[Y1] Biological Molecules Flashcards
(130 cards)
1
Q
What are monomers?
A
Small molecules that combine to form larger chains of molecules.
2
Q
What are polymers?
A
Large molecules made up of repeated smaller molecules.
3
Q
What are the two main usages of carbohydrates?
A
- respiritory substrates
- structural components
4
Q
What are carbohydrate monomers called?
A
Monosaccharides
5
Q
What are carbohydrate dimers called?
A
Disaccharides
6
Q
What are carbohydrate polymers called?
A
Polysaccharides
7
Q
Give 3 examples of monosaccharides?
A
- Glucose
- Galactose
- Fructose
8
Q
What is the structure of Glucose?
A
Hexosugar (hexose)
- contains 6 carbon atoms.
- contains hydrogen.
- contains oxygen.
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9
Q
What are isomers?
A
The different structures of the same monomers.
10
Q
What is the difference between the isomers of Glucose?
A
α - Hydroxyl group below.
β - Hydroxyl group above.
https://s3mn.mnimgs.com/img/shared/ck-files/ck_55f311ac700e0.jpg
11
Q
How are monosaccharides joined together?
A
Condensation reactions
12
Q
What happens during a condensation reaction (in sugars)?
A
- 2 monosaccharides (or polysaccharide chain ends) bond together to form a disaccharides (or longer polysaccharide chains).
- Water is released.
- made from one hydroxyl group and the other hydrogen.
- ∴ it is a condensation reaction. - A glycosidic bond is formed from the remaining oxygen.
13
Q
Give 3 examples of disaccharides and what monomers make them up.
A
Glucose + α-Glucose ==> MALTOSE
Glucose + Fructose ==> SUCROSE
Glucose + Galactose ==> LACTOSE
14
Q
Give 3 examples of polysaccharides and what monomers make them up.
A
Many x β-Glucose ==> CELLULOSE
Many x α-Glucose ==> GLYCOGEN
Many x α-Glucose ==> STARCH
15
Q
How are polysaccharides broken apart?
A
Hydrolysis reactions
16
Q
What happens during a hydrolysis reaction?
A
- Water is required for this to take place.
- Poly/Disaccharides break down into monomers/ smaller polymers.
- The bonds are broken. (Name the relevant bond)
17
Q
What is the general formula for monosaccharides?
A
(CH₂O)n
- n = number of carbons.
18
Q
What are the names and formulae of the different monosaccharides, given the number of carbons.
3 4 5 6 7
A
3 TRIOSE C₃H₆O₃
4 TETROSE C₄H₈O₄
5 PENTOSE C₅H₁₀O₅
6 HEXOSE C₆H₁₂O₆
7 HEPTOSE C₇H₁₄O₇
19
Q
What are the formulae of Glucose, Fructose, and Galactose?
A
- They are all C₆H₁₂O₆.
- But they are still different from each other structurally.
- ∴they are structural isomers of each other.
20
Q
Describe the test for reducing sugars.
A
- Benedict’s solution is added in excess.
- The solution is heated in a water bath.
- If the test is +tive you will get a colour change.
- The colour change follows the gradient:
Green (low) → Yellow → Orange → Red (High). - If the test is -tive the solution will remain Blue.
21
Q
Is the Benedict’s test quantitative?
A
No. It’s Semi-Quantitative.
22
Q
How does the Benedict’s test work?
A
- It works by causing the reducing sugar to give an electron to the solution (reduces the Benedict’s solution).
23
Q
How would you get a quantitative reading from the Benedict’s test? Why does this work?
A
- Use a pH probe.
- ∵the sugar solution ionises (gains hydrogen) you can read the concentration of reducing sugars in a sample by reading the concentration of H.
24
Q
What are Lipids made of and there proportion?
A
C, H, O
- has lower proportion of O to C and H (than carbohydrates)
25
Are lipids insolube?
