GENETICS FINAL 2020 w QUIZZES
DNA of the same polarity as mRNA is called the ___ strand (+ or -)
+
mRNA is ready to be translated is assigned the __ strand polarity (+ or -)
+
in ambisense genomes, the + strand is aka the ___ and the - strand is aka the ____
+ strand aka genome - strand aka anti-genome
what strand is used as mRNA template with ambisense RNA viral genome
+RNA
is flaviviridae +/- ds/ss RNA/DNA?
+ssRNA
which genome can be translated directly to make protein by the host cell?
+ssRNA
flaviviridae genome
+ssRNA 10-12 kb length cap at 5' end
togaviridae genome
+ssRNA 10-13 kb long 5' cap 3' poly A tail
picornaviridae genome
+ssRNA 7-8.5 kb length polyadenylated
Of the 7 viral types, which is HBV categorized under?
+ssRNA from retroviruses using RTase step
why are genome type IV viruses unusual?
+ssRNA genomes that go through DNA intermediate. when infect host cell, genome is NOT translated copied into - strand DNA by RTase
How to get mRNA production for RNA viruses
+ssRNA retrovirus to dsDNA to +mRNA (RT makes DNA from RNA) DsRNA to +mRNA (transcription of - strand) +ssRNA to +mRNA (direct use as mRNA) -ssRNA to +mRNA (transcription of - strand)
genome type IV is
+ssRNA virus
genome type VI
+ssRNA viruses that don't use genome directly as mRNA retroviridae family
RNA and DNA compliments of + strands are called __ strands
-
S layer surface coating
- 1000s of copies of a single protein linked together - provides protection from the environment - adhesin is protection from host immunity
Map of human mtDNA
- 13 mRNA (green) - 22 tRNA (violet) - 2 rRNA (blue) - the major NCR region contains heavy strand promoter (HSP) and light strand promoter (LSP)
Alkylating Agents - Induced DNA Damage
- add an alkyl group (-CH3 or CH2CH3) to amino or ketone groups in nucleotides - alkylated nucleotides exhibit abnormal base pairing ex: ethyl guanine pairs with T - creates Mustard Gas (agent used in WWI) which caused burns, blindness, and tumors
UV light and Low Energy Radiation - Induced DNA Damage
- all electromagnetic radiation having wavelengths shorter than visible light (~380 nm) are very energetic - Disrupt DNA and other macromolecules - UV light (~260 nm) is very mutagenic - causes adjacent pyrimidine bases to fuse to each other = called pyrimidine dimers (two thymines) - pyrimidine dimers prevent DNA pol from replicating normally - cells containing too many of these will kill themselves
how do you blot during southern blot
- blot with a piece of blotting paper (nitrocellulose paper) - push down paper onto gel - blotting paper will have copy of DNA on it
Depictions of Mitochondrial DNA
- children receive mitochondrial DNA from mom - H-strands = Guanine
exam guidelines for ppl at risk for HNPCC
- colonoscopy every 1-3 yrs starting at age 25 y/o OR 5-10 yrs before age of earliest CRC dx in the family - annual hemoccult test starting when colonoscopy begins - women only - endometrial screen w/ biopsy (consider vacuum cutterage/Pipel biopsy) start age 25 y/o and cont annually - surgery rec if polyps detected
High-Energy Radiation (Ionizing Radiation) - Induced DNA Damage
- electromagnetic radiation with shorter wavelengths even worse are X-rays, gamma rays, cosmic rays - mutates DNA by creating thymine dimers, breaking phosphodiester bonds, and producing free radicals (ionization)
external bacterial cell structures
- flagella - fimbriae - pili - slime layer - capsules - s layers - cell wall - periplasm - cytoplasmic membrane
characteristics of pathogenecity islands
- may be quite large (up to 100s of kbs) - may be unstable and spontaneously lost
inclusion of bacterial structure
- metachromatic granules (volutin): phosphate reserves - polysaccharide granules: energy reserves - lipid inclusions: energy reserves - sulfur granules: energy reserves - carboxysomes: RuBisCO enzyme for CO2 fixation during photosythesis - gas vacuoles: protein-covered cylinders that maintain bouyancy - magnetosomes: FeO2 inclusion. destroys H2O2
