GENOMICS REVISION PART 1

Question 1

• Describe the structure of chromosomes, explaining the main function of centromeres and telomeres;

Answer 1

Chromosomes are the structures formed by the packaging and compaction of DNA wrapped around octamers of small proteins called histones - this combination of DNA and histone proteins is called chromatin. Chromosomes have key structural regions; the centromere in the middle (or approximately so); and the telomeres at each end.

Telomeres protect the chromosome from degradation, is highly repetative.

• Telomerase repairs telomeres but it is only active in certain cell types
• If telemorase is switched on in the wrong cells this can lead to cancer

Whilst centromeres are important for keeping sister chromatids together (after replication has occurred in S phase of the cell cycle) and for attaching to microtubules during cell division.

• Rich in heterochromatin
• Normally highly reptative.

Question 2

What are the 4 different types of chromosomes based on the position of their centromere and the length of their p arms?

not in order:

• telocentric
• submetacentric
• acrocentric
• metacentric

Answer 2

firstly the p arm is the short arm (petite) and the Q arm is the long arm.

metacentric -centromere in middle

submetacentric- centromere slightly above the middle (what you normally see how chromosomes look like)

acrocentric- centromere very high up so has a very short p arm

telocentric- centromere connect the two chromosomes at the top. no p arm only q. not in humans though.

Question 3

• Define the genome, the exome and the epigenome;

Answer 3

genome:

Question 4

• Define the genome, the exome and the epigenome;

Answer 4

genome: -An organisms complete set of DNA
exome: The exome is the part of the genome composed of exons, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing and contribute to the final protein product encoded by that gene.
epigenome: An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism’s offspring via transgenerational stranded epigenetic inheritance.

Question 5

which end is the promoter region on on DNA

Answer 5

5’

Question 6

What is the difference between the nuclear and mitochondrial DNA?

Answer 6

Technically all the DNA in a cell is nuclear + mitochondrial DNA
Nuclear DNA has 22 pairs of autosomes and 1 pair of sex chromosomes whereas mitochondrial DNA is much less and is inherited from the mother only.

Question 7

Explain purines and pyrimidines when it comes to DNA bases

Answer 7

The purines in DNA are adenine and guanine, the same as in RNA. The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil. Purines are larger than pyrimidines because they have a two-ring structure while pyrimidines only have a single ring.

Question 8

Explain gene expression

Answer 8

• Every cell has the whole of the genome HOWEVER only some genes in a genome are expressed in particular cells which explains why different cells differentiate differently.
• Controlled by DNA sequence and epigenome.

Question 9

What are the 3 key features used to identify chromosomes?

Answer 9

1. Size
2. Banding pattern
3. Centromere position

Question 10

in the nucleotides g-c and a-t connection which has 3 bonds and which has 2

Answer 10

g-c is lit so has 3

a-t 2

Question 11

What is the process of transcription?

Answer 11

-Transcription is the process of making RNA from a DNA -involves DNA, transcription factors (TFIID, TFIIA,TFIIB), RNA polymerase and ATP.

The DNA separates and the strand is transcribed in 5’ to 3’ direction. The strand being trascribed starts with a TATA box.

• Transcription factors are needed for successful transcription. TFIID is the largest TF. One of its parts called TBP binds to the DNA using the TATA box to position TPIID near the transcription site.
• Other transcription factors (TFIIA + TFIIB) then attach. These complexes prepare DNA for the successful binding of RNA polymerase.
• Once RNA Polymerase is bound other TF’s complete the mature transcription complex.
• Now ATP must be added so transcription can begin & ATP reduced to ADP and Pi.
• Most TF’s are released after transcription begins. When the end of transcription unit is reached RNA polymerase dissociates and the newly formed strand of RNA is released.

Question 12

What are the three steps involved in post transcriptional modification and their functions?

Answer 12

Methylation - Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA

• The methylated cap provides protection against degradation by exonucleases
• It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)

Polyadenylation - Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript
The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus

Splicing - Within eukaryotic genes are non-coding sequences called introns, which must be removed prior to forming mature mRNA
The coding regions are called exons and these are fused together when introns are removed to form a continuous sequence
Introns are intruding sequences whereas exons are expressing sequences
The process by which introns are removed is called splicing

Question 13

What happens in the process of mRNA Splicing? Read question from mind map MRNA Splicing part.