Yes (in water).
| However they are soluble in organic substances (e.g. alcohol, asetone)
26
What are the functions of lipids?
- Energy storing.
- Water-proofing.
- Insulating.
- Physical protection.
27
What two types of lipids can you get (and at what conditions)?
Fats (solid at room temp)
Oils (liquid at room temp)
[Room temp = 10-20 degrees C]
28
Describe the structure of Triglycerides.
A glycerol head bonded to three fatty acid tails through ester bonds.
29
What are saturated lipids?
- no double bonds
| - usually fats
30
What are monounsaturated lipids?
- one double bond
| - usually oils
31
What are polyunsaturated lipids?
- multiple double bonds
| - usually oils
32
What is the general rule determine how (un)saturated a lipid is?
more unsaturated = more kinks
33
How does triglyceride's specific structure determine their function?
- a high ration of energy-storing carbon-hydrogen bonds
- have a low mass to energy ratio
- are large and insoluble
- has a high ratio of hydrogen: oxygen and so releases water when oxidised
34
Describe the structure of Phospholipids.
- a phosphate head with two fatty acid tails.
| - they are polar ( hydrophobic tail, hydrophilic head)
35
What is a Licence structure?
Single-layer spherical arrangement of phospholipids
36
What is a Liposome structure?
Double-layer spherical arrangement of phospholipids
37
What is a Bilayer structure
Double-layer flat arrangement of phospholipids
38
How does phospholipid's specific structure determine their fuvtion?
- their polarity is useful in various cellular functions (in aqueous)
- the hydrophilic phosphate head helps hold at the surface of cell membranes
- combined with carbohydrates makes glycolipids within the cell-surface membrane (these are important in cell recognition).
39
What is the test for lipids? (name of the test)
The emulsion test.
40
How do we test for lipids? (describe steps)
- take a dry, grease-free test tube.
- add ethanol to the sample.
- shake thoroughly to dissolve any lipids.
- add water and shake gently.
- as a control, repeat the procedures using water instead of the sample (this should stay clear).
41
What will happen if the test for lipids is positive?
A cloudy emulsion will form.
42
Why does the test for lipids work?
- The cloudy emulsion id due to any lipid in the sample being finely dispersed in the water,
- Therefore when light passes through the emulsion it is refracted as it passes from oil droplets to water
- Making it appear cloudy.
43
What is the structure of an amino acid?
- A central Carbon
- An amino group (-NH₂)
- A carboxyl group (-COOH)
- A hydrogen atom (-H)
- R (side) group
44
How many naturally occurring amino acids are there?
20.
45
How do amino acids differ?
Through the R group being a variety of different chemical groups.
46
How a dipeptides made?
The removal on water in a condensation reaction.
The water is made by combining a hydroxyl (-OH) from the carboxyl group to one amino acid with a hydrogen (-H) from the amino group.
The two amino acids then link via a peptide bond.
47
How are peptide bonds connected?
Between the carbon atom of one amino acid and the nitrogen of the other.
48
How are peptide bonds broken?
Hydrolysis reaction.
49
What is the primary structure of proteins?
Amino acid monomers joining together in a process called polymerisation.
This gives many hundreds of amino acids called a polypeptide.
50
Why is there a limitless number of types of primary protein structure?
The 20 naturally occurring amino acids can join together in different sequences.
51
Why is the primary structure of proteins important?
A change in just a single amino acid in the primary structure can lead to a change in shape and therefore function.
52
What is the secondary structure of proteins?
Long polypeptide chains being twisted into a 3D shape, such as:
- a coil (α-helix).
- sheet (β-pleated sheet).
53
Why can a secondary protein structure form?
- Linked amino acids that make up a polypeptide both have a -NH and a -C=O group on either side of every peptide bond.
- The Hydrogen in the -NH has an overall +tive charge.
- The Oxygen in the -C=O has an overall negative charge.
- These two groups, therefore, readily form weak hydrogen bonds.
54
What is the tertiary structure of proteins?
