Week 01 Genomes, Genes, Mutations Flashcards
genome
the entire collection of genetic material within an organism
chromosome
structure consisting of DNA and associated proteins that carries and transmits genetic information
Each unreplicated chromosome consists of a single molecule of DNA.
Compare the chromosomes of prokaryotes vs eukaryotes with respect to:
- number
- shape
- location
- extra dna
- accompanying proteins
- replication
- percentage expressed
- repeats
-
number:
- prokaryotes: 1
- eukaryotes: >1
-
shape:
- prokaryotes: circular
- eukaryotes: linear
-
location:
- prokaryotes: cytoplasm
- eukaryotes: nucleus
-
extra dna:
- prokaryotes: plasmids
- eukaryotes: in organelles (e.g. mitochondria, chloroplasts)
-
accompanying proteins:
- prokaryotes: no, ‘naked’
- eukaryotes: packaged with histones to form chromatin
-
replication:
- prokaryotes: binary fission
- eukaryotes: mitosis and meiosis
-
percentage expressed:
- prokaryotes: >90% expressed
- eukaryotes: <10% expressed
-
repeats:
- prokaryotes: very few repeats
- eukaryotes: many repeats
ploidy
the number of sets of homologous chromosomes in the genome of a cell or an organism (e.g. monoploid, diploid, triploid, polyploid)
haploid number
The haploid number (n) refers to the total number of chromosomes found in a gamete (a sperm or egg cell produced by meiosis in preparation for sexual reproduction).
Depending upon the polidy of the organism, the chromosome number in somatic cells will be some multiple of this e.g. diploid = 2n, triploid = 3n
total chromosome number
Depending upon the ploidy of the organism, the chromosome number in somatic cells will be some multiple of the haploid number e.g. diploid = 2n, triploid = 3n.
Most animals are diploid, so e.g. humans have 2n where n = 23 so 2n = 46 chromosomes
euploidy
The state of a cell or organism having or ganing one or more than one set of the same set of chromosomes, possibly excluding the sex-determining chromosomes.
For example, most human cells have 2 of each of the 23 homologous monoploid chromosomes, for a total of 46 chromosomes.
A human cell with one extra set of the 23 normal chromosomes (functionally triploid) would be considered a case of abberant euploidy. This would also result in polyploidy, the organism’s having >2 sets.
aneuploidy
Aneuploidy is the state where one or more individual chromosomes of a normal set are absent or present in more than their usual number of copies (excluding the absence or presence of complete sets, which is considered euploidy).
Unlike euploidy, aneuploid karyotypes will not be a multiple of the haploid number.
Examples: Down syndrome = extra copy of chromosome 21; Turner syndrome = partly or missing X chromosome
Veterinary example: XXY trisomy in male tortoiseshell cats (Klinefelter syndrome)
karyotype
The complete set of chromosomes possessed by an organism
usually presented as a picture of a complete set of its metaphase chromosomes
Can be used to identify chromosomal abnormalities
chromatin
Material found within the eukaryotic nucleus; consists of DNA and histone proteins
Chromatine regulates gene expression
What are the three essential elements of a functioning (eukaryotic) chromosome?
- Centromere
- Pair of telomeres
- Origins of replication
centromere
- appears as a constricted region on the chromosome
- serves as the attachment point for spindle microtubules
- Before cell division, a multiprotein complex called the kinetochore assembles on the centromere; later, spindle microtubules attach to the kinetochore
- Chromosomes lacking a centromere cannot be drawn into the newly formed nuclei; such chromosomes are lost, often with catastrophic consequences for the cell (p. 22)
telomere
- Telomeres are the specific DNA sequences and associated proteins located at the tips of whole linear chromosomes
- telomeres protect and stabilize the chromosome ends
- telomeres also participate in limiting cell division and may play important roles in aging and cancer
origins of replication
- sites where DNA synthesis begins;
- unlike centromeres and telomeres, they are not easily observed by microscopy
nucleosome
- the basic structural unit of DNA packaging in eukaryotes, comprised of a section of DNA that is wrapped around a core of (histone) proteins
- Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight histone proteins, which are known as a histone octamer
What is the difference between the relaxed and supercoiled states of chromatin?
Relaxed (extended)
- Required for gene expression
- Most of cell cycle
- Not visible under microscope
Supercoiled (condensed)
- NO gene expression
- During mitosis and meiosis
- Visible under microscope
euchromatin
- a lightly packed form of chromatin that is enriched in genes
- is often (but not always) under active transcription
- Euchromatin comprises the most active portion of the genome within the cell nucleus
- ‘beads on a string’
heterochromatin
Heterochromatin
- Generally condensed (not just meiosis)
- Minimal gene expression
- Few recombination events
- Constitutive or Facultative
Constitutive heterochromatin
- ALWAYS condensed
- Centromeres, telomeres, repeat sequences (high numbers of tandem repeats)
tandem repeats
Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other
Facultative heterochromatin
- SOMETIMES condensed
- Not repeat sequences
- Example: X chromosome inactivation in female mammals: one X chromosome is packaged as facultative heterochromatin and silenced, while the other X chromosome is packaged as euchromatin and expressed
In a karyotype image, we typically visualize chromosomes in their [relaxed/supercoiled], [replicated/unreplicated] form during meiosis/mitosis
In a karyotype image, we typically visualize chromosomes in their supercoiled, replicated form during meiosis/mitosis
On the basis of the location of the centromere,
chromosomes are classified into four types. What are the names of these four types?
- Metacentric
- Submetacentric
- Acrocentric
- Telocentric
Where is the location of the centromere in a metacentric chromosome (during metaphase)?
