active site?
A part of an enzyme that attaches to the substrate to catalyse a reaction.
67
Describe the shape of an active site:
• Specific and unique in shape due to the specific folding and bonding in the tertiary structure of the protein.
• This means the enzyme can only attach to the substrate if it is complementary in shape.
68
What is the activation energy?
The minimum amount of energy the reaction requires in order to occur.
69
What happens to the activation energy of a reaction when the enzyme attaches to the substrate?
The activation energy is lowered, therefore speeding up the rate of the reaction.
70
What does the lock and key model suggest?
•Suggests that the enzyme is like a “lock” and the substrate is like a “key” thats fits into it due to their complementarity in shape.
• Further suggests the enzyme active site is a fixed shape and that due to random collisions the substrate can collide and attach to the enzyme - this forms an enzyme-substrate complex.
• Once the enzyme-substrate complex has formed, the charged groups within the active site are ready to distort the substrate, therefore lowering the activation energy. The products are then released and the active site is empty and ready to be reused.
71
What is the induced fit model of an enzyme?
• Substrate binds to active site.
• ES-complex forms
• Active site changes shape slightly so its complementary to substrate.
• Reduces activation energy.
72
How does temperature affect enzyme activity?
• If the temperature is too low, there is not enough kinetic energy for successful collisions between the enzyme and substrate.
• If the temperature is too high, the enzyme becomes denatured: the active site changes shape and the enzyme-substrate complex can no longer form.
73
How does pH affect enzyme activity?
If the pH is too low or high, this interferes with the charge in the amino acids in the active site. This breaks the bonds holding the tertiary structure in place, so the active site changes shape and the enzyme denatures.
74
How does substrate concentration affect enzyme activity?
If there is insufficient substrate, there will be fewer collisions between the enzyme and substrate so the reaction will be slower.
75
How does enzyme concentration affect enzyme activity?
If there is insufficient enzymes, the active site will saturate with substrate, so is unable to work any faster.
76
How does competitive inhibitors affect enzyme activity?
• Similar shape to substrate.
• Inhibitor binds to active site, substrate can no longer bind.
• Prevents ES-complex from forming.
77
How do non-competitive inhibitors affect enzyme activity?
Non-competitive inhibitors bind away from the active site, called the allosteric site. This causes the active site to change shape, therefore the substrate can no longer bind to the enzyme no matter how much substrate is added.
78
What does DNA stand for?
Deoxyribonucleic acid.
79
What does RNA stand for?
Ribonucleic acid.
80
What is the function of DNA?
Store your genetic information.
81
What is the function of RNA?
• Transfer genetic information from DNA to ribosomes.
• Ribosomes are the site of protein synthesis, they read the RNA to make polypeptides via a process called translation.
• Ribosomes are made up of RNA and proteins.
82
What is a polynucleotide?
• Many nucleotides joined together via a condensation reaction between the pentose sugar from one nucleotide and the phosphate group from another.
• This forms a phosphodiester bond (a phosphate group and 2 ester bonds).
• The polynucleotide chain is known as a sugar-phosphate backbone.
83
Describe the DNA structure:
• DNA has a double helix structure, which is formed when two separate polynucleotide strands wind up together to form a spiral.
• DNA molecules are really long and tightly coiled together so can store lots of genetic information in a small space in the cell nucleus.
84
Describe a DNA nucleotide structure:
A phosphate group, the pentose sugar deoxyribose, and a base of either C,G,A or T.
85
Describe the RNA nucleotide structure:
A phosphate group, the pentose sugar ribose, and a base of either C,G,A or U (U replaces T).
86
Describe the complementary base pairing of DNA:
•A pairs with T and forms 2 hydrogen bonds
•C pairs with G and forms 3 hydrogen bonds.
Since these bases always pair with each other, theres always an equal amount of A:T and C:G.
87
What positions are the sugar and phosphate exposed?
3 prime = sugar exposed.
5 prime = phosphate exposed.
88
Describe the RNA structure:
• Consists of the pentose sugar ribose.
• Uracil replaced thymine, and pairs with adenine.
• RNA is a single polynucleotide strand.
• RNA is much smaller than most DNA polynucleotides.
89
Why is DNA replicated?
For cell division so that each new cell has the full amount of DNA.
90
What is the process of DNA replication called and why is it called this?
• Semi-conservative replication.
• Because half of the strands in each DNA molecule are from the original molecule. This means theres a genetic continuity between generations of cells.
91
Describe what happens during the first stage of semi-conservative replication:
• The enzyme “DNA helicase” breaks the hydrogen bonds between the bases of the two polynucleotide DNA strands. Causing the helix to unwind and form two single strands.
92
Describe what happens during the 2nd stage of semi-conservative replication:
• Each original strand acts as a template for a new strand.
