1B - More Biological Molecules Flashcards
1
Q
How much of a cell is water?
A
About 80%
2
Q
What is a metabolic reaction?
A
A chemical reaction that happens in a living organism to keep it alive.
3
Q
What is a metabolite?
A
A substance involved in a metabolic reaction.
4
Q
Give some of the functions of water in living organisms.
A
- Metabolite
- Solvent
- Temperature control
- Water transport
5
Q
Explain how water is used as a metabolite in living organisms.
A
It is involved in many metabolic reactions, including condensation and hydrolysis reactions.
6
Q
Explain how water is used as a solvent in living organisms.
A
Most metabolic reactions happen in solution (in the cytoplasm of cells).
7
Q
Explain how water helps with temperature control in living organisms.
A
It has a high latent heat of vaporisation and a high specific heat capacity so it can be used to regulate temperature.
8
Q
Explain how water is used for water transport in living organisms.
A
Water molecules are very cohesive, which allows plants to transport water around the plant easily.
9
Q
Describe the structure of a water molecule.
A
- One atom of oxygen joined to two atoms of hydrogen by shared electrons.
- The oxygen has a slight -ve charge and the hydrogen has a slight +ve charge.
10
Q
Explain why water is a polar molecule.
A
- Shared electrons are pulled closer to the oxygen, giving it a negative charge while the hydrogens are left with a positive charge.
- Uneven distribution of charge makes the molecule polar.
11
Q
What is the symbol for a slight positive charge?
A
Delta +
12
Q
What is the symbol for a slight negative charge?
A
Delta -
13
Q
What bonds are formed between water molecules?
A
Hydrogen bonds
14
Q
What is the result of water being a polar molecule?
A
Hydrogen bonds form between molecules due to the positive and negative charges.
15
Q
Why is water an important metabolite?
A
- Involved in condensation and hydrolysis reactions
* e.g. Energy from ATP is released through a hydrolysis reaction
16
Q
Why does water have a high latent heat of vaporisation and how is this useful in living organisms?
A
- Takes a lot of energy to break hydrogen bonds between water molecules
- So a lot of energy is used up when evaporating water
- This allows organisms to cool down by evaporating water
17
Q
What is latent heat of vaporisation?
A
The amount of energy required to turn a certain liquid into gas (per unit mass).
18
Q
Give an example of an important condensation reaction in living organisms.
A
Amino acids joining to make a polypeptide.
19
Q
Give an example of an important hydrolysis reaction in living organisms.
A
Energy is released from ATP by hydrolysis.
20
Q
Why can water buffer changes in temperature and how is this useful in living organisms?
A
- Hydrogen bonds between molecules can absorb a lot of energy
- So water has a high specific heat capacity
- Water stays at a stable temperature, maintaining the internal temperature of organisms and the habitats they live in.
21
Q
What is specific heat capacity?
A
The amount of energy required to heat a substance up (per degree per unit mass).
22
Q
Why is water a good solvent and how is this useful in living organisms?
A
• The charged parts of water molecules are attracted to ions in ionic compounds.
• The ions are totally surrounded by the water molecules - this dissolves them.
• This is all due to water’s polarity.
• This allows reactions to happen in solution.
(See diagram pg 21)
23
Q
Why is there cohesion between water molecules and how is this useful in living organisms?
A
- Water’s polarity makes it very cohesive.
- This allows it to flow, so it is useful for transport (e.g. up the xylem).
- This also creates surface tension, which allows certain insects to walk on the surface.
24
Q
Name a way in which surface tension is important in living organisms.
A
Pond skaters and other insects can walk on water.
25
Name a way in which water’s cohesion is important in living organisms.
It allows water to flow up the xylem in plants.
26
What type of molecule are DNA and RNA?
Nucleic acids
27
What does DNA stand for?
Deoxyribonucleic acid
28
What does RNA stand for?
Ribonucleic acid
29
What is the function of DNA?
• Stores genetic information.
30
What is the function of RNA?
* Transfers genetic information from the DNA to the ribosomes
* Makes up some ribosomes (along with proteins)
31
What do ribosomes do and what molecules do they work with?
