Topic 4 - Understanding Genomes

Question 1

What main types of error can occur during DNA replication and which repair systems deal with the resulting damage?

Answer 1

Nucleotide mis-incorporation and replication slippage can occur during replication. Both are reduced by the proofreading activity of DNA polymerase, and those errors that are detected by the mismatch repair (MMR) proteins or by systems to detect and repair chemical damage (e.g. deamination of cytosine), are corrected by base-excision repair (BER), nucleotide excision repair (NER) or MMR proteins.

Question 2

What DNA sequence changes in or around a gene might affect the processes involved in the expression of that gene?

Answer 2

Alterations to the sequence of gene regulatory elements, such as those found in a gene’s promoter and enhancer regions.

Question 3

How would alterations to the sequence of gene regulatory elements, such as those found in a gene’s promoter and enhancer regions, have an impact upon the amount of the mRNA and/or the encoded protein?

Answer 3

Alterations to promoters and enhancers can influence binding of RNA polymerase or transcription factors.

Alterations to the conserved sequences at splice sites can affect patterns of splicing.

Alterations to other signals can affect polyadenylation and mRNA stability.

Question 4

How many chromosomes does each of the parents of a mule (which has 63 chromosomes) have?

Answer 4

A horse has 64 chromosomes while a donkey has 62.

Question 5

What is the dramatic phenotypic consequence of the change in chromosome number in the mule or hinny compared to those of the horse and donkey parents?

Answer 5

The mule or hinny offspring of a horse and donkey are infertile.

Question 6

What is the C-value in genomics?

Answer 6

An estimate of the size of a haploid genome, usually in units of mass. The C-value-paradox is a phrase used to describe the fact that the C value is unrelated to the apparent complexity of the organism bearing the genome.

Question 7

What is flow cytometry?

Answer 7

A technique where cells are separated from each other in a fast moving stream of liquid. The separation is often based upon fluorescence, either to total nucleic acid content, or linked to the detection of a particular antigen. The technique is commonly encountered as fluorescent automated cell sorting (FACS).

Question 8

What term describes the number of copies of a genome present within a cell?

Answer 8

Ploidy.

Question 9

What is a centromere?

Answer 9

The region in eukaryote chromosomes where daughter chromatids are joined together. The centromere is also the position on a chromosome where the spindles attach during mitosis.

Question 10

What are telomeres?

Answer 10

Regions at the ends of eukaryote chromosomes. They consist of non-coding nucleotide repeats, and their presence avoids the loss of coding regions during DNA replication (the 3′ end of each strand cannot be replicated to its end). Erosion triggers local synthesis of long non-coding RNAs that recruit addition of new repeats through the action of a telomerase enzyme.

Question 11

What are transfer RNAs (tRNAs)?

Answer 11

Small RNA molecules that carry a three base anti-codon that pairs with the codon within the ribosome during protein synthesis. Each tRNA is covalently linked (‘charged’) with an amino acids corresponding to the codon/anti-codon base sequence.

Question 12

What are ribosomal RNAs (rRNAs)?

Answer 12

A family of RNA molecules that form the major component of the ribosome, the site of tRNA delivery of amino acids to the growing protein chain that is assembled on the mRNA. Ribosomal RNAs are identified by their size as estimated by centrifugation (in S, or Svedberg units). In eukaryotes the 28S, 5S and 5.8S rRNAs are found in the large (80S) unit and the 18S rRNA in the small (40S) unit. In eubacteria and Archaea, the large ribosomal unit (70S) contains of 23S and 5S rRNAs, and the smaller 30S unit contains the 16S rRNA. rRNAs are universal and their base-sequence is frequently used for bar-coding for molecular phylogeny.

Question 13

What is Giemsa?

Answer 13

A chemical commonly used to differentially stain metaphase chromosomes in order to identify them from their banding patterns. The dark staining regions generated on a chromosome are called G-bands.

Question 14

What is a karyotype?

Answer 14

The complement of chromosomes in a eukaryote cell that is visualised using cytogenetic techniques.

Question 15

What is an ideogram?

Answer 15

A pictorial or schematic representation of an organism’s karyotype, usually showing the G banding pattern for identification.

Question 16

What is polyploidy?

Answer 16

Polyploidy is a state where cells/organisms inherit more than one set of diploid chromosomes. In some cases, and in particular in groups such as plants, polyploidy is the normal, stable, genetic state.