- α-helices of the secondary structure being able t twist and fold even more to give the complex and often specific, 3D structure of a specific protein.
55
What bonds are present in the tertiary structure of proteins?
- Disulfide bridges: these are fairly strong and therefore ar not easily broken.
- Ionic bonds: these are formed between any carboxyl and amino group that are not involved in forming peptide bonds. They are weaker than disulfide bonds and are easily broken by changes in pH.
- Hydrogen bonds: these are numerous but easily broken.
56
What is the quaternary structure of proteins?
The combination of different polypeptide chains and associated non-protein (prosthetic) groups into a large, complex protein molecule.
57
Give an example of a quaternary structure.
iron-containing haem group in haemoglobin.
58
How does the primary structure affect the tertiary structure of proteins?
The order of amino acids ultimately determines how the protein will fold and bond, therefore influencing its shape and therefore it's tertiary structure.
59
What is the test for proteins, and how does it do it?
The Biuret test, which detects peptide bonds.
60
Describe the Biuret test.
- Place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at RTP.
- Add a few drops of very dilute (0.05%) copper(II) sulfate solution and mix readily.
- A purple colouration indicates the presence of peptide bonds and hence a protein.
- If no protein is present, the solution remains blue.
61
What are the two basic types of protein shape, examples, and general function?
- Globular, such as enzymes and haemoglobin, carry out metabolic functions.
- Fibrous, such as collagen, have structural functions.
62
Describe the structure of
| fibrous proteins.
They form large chains which run parallel to one another. These chains are linked by cross-bridges and so form very stable molecules.
63
Describe the specific structure of a fibrous protein (with a named example).
One example is collagen.
- The primary structure is an unbranched polypeptide chain.
- In the secondary structure the polypeptide chain is very tightly wound.
- Lots of the amino acid glycine helps close packing.
- In the tertiary structure the chain is twisted into a second helix.
- Its quaternary structure is made up of three such polypeptide chains wound together in the same way as individual fibres are wound in a rope.
64
How does the structure of the named fibrous protein aid in its function?
Collagen is found in tendons.
Tendons join muscles to bones.
When a muscle contracts the bone is pulled in the direction of the contraction.
65
What type of structure does an enzyme have?
Globluar
66
What is an enzyme?
Enzymes are biological catalyst that alter the rate of reaction by providing an alternative reaction pathway, without being used up.
67
What is the active site of an enzyme? Describe its functions.
A functional region of an enzyme, which is made up of a relatively small number of amino acids.
This forms a small depression within the much large enzyme molecule.
68
What do enzymes act on?
Substrates.
69
What is the enzyme-substrate complex model?
When a substrate fits neatly into the depression of an enzyme's active site.
70
What is the induced fit model?
This proposes that the active site forms as the enzyme and substrate interact.
The enzyme is flexible and can mould itself around the substrate (like a glove on a hand).
As it changes its shape the enzyme puts strain on the substrate, which sistorts a particular bond(s) in the substrate and consequently lower the activation energy needed to break the bond.
71
Why might a change in the environment of an enzyme be bad?
A change in an enzymes environment is likely to change its shape. Therefore meaning it can no longer attach to the specific substrate.
72
What are two ways of measuring enzyme-catalysed reactions?
- The formation of the products.
| - the disappearance of the substrate.
73
Describe an increasing/decreasing graph of volume/mass of substrates by time
[9 points to make]
- At first there is a lot of substrate but no product.
- It is easy for the substrates to come into contact with empty active sites on enzymes.
- All enzymes active istes are filled at any given time and the substrate rapidly becomes a product.
- The amount of substrate decreases whilst the amount of product increases.
- As this continues there is less and less substrate and more and more product.
- It becomes more difficult for the substrate molecule to come into contact with the enzyme molecules as there are very few substrate molecules and the products 'may get in the way'
- It therefore takes longer for the substrate to be broken down so the rate of product produced/substrate used slows down.