• Complementary base pairing means that free-floating DNA nucleotides attract to their complementary-exposed bases on each original template strand (A with T, C with G).
93
Describe what happens during the third stage semi-conservative replication:
• Condensation reactions join up the nucleotides of the new strand together, catalysed by the enzyme “DNA polymerase”.
• Hydrogen bonds form between the bases of the original and new strands.
• Each new DNA molecule is made from a strand of the original DNA molecule and a new strand.
94
Describe the full experiment which led Meselson and Stahl to proving that DNA replicated via semi-conservative replication:
1. Two samples of bacteria were grown for several generations (one in a nutrient broth containing heavy nitrogen, and one in a broth containing light nitrogen). As the bacteria reproduced, they took up nitrogen from the broth to make nucleotides for new DNA, so the nitrogen gradually became part of the bacterium’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 down the centrifuge tube than the DNA from the light nitrogen bacteria - because its heavier.
3. The bacteria grown in a heavy nitrogen broth was then put in a broth only containing light nitrogen. The bacteria was left for one round of DNA replication before a sample of DNA was taken from the broth and spun in a centrifuge.
4. If DNA replicated conservatively then the original DNA containing heavy nitrogen bacteria would still be together and would settle at the bottom, whilst the new light nitrogen bacteria would settle at the top.
5. If replication was semi-conservative, the new bacterial molecules would contain one DNA strand from the original DNA containing heavy nitrogen bacteria, and one strand from the new DNA containing light nitrogen bacteria. So the DNA would settle out in between where the heavy nitrogen settled out and the light nitrogen settled out.
• Result: The DNA settled in the middle, showing that it contained a mixture of heavy and light nitrogen, meaning that it replicated semi-conservatively in the light nitrogen.
95
Outline the importances of water:
• metabolite in many metabolic reactions e.g. condensation, hydrolysis reactions.
• universal solvent: many substances dissolve in it. Most metabolic reactions take place in solution, making water essential.
• Helps temperature control due to its high latent heat of vaporisation and high specific heat capacity.
• Cohesive: useful for transporting substances in plants and transport in other organisms.
96
What is a hydrogen bond?
A weak bond between a slightly positively charged hydrogen atom from one molecule and a slightly negatively charged atom from another molecule.
97
Water being a universal solvent:
Many biological reactions contain ions, the positively charged side of the water molecule (oxygen) attracts to the negative ion vice versa.
• Waters polarity makes it a useful solvent, so organisms can take up substances dissolved in water and transport them around the body.
98
Water’s high latent heat of vaporisation:
Lots of energy required to change the state of water from liquid to gas, meaning water loss by evaporation can cool an organism down without it losing too much water.
99
Waters high specific heat capacity:
• Lots of energy required to raise the temperature of 1 gram of water by 1*C.
• Meaning water can buffer (resist) changed in temperature.
100
What are the common factors to investigate when investigating the effect of different factors of the enzyme activity of different enzymes?
• Temperature
• pH
• Substrate concentration
• Enzyme Concentration
•Inhibitors (competitive + non-competitive)
101
What are the common enzymes investigated when investigating the effect of different factors on the enzyme activity of different enzymes?
• amylase
• catalase
• protease
• trypsin
102
What is the equipment needed to investigate the effect of pH on trypsin activity?
• Stop clock
• Photographic film (source of substrate: contains gelatine which trypsin breaks down)
• Test tube
• pH buffers
• Straws with slit cut in them
• Syringe
• Kettle
• 2% trypsin
• Beaker
• Thermometer
103
What is the method used to investigate the effect of pH on trypsin activity?
1. Use forceps to place piece of photographic film onto the slit cut in a straw.
2. Use a syringe to add 4cm^3 of 2% trypsin to a test tube.
3. Use a different syringe to add 4cm^3 of pH 4 buffer solution to the same test tube.
4. Add the test tube to a water bath set to 37*C (use thermometer to check), wait 5 minutes for contents of the tube to reach 37*C.
5. Place straw attached to photographic film into test tube and immediately start a stop clock.
6. Dunk the straw in and out of the test tube every 10 seconds.
7. Once the photographic film has turned completely clear, the reaction is over (compare the film to an already-cleared film to determine the end result). Compare the time taken for the film to clear (if the film doesn’t change at all in the 25 minutes record the time as infinity (no reaction)).
8. Repeat the experiment for all the pH values your going to test (repeat steps 1-7 another 2 times for each pH value and calculate a mean, then calculate a mean rate of reaction using the formula 1/mean time taken).
9. Plot a graph of pH against mean RoR.
104
How to calculate the mean RoR:
1. Calculate a mean from your 3 trials (excluding any anomalies).
2. Use the formula 1/mean time taken to calculate the mean rate of reaction.