describe gapped dsDNA genome
- most of the DNA is ds - part of it is ss DNA, the negative strand = GAP. - there is a protein attached to the 3' end of neg strand - small piece of RNA attached to the plus strand
Triplet Repeats (Expanding Mutations) TNRE
- repeating trinucleotide sequence (most common is CAG) - we all have them and they can be found in coding and non-coding regions of transcribed DNA - abnormal events: copy number increases (we don't know why) - increase in copies is associated with Huntington's disease - TNRE gets worse each generation = called anticipation
Viruses - Induced DNA Damage
- retroviruses randomly insert themselves into our genome... usually junk but if it goes to promoter or coding sequence, gene expression is disrupted (like in transposons) - other viruses produce proteins that inhibit DNA rep, monitoring, or repair mechanisms - can't be removed bc they're seen as part of the DNA motif - exonuclease activity
is it + or - strand RNA that cannot be translated
- strand RNA cell cannot make a copy of it to make RNA
how to make a cDNA library
- transcribe euk DNA template - get primary mRNA transcript - clip out introns to only have expressed sequence to match mature mRNA - isolation of mRNA addition of RT - ssDNA made, degrade mRNA - DNAPol to make dsDNA with NO introns
Horizontal Gene transfer
- transfer of genes between cells of the same generation - transfer of DNA that results in organisms acquiring new genes that did not come directly
Who should be offered genetic counseling?
-family history of genetic disorder -pregnancy over 35 -repeated miscarriages/previous child with genetic disorder -abnormal ultrasound or pregnancy screening
What is not encoded in viral genome
-no genes encoding complete protein synthesis machinery -no ribosomes
genome type V is viruses with ____ genome
-ssRNA genome
bacterial size varies from about ___ to ____
0.1-0.2 um to > 100 um
A population of 150 individuals at equilibrium has an allele frequency of 0.3 for the dominant allele (B) and a frequency of 0.7 for the recessive allele (b). Use the Hardy-Weinberg equation to determine the frequency of the genotype (bb).
0.49
If a population in Hardy-Weinberg equilibrium has an aa genotype frequency of 0.36, what is the frequency of the "a" allele?
0.6
many viruses encode at least ___ protein(s) to which modulate host defenses
1
1 cM = ?
1 million base pair DNA and physical distance is 1 Mb
average bacterial size
1 um
What are 6 causes of Induced DNA damage?
1) Base Analogs 2) Alkylating agents 3) Intercalating Agents 4) UV light 5) High-Energy Radiation (ionizing radiation) 6) Viruses
What are 5 causes of Spontaneous DNA damage?
1) Errors of DNA polymerase 2) Tautomeric Shifts 3) Depurination and Deamination 4) Oxidative damage 5) Transposons
What goes into population genetics?
1) Genetic Factors 2) Environmental factors that surround the genetic frequencies 3) Societal factors *All act to determine the frequency and distribution of alleles and genotypes
How are mutations classified?
1) Size 2) Spontaneous 3) induced 4) lethal 5) conditional - in certain environments 6) Suppressor - intragenic = 2nd mutation in the same gene (mutation 1 alters the structure and mutation 2 alters it back) - intergenic = 2nd mutation in different genes
What types of cells contain mutated DNA?
1) Somatic - arise in the DNA of somatic cells; is not passed on; the earlier in development causes worse outcomes 2) germ-line - mutations arise in the DNA of gamete-forming tissue; can be transmitted to offspring (can cause cancer)
How does DNA damage get converted into permanent mutations?
1) a change in DNA caused by a mutagen, cells are constantly exposed to mutagens. not good or bad 2) Mutations are also errors in replication - DNA pol puts the wrong nucleotide 3) second DNA rep occurs - the wrong serves as a template for complementary wrong nt 4) permanent - can't be removed or repaired 5) random
What can we use to estimate distances in genetic maps?