Centromere is in the middle such that the two arms of the chromosome are almost equal in length
Where is the location of the centromere in a submetacentric chromosome (during metaphase)?
Centromere is not in the middle, such that the dwo arms of the chromosomes are unequal. When unreplicated they form an L shape.
Where is the location of the centromere in an acrocentric chromosome (during metaphase)?
If the p (short) arm is so short that it is hard to observe, but still present, then the chromosome is acrocentric.
From Latin acro- “sharp, tip, peak, extremity” from Ancient Greek ákros “highest, at the extremity”
Where is the location of the centromere in an telocentric chromosome (during metaphase)?
A telocentric chromosome’s centromere is located at the terminal end of the chromosome. A telocentric chromosome has therefore only one arm.
What is the example of chromosome staining in animals discussed in the lectures called? What are the two types of bands that can be visualised and what does this stain tell us?
Giemsa stain in animals
- G bright bands = gene-rich, GC rich, fewer repeats
- G dark bands = gene-poor, AT rich, more repeats
One way to view chromosomes microscopically is to stimulate them to divide mitotically then treat them with . This prevents formation of the apparatus, causing the accumulation of chromosomes in the stage of mitosis. In this form the are clearly visible under the microscope.
One way to view chromosomes microscopically is to stimulate them to divide mitotically then treat them with colichine. This prevents formation of the spindle apparatus, causing the accumulation of chromosomes in the metaphase stage of mitosis. In this form the are clearly visible under the microscope.
What are the three parts of the basic structure of a gene and their basic functions?
- Promoter: Site of RNA Polymerase binding
- Transcribed region: Transcribed into RNA and can include untranslated regions
- Terminator: RNA Polymerase releases – transcription ends
In prokaryotic genes, the promoter is part of the region of the gene.
In prokaryotic genes, the promoter is part of the regulatory region of the gene.
In prokaryotic genes, the transcribed region includes (1) [5’ untranslated region/3’ untranslated region/both], (2) the protein coding region, and (3) [introns/no introns].
In prokaryotic genes, the transcribed region includes (1) both 5’ and 3’ untranslated regions, (2) the protein coding region, and (3) no introns.
Some genes in bacteria are in operons (this not true in eukaryotes). What does this mean?
Several genes are controlled by the same promoter.
In eukaryotic genes, both exons and introns exist in the transcribed region. Exons are [transcribed and/spliced out and not] translated into proteins. Introns are [transcribed and/spliced out and not] translated into proteins.
In eukaryotic genes, both exons and introns exist in the transcribed region. Exons are transcribed and translated into proteins. Introns are spliced out and not translated into proteins.
The three main types of transcription factors in eukaryotic genes are:
- General transcription factors
- Positive transcription factors (activator proteins)
- Negative transcription factors (repressors)
Over 80% of what used to be called “junk” DNA we now know is translated into RNA. What are some of these types of RNA?
What are four sites for the control of gene expression?
- Transcription factors
- Bind promoters and enhancers
- Affect binding of RNA polymerase
- Most genes are affected by several transcription factors
- Chromatin
- Nucleosome packaging
- Histone modifications (eg: acetylation)
- DNA modifications
- eg: methylation of CpG nucleotides in gene promoters to suppress gene expression
- RNAi
- Affects abundance of mRNA
Epigenetics
Stable, heritable phenotypes resulting from changes in a chromosome without alterations in the DNA sequence (e.g. Chromatin modifications, DNA modifications, Small RNA)
May or may not be transgenerational (ie can be somatic or germline)
e.g. agouti mice
Term for a base substitution that results in a different amino acid in the protein?
missense mutation
Term for a mutation that changes an amino acid specifying codon into one that terminates translation (a stop codon)?
Nonsense mutation
If a nonsense mutation occurs early in the mRNA sequence, the protein will be truncated and usually nonfunctional
Term for a mutation that changes a codon to a synonymous codon that specifies the same amino acid?
Silent mutation
What is the difference between a somatic and a germline mutation?
What is the name for a mutation where a section of a genetic sequence gets flipped around and reversed end-to-end?
inversion
What are the terms for:
(a) the spontaneous replication error that arises through changes in how protons (H ions) are positioned in DNA bases, leading to non-standard base-bairings (e.g. C-A instead of C-G), and
(b) the phenomenon that causes conditions in which normal, protonated, and other forms of the bases are able to pair because of flexibility in the DNA helical structure
(a) Tautometric shifts
(b) wobble
What are the four basic types of chromosome rearrangements?
- duplications
- deletions
- inversions
- translocations
What is the term describing when genetic material moves from one chromosome to another (translocation) with an exchange also in return of material from that chromosome to the first?
reciprocal translocation
- Errors in chromosome alignment during meiosis (subfertility)
- Balanced = complete chromosome complement (Phenotypic effects unlikely; reduced fertility)
- Unbalanced = duplication and deletion (Lethal or phenotypic effects likely; segregation problems during meiosis)
What are the two types of polyploidy?
autopolyploidy, in which all chromosome sets are from a single species, and allopolyploidy, in which chromosome sets are from two or more species (e.g. wheat)
What are the consequences of nondisjunction during meiosis I for gametes and zygotes?
- homologous pair fails to split
- 100% abnormal gametes
- Zygotes (assuming second parent normal):
- 50% Trisomy
- 50% Monosomy
- Lethal or phenotypic effects likely
What are the consequences of nondisjunction during meiosis II for gametes and zygotes?
- set of sister chromatids fail to split
- Gametes
- 50% normal gametes
- 50% abnormal gametes
- Zygotes (assuming second parent normal):
- 50% Normal
- 25% Trisomy
- 25% Monosomy
- Lethal or phenotypic effects likely
