Genomemetronomechickenboneashytone ass nigga Flashcards
where are chromosomes located
nucleoplasm
what are the closed and open chromatid regions in interphase chromosomes called
closed - heterochromatin
open - euchromatin
out of euhcromatin and heterochtomatin, which one transcribed and why
euchromatin is typically transcribed because it is relaxed and open
what is the function of chromosomal territories (TAD’s)
topologically associated domains help separate heterochromatic and euchromatic regions
what determines wether a chromatin is open or closed
histone modifications dictate wether the chromatid is a eu/heterochromatid
difference between cis/trans-acting non-coding regions
cis - is not transcribed
trans - are transcribed - RNA
what are the 4 flavours of gene variations
SNP - single nucleotide polymorphisms
IDP - insertion deletion polymorphisms
SSR - simple sequence repeats
CNV - copy number variants
why do CNV class of mutations occur and what are the consenquences
unequal crossing over during mitosis 1
phenotypes can vary tremendously
Mendel’s first postulate
an organism inherits 2 alleles for each gene, one from each parent
Mendel’s second postulate
if the alleles are heterozygous, the dominant allele determines the phenotype
Mendel’s 3rd postulate, 1st law
during gamete formation, the two alleles segregate randomly, one to each pole
if they are homozygous them all the gametes will contain the same allele
if heterozygous, the half of the gametes will contain one and the other half will contain the other allele
what is the genotypic and phenotypic ratio of F2 of parents that are homozygous recessive and the other homozygous dominant
genotypic ratio - 1:2:1
phenotypic ratio - 3:1
Mendel’s 4th postulate, 2nd law
independent assortment - genes on a chromosome assort independently on their gene locus to other genes on different loci
evident in dihybrid inheritance
in dihybrid inheritance with parents with both genes heterozygous (TtRr x TtRr) what is the phenotypic ratio
9:3:3:1
what is reciprocal recessive epistasis, and what is the ratio
in dihybrid inheritance, a dominant allele must be present in both genes for the gene to be expressed
9:7
what is dominant epistasis, and the ratio
one dominant allele on one gene produces the same phenotype regardless of the status of the alleles on the other gene
12:3:1
what are duplicate dominant genes with cumulative effects and the phenotypic ratio
when a single dominant allele on a gene changes supresses a specific phenotype, both alleles on a single gene must be recessive for the gene to be expressed,
when both genes are homozygous recessive, it produces another phenotype
AaBb - 9
Aabb/BBaa - 6
aabb - 1
dominant and recessive, and the ratio
dominant allele from one gene and a recessive allele from the other gene produce the same phenotype
13:3
difference between differentiation and determination
determination - internal mechanisms determine the identity of the cell
differentiation - changes in cell morphology and other characteristics to become specialised
difference between pluri/multipotent cells and totipotent
pluripotent - can become several cells
totipotent - can become all cell types
what is loose binding
the core of RNA polymerase has a specificity for DNA
in bacterial RNA polymerase what is the function of the alpha sub-units
enzyme assembly
promotor recognition
binds to some activators
what is the function of the beta sub-units in bacterial RNA polymerase
they are the catalytic centre of the enzyme
what is the function of the sigma sub-unit in bacterial RNA polymerase
promoter specificity, ensures binding at promoter sequence only
what sub-unit of bacterial RNA polymerase is required for the initiation step
sigma
what part of bacterial RNA polymerase is required for elongation
core enzyme
what is sigma sub-unit 32 induced by
high temperatures
what sigma sub-units are for general use and nitrogen
general - sigma sub-unit 70
nitrogen - sigma sub-unit 54
when a promotor region is poorly recognised by RNA polymerase, what is used to activate it
catabolic activator protein (CAP)
how does glucose affect the lac operon
high glucose leads to low cAMP which leads to low CAP leading to no transcription
vice versa for low glucose levels
out off the following, which is the only one that would lead to an active lac operon low glucose, low lactose high lactose, low glucose high lactose, high glucose high glucose, low lactose
high lactose, low glucose
how does lactose affect the lac operon