- This continues to slow until there is so little substrate it can no longer be measured.
- The graph must therefore plateau out
74
How do you measure the rate of change on a graph?
Find the tangent at that point.
75
What must be a constant when measuring the effect of temperature on the rate of enzyme activity?
- pH.
- enzyme concentration.
- substrate concentration.
76
What word describes the relation between an enzyme's active site and a substrate?
Complementary.
77
How does temperature affect the rate of an enzyme-catalysed reaction?
- Rise in temp = more kinetic energy.
- molecule moves more rapidly and collide more often.
- therefore they are more likely to collide with the enzymes in a given time.
- resulting in more successful collisions and the rate of reaction increasing.
- However the rise in temp also causes H-bonds in the enzyme to break, resulting in a change of shape of an active site.
- This continuous as the temp rises and causes the enzyme to stop working all together.
- This is know as denaturing (this begins after the optimum temp has been reached.)
78
Why is body temp around 37oC and not 40oC (the optimum temp for a lot of enzymes)
- Although a higher temp would increase the metabolic rate, the advantages are offset by the additional energy needed to maintain the said temperature.
- Other proteins (non enzymes) may denature at higher temperatures.
- At higher temperatures, any further rise (eg like during illness) could cause denaturing.
79
How is the pH of a solution calculated?
pH= -log10( [H+] )
80
How does pH affect the rate of an enzyme-catalysed reaction?
- A change in pH alteres the charge on the amino acid that make up the active site of the enzyme.
- Therefore, the substrate can no longer become attached to the active site and so the enzyme-substrate cannot be formed.
- Depending on the magnitude of the change in pH, it may cause the bonds in the tertiary structure to break. Therefore changing the active site.
81
When does an increase in the amount of enzymes lead to a proportional increase in rate of reaction?
When there is an excess of substrate.
82
When does an increase in the concentration of substrate lead to a proportional increase in rate of reaction?
When the concentration of enzymes re fixed.
When the substrate concentration slowly increase.
83
What is an enzyme inhibitor?
Substances that directly or indirectly interfere with the function of the active site of an enzyme and so reduce its activity.
84
What are two different types of inhibitors?
Competitive inhibitors: which bind to the active site of the enzyme.
Non-competitive inhibitors: which bind to the allosteric site of the enzyme.
85
What determines the effect an inhibitor has on the enzyme activity?
- Inhibitor concentration: More = less enzyme activity.
| - Substrate concentration: More = more enzyme activity.
86
Why does an increase in substrate concentration slow down the effect a competitive Inhibitor have on the enzyme activity?
Inhibitors can only bind to enzymes for a set amount of time.
Therefore if there are more substrates it is more likely that a substrate will bind to the enzyme meaning the enzyme activity is greater than if there were a higher concentration of inhibitors.
87
How does a non- competitive inhibitor work?
They attach to a bonding site on an enzyme which isn't its active site.
This alters the shape of the enzyme and thus the sahep of the active site, meaning the complimentary substrate can no longer bond to it.
88
What three components make up a nucleotide
- A pentose sugar
- a phosphate group
- a nitrogenous organic base .
89
What are the five nitrogenous bases?
```
A∣Adenine
T∣Thymine
C∣Cytosine
G∣Guanine
U∣Uracil
```
90
What bond is formed between two mononucleotides?
Phosphodiester bond
91
How are two strands of DNA held together?
Hydrogen bonds between complementary base pairs.
A to T
C to G
92
How is DNA antiparallel?
each strands run in different direction:
one from 3` to 5`
the other 5` to 3`
93
Why is DNA a stable molecule?
- The phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.
- hydrogen bonds link the organic base pairs forming bridges (rungs) between phosphodiester uprights.
94
Why is a C-G bond more stable than an A-T bond?
C-G bond with 3 hydrogen bonds whereas A-T bond with 2.
95
How is DNA adapted to carry out its function?