1) anonymous markers can be detected using molecular techniques. 2) Single nucleotide polymorphisms (SNP's) - at 1 nucleotide, there is a base change, which we can connect to a certain gene and estimate positions within the genome.
3 Small Gene Mutations
1) base-pair substitutions 2)Insertions/deletions
How is amount of gene product regulated?
1) epigenetic factors 2) regulation of transcription, RNA processing, and translation 3) regulation of post-translation events 4) protein processing and disposal
Two main forms of hereditary colon cancer
1) familial adenomatous polyposis (FAP) - many colonic polyps -- 1% 2) hereditary nonpolyposis colorectal cancer (HNPCC) - few if any polyps -- 5-10%
2 types of Repair Mechanisms for DNA Mutations
1) photo repair 2) Excision Repair
What are the 5 assumptions of the Hardy-Weinberg Principle?
1) that the population is very large 2) that there is no immigration or emigration of individuals in the population 3) there is no mutation 4) there is random mating 5) no natural selection
What is hydroxyurea used for?
1) treat certain leukemia 2) reduce the need for blood transfusions in sickle cell anemia and prevents the formation of sickle-celled RBC 3) class of medications called antimetabolites 4) treats cancer by slowing/stopping the growth of cancer cells
plasmids are ___% the size of a bacterial chromosome
1-5%
How to get from +ssDNA to +mRNA for DNA viruses
1. +ssDNA 2. Synthesis of - strand 3. dsDNA intermediate 4. Transcription of - strand 5. + mRNA
process of +ssRNA genome replication
1. +ssRNA strand copied to make -ssRNA 2. - strand RNA copied again to make more + strands via RdRp
Types of DNA markers for linkage analysis
1. 2 allele RFLP 2. Microsatellite 3. VNTR's 4. SNP's
Examples of common dsDNA viruses
1. Adenoviridae 2. Herpesviridae 3. Papillomaviridae 4. Polyomaviridae 5. Poxviridae
Example of larger dsDNA viruses
1. Adenovirus 2. Herpesvirus 3. Pox viruses (largest(
how would you make vax out of HSV
1. DNA extracted from virus 2. herpes simplex gene isolated 3. DNA is extracted and cleaved 4. put DNA in attenuated/harmless cowpox virus 5. recombo DNA piece 6. goes into virus 7. attenuated virus inj to human but contains DNA from virus to which human will recognize
BRCA2 function
1. DNA repair: homologous recombo 2. cell-cycle checkpoint control: interacts w/ p53 3. chromatin remodeling
7 viral genome types
1. DsDNA 2. +ssDNA 3. DsRNA 4. +ssRNA 5. -ssRNA 6. +ssRNA from retroviruses with RTase step 7. Gapped dsDNA with RTase step
Steps of viral multiplication
1. Host cell recognition 2. Attachment to the host cell 3. Unloading 4. Synthesis 5. Assembly 6. Release
exon 11 of BRCA2 contains which two regions required for binding to RAD51
1. OCCR - ovarian ca cluster region 2. 8 BRC repeats
Examples of dsDNA viruses with small genomes
1. Polyoma virus 2. Papilloma virus
BRCA1 domains
1. RING-finger domain is a protein-protein interaction and binds BRCA-1 associated RING domain 1 (BARD1)
what are found in some bacteria
1. S layer 2. Fimbriae 3. outer membrane 4. cell membrane 5. actin cytoskeleton 6. pilus
what is the two-step approach to evaluating FHx?
