Chapter 2: Nucleic Acids Flashcards
1
Q
draw the structure of a nucleotide
A
- google image *
- phosphate group
- nitrogen-containing base
- pentose sugar
2
Q
name two types of nucleic acids
A
Ribonucleic acid (RNA) Deoxyribonucleic acid (DNA)
3
Q
Name the pentose sugars in DNA &
RNA.
A
DNA: deoxyribose
RNA: ribose
4
Q
State the role of DNA in living cells
A
Base sequence of genes codes for functional RNA & amino acid sequence of polypeptides.
Genetic information determines inherited characteristics = influences structure & function of organisms.
5
Q
Role of RNA
A
transfers genetic information from DNA to ribosomes
6
Q
How do polynucleotides form?
A
Condensation reactions between nucleotides form strong phosphodiester bonds (sugar-phosphate backbone)
7
Q
whats a mononucleotide?
A
a single nucleotide
formed via condensation reactions of pentose sugar, phosphate group and organic base
8
Q
Describe the structure of DNA
A
- double helix of 2 polynucleotide strands
(deoxyribose) - polynucleotide strands held together by H bonds between specific complementary base pairs (A+T, C+G)
9
Q
whats a polynucleotide?
A
polymer of nucleotides
10
Q
Which bases are purine and which are pyrimidine?
A
A & G = 2-ring purine bases
T & C & U = 1-ring pyrimidine bases
11
Q
Name the complementary base pairs in DNA
A
2 H-bonds between
adenine (A) + thymine (T)
3 H-bonds between
guanine (G) + cytosine (C)
12
Q
Name the complementary base pairs in RNA
A
2 H-bonds between
adenine (A) + uracil (U)
3 H-bonds between
guanine (G) + cytosine (C)
13
Q
Relate the structure of DNA to its functions.
A
● sugar-phosphate backbone protects bases
● long, large molecule stores lots of information
● helix/coiled SO compact (for storage in nucleus)
● base sequence of triplets codes for amino acids
● double-stranded for semi-conservative replication/each strand acts as a template
● weak H-bonds break so strands separate for replication
● complementary base pairing for accurate replication
14
Q
Describe the structure of messenger RNA (mRNA).
A
● Long ribose polynucleotide (but shorter than
DNA).
● Contains uracil instead of thymine.
● Single-stranded & linear (no complementary
base pairing).
● Codon sequence is complementary to exons of 1
gene from 1 DNA strand
15
Q
Relate the structure of messenger RNA
(mRNA) to its functions
A
● long polynucleotide but shorter than DNA: Breaks down quickly so no excess polypeptide forms.
● single-stranded and linear: Ribosome can move along strand & tRNA can bind to exposed bases.
● codon sequence complementary to exons of 1 gene from a DNA strand: Can be translated into a specific polypeptide by
ribosomes.
16
Q
Describe the similarities between DNA and RNA
A
1 both are polymers of nucleotides
2 both nucleotides are made of an organic base, pentose sugar and a phosphate group
17
Q
Describe the differences between RNA and DNA
A
- RNA has a ribose sugar, DNA has a deoxyribose sugar
- RNA has organic base uracil (U) instead of DNA base thymine (T)
- DNA is double stranded whereas RNA is a single polynucleotide chain (much shorter than most DNA polynucleotides)
18
Q
Describe the phosphodiester bond
A
- A bond that forms between the phosphate group of one nucleotide and the 3’ Carbon of deoxyribose sugar on the next (via condensation reaction of nucleotides)
- the bonds form the sugar-phosphate-sugar backbone of DNA and RNA
19
Q
Why are the two polynucleotides of DNA antiparallel?
A
Because the two strands of DNA run in the opposite direction to one another
20
Q
Why can the structure of DNA be likened to a ladder?
A
- alternating phosphate and deoxyribose molecules make up the uprights and organic bases pairs are the rungs (steps of the ladder)
- The uprights run in opposite directions to one another i.e. are anti parallel.
21
Q
Describe the structure of transfer RNA
tRNA
A
● Single strand of about 80 nucleotides.
● Folded into clover shape (some paired bases).
● Anticodon on one end, amino acid binding site
on the other:
a) anticodon binds to complementary mRNA codon
b) amino acid corresponds to anticodon
22
Q
Order DNA, mRNA and tRNA according
to increasing length
A
tRNA
mRNA
DNA
23
Q
Why did scientists initially doubt that DNA carried the
genetic code?
