Genome Anatomy Flashcards
What makes DNA good for storage?
Structure - far more stable
What sugar is DNA based off?
2’-deoxyribose
How does structure of RNA differ? How does this affect its
Has an OH on 2’ carbon –> chemically unstable Used instead for transient information transfer
In what direction is DNA and RNA synthesised?
In a 5’ to 3’
Does the sense or anti sense strand end up in the mRNA?
Sense –> this is the strand that would usually be written out for a gene
What is chromatin? What is a nucleosome?
Chromatin: Chromatin is the material that makes up a chromosome that consists of DNA and protein. The major proteins in chromatin are proteins called histones.
Nucleosome: The fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones
What is a chromatid?
1/2 of a replicated chromosome. Prior to cell division, chromosomes are copied and identical chromosome copies join together at their centromeres. Each strand of one of these chromosomes is a chromatid. Joined chromatids are known as sister chromatids.
What is the core of a nucleosome?
A histone octamer –> a set of 8 proteins
What is the centromere?
Narrowing near centre of chromosome where mitotic spindle is attached
What separates the short from the long arm of the chromosome?
Centromere
What is the short and long arm of the chromosome referred to respectively?
Short - (p) Long (q)
What is a telomere (tel)?
A region of repetitive nucleotide sequences at each end of a chromosome e.g. qtel / ptel
What is function of telomere?
Protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes
What is a chromosome ideogram?
Provide a schematic representation of chromosomes. They are used to show the relative size of the chromosomes and their characteristic banding patterns.
What is the maximum resolution achievable in the human genome using ideograms?
About 850 bands
What is typically used to describe location of genetic variants / genetic features?
Chromosome coordinates
What is haploinsufficiency?
Haploinsufficiency describes the situation where having only a single functioning copy of a gene is not enough for normal function, so that loss‐of‐function mutations cause a dominant phenotype.
Are all autosomes haploinsufficient?
Yes
What is exempt from haploinsufficiency?
X chromosome - Only one working copy is necessary/sufficient for normal expression of the gene’s function. The functional allele of a haplosufficient gene is dominant. The non-functional allele of a haplosufficient gene is recessive.
What are the pseudoautosomal regions?
Homologous sequences of nucleotides on the X and Y chromosomes
What does the term ‘x-unique’ refer to?
Many genes are unique to the X chromosome, but genes in the pseudoautosomal regions are present on both sex chromosomes.
X-unique genes are unique only to the X chromosome. This means males are hemizygous for most genes on sex chromosomes (has only one member of a chromosome pair or chromosome segment rather than the usual two)
What does hemizygous mean? Does this feature in males or females?
Hemizygous is a condition in which only one copy of a gene or DNA sequence is present in diploid cells.
Males are hemizygous for most genes on sex chromosomes, having only one X and one Y chromosome.
What makes up the majority of the Y chromosome?
Heterochromatin
What is heterochromatin?
a tightly packed form of DNA
There are only a few unique genes on the Y chromosome. What is the most important one?
SRY –> sex determining region
What is SRY responsible for?
Testes formation
Does the number of chromosomes remain constant thoughout the life cycle of a cell? Does the DNA content?
Yes
No –> replication (4n), separation
What are sister chromatids?
Identical copies formed by the DNA replication of a chromosome, joined together by a centromere. Is ‘one-half’ of the duplicated chromosome.
4n
How are sister chromatids formed?
Chromosome replicates (2n becomes 4n)
What then happens to sister chromatids?
Separate at mitosis
What proportion of our genome is non coding DNA?
>90%
What is mitochrondrial DNA? Where is it found?
The small circular chromosome found inside mitochondria (powerhouse of cell)
Describe difference in location between nuclear and mitochondrial DNA?
Nuclear DNA is located within the nucleus of eukaryote cells while mitochondrial DNA is located in the mitochondria in cytoplasm
How many genes does the mitochondrial DNA contain?
37
Describe difference in structure between mitochondrial and nuclear DNA
Circular vs linear
How is mitochondrial genome inherited?
Maternal (oocyte) inheritance –> passed on in cytoplasm of oocyte
What 2 sequences can the human genome be broken down into?
- Single-copy sequences (non-repetitive)
- Repetitive sequences
How do single-copy and repetitive sequences differ?
Single-copy sequences are unique and are translated and code for proteins
Repetitive sequences are not translated (typically non-coding)
Are genes single-copy sequences or repetitive?
Single-copy (are translated)
What 2 main types can repetitive sequences be subdivided into?
- Satellite DNA
- Interspersed repeats
What does satellite DNA consist of?
