Molecular genetics exam 2 Flashcards
2 categories of mutations
somatic vs germline
somatic mutation
cannot be passed to offspring
Germline mutation
can be passed to offspring bc mutation occurs in oocyte and sperm
Point mutations
change of a single base
Silent or synonymous mutation
when the change results in the same AA
Missense mutation
when the change results in a different AA
Conservative mutation
when the change is still the same type of aa such as polar or np
Nonconservative mutation
when the change results in a different type of AA such that it results in a differently folded protein
Nonsense mutation
Leads to a premature stop codon and degradation of protein occurs
Transitions
changing to the same type of base
transversions
changing to a different type of base
Frameshift mutation
when the insertion or deletion of a nucleotide changes the reading Frame and the sequence of aa
What does a single nucleotide change in hemoglobin result in?
A sickle shaped red blood cell that is sticky
Normal individuals may have fewer than __ nucleotide repeats
30
Over 20 disorders exhibit over __ nucleotide repeats
200
Examples of disorders with over 200 nucleotide repeats
Fragile X syndrome, Huntington’s diseases and myotonic dystrophy
isoallele impact on phenotype
none or small that can only detected by special techniques
Null allele impact on phenotype
No gene product or nonfunctional gene product
Recessive allele impact on phenotype
Alter only when homozygous
Gain of function impact on phenotype
produce new
neutral impact on phenotype
no effect due to degeneracy and order in genetic code
induced mutation
result from the influence of an extraneous factor, either natural or artificial
4 examples of induced mutations
radiation, UV, natural and synthetic chemical
spontaneous mutations
usually linked to normal biological or chemical processes in the organism
During DNA replication, DNA polymerase occasionally inserts incorrect nucleotides due to misfiring and predominantly leads to
point mutations through addition or deletion of nucleotides
Replication slippage
If a DNA strand loops out and becomes displaced or if DNA polymerase slips, small insertions and deletions can occur
where is replication slippage common
in repeat sequences
Deamination
Amino group in cytosine or adenine is converted to uracil, and adenine is converted to hypoxanthine
what does Deamination result in?
base pair change during replication mispairing
Depurination
loss of one of the nitrogenous bases (usually a purine) in an intact double helical DNA molecule
what does deportation result in?
Frameshift because pairing cannot occur during replication
Oxidative damage
induced by the by products of normal cellular processes and exposure to high energy radiation
examples of things that cause oxidative damage
superoxides, hydroxyl radicals, and hydrogen peroxide
what does oxidative damage result in?
DNA breaks
Mutagens
natural or artificial agents that induce mutations
examples of mutagens
fungal toxins, cosmic rays, UV, industrial pollutants, medical x rays, and chemicals in smoke
Base analogs
mutagenic chemicals that substitute for purines or pyrimidines during nucleic acid replication
Specific mispairing
alter base such that it will mispair
alkylating agents
donate an alkyl group to amino or keto groups in nucleotides to alter base pairing affinity
what mutations result from alkylating agents?
transition mutations result
Intercalating agents
Chemicals that have dimensions and shapes that allow them to wedge between DNA base pairs, causing base pair distortions and unwinding
examples of intercalating agents
ethidium bromide and chemotherapeutic agents
Pyrimidine dimers
distort the DNA conformation in such a way that errors tend to be introduced during DNA replication
what causes pyrimidine dimers?
UV radiation
Transposable elements
Sequences that can move about the genome and when they leave it results in DNA damage
what is an example of something that acts as a transposable element?
Virus which is why hpv leads to cancer
Ionizing radiation causes __ damage
base
What causes ionizing radiation
x rays, gamma rays and cosmic rays
what happens during ionizing radiation?
stable molecules and atoms are transformed into free radicals
what 3 things does ionizing radiation do?
alter purines/pyrimidines, break phosphodiaster bonds, and produce deletions, translocations, and fragmentation
mismatch repair
responds after damaged DNA has escaped repair and failed to be completely replicated.
Base excision repair
corrects DNA containing a damaged DNA base
3 steps of Base excision repair
Exonuclease cuts base, DNA polymerase inserts complementary nucleotides into gap and DNA ligase seals the nick
2 steps of mismatch repair
excision of segment of DNA that contains a base mismatch followed by repair synthesis. Through a process of recombination
Nucleotide excision repair
Repairs bulky lesions that alter/distort the double helix
3 steps of NER
Exonuclease cuts distortion, DNA polymerase inserts nucleotides and DNA ligase seals nick
NER may repair
pyrimidine dimers
Double strand breaks are caused by
ionizing radiation
DSB have 2 options for repair
homologous recombination and non nonhomologous end joining
what us the preferred option of repairing DSB
homologous recombindation
what does non homologous end joining involve?
bringing the 2 ends together but it may result in the deletion of some bases
steps of homologous recombination
Damaged chromosome finds its homologous chromosome (same genes but not exactly the same sequence)
One strand of the damaged chromosome inserts itself into the homologous chromosome between the strands on DNA. It copies the sequence until it has copied all the DNA that was deleted
The damaged chromosome (blue one) will leave the homologous chromosome
The overlap area will match up
The gaps in the DNA will be filled in by DNA polymerase
Chromatin modifications can occur in 3 different ways
Histone modifications, nucleosomal remodeling, and dna methylation
Nucleosome organization
DNA molecule is wound 1 and 3/4 turns around a histone October called core particles
what are histones made of
4 different subunits
chromatin remodeling must occur to
allow the DNA to be accessed by DNA binding proteins to allow replication and gene expression
Histone tails are potential targets along the chromatin fiber for chemical modifications that may include
acetylation, methylation, ubiquitination, and phosphorylation
Regulating genes via nucleosomes
addition or removal of certain groups to the tails of histone proteins disrupts chromatin structure allowing transcription to take place
Epigenetic inheritance
involves the copying of the histone modifications after the DNA has been replicated
how does DNA methylation inhibit transcription?
