Module 2: Molecular Biology & Genetics And Module 3: Human Molecular Genetics Flashcards
Aneuploidy
An abnormal number of a particular chromosome
Example of aneuploidy, and what causes it
Down syndrome caused by trisomy 21.
Three copies of chromosome 21, caused by failure of chromosomes to separate during meiosis.
Nondisjunction
Failure of chromosomes/ chromatids to separate during anaphase of cell division
What does XXY cause?
Klinefelter syndrome
What does XO cause?
Turner syndrome
Polyploidy
Possession of multiple sets of chromosomes
How does polyploidy come about?
Gametes contain same number of chromosomes as parent cell (2n). When fertilised, the two gametes produce a tetraploid (2n + 2n = 4n)
Example of a triploid species
Bananas
What is a sure cause of infertility? Why?
Odd number of chromosome sets. Not all chromosomes will have homologous chromosomes to pair with due to gametes having different chromosome set numbers
What are the four chromosomal aberrations?
Deletion
Duplication
Inversion
Translocation
Deletion, and what disease can it cause?
Small part of a chromosome is removed
Lejeune syndrome/ cri du chat: deletion of the top of short arm on chromosome five
Duplication
One part of a chromosome is repeated
Inversion, and what effect does it have?
Part of a chromosome is taken out, then re-added in the reverse order.
Inversion prevents the production of viable zygotes during meiosis, because crossing over results in uneven chromosomes.
Translocation
Part of a chromosome is moved to a non homologous chromosome
Can be reciprocal
Philadelphia translocation
Ends of chromosomes 9 and 22 are swapped (translocated)
95% of the time this results in myeloid leukaemia
Familial Down syndrome
One 14 chromosome and one 21 chromosome are joined in the parent.
A potential gamete, when fertilised, will produce an embryo with three chromosome 21’s.
Why do we inactivate an X chromosome?
Because only one X is necessary- females have an extra one.
What does the inactivated X chromosome show up as?
Barr body
When is the X chromosome inactivated?
After four days- after the cell has divided several times
How is the X chromosome inactivated, and which one is chosen?
DNA is packed closer together, and methyl groups are added to prevent enzymes from interacting with it.
Can be from mother or father
Describe the three components of the Central Dogma of Molecular Biology and their roles
DNA- information
RNA- messenger
Protein- worker
Which five processes occur in the central dogma of molecular biology?
Transcription Translation Reverse transcription DNA replication RNA replication
Gene expression
Process by which information from a gene is used in the synthesis of a functional gene product
Functional gene product (2)
Protein or non-coding RNA
Product of gene expression
What does a gene do?
Produces a type of RNA with a specific function
Transcription
Synthesis of double-stranded DNA from a single-stranded RNA
Which enzyme catalyses transcription?
RNA polymerase
Coding strand
The DNA strand containing the information the cell needs
Non-coding strand
The strand that doesn’t contain information the cell needs. Is there for replication
Other name for non-coding strand
Template strand
In which direction along the template strand does RNA synthesis occur?
3’-5’
Three stages of transcription
Initiation
Elongation
Termination
Which stage of transcription differs between eukaryotes and prokaryotes?
Termination
Where does initiation of transcription start?
At the TATA box in the promoter region of the template strand
TATA box
A segment of DNA that contains bases T,A,T,A / is AT heavy
How does initiation of transcription start?
TATA box allows transcription factors to bind
Transcription factors
Proteins that bind to DNA and help bind the RNA polymerase
What is the name of the complex which includes transcriptions factors and RNA polymerase?
Transcriptional initiation complex
RNA polymerase function
Starts mRNA synthesis, contains hydroxyl group which means it doesn’t need a primer
Elongation (transcription)
RNA polymerase continues to synthesise mRNA from template strand in the 5’-3’ direction
Which regions flank the coding sequence in a gene?
5’UTR and 3’UTR
UTR
Untranslated region
- a region which is copied in transcription but is not translated
Which nucleotide connects to the 5’UTR before translation?
5’G cap
A chemically modified guanine nucleotide
5’G cap function
Prevents enzymes from degrading mRNA
What connects to the end of the 3’UTR?