Large blocks of repetitive sequences (heterochromatin) at specific locations
Where are interspersed repeats found?
Scattered throughout genome
What is transcription?
Information in strand of DNA is copied into RNA
What is translation?
Turning RNA into protein
Where does translation occur?
Cytoplasm
Gene structure
What are introns?
A portion of a gene that does not code for amino acids so is not expressed –> have to be removed from primary RNA transcript by splicing
What is splicing governed by?
Specific sequences at junctions between exons and introns –> splice doner and splice acceptor sites
What is the TATA box?
Promoter sequence –> specifies to other molecules where transcription begins
What is alternative splicing?
A process by which exons or portions of exons or noncoding regions within a pre-mRNA transcript are differentially joined or skipped, resulting in multiple protein isoforms being encoded by a single gene
What is exon skipping?
A form of alternative splicing
Certain exons are skipped resulting in various forms of mature mRNA
What is mutually exclusive exon choice?
A form of alternative splicing where only one of two or more candidate exons is spliced into the mature mRNA isoform
What does alternative splicing give rise to?
2 different proteins which are identical at end terminal regions but differ in small domain in centre
What are pseudogenes?
Nonfunctional segments of DNA that resemble functional genes
How do psuedogenes come about?
Unnecessary copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript
What are processed genes?
Intronless copies of other genes, usually remote from the parent gene.
How do processed genes come about?
Copies of messenger RNAs have been reverse transcribed into DNA and inserted into the genome
What is reverse transcription and where is it commonly seen?
Te reverse process of the normal transcription in which the RNA template is copied to form a cDNA molecule in retroviruses (e.g. HIV)
Are processed genes functional or non-functional?
Mostly non-functional
What is satellite DNA?
Large blocks found at centromeres consisting of heterochromatic chromosomal regions –> simple tandemly repeated sequences
What is genetic polymorphism?
- The inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater.
- Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
What type of DNA is alphoid DNA?
- A type of satellite DNA found at centromeres
- 171-bp repeat unit
What is alphoid DNA required for biologically?
The assembly of the centromere
What is FISH?
- A molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with a high degree of sequence complementarity
- Detects and localises the presence or absence of specific DNA sequences on chromosomes
- FISH can also be used to detect and localise specific RNA targets (mRNA, lncRNA and miRNA) in cells, circulating tumor cells, and tissue samples
Why is FISH able to be used with alphoid DNA?
Repeat unit sequence shows chromosome specific sequence variation
How does FISH work?
The first step is to prepare short sequences of single-stranded DNA that match a portion of the gene the researcher is looking for. These are called probes. The next step is to label these probes by attaching one of a number of colors of fluorescent dye.DNA is composed of two strands of complementary molecules that bind to each other like chemical magnets. Since the researchers’ probes are single-stranded, they are able to bind to the complementary strand of DNA, wherever it may reside on a person’s chromosomes. When a probe binds to a chromosome, its fluorescent tag provides a way for researchers to see its location.
How are alphoid probes generated?
Generated from repetitive sequences found in the middle of each chromosome
How does the dispersion of interspersed repeats differ from satellite DNA?
Scattered around the genome, not in large blocks
What is the most widespread of the interspersed repeats?
Alu repeat which is a member of SINE family (short interspersed nuclear element)
How much of your genome is composed of Alu repeats?
5%
What is retrotransposition?
Insertion of DNA sequences mediated by an RNA intermediate
How are Alu repeats dispersed?
By retrotransposition
What is the difference between repetitive and single-copy DNA?
Single-copy: a unique sequence that code for proteins and undergoes transcription.
Repetitive: the sequence that has repeated sequences of nucleotides in the DNA and that don’t code for proteins.
Where is single-copy DNA found?
In exons or euchromatin
Where is repetitive DNA found?
In introns or the heterochromatin
What is the difference between satellite and interspersed DNA?
Interspersed nuclear fragments, including MIRs and LINEs, are distributed throughout the genome, whereas satellite sequences are clustered in discrete areas (e.g. centromeres)
What is alternative splicing? What is its function?
Alternative splicing is a process that enables mRNA to direct synthesis of different protein variants that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exons that are joined by splicing to alter the mRNA coding sequence.
What is alphoid DNA and where is it found?
A complex family of repetitive DNA sequences found in the centromeric heterochromatin of human chromosomes.
Alphoid vs Alu?
Alu - interspersed
Alphoid - satellite
What are retrotransposons?
Retrotransposons copy and paste themselves into different genomic locations by converting RNA back into DNA through the process reverse transcription