They read RNA to make polypeptides (proteins).
32
What is translation?
The process by which ribosomes read RNA to make polypeptides (proteins).
33
What are nucleic acids?
* Polymers of nucleotides
| * Examples: DNA and RNA
34
What are nucleotides made from?
* Pentose sugar (with 5 carbon atoms)
* Nitrogen-containing organic base
* Phosphate group
35
What is the sugar in DNA called?
Deoxyribose
36
What is the sugar in RNA called?
Ribose
37
What two things can be different in a nucleotide?
* The sugar
| * The base
38
Describe the structure of a DNA nucleotide.
* Deoxyribose
* Phosphate group
* A, T, C or G base
39
What are the 4 types of possible base in a DNA nucleotide?
* Adenine (A)
* Thymine (T)
* Cytosine (C)
* Guanine (G)
40
Describe the structure of an RNA nucleotide.
* Ribose
* Phosphate group
* A, U, C or G base
41
What are the 4 types of possible base in an RNA nucleotide?
* Adenine (A)
* Uracil (U)
* Cytosine (C)
* Guanine (G)
42
What is the difference in possible bases in a DNA and RNA nucleotide?
In RNA, uracil replaces thymine.
43
What do nucleotides join to form?
Polynucleotides
44
Through what type of reaction do nucleotides join?
Condensation reaction
45
What is the bond between two nucleotides called?
Phosphodiester bond
46
Between which parts of nucleotides are phosphodiester bonds formed in a polynucleotide?
The phosphate group of one nucleotide and the sugar of another.
47
Why is a phosphodiester bond called that?
It consists of a phosphate group with two ester bonds joining it to each sugar on either side.
(See diagram pg 17)
48
Remember to revise the structure of a phosphodiester bond.
Diagram pg 17
49
What is the full name of the A base?
Adenine
50
What is the full name of the C base?
Cytosine
51
What is the full name of the T base?
Thymine
52
What is the full name of the G base?
Guanine
53
What is the full name of the U base?
Uracil
54
Describe the structure of DNA.
* Two antiparallel polynucleotide strands
* Joined by hydrogen bonding
* In a double helix
55
What is the chain of phosphates and sugars joined by phosphodiester bonds called?
The sugar-phosphate backbone.
56
What holds the two polynucleotide chains together in DNA?
Hydrogen bonds between bases.
57
What is complementary base pairing?
The idea that each base can only join with one particular other base.
58
Adenine (A) always pairs with...
Thymine (T)
59
Cytosine (C) always pairs with...
Guanine (G)
60
How are the amounts of each base in DNA related?
There is always the same amount of adenine and thymine as well as the same amount of cytosine and guanine.
61
What are the complementary base pairs?
* A-T
| * C-G
62
What does antiparallel mean?
Running in opposite directions.
63
Remember to revise the structure of a DNA molecule.
Diagram pg 17 of revision guide.
64
Why did scientists at first doubt that DNA was the carrier of genetic code?
It had relatively simple chemical composition.
65
Describe the structure of an RNA molecule compared with a DNA molecule.
* It is made of only one polynucleotide chain.
| * The polynucleotide is shorter than most DNA polynucleotides.
66
What is the process of DNA replication called?
Semi-conservative replication
67
Why is semi-conservative replication called that?
Half of the strands in each new DNA molecule come from the original DNA molecule
68
What does semi-conservative replication result in?
Genetic continuity between generations of cells (i.e. the cells produced by cell division inherit their genes from their parent cells)
69
What enzyme breaks the hydrogen bonds in semi-conservative DNA replication?
DNA helicase
70
What enzyme joins the phosphate-sugar backbones kin semi-conservative DNA replication?
DNA polymerase
71
Describe the process of semi-conservative DNA replication.
