0
Q
Definition of locus
A
The specific place on a chromosome that a gene occupies
1
Q
What is a gene?
A
A length of DNA; a sequence of nucleotide bases that codes for one or more polypeptides
2
Q
Give examples of polypeptides that genes code for
A
- Structural proteins, e.g. Collagen, keratin
- Haemoglobin
- Immunoglobulins
- Cell surface receptors
- Antigens
- Actin and myosin in muscle cells
- Tubulin proteins in the cytoskeleton
- Channel proteins
- Electron carriers
- Enzymes
3
Q
Name some characteristics of the genetic code
A
- It is a triplet code: a sequence of 3 nucleotide bases codes for an amino acid
- It is a degenerate code (all amino acids except methionine have more than 1 code)
- Some codes don’t correspond to an amino acid but indicate ‘stop’ (end of the polypeptide chain)
- It is widespread but not universal (generally the same base sequence will code for the same amino acid in most organisms)
4
Q
Where are proteins assembled?
A
In the cytoplasm, at ribosomes
5
Q
What are the 2 stages involved in protein synthesis?
A
Transcription
Translation
6
Q
How does transcription occur?
A
- The enzyme helicase breaks the hydrogen bonds between the bases in a region of DNA in the nucleus causing the 2 strands to separate
- RNA polymerase binds to a sequence called the promoter region
- RNA polymerase moves along the strand forming a complementary mRNA strand from free RNA nucleotides in the nucleus
- As the mRNA strand is produced the 2 strands of DNA start to recoil behind it
- When a terminator region is reached the DNA is no longer copied
- The mRNA is released from the DNA and passes out of the nucleus, through a pore in the nuclear envelope, to a ribosome
7
Q
Which strand of DNA is mRNA made from?
A
The template strand, so that it has the same sequence as the coding strand
8
Q
What are codons?
A
Triplets of nucleotide bases
9
Q
Why is the sequence if amino acid in a protein critical?
A
- It forms the primary structure of a protein
- The primary structure determines the tertiary structure
- The tertiary structure is what allows a protein to function
- If the tertiary structure is altered, the protein can no longer function so effectively, if at all
10
Q
What is the structure of tRNA?
A
- Lengths of RNA that fold into 3 hairpin shapes
- It has 3 exposed bases at 1 end where a particular amino acid can bind
- At the other end are 3 unpaired nucleotide bases, known as an anticodon. Each anticodon can bind temporarily with its complementary codon on a mRNA molecule
11
Q
How does translation occur?
A
- The mRNA strand formed during transcription attaches at the start codon to a ribosome in the cytoplasm
- The tRNA molecules contain a sequence of 3 bases called an anticodon which binds to a complementary codon on the mRNA
- The tRNA has an amino acid attached to it
- As the ribosome moves along the mRNA, another tRNA attaches, carrying a corresponding amino acid
- The 2 amino acids join together with a peptide bond
- Another tRNA molecule attaches to the mRNA
- The first tRNA molecule is released (now free to collect another amino acid)
- This process continues until a stop codon is reached on the mRNA
- The polypeptide chain is then released
12
Q
What is a mutation?
A
A change in the amount of, or arrangement of, the genetic material in a cell
13
Q
What is chromosome mutation?
A
A change to the structure of a chromosome
E.g. Deletion, inversion or translocation
14
Q
What are mutagens?
A
Substances that may cause mutations
15
Q
What are DNA mutations?
A
Changes to genes due to changes in nucleotide base sequences
16
Q
What are the 2 main classes of DNA mutations?
A
Point mutations
Insertion/deletion mutations
17
Q
When do DNA mutations occur?
A
When DNA is replicating before nuclear division, by either mitosis or meiosis
18
Q
What is point mutation?
A
One base pair replaces another
Also called substitutions
19
Q
What are insertion/deletion mutations?
A
When one or more nucleotide pairs are inserted or deleted from a length of DNA
These cause a frameshift
20
Q
What is a missense mutation?
A
A mutation in which a base pair has been replaced, causing a change to the polypeptide sequence
21
Q
What is a nonsense mutation?