Answer 13

Key points

• Intron structure: GU (at the beginning of intron), The A branch site, A Pyr-rich region, the 3’ AG (at the end)
• GU + AG sequence define beginning and end of sequence.
• Splicing regulated by spliceosome

Question 14

What is the process of translation?

Answer 14

• Translation is the synthesis of protein from an RNA template with the key factors being mRNA, ribosome (small + large subunit), tRNA and release factor.
• Initiation: initiation begins when the small subunit of the ribosome attaches to the methylated cap at the 5’ end and moves to the translation initiation site.
• tRNA contain anti-codons which is complementary to the codon to which it binds. The first mRNA codon is typically AUG which binds to UAC
• Attached to the end of the tRNA is the corresponding amino acid, methionine (met) which corresponds to the AUG codon.
• The large subunit of the ribosome now binds to create the P site and A site.
• Elongation: the first tRNA occupies the P (peptidyl) site the second tRNA occupies the A site (Aminoacyl) and is complementary to the 2nd mRNA codon. (Initiation start at the P site but in elongation it starts at the A suite)
• The methionine is then transferred to the A site amino acid. The first tRNA exits, the ribosome moves along the mRNA unto the new tRNA each time- these are basic steps of the elongation.
• Termination: As elongation continues the growing peptide is continually transferred into the A site tRNA.
• The ribosome moves across the mRNA and new tRNA’s enter. When a stop codon is encountered at the A site a release factor enters the A site and translation is terminated
• When termination is reached the ribosome dissociates and the newly formed protein is reached.

Question 15

What is the central dogma?

Answer 15

The central dogma is the idea that DNA to RNA to protein only happens in that direction and not the other way around.

Question 16

What is the difference between the sense and anti-sense strand of DNA?

Answer 16

• The sense strand has the same sequence as the mRNA molecule
• The anti-sense strand is used as a template to generate this identical mRNA strand except T is replace with U

Question 17

What is the triplet code and what is meant by degeneracy?

Answer 17

• The triplet code is that RNA is read in groups of 3 bases called codons
• There are 64 possible combinations of 3 bases but only 20 amino acids this is because of degeneracy
• It is degenerate because more than 1 codon can code for the same amino acid.

Question 18

what with UAC translate to and what is special about this codon

Answer 18

AUG this is the start codon

Question 19

The same nucleotide sequence can be used differently explain how the sequence of nucleotides is an open reading frame.

Answer 19

• This is because when reading mRNA there are 3 bases that you can start from which will each code for a completely different sequence of codons.
• It is only the first 3 bases because when you get to the 4th base you will get the same sequence as the first base (just missing the first amino acid)

Question 20

When and where does translation and transcription occur?

Answer 20

When and where does translation and transcription occur?

• Transcription and RNA editing occurs in the nucleus and translation in the cytoplasm
• This takes place during interphase in the cell cycle- so basically everything apart from mitosis and cytokinesis

Question 21

What is not translated from the mRNA?

Answer 21

• The methylates cap, the UTR’s, Poly A tail

- Basically, only the RNA from the coding exons

Question 22

• Compare and contrast DNA and RNA

Answer 22

RNA is single-stranded while DNA is double-stranded.
RNA contains uracil while DNA contains thymine.
RNA has the sugar ribose while DNA has the sugar deoxyribose.

Question 23

Summarise the cell cycle.

Answer 23

Interphase
G1 – First intermediate gap stage in which the cell grows and prepares for DNA replication
 S – Synthesis stage in which DNA is replicated
 G2 – Second intermediate gap stage in which the cell finishes growing and prepares for cell division

M phase
The period of the cell cycle in which the cell and contents divide to create two genetically identical daughter cells
This phase is comprised of two distinct stages:
 Mitosis – Nuclear division, whereby DNA (as condensed chromosomes) is separated into two identical nuclei
 Cytokinesis – Cytoplasmic division, whereby cellular contents are segregated and the cell splits into two

Question 24

What is the process of DNA replication?

Answer 24

• Helicase unzips DNA to make a replication fork so both strands now form a template
• Primase starts the process by putting down a primer
• DNA polymerase adds bases but can only go in a 5’ to 3’ direction
• The leading strand is made continuously but this can’t happen in the lagging strand so only small Ozark fragments can be made.
• Each fragment is started with an RNA primer.
• The enzyme exonuclease removes all RNA primers from both strands of DNA and DNA polymerase fills in the gap.
• Finally, DNA ligase seals the fragments.