1. did CRC occur in 1st deg relative or 2nd? 2. are characteristics suggesting high risk present? (2+ relatives affected w/ CRC w/ one dx'd before 50 y/o
examples of hosts in host-vector systems
1. e. coli (bacteria) 2. yeast cells 3. virus 4. mammalian tissue culture cells 5. insect cells
lesions possible with FAP
1. endodermal lesions - small bowel, biliary tree, colorectal, gastric 2. mesodermal lesions - osteoma, desmoid, liver, dental 3. ectodermal lesions - retinal, epidermal, endocrine
two major forms of hereditary colon cancers that have been ID'd
1. familial adenomatous polyposis, FAP: (many colonic polyps) 2. hereditary nonpolyposis colorectal cancer, HNPCC (few, if any polyps)
process of storing genes in a library
1. fragments of DNA from organism's DNA with restriction enz 2. insert to plasmid vector 3. bacterial transformation of vectors 4. store vectors in DNA library
the ease with which Tns move into or out of DNA sequences means that transcription can occur from:
1. from host genomic DNA harboring a transposon to a plasmid 2. from one plasmid to another plasmid 3. from a plasmid to genomic DNA
what is encoded by a viral genome?
1. gene products - genome replication, viral genome packaging, viral assembly 2. regulatory signals - reg/timing of replication cycle
naked virus means it has which two components
1. genome 2. capsid
human viruses come in which nucleocapsid shapes
1. helical 2. icosahedral
various shapes of nucleocapsids come in various
1. helical 2. icosahedral 3. rods 4. cones some viruses are complex & don't fit the typical shape
two methods of how microbes can take up substances from their environment
1. horizontal gene transfer (HGT) 2. vertical gene transfer
how to use biotech to make insulin
1. human insulin made in petri dish 2. amplify seq in bacteria 3. harvest 4. tx DM pts.
different polar flagellar arrangement
1. monotrichous 2. lophotrichous 3. amphitrichous
during molecular cloning, the plasmid must contain which 3 things
1. origin of replication 2. abx resistance gene 3. gene with observable phenotype
what must artificial chromosomes have in order to be viable vectors in host-vector systems?
1. origin of replication 2. functional chromosomes
examples of viridae of genome type V
1. paramyxoviridae 2. rhabdoviridae 3. filoviridae 4. orthomyxoviridae 5. arenaviridae
examples of genome type IV +ssRNA viruses
1. picornaviridae 2. caliciviridae 3. coronaviruses
examples of vectors in host-vector systems
1. plasmids (most commonly used) 2. artificial chromosomes
four steps of RNA virus and host cell
1. recognize and bind host 2. uncoat 3. synth 4. mRNA
how to use cloned DNA as a probe to identify the same gene in a DNA library?
1. restriction endonuclease breakdown DNA 2. release fragments of DNA 3. separate fragments of DNA using electrophoresis 4. denature DNA in a gel to have ssDNA stuck in the gel 5. look for genes of interest with probe
process of DNA fingerprinting with RFLPs
1. restriction endonuclease cut at specific RFLP sites 2. cut DNA w/ one fragment containing gene of interest 3. run through gel 4. notice banding pattern
two forms of colon cancer
1. sporadic 2. inherted
process of gene therapy (stepwise)
1. stem cells removed from pt 2. working copy of gene inserted into virus 3. virus delivers working gene to pt's extracted stem cells by infecting them 4. grow stem cells w/ working gene and return to pt
two major functions of BRCA1
1. transcription factor: involved in reg of estrogen receptor activity and related to the control of estrogen-induced proliferation of breast tissue 2. DNA repair: homologous recombo & repair of transcription-coupled oxidation-induced DNA damage. cell-cycle checkpoint control interacts w/ RB, ESF1, p53. Chromatin remodeling.
main routes of horizontal gene transfer (HGT)
1. transformation 2. transduction 3. conjugation
gene therapy is being researched to treat which diseases
1. type I DM 2. cystic fibrosis 3. hemophilia 4. hereditary blindness 5. cancers 6. PD
how is the HBV genome replicated?
1. virus starts w/ mRNA 2. plus RNA converted to minus strand DNA via RTase 3. minus strand DNA converted dsDNA 4. the gaps, protein, small piece of RNA are all introduced to the molecule and packaged into the new virus particles
when the new TCGA system is used, as many as ___ in 10 cancers may be reclassified
1/10 new classification system for cancer can also affect drug development or recruitment of pts into clinical trials
what is meant by ambisense RNA viral genome
1/2 of the genome has + polarity and other 1/2 has - polarity green is + orange is -
reoviridae genome
10 dsDNA segments
in a woman with HNPCC, the lifetime risk of ovarian cancer is ___%
10-15%
___ different well-known human STRs are used in the US federal profiling database, CODIS (combined DNA index system)
13
Size of herpesvirus
130-365 Kb in length
approx ___% of apparently sporadic CRC and variable portion of other cancers also show this abnormality.