Question 17

What is non-disjunction?

Answer 17

When chromosomes fail to separate to poles of a cell during the reduction phase of mitosis or meiosis. The result is an uneven distribution of chromosomes between daughter cells or gametes.

Question 18

What is a dideoxy nucleotide (ddNTP)?

Answer 18

A form of nucleotide without a hydroxyl group on the 3’ C atom of the ribose sugar that terminates DNA synthesis. Dideoxy forms of nucleotides are used in a DNA sequencing method involving the production of polynucleotide chains that terminate at specific nucleotide positions due to the incorporation of a dideoxynucleotide.

Question 19

What is the template base sequence for a stretch of DNA with a base sequence of 5′ CCTCTT? Give your answer in the 5′ to 3′ direction.

Answer 19

5′ AAGAGG.

Question 20

What is parallel sequencing?

Answer 20

The technique of carrying out many different sequencing reactions simultaneously; for example, on beads or in wells on a glass slide. Parallel sequencing allows large amounts of sequence data to be collected from a complex template DNA.

Question 21

What roles do paired primers play in PCR?

Answer 21

The forward and reverse primers ensure that synthesis occurs in two directions, i.e. along both of the denatured DNA strands. This ensures that the primer binding site for each primer is regenerated, allowing exponential amplification.

Question 22

What is a reference sequence?

Answer 22

The base sequence that is accepted as the standard sequence for a particular species, against which all others are compared. Reference sequences are often annotated to indicate all base variants found in individual members of that species.

Question 23

Why are sequences of repetitive DNA regions impossible to localise to a specific location in a genome?

Answer 23

Short sequences obtained from repetitive regions of a genome will not contain sufficient unique (non-repetitive) stretches of sequence to categorically assign them to one region.

Question 24

What are DNA barcodes?

Answer 24

Codes used for identification of species on the basis of one or a few DNA base sequences, regardless of the phenotypes.

Question 25

Why is it important for a barcode sequence to be more variable between species than within species?

Answer 25

If variation in a particular sequence between individuals of the same species was comparable to that between different species, it would not be possible to distinguish between species on the basis of that variation.

Question 26

Other than DNA, which other nucleic acid is found in cells and what roles does it play?

Answer 26

RNA copies of DNA strands are present in mRNA, and other RNA species perform functions in translation, including tRNAs and rRNAs.

Question 27

What is a transcriptome?

Answer 27

A record of all transcribed RNA molecules found in a cell. Transcriptomes can be obtained by DNA sequencing of the RNAs or through quantitative analysis of genes using hybridisation strategies such as with micro-arrays or gene chips. Transcriptomes often record both which genes are expressed and how much of each of those genes is expressed in a particular cell type.

Question 28

What is meant by ‘metagenomics’?

Answer 28

The study of DNA or RNA sequences obtained from large complex biological samples, such as environmental samples. Species and genes are identified by compared individual sequences with databases containing reference genome sequences. The DNA sequences obtained represent a record of which species are present and how much of each species is present.

Question 29

How could individual species be identified from a mixed sample of genomic DNA sequences?

Answer 29

By comparing each short sequence obtained to all available reference sequences in the various genomic databases.

Question 30

What is a microbiome?

Answer 30

The total genome sequence (as DNA and also RNA sequence) of all micro-organisms in a specific environment or niche.

Question 31

What is a hologenome?

Answer 31

The entire genome material (and its implied biological function) for an organism and its microbiota.

Question 32

What is Paleogenomics?

Answer 32

Paleogenomics is the analysis of samples from extinct or very old biological samples or from bones, etc. In most cases, genomic DNA is chemically broken down during the decay of an organism’s remains, leading to only short segments of the original genomic DNA remaining.

Question 33

What roles do segments of both mitochondrial and chloroplast genomes play in species identification projects?

Answer 33

They can be used for the generation of DNA barcodes for animals (mitochondria) and land plants (chloroplasts and mitochondria).

Question 34

What is the mitochondrial genome (mtDNA)?

Answer 34

The DNA sequence resident in eukaryotic mitochondria (mtDNA) that is inherited separately from the nuclear genome.

Question 35

What is meant by the ‘molecular clock’?

Answer 35

Use of the molecular difference between pairs of taxa as a proxy for estimating the time elapsed since a shared common ancestor, based upon the assumption of more or less constant rates of molecular evolution. Molecular clocks are often time-calibrated using fossils.