Question 25

What is the process of DNA replication?

Answer 25

- Helicase unzips DNA to make a replication fork so both strands now form a template - Primase starts the process by putting down a primer - DNA polymerase adds bases but can only go in a 5’ to 3’ direction - The leading strand is made continuously but this can’t happen in the lagging strand so only small Ozark fragments can be made. - Each fragment is started with an RNA primer. - The enzyme exonuclease removes all RNA primers from both strands of DNA and DNA polymerase fills in the gap. - Finally, DNA ligase seals the fragments.

Question 26

there are two main types of variants/mutations which are single base substitutions or indels. in terms of base substitutions what is the diffenrce between synonymus, missense and nonsense variants/substitutions? (insertions and deletions) – less than 1kb

Answer 26

synonymus- silent mutation where nucleotide changes but no AA change. Missense- -When amino acid sequence is affected as incorrect amino acid produced -Can be pathogenic or the protein can still function normally even if the sequence changes nonsense- - Change in amino acid sequence to produce a stop codon hence causing a premature termination of a protein.

Question 27

In InDels variants what is the difference between a In-frame and a frameshift?

Answer 27

- This relates to the open reading frame. - In-frame insertions/deletions are in multiples of three - Whereas as frameshifts are not in multiples of three

Question 28

What are the different types of functional effects of variants?

Answer 28

- Loss of function - - Reduced activity/decrease stability = hypomorph - Complete loss of gene product = null allele/amorph - Gain of function - Increased levels of gene expression - New function for protein product - Dominant negative - Mutant allele produces gene product that interferes with correct role

Question 29

Give an example of the dominant and recessive loss of function?

Answer 29

Give an example of the dominant and recessive loss of function? Loss of function recessive  Classic examples are sickle cell anaemia, phenylketonuria, cystic fibrosis, Gaucher’s disease, haemochromatosis…..  One healthy copy of gene is sufficient to produce enough protein for individual to be healthy (or at least sub-clinical)  Recessive diseases Loss of function dominant  Haploinsufficiency • When loss of one allele is sufficient to cause problem • Gene dosage • Full amount of protein product is required • Example MonoMac syndrome (lack of GATA2 leads to monocyte and B cell deficiencies), CHARGE syndrome, Dravet syndrome, Marfan syndrome, Ehlers-Danlos syndrome….

Question 30

What is the difference between germline and somatic?

Answer 30

 Germline affects the gametes therefore can be inherited and passed down through the generations  Somatic – only affects non-germline cells therefore cannot be passed down "Somatic cells" is a fairly general term which refers to essentially all the cells of the body except for the germ line; the germ line being the cells in the sexual organs that produce sperm and eggs.

Question 31

Rank the following different mutation types in order of how likely they are to cause human disease from 1: most likely to 4: least likely Synonymous mutation, Nonsense mutation, Missense mutation, Deep intronic mutation

Answer 31

1 Nonsense mutation 2 Missense mutation 3 Synonymous mutation 4 Deep intronic mutation 4: Mutations in these sequences may lead to retention of large segments of intronic DNA by the mRNA, or to entire exons being spliced out of the mRNA. very difficult to predict.

Question 32

Briefly what is the difference between mitosis and meiosis?

Answer 32

- Mitosis is the cell division where somatic/ autosomal cells are produced. 2 identical cells produced - Meiosis is the cell division process where gametes are produced. 4 non-identical cells produced They are both proceeded by interphase where DNA replication takes place.

Question 33

Explain the process of mitosis

Answer 33

Prophase:  DNA supercoils and chromosomes condense (becoming visible under microscope)  Chromosomes are comprised of genetically identical sister chromatids (joined at a centromere)  Paired centrosomes move to the opposite poles of the cell and form microtubule spindle fibres  The nuclear membrane breaks down and the nucleus dissolves Metaphase:  Microtubule spindle fibres from both centrosomes connect to the centromere of each chromosome  Microtubule depolymerisation causes spindle fibres to shorten in length and contract  This causes chromosomes to align along the centre of the cell (equatorial plane or metaphase plate) Anaphase:  Continued contraction of the spindle fibres causes genetically identical sister chromatids to separate  Once the chromatids separate, they are each considered an individual chromosome in their own right  The genetically identical chromosomes move to the opposite poles of the cell Telophase:  Once the two chromosome sets arrive at the poles, spindle fibres dissolve  Chromosomes decondense (no longer visible under light microscope)  Nuclear membranes reform around each chromosome set  Cytokinesis occurs concurrently, splitting the cell into two