15% the genetic background of microsatellite instability may not be same in HNPCC and various sporadic cases
first and second hit of DNA MMR gene mutations in human cancers diagram
1st hit: inherited mutation in one copy of MMR gene (every cell) 2nd hit: loss of heterozygosity, somatic mutation inactivation of remaining WT copy cancer
tandem is
2 letter
onset of colorectal polyps with FAP is usually in ___ decade of life and the penetrance is __%
20's, 30's 100% penetrance
when was SARS outbreak in china
2002-2003
2pq
2Aa
When do women get an ultrasound?
2nd trimester - 18-20 weeks
What is 30% recombination frequency in centimorgan (cM) and in map units (mu)?
30% recombination freq = 30 cM = 30 mu
Size of adenoviruses
36-48 Kb
in a woman with HNPCC, the lifetime risk of colon cancer is ___%
40-60%
in a woman with HNPCC, the lifetime risk of endometrial cancer is ___-___%
40-60%
lynch syndrome I (HNPCC) excess of synchronous and metachronous CRC
46% metachronous CRC w/in 10 yrs following initial CRC when less than a subtotal colectomy has been performed
GP mRNA is translated and accesses the __' genome
5'
Hereditary nonpolyposis colorectal cancer (HNPCC) accounts for which percentage of all dx'd colon cancers
5-10%
Size of polyoma and papilloma viruses
5-8 Kb in length (kilo base pairs)
If the recombination frequency between genes (A) and (B) is 5.3%, what is the distance between the genes in map units (CM) on the linkage map?
5.3cM
70S ribosome is made up of ___ subunits
50S + 30S subunits
describe genome of genome type IV viruses
7-10 kb long mRNA 5' cap and 3' poly A tail mRNA is made from dsDNA
There are ___ different herpes viruses
8
lynch syndrome I (HNPCC) genetic penetrance
85-90%
about ___% of CRC from HNPCC pts show microsatellite instability and a majority of microsatellite loci are apparently involved
90% in HNPCC tumors, total # mutations at microsat loci alone could be as high as 100k per cell
FAP represents what percentage of all colorectal cases drs dx yearly
< 1%
1. The family below is segregating an autosomal dominant form of Ehlers-Danlos syndrome. Shaded individuals are affected with the disorder. You type each of the family members for a polymorphic DNA linked marker, with results shown below each individual (A-D represent individual alleles for the DNA marker).The disease in this family is linked to which allele of the marker? Ignore Individual III-5.
A
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. UAA, UAG, UGA
missense mutation
A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid.
Chorionic Villus Sampling (CVS)
A technique associated with prenatal diagnosis in which a small sample of the fetal portion of the placenta is removed for analysis to detect certain genetic and congenital defects in the fetus.
Epistasis
A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited; - the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another. skewing of ratios in F2 generations (you can see original phenotypes again)
A mother with blood type A has a child with blood type A. Give all possible blood types for the father of this child.
A, B, AB, O
Which of the following base changes in DNA is an example of a transition?
A-to-G
p^2
AA (dominant)
principle of codominance
AB is not an intermediate phenotype
screening for colorectal cancers
ACS (american cancer society) has recommended colon cancer screening for everyone over 50 y/o. only small % pop actually does.
Damaging Agent: Replication Errors
AG mismatch and TC mismatch, insertion and deletion Repair process: mismatch repair
FAP is linked to the ___ gene whose protein is involved in beta-catenin signalling.
APC
If maternal UBE3A is deleted or methylated
AS
Which dsDNA viral genomes are large enough to have genetic space to code their own DNAPol?