A
A mutation in which a base pair is replaced, causing the polypeptide to end early
22
Q
What is a silent mutation?
A
A mutation in which a base pair has been replaced but it does not affect the polypeptide chain (the codon still codes for the same amino acid)
23
Q
What is a frameshift?
A
An insertion/deletion mutation
24
What is an allele?
An alternative version of a gene
25
What are mutations with neutral effects?
- A mutation in which the base triplet still codes for the same amino acid
- Or a mutation that causes a different characteristic which gives no particular advantage or disadvantage to the organism
26
What is the lac operon?
A section of DNA within E. Coli's DNA
27
In the lac operon what are the structural genes?
Z codes for the enzyme β-galactosidase
Y codes for the enzyme lactose permease
Each consists of a sequence of base pairs that can be transcribed into a length of mRNA
28
In the lac operon what is the operator region?
- A length of DNA next to the structural genes
- It can switch them on and off
- Shortened to 'O'
29
In the lac operon what is the promoter region?
- A length of DNA to which the enzyme RNA polymerase binds to begin the transcription of the structural genes, Z and Y
- Shortened to P
30
What is the regulator gene?
- It is not part of the operon
- Shortened to I
- Produces a repressor protein
31
What are the enzymes β-galactosidase and lactose permease used for?
β-galactosidase = catalyses the hydrolysis of lactose to glucose and galactose
Lactose permease = transports lactose into the cell
32
What happens when lactose is absent from the medium surrounding the lac operon?
- A repressor protein is produced by the expression of the regulatory gene
- The repressor protein binds to the operator region, blocking part of the promoter region
- This prevents RNA polymerase from attaching to the promoter region
- So transcription cannot occur: β-galactosidase and lactose permease are not synthesised
33
What happens when lactose is present from the medium surrounding the lac operon?
- Lactose molecules bind to the repressor protein
- This causes the shape of the protein to change, preventing it from binding to the operator region
- This allows RNA polymerase to bind to the promoter region
- Transcription of mRNA can then occur for Z and Y
- β-galactosidase and lactose permease are synthesised
- The E. Coli can now take up lactose from the medium and convert it to glucose and galactose
34
What is an organism's body plan?
The general structure or layout of an organism
35
What are homeobox genes?
- Genes that control the development of the body plan of an organism, including the polarity (head and tail ends) and positioning of the organs
- They are each a sequence of 180 base pairs (60 amino acids)
- They code for transcription factors
36
Which homeobox genes determine what?
- Embryo's polarity (head/tail) = maternal effect genes
- Polarity of each segment = segmentation genes
- What each segment looks like, e.g. Abdomen, thorax, head = homeotic selector genes
37
What is the effect of a mutation in a homeobox gene?
- Can cause changes in the body plan
| - Can change one body part to another
38
How are homeobox genes arranged?
- In clusters known as Hox clusters
| - These usually contain 9-11 genes
39
How are homeobox genes activated?
In the same order as they are expressed along the body (from head to tail)
40
What is a morphogen?
A substance that governs the pattern of tissue development
41
What is apoptosis?
Programmed cell death
42
When and where does apoptosis occur?
In multicellular organisms
| After about 50 mitotic divisions
43
What is necrosis?
Cell death that occurs after trauma
44
What is the sequence of events that occur during apoptosis?
- Enzymes break down the cell cytoskeleton
- The cytoplasm becomes dense, with organelles tightly packed
- The cell surface membrane changes and small bits called blebs form
- Chromatin condenses and the nuclear envelope breaks. DNA breaks into fragments
- The cell breaks into vesicles that are taken up by phagocytosis. The cellular debris is disposed of and does not damage any other cells or tissues
- The whole process occurs very quickly
45
How is apoptosis controlled?
By a range of cell signals (some from inside the cell and some from outside)
These include:
- Cytokines made by cells of the immune system
- Hormones
- Growth factors
- Nitric oxide
46
How does nitric oxide induce apoptosis?
- By making the inner mitochondrial membrane more permeable to hydrogen ions and dissipating the proton gradient
- Proteins are released into the cytosol
- These proteins bind to apoptosis inhibitor proteins and allow the process to take place
47
What is the role of apoptosis?