Question 34

Explain the process of meiosis

Answer 34

Meiosis I The first meiotic division is a reduction division (diploid → haploid) in which homologous chromosomes are separated  P-I: Chromosomes condense, nuclear membrane dissolves, homologous chromosomes form bivalents, crossing over occurs  M-I: Spindle fibres from opposing centrosomes connect to bivalents (at centromeres) and align them along the middle of the cell  A-I: Spindle fibres contract and split the bivalent, homologous chromosomes move to opposite poles of the cell  T-I: Chromosomes decondense, nuclear membrane may reform, cell divides (cytokinesis) to form two haploid daughter cells Meiosis II The second division separates sister chromatids (these chromatids may not be identical due to crossing over in prophase I)  P-II: Chromosomes condense, nuclear membrane dissolves, centrosomes move to opposite poles (perpendicular to before)  M-II: Spindle fibres from opposing centrosomes attach to chromosomes (at centromere) and align them along the cell equator  A-II: Spindle fibres contract and separate the sister chromatids, chromatids (now called chromosomes) move to opposite poles  T-II: Chromosomes decondense, nuclear membrane reforms, cells divide (cytokinesis) to form four haploid daughter cells Anaphase II, In anaphase I, the homologous pair of chromosomes are pulled apart from one another but it is in anaphase II that the sister chromatids of each chromosome are pulled apart allowing the final gametes to be haploid.

Question 35

What is the difference between haploid, diploid, polyploid and aneuploid?

Answer 35

Haploid- one set of chromosomes (n=23 as a normal gamete) Diploid- Cell contains 2 sets of chromosomes (2n= 46 normal in somatic/autosomal cells) Polypoid- a multiple of a haploid number (e.g. 4n=92) – not compatible with life Aneuploid: chromosome number which is not an exact multiple of haploid number due to extra or missing chromosomes (e.g 2n+1=47) can be trisomy or monosomy and is caused by non-dysjunction

Question 36

What leads to genetic variation?

Answer 36

Independent assortment and crossing over

Question 37

What are some examples of autosomal aneuplodies?

Answer 37

Trisomy 23- downs Trisomy 18 - Edwards Trisomy- 23 – Patau (mediun survival time 7-10 days))

Question 38

What are some examples of sex chromosome aneuplodies?

Answer 38

Turners syndrome (45,X missing an X) only affects females Tripple X syndrome (47, XXX) 1 IN 1000 female births Klinefelter’s (47 XXY) 1 IN 100 male births

Question 39

Explain mosaicism and the two different types relate this to when non-disjunction happens?

Answer 39

Mosaicism describes the occurrence of cells that differ in their genetic component from other cells of the body. ... Mosaicism can be germline (affecting only egg or sperm cells), somatic (affecting cells other than egg or sperm cells), or a combination of both. If non- disjunction occurs in meiosis then it affects the zygote but if it occurs in mitosis then this is post- zygotic and will only affect some of the cells whereas zygomatic non-disjunction affects every cell. Mosaicism can also happen when the body realises the trisomy for example and then tries to fix it or when non-disjunction starts normally but then becomes faulty down the line. This explains why something like downs syndrome is more severe is some people as they may have mosic of the chromosome of fully.

Question 40

How many and what type of daughter cells does meiosis produce? * 4 haploid * 4 diploid * 2 diploid * 2 haploid

Answer 40

A-4 haploid

Question 41

What structure is most important in forming the tetrads (bivalent)? * synaptonemal complex * kinetochore * chiasma * centromere

Answer 41

A- synaptonemal complex not chiasma as A chiasma is the point of contact between a homologous pair of chromosomes at which recombination (crossing over) occurs.

Question 42

At which stage of meiosis are sister chromatids separated from each other? * prophase II * anaphase I * anaphase II * prophase I

Answer 42

answer- Anaphase II, In anaphase I, the homologous pair of chromosomes are pulled apart from one another but it is in anaphase II that the sister chromatids of each chromosome are pulled apart allowing the final gametes to be haploid.