the addition or removal of methyl groups from the bases of DNA can repress transcription by binding to transcription factors in DNA
Cis acting elements
postion regulator proteins in regions where those proteins can act to stimulate or repress transcription of the associated gene
Promotors
nucleotide sequences that serve as recognition sites for transcription machinery that are critical for the initiation of transcription and are located adjacent to the genes regulated
Examples of cis acting elements
enhancers or activators and silencers or repressors
activators ___ transcription intitiation whereas repressors ___ TI
increase, decrease
What do transcription factors do?
bind to cis-acting elements
2 parts of the transcription factors
DNA binding domain and trans activating domain
what is the DNA binding domain?
Binds to specific DNA sequences in the cis-acting regulatory site
what is the trans activating domain
Activates or represses transcription by biding to other transcription factors or RNA polymerase
What is DNA looping?
bending of the DNA such that the transcription factors interact wit the DNA of the transcription complex
Enhancer
DNA sequence stimulating transcription a distance away from the promotor
insulator
dna sequence that blocks or insulates the effect of enhancers
2 types of post transcriptional processing
alternative splicing and RNAinterference
Alternative splicing
generate different forms of mRNA from identical pre-mRNA giving rise to a number of proteins from one gene
Steady state level of mRNA
amount in cell
The steady state level of mRNA can be regulated by
in response to cell needs, through removing cap and tail, and through rna interference
How does RNAi occur?
Short interfering RNA (siRNA) and microRNA (miRNA) represses mRNA translation ad triggers degradation
Explain the process of miRNAs
miRNAs are transcribed from DNA to form a hairpin loop which targets them to degradation because they are double stranded. Dicer cleaves the miRNA into smaller pieces where it is packed up by RISC and the short strands target any other mRNA with that sequence
Translational control
regulates the rate of protein synthesis
Posttranslational modifications
Stability of a protein can be modulated. protein can change its structure and its activity
translation can be regulated to
produce the correct quantity of a protein
Recombinant DNA technology (genetic engineering)
Techniques for locating, isolating, altering, and studying DNA segments
Molecular genetics
Biotechnology, the use of these techniques to develop new products
What do restriction enzymes do?
Recognize and cut DNA at specific nucleotide sequences
2 ends made by restriction enzymes
Blunt and cohesive ends
cohesive ends
fragments with short, single stranded overhanging ends
blunt ends
even length ends from both single strands
sticky ends allow for
2 strands of DNA to come together due to base pairing
CRISPR-Cas genome editing
makes a double stranded cut at a specific sequence and the dna repair mechanism in the cell repairs the break. Repaired by non homologous end joining or homologous recombination
where is CRISPR-Cas found?
bacteria and archaea
Gel electrophoresis
Separates molecules such as DNA or protein based on size and electrical change
Southern blotting
detect DNA
Northern blotting
detect RNA
western blotting
to detect protein
Probe
dna or rna with a base sequence complementary to a sequence in the gene of interest
Purpose of southern blotting
determine the presence of a specific gene sequence
Purpose of western blot
to determine if a protein is being expressed
cloning vector
a replicating DNA molecule attached with a foreign DNA fragment to be introduced in cell
3 things a cloning vector must have
origin of replication, selectable markers-traits, and a cleavage site
why is an OOR needed in a cloning vector?
So that it is replicated along with the DNA that it carries
Why are selectable markers needed in a cloning vector?
Enables cells containing the vector to be identified or selected
why is a cleavage site needed on a cloning vector?
it needs a site for each of one or more restriction enzymes used
what are plasmids?
circular DNA molecules from bacteria
what are linkers?
synthetic DNA fragments containing restriction sites
how does foreign DNA get inserted into plasmids?
restriction enzymes
what are selectable markers used for in recombinant plasmids?
to confirm whether the cells have been transfromed
DNA markers
short segments of DNA whose sequence and location are known and they represent landmarks along chromosome
Name the different types of molecular markers
Single nucleotide polymorphisms, restriction fragment length polymorphisms, and microsatellites
what are the molecular markers used for?
Crime scene investigation, parental disputes, disease diagnosis, determining the type of species in cases of poaching
what are micro satellites?
short tandem repeats (STR) variable number of copies of repeat sequences possessed by many organisms
what are micro satellites detected by?
PCR
Homozygotes show a
single tail peak
heterozygotes show
2 shorter peaks
Forward genetics
begins with a phenotype to a gene that encodes the phenotype
reverse genetics
begins with a gene of unknown function, first inducing mutations and then checking the effect of the mutation on the phenotype
transgenic techniques
an organism permanently altered by the addition of a DNA sequence to its genome
Knockout mice
a normal gene of a mouse has been fully disabled
transgene
the foreign DNA that a transgenic organism carries
How are GMOs produced?
alteration of an organisms genome using recombinant DNA technologies to add or remove a gene from the genome
what is biotechnology?
use of living organisms to create a product or a process that helps improve the life of humans or other organisms
Biopharming
production of proteins in genetically modified plants and animals
Bi transgenic crops
have built in insecticide protection from insect pests
where are bi transgenic crops found
in many plants including corn, cotton, tomatoes, and tobacco