- It removes ineffective or harmful T-lymphocytes
| - During limb development,not causes fingers and toes to separate
48
What happens if the rate of cells dying does not balance the rate of cells produced by mitosis?
Not enough apoptosis = formation of tumours
| Too much apoptosis = cell loss and degeneration
49
What does genotype mean?
Alleles for a particular trait/characteristic present within cells of an individual
50
What does phenotype mean?
Observable characteristics of an organism caused by the genotype
51
What does homozygous mean?
An organism with 2 identical alleles for the same gene
52
What does heterozygous mean?
An organism with 2 different alleles of the same gene
53
What is a dominant allele?
An allele that is always expressed in the phenotype, even if a different allele for the same gene is present in the phenotype
54
What is a recessive allele?
An allele that is only expressed in the phenotype if another identical allele is present, or if a dominant allele is absent
55
What are the differences between apoptosis and necrosis?
Apoptosis:
- Does not cause any damage to nearby cells (doesn't release any toxins)
- Caused by ageing
- Natural process
Necrosis:
- Causes damage to nearby cells (releases hydrolysis enzymes)
- Can leave scars
- Caused by damage to the cell
- Not a natural process
56
What is a zygote?
The cell formed, during sexual reproduction, form the fusion of 2 gametes
57
What does haploid mean?
Eukaryotic cell or organism having only 1 set of chromosomes
58
Why do gametes need to be haploid?
To ensure that, after fertilisation, the original chromosome number is restored (during fertilisation 2 gametes fuse to make 1 cell, and so the chromosomes are combined into 1 nucleus)
59
What happens during interphase and when does it occur?
The DNA replicates - before meiosis I
60
What happens during prophase I?
- The chromatin condenses and undergoes supercoiling so that chromosomes shorten and thicken
- The chromosomes come together in their homologous pairs to form a bivalvent
- The non-sister chromatids wrap around each other and attach at points called chiasmata
- They may swap sections of chromatids with 1 another in a process called crossing over
- The nucleolus disappears and the nuclear envelope disintegrates
- A spindle forms. It is made of protein microtubules
61
What are homologous pairs?
Each member of the pair has the same genes at the loci. Each pair consists of 1 maternal and 1 paternal chromosome
62
How long does prophase I last?
For days, months or even years, depending on the species and on the type of gamete (male or female) being formed
63
What happens during metaphase I?
- Bivalents line up across the equator of the spindle, attached to spindle fibres at the centromeres. The chiasmata are still present
- The bivalents are arranged randomly with each member of a homologous pair facing opposite poles
- This allows the chromosomes to independently segregate when they are pulled apart in anaphase I
64
What happens during anaphase I?
- The homologous chromosomes in each bivalent are pulled by the spindle fibres to opposite poles
- The centromeres do not divide
- The chiasmata separate and lengths of chromatid that have been crossed over remain with the chromatid to which they have become newly attached
65
What happens during telophase I?
- In most animal cells 2 new nuclear envelopes form - 1 around each set of chromosomes at each pole - and the cell divides by cytokinesis. There is a brief interphase and chromosomes uncoil
- In most plant cells the cell goes straight from anaphase I into meiosis II
66
What happens during prophase II?
- If a nuclear envelope has reformed, it breaks down again
| - The nucleolus disappears, chromosomes condense and spindles form
67
What happens during metaphase II?
- The chromosomes arrange themselves on the equator of the spindle. They are attached to the spindle fibres at the centromeres.
- The chromatids of each chromosome are randomly assorted
68
What happens during anaphase II?
- The centromeres divide and the chromatids are pulled to opposite poles by the spindle fibres. The chromatids randomly segregate
69
What happens during telophase II?
- Nuclear envelopes reform around the haploid daughter nuclei
- In animals, the 2 cells now divide to give 4 haploid cells
- In plants, a tetrad of 4 haploid cells is formed
70
What does the chi-squared test test?
- The null hypothesis
| - It tests if the difference between observed categorical data and expected data is small enough to be due to chance
71
What criteria is there for the chi-squared test?