A
- it’s a chemically simple molecule with few
components
24
Q
Why is DNA replication described as
‘semiconservative’?
A
● Strands from original DNA molecule
act as a template.
● New DNA molecule contains 1 old
strand & 1 new strand.
25
Outline the process of semiconservative
| DNA replication
1. H bonds between bases on the two polynucleotide DNA strands are broken to separate the strands by DNA helicase. This unwinds the double helix.
2. Each original strand acts as template
3. Free floating nucleotides are attracted to exposed complementary organic base pairs
4. Condensation reactions join nucleotides of new strands together and is catalysed by the enzyme: DNA polymerase. Hydrogen bonds form between the bases on the original and new strands.
5. Each new DNA molecule contains one strand from the original DNA molecule and one new strand. This is semi-conservative replication.
26
what did Meselson and stahl do to provide evidence for semi conservative replication?
They cultured bacteria in a medium of heavy nitrogen, then moved them to a medium of light nitrogen allowing the bacteria to replicate and divide. The new bacterial DNA consisted of one heavy strand and one light strand.
27
Explain how the Meselson-Stahl
experiment validated semiconservative
replication
- DNA settled out in middle, showing that DNA molecules contained a mixture of heavy and light nitrogen
- so bacterial DNA had replicated semi-conservatively in the light nitrogen
28
What twists to form DNA double helix?
Two antiparallel polynucleotide strands
29
Describe the structure of adenosine triphosphate
| ATP
- nucleotide with a molecule of ribose, a molecule of adenine and has 3 phosphate groups
- It is the immediate source of energy in a cell
30
Why are the 3 Phosphate groups key to how ATP stores energy?
- bonds between these phosphate groups are unstable and have a low activation energy, which mean they are easily broken. When they do break they release a considerable amount of energy
- most energy released when first phosphate broken off, less when 2nd broken off and even less when final broken off
31
How is ATP converted to ADP?
- by a hydrolysis reaction.
| - catalysed by ATP hydrolase (ATPase).
32
Word equation for ATP into ADP?
ATP + H2O --> ADP + Pi + Energy
33
What is AMP?
| What is ADP?
AMP is Adenosine Monophosphate
| ADP is Adenosine Diphosphate
34
What is Pi?
Inorganic Phosphate
| A single phosphate
35
Why is ATP referred to as a nucleotide derivative?
Because it's a modified form of a nucleotide
36
What does ATP do once made?
ATP diffuses to the part of the cell that needs energy
37
What happens when energy is needed by a cell?
When energy is needed by a cell, ATP is broken down into ADP and Pi
38
Explain the role of ATP in cells
ATP hydrolase catalyses ATP → ADP + Pi
- ATP hydrolysis can be coupled to metabolic reactions so energy released can be used directly to make coupled reactions happen rather than being lost as heat.
- Pi released during ATP hydrolysis can be used to phosphorylate other compounds, making them more reactive. (Phosphorylation)
39
How is ATP resynthesised in cells?
● ATP synthase catalyses condensation
reaction between ADP & Pi
● during photosynthesis & respiration
40
Explain why ATP is suitable as the
| ‘energy currency’ of cells.
● High energy bonds between phosphate groups.
● Small amounts of energy released at a time =
less energy wasted as heat.
● Single-step hydrolysis = energy available
quickly.
● Readily resynthesised.
41
what is hydrogen helicase?
- enzyme that breaks down the hydrogen bonds between the two polynucleotide strands
42
What is Photophosphorylation?
Conversion of ATP to ADP in chlorophyll-containing plant cells during photosynthesis
43
What is oxidative phosphorylation?
Conversion of ATP to ADP in animal cells during respiration
44
What is Substrate-Level Phosphorylation?
- chemical reaction coupled to ATP synthesis
- metabolism reaction that results in the production of ATP by the transfer of a phosphate group from a substrate directly to ADP
(in animal and plant cells)
45
what's DNA polymerase?
- enzyme that synthesizes DNA molecules from deoxyribonucleotides
- enzymes play an essential role in DNA replication, usually working in pairs to produce two matching DNA stranges from a single DNA molecule
46
Why is water a polar molecule?
- O is more electronegative than H, so
attracts the electron density in the
covalent bond more strongly.
- forms O 𝛿- (slight negative charge) &
H 𝛿+ (slight positive charge)
47
what are metabolic reactions?