high lactose leads to lactose binding to the repressor protein, inactivating it, activating the lac operon
vice versa for low lactose
what is SP1, where is it found and what does it bind to
a transcriptional activator that confer general expression
found in all cell types
binds to GGGCGG
what is MyoD, where is it found and what does it bind to
a transcriptional activator that confers tissue specific expression
muscle-specific
binds to CANNTG
name a transcriptional factor that confers response to specific stimuli
oestrogen
how do histone acetyl transferase allow RNA polymerase to bind to a histone
acetylation of the lysines in the tail of the histone neutralises the charge
leads to a reduced affinity in the tail for DNA
opens up DNA for RNA polymerase to bind
what are the 2 domains of a histone
amino-tail
globular
purpose of histone de-acetylase
removes the acetyl group from the lysines in the tail to restore affinity and close down the DNA
preventing RNA polymerase from binding
what base is usually methylated in DNA
C
what is the gene number and genome size of humans
gene number - 31,000
genome size - 3,200
what is the gene number and the genome size of bacteria
gene number - 4000
genome size - 4
what is gene density
number of genes per genome size(mb)
what are the gene densities of human, mice, fly, yeast
human - 9
mice - 14
fly - 83
yeast - 512
what can causes chromosomal abnormalities
chemicals
radiation
errors in replication
what is monosomy
loss of a single chromosome
what is cri-du-chat syndrome
missing a small part of chromosome 5
1/50,000 infants
severe mental retardation
physical abnormalities
what is trisomy
gain of chromosome to a diploid chromosome
what causes down syndrome and the effects
trisomy at chromosome 21, only trisomy with a longer survival rate
respiratory diseases
heart malformations
15x higher leukemia rate
what are spontaneous causes for mutation
replication errors
deamination
tautomerisation
induced causes of mutation
radiation/UV
base analogues
intercalating agents
what are the chances normal replication will introduce an incorrect base
once every 10 to the power of 10
good chance it gets repaired as well
what are spontaneous structural alterations in DNA bases called
tautomerizations
what does the amino group of A and C tautomerize into
NH, imino group
what does the C=O, keto group of G and T tautomerize into, and what are the effects
C-OH, enol group
enol group binds a G instead of an A
example of an intercalating agent
ethidium bromide
example of a base analogue
bromouracil (T analogue)
what does CFTR (cystic fibrosis transmembrane conductance regulator) encode for
Cl- ion transporter
what does a mutant CFTR cause
doesn’t allow transport of chlorine ions out the cell which causes sticky mucus to build up around the cell
what is the location and name of the amino acid that is deleted that causes cystic fibrosis
deletion of phenylalanine at 508
what causes huntington’s disease
a tri-nucleotide repeat
inheritance of a defective huntingtin gene
what trinucleotide is repeated that causes huntingon’s disease
CAG
what type of genetic disease is huntington’s and cystic fibrosis
huntington’s - dominant autosomal
cystic fibrosis - recessive autosomal
what mutation causes breast cancer
mutation in BRAC1 or 2
where are BRAC1 and 2 located
BRAC2 - chromosome 13
BRAC1 - chromosome 17
what does the lack of factor VIII cause
haemophilia
how can chromosomes be visualised for a light microscope
giemsa stain
definition of epigenetics
processes that induce long term and stable changes in gene activity without a change in gene sequence
what diseases does DNA methylation cause
obesity cancer depression heart disease hypertension anxiety
what % of breast cancer is inherited
5%
what causes sporadic breast cancer
DNA hypermethylation of BRAC1
what is the warburg effect
when cancer cells use glycolysis regardless of oxygen levels
what is aneuploidy
chromosome instability, causes more mutations
difference in growth type between benign and malignant tumours
benign - expansive
malignant - infiltrative
difference in outcomes from spontaneous evolution between benign and malignant tumours
benign - usually favourable outcomes
malignant - always fatal
what do tumours consist of
malignant cells
host cells
secreted factors
extracellular matrix protein
what is the normal and mutated function of proto-oncogenes and their genetic properties
normal - promote cell survival and proliferation