Question 43

Which part of meiosis is similar to mitosis? * anaphase I * metaphase I * meiosis I * meiosis II

Answer 43

• meiosis II Answer- meiosis II remember meiosis II as a whole is very similar to mitosis as this is when sister chromatids of each chromosome are being pulled apart

Question 44

If a muscle cell of a typical organism has 32 chromosomes, how many chromosomes will be in a gamete of that same organism? * 32 * 16 * 64 * 8

Answer 44

A-16

Question 45

In a comparison of the stages of meiosis to the stages of mitosis, which stages are unique to meiosis and which stages have the same events in both meiosis and mitosis?

Answer 45

All of the stages of meiosis I, except possibly telophase I, are unique because homologous chromosomes are separated, not sister chromatids. In some species, the chromosomes do not decondense and the nuclear envelopes do not form in telophase I. All of the stages of meiosis II have the same events as the stages of mitosis, with the possible exception of prophase II. In some species, the chromosomes are still condensed and there is no nuclear envelope. Other than this, all processes are the same.

Question 46

# fill in the gaps Random alignment of chromosomes leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-producing individual came equally from the …………………………… and the ………………………….. . In ……………………… , the duplicated copies of these maternal and paternal ……………….. chromosomes line up across the centre of the cell. The orientation of each tetrad or ………………………….. is random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the ……………………… are pulled apart in ……………………….. , any combination of maternal and paternal chromosomes will move toward each pole. The …………………………….. formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents.

Answer 46

1 and 2: mother father egg sperm 3 metaphase 1 4 homologus 5 bivalent 6 chromosomes, homologus chromosomes 7 anaphase 1 8 gamete

Question 47

What is translocation?

Answer 47

A chromosome abnormality where there is an exchange of 2 segments between non-homologous chromosomes (not the same)

Question 48

What is reciprocal translocation?

Answer 48

Reciprocal translocation happens due to non-homologous end joining going wrong. NHEJ normally repairs breaks in chromosomes but sometimes it can switch the chromosomes and instead of attaching a to a and b to b it attaches a to b and b to a. This causes a derivative to be formed. This doesn’t necessarily cause a problem because you still have the right quantity of chromosomes just in the wrong places. The consequences of this happens when a person gives birth as become chromosomes are in the wrong place when the derivative meets with the normal chromosome of the mother/father DNA the chromosomes are either going to be trisomic or monosomic which is either not compatible with life leading to miscarriage or will leave to a child with learning disabilities.

Question 49

What is Robertsonian translocation?

Answer 49

Robertsonian translocations only happens with the acrocentric chromosomes (the ones with the really small p arm). It happens when the p arms of two chromosomes break off and two q arms join together. NOTE= a balanced carrier will have 45 chromosomes. This is because the other pair of the acrocentric chromosome has the same chromosomes so all of the chromosomes are still present. In fact, if 46 chromosomes are present including the Robertsonian derivative then it must be unbalanced.

Question 50

What is the difference between reciprocal and Robertsonian translocation in terms of the number for a balanced carrier and what would show up on a karyotype?

Answer 50

In reciprocal translocation a balance carrier will have 46 whereas In Robertsonian translocation a balanced carrier will have 45 Trisomy 21 due to reciprocal translocation and Robertsonian translocation would clinically present the same but different on a karyotype. When the cause in NHEJ there would be 3 chromosomes for 21 but for RT there would be 2 chromosome 21s but then elsewhere e.g at chromosome 14 attached would be the q arm of 21 (remember 13, 14, 15, 21, and 22 are acrocentric).

Question 51

Explain how unequal crossing over can result in deletions and duplications;

Answer 51

When the chromosomes do not line up/ align together properly during crossing over this can lead to deletions and dupplications

Question 52

Explain briefly how structural abnormalities may be detected using stained metaphase chromosomes, FISH and array-CGH.

Answer 52

Chromosome staining/ stained metaphase chromosomes- uses Giemsa banding (G-banding), the banding comes from euchromatin (GC rich, loosely packed, genes active) vs heterochromatin (AT rich, tightly packed, genes inactive). Takes a few days as has to be done in metaphase. Can’t see microdeletions looks for aneuploidies, translocation and very large deletions. FISH- florescent in situ hybridisation. A florescent probe which is a single stranded DNA binds to the SPECIFIC part of the genome you’re after and lights it up. Again takes a few days as has to be done in metaphase. Can’t see microdeletions looks for aneuploidies, translocation and very large deletions. Array CGH- patient DNA labelled green and control DNA red they are then compared to detect for abnormalities. Uses extracted DNA looks for microdeletions and microduplications.