- sum of all of the chemical reactions that are involved in catabolism and anabolism
48
catabolism vs anabolism
Anabolism requires energy to grow and build. Catabolism uses energy to break down
49
why is ATP not a good long term energy store?
- instability of its phosphate bonds
| - so cells don't store large quantities of ATP, this is okay b/c ATP rapidly reformed
50
why is ATP a better immediate energy source than glucose?
- ATP releases less energy so energy for reactions released in SMALLER, MORE MANAGEABLE quantities than glucose molecule
- ATP hydrolysis is a single reaction that releases immediate energy, glucose breakdown is a long series of reactions so energy released takes longer
51
Uses of ATP in energy requiring processes in cells
```
Metabolic processes
Movement
Active Transport
Secretion
Activation of molecules
```
52
why is ATP important in metabolic processes?
ATP provides the energy needed to build up macromolecules from their basic units i.e. making starch from glucose.
53
describe the importance of ATP in movement
- ATP provides the energy for muscle contraction
| - by providing the energy for muscle filaments to slide past on another and shorten overall length of muscle fibre.
54
describe the importance of ATP in active transport
- provides the energy to change the shape of carrier proteins in plasma membranes
- allows molecules or ions to be moved against a concentration gradient.
55
describe the importance/role of ATP in secretion
needed to form the lysosomes necessary for the secretion of cell products
56
describe the importance of ATP in activation of molecules
- Pi released during ATP hydrolysis can be used to phosphorylate other compounds to make them more reactive, thus lowering the Ea in enzyme-catalysing reactions
57
Explain five properties that make water important for organisms (5 marks)
1. A metabolite in condensation/hydrolysis/photosynthesis/respiration
2. A solvent so (metabolic) reactions can occur
3. High heat capacity so buffers changes in temperature
4. Large latent heat of vaporisation so provides a cooling effect (through evaporation)
5. Cohesion (between water molecules) so supports columns of water (in plants)
6. Cohesion (between water molecules) so produces surface tensions supporting (small) organisms
58
why is water a dipolar molecule?
- Molecule has no overall charge but oxygen atom has a slightly negative charge, while hydrogen have a slightly positive one.
- Water molecule has both + and - poles and is therefore dipolar.
59
describe hydrogen bonding in water
- partial negative charge on the O of one molecule can form a hydrogen bond with the partial positive charge on the hydrogens of other molecules
- gives water its cohesive property i.e. 'stick together'
60
Explain why water is significant to living organisms
● Solvent for polar molecules during metabolic
reactions.
● Enables organisms to avoid fluctuations in
core temperature.
● Cohesion-tension of water molecules in
transpiration stream.
61
describe 'high specific heat capacity' as a property of water
i.e. water can buffer (resist) changes in temp
- therefore can absorb large amounts of heat energy before its temperature raises a significant amount
- so helps maintain constant internal body temp (and environment for organisms that live in water)
62
discuss 'large latent heat of vaporisation' as related to water
- its amount of energy needed to evaporate 1g of water (i.e. convert it to gas at a constant temp)
- H bonding between water molecules so a lot of energy required
- evap of water like sweat is very effective for cooling b/c body heat used to evap water
63
what's a metabolite?
refers to any substance involved in metabolism (e.g. water is used in hydrolysis reactions)
64
discuss water as a metabolite
water used in hydrolysis e.g. proteins to amino acids
water produced in condensation reactions
chemical reactions take place in aqueous medium
water is a major raw material in photosynthesis
65
discuss water as important solvent in which metabolic reactions occur
- lots of substances in metabolic reactions are ionic, water is polar and so is attracted to it and dissolves these substances e.g. :
CO2 and O2
Ammonia and Urea
Inorganic ions and small hydrophilic molecules such as amino acids, monosaccharides and ATP
Enzymes, whose reactions take place in solution
66
describe 'cohesion' and 'surface tension' as a property of water
- strong cohesion helps water to flow, making it great for transporting substances, it's how water travels in columns up the xylem in plants
- strong cohesion also means water has high surface tension. Where water meets air they tend to be pulled back to into the body rather than escaping from it. This force is surface tension and means water surface acts as an elastic sheet and strong enough to support small organisms like pond skaters.
67
What does water's evaporation do in organisms?
its evaporation cools organisms and allows them to control their temp
68
How is water good for support?
It is not easily compressed and therefore provides support
69
Discuss the advantage of water's transparency
- aquatic plants can photosynthesise
| - light rays can penetrate the jelly-like fluid that fills the eye and so reach the retina.