Poly-A tail
Functions of poly-A tail (2)
Prevents enzymes from degrading RNA
Facilitates transport of mRNA from nucleus into cytoplasm, through a nuclear pore
What connects to the 5’UTR before transcription?
Promoter region, including TATA box
What changes does the gene undergo after transcription?
Promoter region is lost
5’G cap and poly-A tail are added
Which part of the gene makes it through translation?
Coding sequence
Introns
Non-coding regions
Exons
Coding regions
Splicing
Process of removing introns and joining exons together in the coding sequence before translation
Before splicing, what kind of RNA exists?
Pre-mRNA (precursor)
After splicing, what kind of RNA exists?
mRNA (mature)
What is the name of the triplet-based genetic code?
Triplet codon hypothesis
How many possible codons are there? How many codons code for amino acids?
64
61
UAA UAG UGA are what kind of codons?
Stop codons
Start codon
AUG
Adaptor molecule between mRNA and amino acid
tRNA
Structure of tRNA
Single strand of RNA, 70-80 nucleotides in length
Looped and twisted into 3D L-shape
Where does the tRNA connect the amino acid?
At the amino acid attachment site
Anticodon-triplet
The triplet of bases on a tRNA which base pairs to the mRNA strand
What happens at the amino a acid binding site?
An enzyme joins tRNA to an amino acid by using ATP to form a covalent bond
Different enzyme for each amino acid
In general, it’s called aminoacyl-tRNA synthetase
Three stages of translation
Initiation
Elongation
Termination
Ribosome structure
Small subunit
Large subunit with A P and E sites
- above the P site is the exit tunnel
Locations of ribosomes (2) and where the proteins go
Bound to the rER- used within the plasma membrane or exit (exocytosis)
Free in the cytosol - released into the cytosol and used in the cell
Describe initiation (translation)
Small subunit meets tRNA molecule carrying methionine
They find and bind to the 5’G cap of the mRNA
They scan along the mRNA until the start AUG codon, where large subunit joins and methionine is carried by P site
Describe elongation (translation)
A charged tRNA arrives at the A site of the large subunit
Simultaneously:
- amino acid at P site attaches to new amino acid at A site- forming peptide bond
- ribosome moves along mRNA, shifting positions of the tRNAs so the growing polypeptide sits in the exit tunnel
Then the uncharged tRNA exits out the E site by detaching from its codon
Charged tRNA
tRNA molecule with an amino acid attached
Describe termination (translation)
Release factor enters A site once ribosome reaches a stop codon
- breaks bond between P site and final amino acid using water
Polypeptide chain detaches from the tRNA, and both subunits and mRNA dissociate
Genotype
Set of genes/ DNA combinations responsible for a particular trait
Phenotype
Physical expression of a genotype
Defined by what happens at the protein level
_____ variation commonly leads to _____ variation
Genetic
Phenotypic
F1
First filial generation
F2
Second filial generation
Monohybrid
A cross that is heterozygous with respect to one specific gene
What does Mendel’s peas experiment show about how information is inherited?
Information is passed on to offspring packaged in particles called genes
Test cross
Crossing a dominant phenotype with a homozygous recessive genotype to find the genotype of the first one
Mendels law of segregation
Genes segregate at meiosis so that each gamete contains only one of the two possessed by the parent
(Diploid—> haploid)
Mendels law of independent assortment
Alleles of different genes assort independently during gamete formation
(Where R or r goes does not determine where Y or y goes)
Product rule is for ?
Independent events
Sun rule is for ?
Mutually exclusive events
Polymorphism
When one gene controls more than one allele
Incomplete dominance
One allele is partially dominant, so a new phenotype is produced
This is not blending
Co-dominance
Both phenotypes exist side by side
Example of co-dominance
AB blood type
Polygenic traits
Traits that are controlled by groups of genes
If you graphed a polygenic trait of the population, what would it look like?
Normally distributed
How does the environments effect on a phenotype change the variation?
It smooths out differences
What is the name of a trait which is determined by genes on the X or Y chromosome? Give an example
Sex-linked trait
Red-green colour blindness
Hemizygous
Describes an individual who only has one allele. Often a male, referring to a gene on the X chromosome.
Will the sons of a father with red green colour blindness also have this?