- The sample size must be relatively large
- Only raw counts, not percentages or ratios, can be used
- There are no 0 scores
- There must be a strong biological theory that we can use to predict expected values
- The data must be in categories
72
Given that the formula for calculating chi-squared is:
[The sum of (observed numbers (O) - expected numbers)^2]/[expected numbers (E)]
How can you design a table to make this simpler?
Columns:
- Category
- Observed
- Expected
- O - E
- (O - E)^2
- (O - E)^2/E
73
How do you find the critical value for the chi-squared test?
Look in a distribution table:
- The probability value is 0.05
- The degrees of freedom are correct (number of categories - 1)
- Using these, you will find the critical value
74
How do you know if the difference (using the chi-squared test) is significant or not?
- If the value from the chi-squared test is smaller than the critical value then we say that the difference is due to chance and not statistically significant
75
What is a genotype?
- The genetic make up of an organism
| - It describes the organism in terms of the alleles it contains
76
What does homozygous mean?
An organism with 2 identical alleles for a particular gene
77
What does heterozygous mean?
An organism with 2 different alleles for the same gene
81
What is a phenotype?
The characteristics that are expressed in the organism
- The features that can be observed
- They are determined by the genotype and the environment in which the organism has developed
82
What is a dominant allele?
An allele that is always expressed in the phenotype, even if a different allele for the same gene is present in the genotype
83
What is a recessive allele?
An allele that is only expressed in the phenotype in the presence of another identical allele, or in the absence of a dominant allele, for the same gene
84
What are codominant alleles?
2 alleles of the same gene that are both expressed in the phenotype of a heterozygote
85
What is linkage?
Genes for different characteristics that are present at different loci on the same chromosome are linked
86
What is the advantage of linkage?
It reduces the number of phenotypes resulting from a cross
- The linked alleles are usually inherited together because they do not segregate independently at meiosis (unless chiasmata have formed between them)
- At crossover, the alleles from 1 chromatid become linked to alleles on the other chromatid
87
What is a sex linked characteristic?
The gene that codes for the characteristic is found on one of the sex chromosomes (X and Y)
- Sex-linkage usually occurs on the X-chromosome because the Y-chromosome has fewer genes
88
Explain sickle-cell anaemia
- All individuals with the disease have the same mutation
- The β-strands of haemoglobin differ by 1 amino acid at position 6
- When this abnormal haemoglobin is deoxygenated it is not soluble and becomes crystalline and aggregates into more linear and less globular structures. This deforms the red blood cells, making them inflexible and unable to squeeze through capillaries
- After many cycles of oxygenation and deoxygenation, some cells become irreversibly sickled. Some are destroyed
- If enough sickle-cells become lodged in capillaries blood flow is impeded. Organs, particularly bones, do not receive enough oxygen, leading to a painful crisis
- Eventually organs become damaged
89
What is epistasis?
The interaction of genes concerned with the expression of 1 characteristic
- The genes may work against each other, resulting in masking
- The genes may work together in a complementary fashion
90
What is recessive epistasis?
- The homozygous presence of a recessive allele may prevent the expression of another allele at a second locus
- The alleles at the first locus are epistatic to the alleles at the 2nd locus (which are described as hypostatic)
91
What is dominant epistasis?
A dominant allele at 1 gene locus masks the expression of the alleles at a 2nd gene locus
92
What is complementary epistasis?
A dominant allele must be present for both gene loci
93
What is discontinuous variation?
The qualitative differences between phenotypes
- The genes interact in an epistatic way if more than 1 gene is involved
- If only 1 gene is involved, it is monogenic
- Different alleles at a single gene locus have large effects on the phenotype
- Different gene loci have quite different effects on the phenotype
94
What is continuous variation?
Quantitative differences between phenotypes
- There is a wide range of variation within the population, with no distinct categories
- Traits exhibiting continuous variation are controlled by 2 or more genes
- Each gene provides an additive component to the phenotype
- Different alleles at each gene locus have a small effect on the phenotype
- A large number of different genes may have a combined effect on the phenotype (polygenic)
95
How does the environment contribute to the phenotype?
```
Some traits (such as intelligence) can be partly determined by genes and partly by the environment
- Different environmental factors may limit the expression of these genes
```
96
Is the expression of polygenic traits or monogenic traits influenced more by the environment?