mutated - normal function but amplifies and unregulated
dominant
what is the genetic properties of a tumour suppressant gene
recessive
what is the normal and mutated function of a care taker gene and its genetic properties
normal - repair/prevent DNA damage
mutated - loss of functions allows accumulation of mutations
recessive
why is C-Myc highly regulated
its mRNA is short lived and protein levels are low
where does translocation of c-myc occur and what does it cause
burkitt’s lymphoma
enhanced expression
where is c-myc translocated from and to
from chromosome 8 to chromosome 14, near an antibody gene enhancer
what is HER2
type 1 transmembrane growth factor receptor
what happens upon ligand binding of HER
HER proteins undergo dimerization and transphosphorylation of their intracellular domains
what promotes receptor dimerization and activity in HER
a V664E mutation
what are the 5 classes of tumour suppressant genes
proteins that arrest cell cycle enzymes that check and repair DNA proteins that promote apoptosis checkpoint control proteins receptors/hormones that function to inhibit cell proliferation
where is p53 located
chromosome 17
how does p53 regulate cell division
binds DNA, stimulating p21 which binds to CDK-cyclin complex - inactivating it
what is loss of heterozygosity
when there is an inherited mutation in a tumour suppressant gene but the other copy is normal
loss of the remaining functional allele of that gene is LOH
what does LOH cause
breast cancer
colon cancer
retinoblastoma
what causes retinoblastoma
mutation in the RB gene
function of RB
regulates cell cycle entry
genetic properties of RB
can be hereditary but is recessive
what happens if LOH occurs to an individual with hereditary mutation in their RB gene
they become homozygous for the mutant RB gene and develop a tumour in the retina
what is a direct acting mutagen
chemicals that react with nitrogen and oxygen in DNA to alter base pairing
what is an indirect acting mutagen
has little mutagenic effect until modified by cellular enzymes
where does squamous cell carcinomas arise from and what are the causes and a common element between them
arises from stratified squamous and non-squamous epithelial cells
alcohol, smoking, UV
oxidative stress
what is a retrovirus and an example that causes cancer
RNA viruses that incorporate into the genome of the host
HTLV-1
how is devil facial tumour spread
tumour cells passage between individuals during biting behaviours
what can gene therapy do for cancer treatment
target cancer cells or surrounding cells
what has accelerated cancer gene therapies
CRSPR/Cas9
what is the difference between germ-line and somatic gene therapy in terms of offspring
unlike germ-line therapy, somatic gene therapy doesn’t pass on the permanent changes down to offspring
what are the 2 strategies used to deal with diseases
1 - modify diseased cells to alleviate disease
2 - kill diseased cells
when is gene augmentation implemented to treat disease
when the diseased cell is altered due to a loss of function mutation
when is gene silencing used to treat diseases
when the diseased cell is altered due to a gain of function mutation
how is gene silencing achieved
turning off gene transcription of the harmful gene
what is gene repair
restoring normal gene function or to minimize effect of mutation
how do you directly kill cells
directly targeting the harmful cells with a gene that will kill them - suicide gene
explain indirect cell targeting
enhancing the immune systems response to the harmful gene - initiating cell death
what are the 2 general methods for gene delivery
in-vivo - directly
ex-vivo - cell-based delivery
why do short lived cells pose a challenge to gene therapy
short lived cells need to divide more often, and they may not pass on the desired genetic material leading to:
loss of therapeutic effectiveness
what is a non-viral vehicle for gene delivery
liposomes
what are the viral vehicles for gene therapy
retrovirus
lentivirus
adenovirus
adeno-associated virus
what is needed to achieve high levels of expression
gene needs to be place in a plasmid expression vector
why is the cytomegalovirus (CMV) promotor used in expression vectors
strongest promotor
drives transcription
works in all eukaryotic cells
what is the polyadenylation (A) site for
efficient termination of transcription
what expression vector contains cytomegalovirus promotor
pJ7
what happens when the plasmid enters the nucleus
RNA polymerase binds to cytomegalovirus transcription