- Stable structure: able to pass from gen to gen without change. Makes mutation rare as they are often repaired.
- Hydrogen bonds between strands: can separate during DNA replication and protein synthesis.
- Extremely large: carries a lot of genetic information.
- Base pairs within the helical cylinder of the deoxyribose-phosphate: the genetic info is protected from outside chemicals or physical forces.
- Complementary base pairing: DNA is able to replicate and transfer info as mRNA
96
How are zygotes formed?
Cellular fusion.
97
What are the two main stages of cell division?
Nuclear division: the process by which the nucleus divides.
Cytokinesis: the process by which the whole cell divides.
98
What are the two types of cell division?
- Mitosis
| - Meiosis
99
Why must DNA be replicated before division?
To ensure all the daughter cells have the genetic information to produce the enzymes and other proteins that they need.
100
What four requirements must there be for semi-conservative replication?
- The four types of nucleotides must be present.
- Both strands of the DNA molecule.
- DNA polymerase.
- A source of chemical energy (to drive the process).
101
What are the steps in semi-conservative replication?
- DNA helicase breaks H-bonds linking base pairs of DNA
- As a result, the double helix separates into 2 strands and unwinds.
- Complimentary free nucleotides bind to each exposed polynucleotide on the template strand by specific base pairing
- Nucleotides are joined together in a condensation reaction by DNA polymerase.
- Each new DNA molecule contains one of the original DNA strands. Therefore half of the original DNA has been saved and built into each DNA molecule. Hence it is called semi-conservative replication.
102
How was the conservative replication model disproven?
This was disproven because of three fact:
- All DNA bases contain nitorgen
- Nitrogen has two isotopes: ¹⁴N and ¹⁵N
- Bacteria will use nitrogen from their growing medium in new DNA they make.
Therefore bacteria growing in ¹⁴N would have lighter DNA than in ¹⁵N.
They grew bacteria in ¹⁵N and then for one generation moved it to ¹⁴N. They separated the DNA in a centrifuge and measured its mass.
103
What does ATP stand for?
Adenosine triphosphate.
104
What type of molecule is ATP?
A phosphorylated macromolecule.
105
What is ATP made up of?
Adenine: A nitrogenous organic base.
Ribose: A pentose sugar.
Phosphates: a chain of 3 phosphate groups.
106
How is ATP an energy store?
Bonds between its phosphate groups are unstable and have a low EA so can be easily broken.
When they break they release a considerable amount of energy.
107
What is the equation to show the breaking of ATP?
ATP + H₂O → ADP + Pᵢ + E
Adenosine Triphosphate + Water → Adenosine Diphosphate + Inorganic Phosphate + Energy
108
What type of reaction is the conversion of ATP into ADP?
A hydrolysis reaction.
109
How can the reaction that converts ATP into ADP be catalysed?
By the enzyme ATP hydrolase (ATPase).
110
How is ATP Synthesised?
Energy is used to add an inorganic phosphate to ADP.
111
How can ATP Synthesis by catalysed?
ATP synthase.
112
What type of reaction is the synthesis of ATP?
A condensation reaction.
113
What is the equation to show the synthesis of ATP?
ADP + Pᵢ + E → ATP + H₂O
| Adenosine Diphosphate + Inorganic Phosphate + Energy → Adenosine Triphosphate + Water
114
In what three ways can ATP being synthesised from ADP occur?
Photophosphorylation: in chlorophyll-containing plant cells during photosynthesis.
Oxidative phosphorylation: in plant and animal cells during respiration.
Substrate-level phosphorylation: in plant and animal cells when phosphate groups are transferred from donor molecules to ADP.
115
Why is ATP a better immediate energy source than glucose?
- MORE MANAGEABLE: ATP released less energy making it more manageable as opposed to glucose releasing a large amount of energy.
- QUICKER: The hydrolysis of ATP into ADP is a single reaction that releases immediate energy. The breakdown of glucose is a long series of reactions and therefore energy release in longer.