Adenoviruses Herpesvirus Poxvirus Viral DNA replication is independent of the host cell
Monoallelic Expression
Allelic imbalance is exhibited in 5-20% of autosomal genes - only ONE GENE IS EXPRESSED - can occur via genomic imprinting and X-inactivation
What protein is made by a developing baby?
Alpha-fetoprotein (AFP)
Some viral genomes do contain genes that encode components of the translation system including
Amino acyl tRNA synthetases Initiation factors Transfer RNAs
When specific non-imprinted genes from the mother's chromosome 15 is deleted, it leads to:
Angelman syndrome
What phenomenon describes a genetic trait that is expressed more strongly or earlier in development with each generation?
Anticipation
other than YACs, what are the other form of artificial chromosomes as vectors?
BACs - Bacterial artificial chromosomes began to develop mammalian artificial chromosomes in cell culture
For a physical map of a chromosome, distances are measured in units of:
Base pairs
APC is now thought to be the gene for ___ cancer
CRC
____ ____ system allows for greater and more specific gene targeting for gene therapy
CRSPR/Cas 9
Forward Mutation
Changes the wild-type phenotype to a mutant phenotype
Base Analogs - Induced DNA Damage
Chemicals that resemble normal nucleotides and can substitute for them during DNA replication; they resemble abnormal base-pairing properties ex: 5-bromouracil resembles thymine - DNA pol will incorporate 5BU instead of thymine during DNA rep - 2nd round of rep, G is put across from 5BU - 3rd round of rep, G is used as wrong template and C is placed
The human ABO blood group alleles are an example of :
Codominance
Diff diseases caused by the 8 diff herpesviruses
Cold sores, fever blisters, genital herpes, chickenpox, shingles, mono, etc.
DNA-dependent RNAPol transcribes ____ to get mRNA
DNA
transformation involves capturing ____ from solution
DNA
dsRNA genomes use which Pol
DNA dep RNA Pol
what are genomic libraries
DNA libraries that contain a representation of an organism's entire genome
central genome core of virus contains
DNA or RNA
Proofread Mechanism for DNA Mutations
DNA polymerase can mistakes. It has exonuclease activity (5' to 3'). This means that they go down the template strand (3' to 5') and if they accidentally add wrong nucleotides, they can excise it and replace it with the proper nucleotide - first line of defense against replication errors
genomic island refers to the
DNA seqs similar to patho islands (PAIs) but not contributing directly to virulence or pathogenicity
Important protein missing by small dsDNA viruses (polyoma/papilloma viruses)
DNAPol (enz that replicates the DNA genome - DNA dependent DNAPol) Have to use host DNAPol so their genomes are replicated
Human cells can only make mRNA from ____ templates
DsDNA
When ssDNA viruses infect a host cell, the ssDNA is converted to
DsDNA Reason - dsDNA -> mRNA using host DNA-dep RNA pol
JC virus is caused by ds_____ virus called _____
DsDNA virus called polyomaviridae
Photo Repair Mechanism for DNA Mutations (direct repair)
EUKS: a mechanism specific to damage from UV light. Photolyase uses Energy from light to repair thymine dimers PROK: same as above but uses photoreactivation enzyme
Genome type II can package _____ (+/-) strand of DNA
Either + or -
mRNA is ____ for protein production
Essential
Excision Repair Mechanism for DNA Mutations (indirect repair)
Excision repair enzymes recognize damaged DNA. The excision enzyme cleaves out the damaged DNA. DNA polymerase 2 resynthesizes the DNA (replaces the removed nucleotides) - DNA ligase seals in the nicks (phosphodiester bonds) - BER and NER
Genomic Imprinting
For some genes, only one copy is expressed. Expression of these genes is variable depending on which parent the gene came from - occurs on only 9 chromosomes - occurs by a pattern of methylation, meaning the copy of the gene to be inactivated is coated with methyl groups (epigenetically silenced due to methylation) takes place in the egg and sperm - reversible form of gene inactivation and is not a mutation - basically, we get one copy of the chromosome from each parent. in somatic tissue, our chromosomes are imprinted (from father and mother) but once it enters gametes, it gets converted to whatever gender the person is.
from the anti-genome (- strand) we can make mRNA called
GP mRNA - it is translated
What term is given to the total genetic information carried by all members of a population?