the RNA is cleaved and polyadenylated
then its spliced
why is plasmid entry into the nucleus very inefficient
due to the plasmid size it cannot pass through the nuclear pores
what are the methods used to get plasmids to enter the nucleus
- conjugating specific DNA or protein sequences that are known to facilitate nuclear transport
- compacting the DNA so that its small enough to enter via the nuclear pores
how many people does cystic fibrosis affect
1/2500
what are the disadvantages of using liposomes for gene transfer
- inefficient transfer of DNA to target cells
- cannot target particular cell types
- poor expression
what is a capsid
surrounds genetic material in a virus
what is the retrovirus genome
ssDNA
7-9Kb
in a retrovirus what do the 3 regions code for
GAG
POL
ENV
GAG - capsid proteins
POL - reverse transcriptase
ENV - envelope proteins
what are most retrovirus used for gene therapy used for
moloney murine leukaemia virus (MoMLV)
how is a viral vector packaged
using a packaging line
what is ADA deficiency
defective adenosine deaminase gene
ADA codes for a gene in the purine salvage pathway
what is most affected by dATP
T-lymphocytes
advantages of retroviral vectors
high efficiency of gene transfer
high levels of expression
disadvantages of retroviral vectors
max insert is 7-7.5kb
only infects dividing cells
toxic - insertional mutagenesis
disadvantages of retroviral vectors
max insert is 7-7.5kb
only infects dividing cells
toxic - insertional mutagenesis
what is a risk of being treated for severe combined immunodeficiency using retroviral vectors
high level of constitutive expression of proto-oncogenes
causes cancer
what is the genome of lentivirus
ssRNA
around 9Kb
how is the safety profile of lentiviruses increased compared to retroviruses
engineered to reduce the strength of promotors and enhancers to reduce the risk of proto-oncogene expression
what is the genome of adenovirus
dsDNA
around 36Kb
what is the life cycle of adenoviruses
1 - early genes are expressed E1a and E1b
2 - expression of E1-E4 followed by viral DNA replication
3 - expression of late genes
4 - packaging of new virus particles and cell lysis
what happens to first generation adenoviral vectors
E1 and E3 removed to allow insertion of transgene and to stop viral replication
low level transcription of viral genes
led to innate host response
cloning capacity of 7.5Kb
what happens to second generation adenoviral vectors
all early genes deleted
have decreased toxicity and prolonged gene expression
cloning capacity of 35Kb
disadvantages of adenoviral vectors
do not insert genes into host chromosome
temporary protein expression
doesn’t work well on dividing cells
requires repeat treatment
what naturally occurring mechanism does gene silencing take advantage of
RNA interference (RNAi)
what triggers gene silencing
double stranded RNA
what are the components of gene silencing
ribonuclease - dicer
siRNA - short interfering RNA
RISC - RNA induced silencing complex
what is direct siRNA therapy
synthesis of RNA oligonucleotides that are complementary to the target transcript
formation of a double stranded siRNA duplex
packaged into a liposome for delivery across the lipid bilayer
how is shRNA converted into siRNA
a gene with inverted repeats is transcribed in the nucleus as short hairpin RNA
dicer cleaves it to create siRNA
disadvantages of RNAi therapy
risk of off-target effects
delivering sufficient RNA to target cells can be difficult
what model organism is used for cancer
oryzias latipes
what model organisms are used for behaviour
rattus norvegicus
macaca mulatta
what model organism is a gram negative gut bacteria
escherichia coli
how many genes does eschericha coli have
4500
what is the life cycle of eschericha coli
20 minutes
at 37 degrees
what is the yeast model organism
saccharomyces cerevisiae
what is the life cycle and gene number of saccharomyces cerevisiae
6000
1.5-2 hour life cycle
what is the chromosome number and gene number size of caenorrhabditis elegans
6 chromosomes
20,000
what is the life cycle of caenorrhabditis elegans
3 days
how many chromosomes and what is the gene number of the drosophila melanogaster
4 chromosomes
14,000 genes
what is the life cycle of the drosophila melanogaster
10-14 days
what is the danio rerio model
a fish
what is the gene number and chromosome number of a danio rerio
25
26,000
what is the life cycle of the danio rerio
3 months
chromosome number and gene number of mus muculus
20
23,000
life cycle of the mus musculus
2 months