No- it is a trait on the X chromosome- which fathers do not give to sons
Recombinant type
A new genotype which wasn’t one of the parents
Parental type
A genotype of one of the parents
How do recombinant types occur?
They are a result of crossing over during meiosis, where homologous chromosomes exchange parts of a gene and form chiasmata
The smaller the distance between two genes, the _____ the recombination frequency?
Smaller
Recombination frequency
Percentage of gametes expected to be recombinant types
centiMorgan cM
A unit of recombination (1% = 1cM) used for a genetic map
Hardy-Weinberg equation (proportions of alleles)
p^2 + 2pq + q^2 = 1
If 1 in 2500 people have a rare disease, how is this expressed in p and q terms?
q^2 = 1/2500
Causes of genetic change in a population (7)
Non-random mating Random genetic drift - bottleneck effect - founder effect Natural selection Gene flow or migration Mutation
Two types of non-random mating
Inbreeding Assortative mating (mating within same phenotype)
Random genetic drift
A random change in allele frequencies due to sampling error over generations
Sampling error
Who happens to leave offspring out of a population
Which factor will increase random genetic drift?
Size of the population (smaller)
Bottleneck effect
An event causes most of the population to die, and the remaining alleles don’t show as much genetic diversity
Founder effect
genetic diversity of new population in a new location is limited by the genotypes of the founding organisms
Stabilising selection
Mean stays the same, variation is reduced
Type of natural selection
Directional selection
Type of natural selection
Mean changes toward one extreme
Disruptive selection
Type of natural selection
Favours the two extremes of the population
Sexual selection
A type of natural selection
Favours the phenotype that attracts females more (or males)
Frequency dependent selection
Type of natural selection
Favours the rarer phenotype
Cline
Geographic change in genetic/ phenotypic composition
As location changes, frequency of a genotype changes
Comparative genomics
Comparing genomes to find what is conserved and what is different between or within species
Aligning (sequences)
The process of lining sequences up next to each other and marking each point where sequences are the same
What might differences in genomes within a species be associated with? (3)
- disease
- characteristics
- evolutionary history
Which two species are the closest relatives of humans?
Chimpanzee and bonobo
We share all our genes with chimps. How do we differ genetically?
We use the genes in different ways
What happens when DNA degrades?
It’s sequence changes
What can ancient DNA be used for?
To determine the relationships of extinct animals
Closest relative of modern humans
Neanderthal
Why are Neanderthal remains good for DNA extraction?
They are in cold, sealed caves
What types of Neanderthal evidence have been found?
Tools, art, jewellery
Some people carry Neanderthal DNA. What does this mean?
They carry alleles that arose in Neanderthals rather than in modern humans
Why do some people carry Neanderthal DNA
When homosapiens left Africa, some interbred with Neanderthals
What allele does Denisovan contribute to the Tibetan population?
One that allows them to handle hypoxia (low oxygen)
How can we work out what the function of a gene is?
By studying organisms that are mutant for that gene
Polydactyly
Above average number of fingers or toes
What is the role of the gene which causes polydactyly?
To prevent polydactyly
The mutant form of this gene is unable to do this, so extra fingers or toes grow
Does variation in a gene always affect phenotype?
Only sometimes
How is mutation linked to variation?
Mutation is a subset of variation
Do mutations affect fitness?
Not all the time
Myotonia congenita
Inherited condition in which muscles fail to relax after contraction,
Due to defect in the gene which encodes a chloride channel receptor
Three functional molecular genetics techniques
Genetic screen
Transgenesis
Targeted mutation
Genetic screen
Mutations are introduced to a gamete by treating them with mutagens
The organism is studied for any changes in phenotype
Mutagen example
X rays or chemicals
What makes a model organism
It can be easily raised in a controlled environment (not too large or too long lifespan)
Easy to manipulate genetically
Transgenesis
Foreign DNA is added from one organism into another (inserted into embryo pronucleus)
DNA code is universal- DNA from one organism can be used in another
Transgenesis
The gene placed into another organism during transgenesis
Novel variant
A variation of a gene in an organism which isn’t present in the parents’ genomes
Targeted mutation
Damage or modify the gene we are interested in to work out its normal function
Explain the components of the Cas9- guide RNA complex
Cas9 is a protein with active sites that can cut the DNA
It forms a complex with a guide RNA with a complementary sequence that can bind to a target gene
By designing the guide RNA, we can choose which gene is cut by Cas9
Explain targeted mutation with CRISPR-Cas9
Complex enters nucleus and finds target sequence (complementary to the guide RNA) on the DNA
Cas9 makes a double stranded break in DNA at the target site
DNA enzymes try to repair the cut- resulting in small insertions/ deletions in the gene (no template, causes errors)
- this causes mutated gene
We can provide a specially designed repair template for the enzymes to copy, to create our own gene
Two conditions for using targeted mutation to treat genetic disease
Targets only the cells or organs affected
Is not a change to the germ line/ doesn’t affect next generation
Example of gene editing for genetic disease
Sickle cell disease
CRISPR-Cas9 used to break a gene (BCL11A) which shuts down gamma genes at birth
Gamma chains help make haemoglobin
Sickle cell disease
Red blood cells have sickle shape due to two recessive copies in the HBB gene
What is cystic fibrosis caused by?