Gene Pool
Enumeration of Progeny constructs what from test crosses?
Genetic maps - they calculate percent recombination Start by finding recombinant phenotypes (least frequent phenotypes), add them together, and divide by total progeny
Preimplantation Genetic Diagnosis (PGD)
Genetic testing on embryos for genes that cause untreatable or severe diseases. - usually uses Blastocyte biopsy (5 trophoectoderm cells); when they become trophoblasts, they get implanted - requires IVF
viruses part of the retroviridae family
HIV HTLV (human t lymphotrophic virus)
How does sickle cell occur?
Hemoglobin usually has 2 alpha subunits and 2 beta subunits. The change occurs when Glu becomes Val (going from a polar molecule to non polar). This causes an aboral deoxygenated tetramer with sticky non-polar sites to stick together, causing a distortion in normal RBC into a sickle shape
____ transfer involves transmission of chromosomal genes from a donor cell to a recipient cell. the plasmid jumps into the chromosome and when the chromosome is duplicated, the plasmid and part of the chromosome are transmitted into a new cell through conjugation. the plasmid/chromosome hybrid then incorporates into the recipient chromosome
Hfr (high frequency transfer)
How do microbes take up substances from their environment?
Horizontal Gene Transfer Vertical Gene Transfer
Viral genome dsDNA is transcribed by _____ ______ to mRNA
Human enzymes - DNA dependent RNA Pol
Viral mRNA is translated by ___ ____ to make proteins
Human ribosomes
Genome type __ is ssDNA
II
insertion sequences (ISs) consist only of ___ on either side of the transposase gene
IRs
JC virus infects everyone but is only a problem for
Immunosuppressed individuals
Differential expression of the genetic material depending on its parentage of inheritance is due to:
Imprinting
The R locus determines flower color in a new plant species. Plants that are genotype RR have red flowers, and plants that are rr have white flowers. However, Rr plants have pink flowers. What type of inheritance does this demonstrate for flower color in these plants?
Incomplete Dominance
Which of the following characterizes the mode of transposition of retrotransposons?
It involves an RNA intermediate AND it involves the initial synthesis of transposase
Transposons - Spontaneous DNA damage
Jumping genes - mobile pieces of DNA found in all living things (45% of the human genome came from this) - they cut or copy themselves and then insert randomly in the host genome - replicative vs nonreplicative transposons encode enzyme transposons - insertion near genes or within genes can disrupt host gene expression and lead to larger chromosomal alterations - control transposes will control movements (methylation and mRNA destruction)
other names for HNPCC are ___ syndrome and cancer family syndrome
LYNCH
____ coronavirus is currently causing outbreaks of serious respiratory disease in Middle East and is transmitted from camels to people
MERS
most HNPCC is caused by mutations in genes called
MLH1 and MSH2
Once dsDNA gets into a cell, it directs production of
MRNA
Xeroderma Pigmentosum
Mutated single strand nucleotide excision repair gene, which prevents repair of thymidine dimers.; Dry skin w/ melanoma and other cancers ("children of the night").
What is needed to get from +ssDNA to +ssRNA?
Neg strand
Proteins made using host ribosomes go on to make ____ viral particles
New
Tautomeric Shifts - Spontaneous DNA damage
Nitrogenous bases can exist in different chemical forms called structural isomers. Normal forms are A-T and C-G and abnormal isomers/base pairing would be T-G or A-C - Conversion between normal and abnormal isomers occurs naturally at some low rate - this is VERY BAD if it occurs right before DNA rep - DNA pol will read rare form and insert the wrong base across - not a major source of mutations (rare but bad)
Do any viruses encode the complete translation system
No
In viral chromosome, are classical centromeres/telomeres found as they are in a standard host chromosome?
No
There are ___ genes encoding proteins involved in energy production or membrane biosynthesis in viruses
No
Is DNA translated?
No - only RNA
What is NIPS and what does it do?