116
Why might cells that require energy possess many large mitochondria?
ATP cannot be stored and so needs to be constantly made within the mitochondria of the cells that need it.
117
What energy-requiring processes in cells use ATP?
- Metabolic processes: needed to build up macromolecules from their basic units (e.g starch from glucose)
- Movement: filaments of muscle to slide past one another and therefore shorten the overall length of muscle fibre (contract)
- Active Transport: change the shape of carrier proteins in plasma membranes.
- Secretion: form the lysosomes necessary for the secretion of cell production.
- Activation of molecules: Phosphate released can be used to phosphorylate other compounds to make them more reactive thus lowering the EA in enzyme-catalysed reactions. (phosphate added to glucose at the start of glycolysis)
118
Describe the polarity of water.
Water is made up of 2 hydrogens bonded to an oxygen.
The Hydrogens are slightly positively charged and the oxygen is slightly negatively charged.
This creates two oppositely charged poles, thus water is dipolar.
119
Why do water molecules stick together?
Opposite poles attract, thus the negative pole of one water will attract to the positive pole of another.
This attractive force is called a hydrogen bond (1/10 as strong as a covalent bond).
120
Why is water a good temperature buffer?
Because water molecules stick together, more energy is needed to separate them that would be needed if they did non form H-bonds.
Thus, the boiling point of water is higher than expected.
This means it takes more energy to heat a mass of water.
And so has a high specific heat capacity.
This means it is a buffer against sudden temperature changes.
This also allows it to stay a liquid at commonly found temperatures on earth (allowing life).
121
How is water being a good temperature buffer important?
It makes the aquatic environment temperature stable.
As organisms are mostly water, it buffers them against sudden temperature changes (especially in terrestrial environments)
122
How is the evaporation of water as sweat an effective means of thermoregulation?
Waters hydrogen bonding between molecules means it requires a lot of energy to evaporate 1g of it.
This means it has a high latent heat.
Therefore for sweat to evaporate, a lot of body heat must be used.
Thus cooling the body.
123
How does water travel up through tubes?
With its hydrogen bonding, water has a tendency to stick together (cohesive force).
This allows it to be pulled up through tubes, such as a xylem vessel in plants.
124
How does water support small organisms (like pond skaters)
When water molecules meet air they tend to be pulled back to the body of water (rather than escaping).
This force is called surface tension, and mean that water acts as a skin and is strong enough to pull small organisms.
125
State the properties of water.
- Stick to each other (due to H-bonds)
- High specific heat capacity (therefore good buffer)
- High latent heat (therefore good thermoregulator)
- Has cohesive force (therefore can be pulled through tubes)
- Has surface tension (can support small organisms)
- Metabolite (involved in metabolic processes)
- Solvent (readily dissolves other substances)
- Difficult to compress (so supports hydrostatic skeletons in animals and turgor pressure in plants)
- Transparent (allowing aquatic plants to photosynthesise, allows light to reach retina)
126
How is water a metabolite?
- Used to break down molecules during hydrolysis reactions.
- Produced in condensation reactions.
- Chemical reactions take place in an aqueous medium.
- A major raw material in photosynthesis.
127
How is water a solvent?
- Dissolves gases (Oxygen and Carbon Dioxide)
- Dissolves waste (Ammonia and Urea)
- Dissolves inorganic ions and small hydrophilic molecules (amino acids, monosaccharides and ATP)
- Dissolves enzymes (whose reactions take place in solution)
128
Where are inorganic ions found in organisms?
In solution inside the cytoplasm of cells and in body fluids as well as part of larger molecules.
129
Give examples of inorganic ions.
- Iron ions in haemoglobin.
- Phosphate ions in DNA, RNA and ATP
- Hydrogen ions in pH control and function of enzymes
- Sodium ions in transport across the plasma membrane
130
What is the test for non-reducing sugars (e.g. starch)?
Iodine/potassium iodide test.