Polygenic traits
97
What is a gene pool?
The set of genetic information carried by a population
98
What do you need to know in order to measure the frequency of an allele?
- The mechanism of inheritance of a particular trait
| - How many different alleles of the gene for that trait are in the population
99
What is the Hardy-Weinberg principle?
A mathematical model used to calculate the allele frequencies of traits with dominant and recessive alleles
If p represents the frequency of the dominant allele, and q of the recessive allele:
p + q = 1
p^2 + q^2 +2pq = 1
101
What assumption does the Hardy-Weinberg model have?
- The population is very large
- The mating within the population is random
- There is no selective advantage for any genotype
- There is no mutation, migration or genetic drift
102
What is "carrying capacity"?
The maximum size that the environment can sustain
103
What isolating mechanisms may split a large population of organisms into sub-groups?
- Geographical barriers
- Seasonal barriers
- Reproductive mechanisms
104
What is selection pressure?
An environmental factor that confers greater chances of survival to reproductive age on some members of the environment
105
What factors offer environmental resistance?
Environmental factors
- Biotic
- Abiotic
106
What is stabilising selection?
When natural selection keeps things the way they are
108
What is genetic drift?
- Fluctuations or changes in allele frequency
- E.g. As the size of populations decreases, the degree of fluctuation will increase
- May lead to the chance elimination of 1 allele from the population
- Reduces genetic variation
- May reduce the ability of a population to survive in a new environment
- Could contribute to the extinction of a population or species
- Could lead to the production of a new species
109
How can small populations occur in nature?
Due to natural disasters
| - E.g. Large volcanic eruption or a disease pandemic
110
What factors are required for evolution?
- Variation
- Heredity
- Means of selection
111
What are the 3 types of selection pressure?
- Disruptive: selection pressure towards the extremes, creating 2 modal values
- Stabilising: selection pressure toward the centre, increases number of individuals at the modal value
- Directional: selection pressure toward 1 extreme, moves the mode in this direction
113
What is "directional selection"?
When the frequency of particular alleles in the gene pool changes, so the frequency of this phenotype within the population also increases
114
What is a population bottleneck?
A shrinkage to a small size
| - Occurs when a large genetically diverse population is drastically reduced by a catastrophic, non-selective event
115
Does genetic drift have a big or small effect on a small population?
Big
116
What is the founder effect?
When a new population is founded from a subset of a much larger one, there will be changes in allele frequency
117
What is speciation?
The formation of a new species
- Occurs when gene flow has effectively stopped between populations where it previously existed
- Requires 2 populations of the same species to become reproductively isolated
118
What is allopatric speciation?
Speciation due to changes in geographical location
119
What is sympatric speciation?
Speciation due to changes in reproductive systems
120
What is the biological species concept?
A group of similar organisms that can interbreed and produce fertile offspring
121
What is percentage divergence?q
(Number of substitutions)/(number of base pairs analysed) x 100
- The differences, caused by base substitutions, between base pair sequences
122
What is a clade?
- A taxonomic group comprising a single ancestral organism and all its descendants
- A mono phyletic group
- Any group of organisms with haplotypes that are more similar to each other than to those in any other group
123
How is cladistic classification different to taxonomic?
- It focuses on evolution (phylogenetic relationships) rather than on similarities between species
- It places great importance on using objective and quantitative analysis
- It uses DNA and RNA sequencing
- It uses computer programmes and the data obtained from nucleic acid sequencing to generate dendrograms or cladograms that represent the evolutionary tree of life
- It makes no distinction between extinct and extant species and both may be included in cladograms
124
How does cladistic classification differ from Linnaean classification?
- Does not use the groups kingdom, phylum or class
- Not helpful to use a fixed number of levels in the classification of living organisms
- Used to confirm the Linnaean classification of organisms
- Can lead to organisms being reclassified
125
What is the phylogenetic species concept?
A group of organisms that have similar morphology, physiology, embryology and behaviour, and occupy the same ecological niche
126
What is a monophyletic group?
One that includes an ancestral organism and all its descendant species
A2 Biology Unit 1
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