1) DNA helicase breaks hydrogen bonds between the bases of the two polynucleotide chains
2) This makes the helix unwind to give two single strands
3) Each strand acts as a template + free-floating nucleotides are attracted to the exposed bases
4) Complementary base pairing means that the correct bases bond to each other
5) DNA polymerase catalyses the condensation reactions that join the sugar-phosphate backbone of each strand
6) Each new DNA molecule contains one strand from the original DNA molecule and one new strand
72
Which carbons are involved in DNA polymerisation?
3' (three prime)
| 5' (five prime)
73
What enzymes are involved in semi-conservative DNA replication and what do they do?
* DNA helicase - Breaks the hydrogen bonds between bases on the two polynucleotide DNA strands
* DNA polymerase - Joins the sugar-phosphate backbone to fully form each strand of DNA
74
What is important to remember about the two strands in DNA?
They are antiparallel.
75
In which direction is a DNA strand formed?
5' to 3' direction
76
Why can a DNA strand only be formed in one direction?
* The active site of DNA polymerase is only complementary to the 3' end of the newly forming DNA strand.
* Therefore, nucleotides can only be added at the 3' end.
* So the strand forms from the 5' to the 3' end.
77
Which way does DNA polymerase move along the TEMPLATE strand in semi-conservative replication and why?
• In the 3' to 5' direction
• Because the two strands are antiparallel, so that the DNA polymerase moves along the NEW strand from 5' to 3', but along the TEMPLATE strand in the 3' to 5' direction (NOTE: It doesn't actually do anything to the template strand!)
(See diagram pg 18)
78
What can be said about the direction in which DNA polymerase works on each strand of the original DNA molecule?
It works in opposite directions (i.e. since each template strand is antiparallel to the other).
(See diagram pg 18)
79
Remember to revise DNA polymerase action.
Pg 18 of revision guide.
80
Who determined the structure of DNA and came up with the theory of semi-conservative DNA replication?
Watson and Crick
81
Who validated the theory of semi-conservative DNA replication?
Meselson and Stahl
82
What were the two main theories of DNA replication?
* Conservative DNA replication
| * Semi-conservative DNA replication
83
Describe the model of conservative DNA replication.
* Original DNA strands stay together
| * New DNA molecules contain two new strands
84
Which element was used in validating the theory of semi-conservative DNA replication and why?
Nitrogen - DNA contains nitrogen, so bacteria take up nitrogen from their surroundings to use in new nucleotide production (when reproducing).
85
What are the two isotopes of nitrogen used in the validation of the theory of semi-conservative DNA replication?
* Heavy nitrogen (15N)
| * Light nitrogen (14N)
86
Describe the experiment used to validate the theory of semi-conservative DNA replication.
1) Two samples of bacteria were grown - one in a nutrient broth containing light nitrogen, one in a broth containing heavy nitrogen
2) As they reproduced, the bacteria took up nitrogen to make new DNA, making the nitrogen part of the DNA
3) A DNA sample from each batch was spun in a separate centrifuge - the heavy nitrogen bacteria DNA settled lower in the tube than the light nitrogen DNA
4) Bacteria grown in the heavy nitrogen were then put in light nitrogen and allowed to replicate once
5) Another DNA sample was taken and spun in the centrifuge
6) If replication was CONSERVATIVE, the original heavy DNA would settle at the bottom and the new light DNA at the top
7) If replication was SEMI-CONSERVATIVE, the new DNA would contain one light and one heavy strand, so it would settle between where the light and heavy DNA would settle out
8) Number 7 happened, proving semi-conservative replication to be correct
87
What would happen in the experiment to prove semi-conservative replication if the process were conservative?
The heavy original strands would settle at the bottom and the new light strands would settle at the top of the tube.
88
Remember to revise the experiment to validate the theory of semi-conservative DNA replication.
Pg 19 of revision guide.
89
What is ATP?
Adenosine triphosphate - a molecule used in cells as an immediate source of energy.
90
Why is there a need for ATP?
* A cell cannot get its energy directly from glucose.
| * Instead, the energy from respiration is used to make ATP, which can diffuse to the part of the cell that needs energy
91
Describe the structure of ATP.
* Adenine (nucleotide base)
* Ribose (pentose sugar)
* 3 phosphate groups
92
What type of molecule is ATP?