70
Name of a negative and positive ion
positive: cation
negative: anion
71
What are inorganic ions and where are they found in
| the body?
```
● atoms with unshared electrons in their outer shell and are thus charges species
● Found in cytoplasm & extracellular
fluid.
● May be in high or very low
concentrations.
```
72
Explain the role of hydrogen ions in the
| body
```
● High concentration of H+
= low (acidic) pH.
● enzyme controlled reactions all affected pH (H+ ions interact with H-bonds & ionic
bonds in tertiary structure of proteins,
which can cause them to denature)
```
73
Explain the role of iron ions in the body
- haemoglobin transports oxygen around body
- haemoglobin made up of 4 polypeptide chain that each contain Fe2+
- Fe2+ is what binds to the oxygen so its a key component
74
Explain the role of sodium ions in the
| body
```
- Involved in co-transport for absorption of
glucose & amino acids in lumen of gut
(Topic 2.3).
- Involved in propagation of action
potentials in neurons (Topic 6.2).
```
75
Explain the role of phosphate ions in the body
● when phosphate ion (PO43-) attached to a molecule its referred to as a phosphate group
● DNA, RNA and ATP all contain phosphate group
● NADP (Topic 5.1)
● cAMP (Topic 6.4)
- in ATP bonds between phoshate groups store energy
- phosphate groups in DNA and RNA allow nucleotides to join up and form polynucelotides
76
role of mRNA, tRNA and rRNA
mRNA: Complementary sequence to 1 gene from DNA
with introns (non-coding regions) spliced out. Codons
can be translated into a polypeptide by ribosomes.
rRNA: component of ribosomes (along with proteins)
tRNA: supplies complementary amino acid to mRNA
codons during translation
77
The enzymes DNA helicase and DNA polymerase are involved in DNA replication.
Describe the function of each of these enzymes.
1. DNA helicase – (unwinding DNA and) breaking
hydrogen bonds / bonds between chains / bases /
strands;
2. DNA polymerase – joins (adjacent) nucleotides
OR forms phosphodiester bond / sugar-phosphate backbone
78
```
Adenosine triphosphate (ATP) is a nucleotide derivative.
Contrast the structures of ATP and a nucleotide found in DNA to give two differences.
```
```
1. ATP has ribose and DNA nucleotide has
deoxyribose;
2. ATP has 3 phosphate (groups) and DNA
nucleotide has 1 phosphate (group);
3. ATP- base always adenine and in DNA
nucleotide base can be different / varies
```
79
In the aseptic technique explain the purpose of:
boiling the agar...
transferring the same volume of liquid culture onto each agar plate...
[2 marks]
1. So no contamination/ other bacteria;
2. So same number of bacteria transferred to
allow comparison
80
Give two features of DNA and explain how each one is important in the semi-conservative replication of DNA.
1. Weak / easily broken hydrogen bonds between
bases allow two strands to separate/unzip;
2. Two strands, so both can act as templates;
3. Complementary base pairing allows accurate
replication;
81
State box and explain the property of water that can help to buffer changes in temperature.
```
1. (water has a relatively) high (specific) heat
capacity;
2. Can gain/lose a lot of heat/energy
without changing temperature;
OR
Takes a lot of heat/energy to change
temperature;
```
82
describe how nucleotides are joined together in DNA (3)
- nucleotides are joined between the phosphate group of one nucleotide and the deoxyribose sugar of the other nucleotide;
- by phosphidiester bonds;
- in a condensation reaction
83
what's the key difference between the conservative and the semi conservative theories of DNA replication?
```
conservative method:
- two DNA strands sperate
- each one acts as a template strand and
a copy is made
- the two new strands come together
- the two original copies then come together
the new DNA contains two new strands
```
semi conservative method:
- two DNA strands seperate
- each one acts as a template strand and a copy is made
- the new DNA contains one new DNA strand and one original DNA strand
84
Comparing the base sequence of a gene provides more information than comparing the amino acid sequence for which the gene codes. Explain why
- more bases than amino acids
- introns
- some AAs already may be coded for (DNA code is degenerate)
85
ATP is useful in many biological processes. Explain why (4 marks)
1. Releases energy in small & easily manageable amounts;
2. Broken down in a one step reaction which makes sure energy is available rapidly;
3. Phosphorylates substances to make them more reactive
4. Reformed/made again rapidly
