Lectures 11-20 Flashcards
What makes the ribose groups of DNA and RNA different?
RNA has an -OH group at ribose C2 (making is less stable as it can be attacked by water)
What are spliced out?
introns
What are repeat elements used for?
Detecting polymorphisms
What are the building blocks for DNA synthesis?
Deoxynucleoside triphosphates
How many Pi groups are released when a phosphodiester bond is formed?
2
What is required for DNA Polymerase to work?
RNA primer (added via primase), which is later removed
How does a phosphodiester bond form?
Why is this significant?
The 3’ OH group on the RNA primer attacks the phosphate, releasing 2 Pi groups
This is why DNA replication is 5’ to 3’
What happens when there is a problem in DNA replication?
DNA polymerase goes back and checks the base, and may excise it
What are the two strands in the replication fork?
The leading and lagging strands
WHat does the lagging strand use to synthesise DNA in the correct direction?
RNA primers.
DNA Polym. 1 replaces DNA Polym 3. and forms a DNA strand from the RNA primer,.
DNA ligase forms a phosphodiester bond between the sections
How is DNA spliced?
RNA containts all the machinery on it, including a spliceosome, allowin splicing to occur contrascriptionally
What would you find in RIbosome small subunits?
A sites (binding site for aminoacyl tRNA) P sites (binding site for peptidyl tRNA)
What codes for stop?
UAA
UAG
UGA
What does AUG code for?
Methionine (START)
How many genes do mitochondria have?
37
Name one property of the transcriptome and proteom
They’re dynamic
What are VNTR’s
Variable number tandem repeats, blockes of repeated sequences
What kinds of satellite DNA are there?
Micro (smaller, 2-6 bases) and mini (10-60 bases)
What is a telomere?
allow replication to tips of chromosomes, and protect chromosomes from fusing to one-another
What are centromeres for?
segregation in cell division
What are the two types of chromatin?
Euchromatin is uncoiled, where heterochromatin in densely packed
What are spindles?
focuses of microtubules (tw o per cell)
What are the different forms of microtubules?
interpolar microtubules elongate and repel spindles
Kinetochore microtubules are attached to the kinetochore
Aster fibres
What splits cells in cytokinesis?
a contractile ring of actin and myosin filaments
Give two reasons as to why meiosis is necessary
reduction division
re-assortment of genes
What kinds of non-harmful polymorphisms are there?
variant is in non-functional DNA, in gene but doesn’t change amino acid, or amino acid change doesn’t change protein function
How can large blocks of DNA be examined?
Microarray analysis or flourescence in situ hybridisation
How can chromosomes be examined?
light microscopy
Why would we sequence DNA?
the location and type of mutation can be found
What advancement has allowed the automation of sequencing?
the use of flourescently labelled ddNTP terminators (fluoroscopes can differ in colour for each base)
When do mutations normally occur?
Cell divison
From intrinsic and extrinsic attacks on DNA
What is the most common mutation?
C to T at CpG
C can methylate and deaminate to thymine
What is the most common effect pf C->T mutations?
CGA->TGA
arginine->STOP
Give 3 extracellular agents causing mutations
UV
chemicals
Ionizing radiation
How would UV light cause DNA damage?
cross-linking of adjacent thymines to from a stable dimer, stalling DNA replication
How would environmental chemicals damage DNA?
interpolate into DNA
cause DNA breaks
chromosome aneuploidy
What would you call a mutation present in an egg or sperm?
What would it be othersie
Germline, they would otherwise be somatic
What happens when the DNA mismatch repair gene is mutated?
leads to the accumulation of somatic mutations, leading to cancers
Ideally, how would DNA double strand breaks be repaires?
The sequence from the other homologous chromosome of the pair would be used to synthesise the missing DNA
What is a missense mutation?
A single nucleotide polymorphism which alters the amino acid being coded for
What are nonsense mutations?
change from an amino acid codon to a stop codon, forminga truncated protein
What effect might silent mutations have on splicing?
They may create a cryptic splice site, where a sit that isn’t normally spliced may interact with the spliceosome.
What measures does the cell have to limit damage done via nonsense mutations?
nonsense mediated decay processes
What are frameshift mutations?
insertion or deletion of base pairs producing a stop codon downstream
what happens when short tandem repeats mispair?
they cause pathogenic deletions and insertions which cause a frameshift
How would you prepare a karyotype from peripheral lymphocytes?
collect venous blood, remove RBC’s, add a culture medium to WBC’s and incubate for 3 days at 37 degrees.
Add colchine and remove the WBC;s, then add a hypotonic saline.
Fix the cells and spread over a slide, to be stained and photgraphed
What are the different arms of chromosomes called?
p - short (petit)
q - long
What are light bands in chromosomes?
less condensed chromatin, replicating early on in S phase (GC rich)
What are the dark bands in chromosomes?
condensed chromatin, replicating late and AT rich
What is the significance of DNA being linear?
Chromosomal anomalies can cause multi-organ problems
Alleles closer together are more likely to be inherited together
What is Array CGH used for?
Array Comparative Genomic Hybridisation - DNA competes for the same probe sites on the microarray, allowing us to look at the whole genome body in greater detail than down the microscope in FISH.
How does Array CGH work?
The patient and reference DNA compete for the same probe sites on the microarray.
If they are in equal amounts, they hybridise equally
What are the types o numerical chromosomal anomalies?
Aneuploidy - monosomy and trisomy
Polyploidy - triploidy
What is the relative severity of anomolies to sex chromosomes?
not too bad tbh
What is a karyotype?
the international representation of genotypes
What is the karyotype of Down Syndrome?
What are thought to be its’ main genetic bases?
47 XX+21
3 copies of 21 ‘Gene dosage effect’
‘amplified developmental instability’
Extra copy of chromosome 21 because of Robertsonian translocation
Mosaicism with normal and trisomy 21 cell lines
What is the karyotype of Edwards syndrome?
47 XX +18
What is the karyotype of Patau Syndrome?
What are the effects of this?
47 XX +13
Affects midline structures particularly incomplete lobation of the brain
What are some sex chromosome anomalies?
Turner syndrome
Klinefelter syndrome
What is the karyotype of Turner syndrome?
45 X
What is the karyotype of Klinefelter syndrome?
47 XXY
results in poorly developed sexual characteristics, but has no effect on learning
From where would errors leading to aneuploidy be inherited?
Most likely the maternal side
BUT NOT 46 XYY, which is lways inherited parentally
Why do trisomies appear to be associated with an increase in maternal age?
lengthly interval between onset and completion of meiosis
Accumulating effects on the oocyte during this phase may damage the cell’s spindle
Wear and tear makes non-disjunction more likely
Name 4 endogenous mechanisms causing DNA damage
depurination
Deamination
reactive oxygen
methylation of cytosines
How does depurination work?
spontaneous fission of link between purine base and sugar, causing the loss of adenine or guanine from helix (deletion of base in new strand)
How does deamination work?
cytosine deaminates to uracil, causing the substitution of A in the new strand
How would oxygen damage DNA?
attacks rings
what is the most common mutation mechanism?
deamination;
C to T at CpG dinucleotide