Nucleotide derivative - a modified form of a nucleotide.
93
How does ATP store energy and how is it released?
* In high energy bonds between the phosphate groups
| * Hydrolysis reactions break these and release the energy
94
What does ATP do after it is made?
Diffuses to the part of the cell that needs energy.
95
Remember to revise the structure of ATP.
Pg 22 of revision guide.
96
Give the equation for the release of energy from ATP.
ATP -> ADP + Pi (+ Energy)
97
What is the catalyst for the release of energy from ATP?
ATP hydrolase
98
What type of reaction is the release of energy from ATP?
Hydrolysis
99
Describe the release of energy from ATP (in terms of products, catalyst and type of reaction).
* ATP is broken down into ADP (adenosine diphosphate) and Pi (inorganic phosphate)
* Catalysed by ATP hydrolase
* Hydrolysis reaction
100
What is the difference between ADP and ATP?
ATP has 3 phosphate groups, while ADP has 2.
101
What is the symbol for an inorganic phosphate group (released in the hydrolysis of ATP)?
Pi (the 'i' is in subscript)
102
What stops energy released in the hydrolysis of ATP from being lost as heat?
* ATP hydrolysis is 'coupled' with energy-requiring reactions in the cell
* The energy released can be used directly to make the the coupled reaction happen (so none is lost as heat)
103
How can the inorganic phosphate group produced by the hydrolysis of ATP be used?
Phosphorylation - The phosphate is added to another compound, often making it more reactive.
104
Give the equation for the production of ATP.
ADP + Pi (+ Energy) -> ATP
105
What is the catalyst for the production of ATP?
ATP synthase
106
What type of reaction is the production of ATP?
Condensation
107
Give some examples of when ATP is produced.
* Respiration
| * Photosynthesis
108
Describe the production of ATP (in terms of reactants, catalyst and type of reaction).
* ATP is made from ADP (adenosine diphosphate) and Pi (inorganic phosphate)
* Catalysed by ATP synthase
* Condensation reaction
109
Remember to revise the ATP hydrolysis and synthesis cycle.
Pg 22 of revision guide.
110
What is an ion?
An atom with an electric charge.
111
What is an ion with a positive charge called?
Cation
112
What is an ion with a negative charge called?
Anion
113
What is an inorganic ion?
An ion which doesn't contain carbon.
114
Where are inorganic ions found?
* Cytoplasm of cells
| * Body fluids of organisms
115
What determines the concentration of an ion in an organism?
Its specific role.
116
Name 4 important ions that you need to know about and give their role.
* Iron - Haemoglobin
* Hydrogen - pH
* Sodium - Glucose and amino acid co-transport
* Phosphate - ATP and DNA
117
What is haemoglobin and what does it do?
A large protein that carries oxygen around the body in RBCs.
118
What is the importance of iron ions?
* In haemoglobin, each of the 4 polypeptide chains has an Fe2+ ion in the middle
* This iron binds to oxygen, allowing it to be transported
119
Describe the structure of haemoglobin.
4 polypeptide chains, each with an iron ion in the middle.
120
How does oxygen bind to haemoglobin?
The Fe2+ ion in each polypeptide temporarily becomes Fe3+ and binds to the oxygen.
121
What is the importance of hydrogen ions?
* The concentration of H+ ions determines the pH of a solution.
* Enzyme-controlled reactions are affected by pH.
122
What is the importance of sodium ions?
• Co-transport of glucose and amino acids across cell membranes uses sodium
123
What can Na+ ions co-transport across cell membranes?
* Glucose
| * Amino acids
124
What is the formula for a phosphate group?
PO4 3-
125
What is the difference between a phosphate ion and a phosphate group?
When a phosphate ion attaches to another molecule, it is known as a phosphate group.
126
Name 3 substances containing phosphate groups.
* DNA
* RNA
* ATP
127
What is the importance of phosphate ions? (2 uses)
In ATP:
• Bonds between phosphate groups store energy
In DNA and RNA:
• Phosphate groups allow nucleotides to join up to form polynucleotides