Mutation to gene which encodes a chloride ion channel
Pre-implantation genetic diagnosis
IVF is used to filter out embryos containing a genetic disease
Three parent babies
If the faulty gene is on mitochondrial DNA
A donor egg is used- with nucleus destroyed- and parents nucleus is transplanted
Contains donor mitochondrial DNA, and prenatal nuclear DNA
How does an embryo begin?
As a small number of totipotent cells
Toro potent
Capable of giving rise to any cell type
Is trophectoderm totipotent like other embryonic stem cells?
No, it’s pluripotent
Pluripotent
Capable of giving rise to several (not any) cell types
During development, cells become more ____ and less ____
Specialised
Flexible
What is cell polarisation in an embryo?
Cells making right connections with each other
Microvilli develop on outer cells at this stage
What do the outer cells of the embryo develop into?
Trophectoderm
What happens once an embryonic cell’s fate is determined?
Certain control genes that code for transcription factors become activated
Why is it difficult for a cell to switch to a different cell type once it’s fate has been determined?
Once transcription factors are made, they make more, which turn on certain genes to transcribe mRNA for cell-specific proteins
What does it mean for a cell to be terminally differentiated?
It has developed into its cell type, fully functioning in the body
Genomic equivalence
The theory that all types of differentiated cells contain all the DNA required to build an entire new organism
(All cells contain full genome)
Is it easier or harder to create a new cell from the nucleus of a fully differentiated cell than from a less differentiated cell?
Harder - but still possible because of genomic equivalence
Where can we get embryonic stem cells? They are ____potent
Harvested from the inner cell mass of mammalian blastocyst embryos
Pluripotent
How are iPS cells made? They are ____potent
Induced pluripotent stem cells are made by reprogramming adult skin cells
Pluripotent
Adult tissue stem cells are ___potent cells
Multi potent
They can divide without limit
Umbilical cord stem cells are ___potent
Multi potent
Stem cells are isolated from blood of umbilical cord, and frozen
Why are umbilical cord stem cells less restricted than adult blood stem cells?
They are younger and immature (less differentiated)
What disease can umbilical cord stem cells be used to treat?
Leukaemia- where affected cells are somatic
What are stem cells in our bodies important for?
Constant renewal of tissues such as skin and blood
Haematopoietic stem cells
Where are they found?
Blood stem cells
In the bone marrow
Three examples of adult stem cells
Fat, bone and white blood cells
A fertilised egg is ___potent
Totipotent (can give rise to all cell types)
What separates totipotent, multi potent and pluripotent cells?
Totipotent cells can divide to create an entire organism- including placenta and embryo
Pluripotent cells can divide into all cell types within an organism, but can’t create an entire organism on their own (like totipotent cells can)
Multi potent cells can differentiate into different cell types, but not all
What is used to persuade stem cells to develop into different kinds of cells?
Different culture conditions
How do we use a virus to correct single gene disorders?
RNA containing the normal allele is inserted into virus (viral RNA)
Virus infects bone marrow cells that have been removed from patient
Viral DNA carrying the normal allele inserts into chromosome
Engineered bone marrow cells are injected into patient
Regenerative medicine is based on the idea that _____
Pluripotent stem cells can be used to repair or replace damaged tissues or organs