Non-invasive Prenatal Screening = through analysis of fetal cell-free DNA. 99% accurate in the detection of aneuploidies. - Millions of DNA particles are mapped to the chromosome of origin extracted from maternal blood - The number of molecules mapped is determined, regardless of fragments fetal or maternal origin - The fraction of molecules assigned to chromosome 13, 18, 21 or X are compared to
Oxidative Damage - Spontaneous DNA damage
Normal process of aerobic cellular respiration creates extremely reactive atoms called free radicals (an atom or group of atoms with an unpaired electron) - free radicals steal an electron from wherever it can get it (proteins, lipids, DNA) - removal of electrons from DNA alters their structures causing the wrong base to be added - cause of cancer and aging
Phenylketonuria
Occurs when phenylalanine can't convert to tyrosine or melanin due to lack of phenylalanine hydroxylase. Phenylalanine accumulates in the blood and causes symptoms. This is toxic to the nervous system and can cause neurological issues.
If paternal SNPRN is deleted or methylated
PWS
What is the largest human virus
Poxvirus
Heteroplasmy
Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrial inherited disease
Crossing over occurs during:
Prophase
dsDNA genomes use which Pol
RNA dep RNA Pol
what type of polymerase is used by genome type III - dsRNA viruses
RNA-dependent RNAPol (RdRp)
dsRNA needs to be worked on with the help of _____ inside the virus particle to get the viral mRNA
RNAPol
some mRNAs are simply copied to make a minus strand by ____ Pol
RNAdep RNAPol
what enzyme is required to be present in dsRNA viruses and why?
RdRp is always encoded in RNA virus genome bc human hosts do not have it. RdRp copies RNA genome and also makes mRNA from genome (replication)
what is the first thing that takes place in an infected cell?
RdRp to make - strand RNA to +mRNA
Damaging Agent: X-rays, oxygen radicals, alkylating agents, and spontaneous reactions
Repair process: Base excision Repair
Damaging Agent: UV light, polycyclic aromatic hydrocarbons
Repair process: Nucleotide excision repair
dsDNA genome has to be
Replicated
Adenoviruses cause ___ & _____ infections
Respiratory and GI
bacterial cells protect themselves from hostile conditions by producing __ ___ and/or ____
S layers and or glycocalyx
___ is used during crime scene investigation
STR
Poliovirus has a ____ life cycle for translation
Short
Which of the following types of mutations leads to the same amino acid sequence of the gene product?
Silent
Principle of Incomplete Dominance
Situation in which one allele is not completely dominant over another allele
Poxviridae causes which viruses (2)
Smallpox to which has been mainly irradicated Molluscum contagiosum virus - skin and genital infection
Which genes predispose colon cancer?
Sporadic genes and inherited forms -most occur sporadically
patho islands are flanked by sequences that look like genes for ____ enzymes
TE
Achondroplasia is a common cause of dwarfism in humans. All individuals with achondroplasia are thought to be heterozygous at the locus that controls this trait. When two individuals with achondroplasia mate, the offspring occur in a ratio of 2 achondroplasia:1 normal. What is the most likely explanation for these observations?
The allele that causes achondroplasia is a recessive lethal allele
What is gene penetrance?
The percentage of people who have a genotype that actually show symptoms
LOD score (Z)
The ratio of probabilities that two genes are linked to the probability that they are not linked, expressed as a log10. Scores of 3.0 or higher are taken as establishing linkage. ex: score of 3 = 103 odds if Z=0 or negative infinity, the loci are not linked the probability ratios must equal 1.
Which of the following is the analog of 5-bromouracil
Thymine
How many viruses can be encoded by polyoma and papilloma viruses
Too small to encode a lot of proteins
Genome type __ is dsDNA viruses
Type I
HPV causes which kind of sx/cancers
Warts Cervical, throat, anogenital cancers
Why do we really care about population genetics and the Hardy-Weinberg Law?
We care because we are given statistics very often about the frequencies of various genetic disorders
Which statement best describes the Hardy-Weinberg principle?
When there is a large population, the mechanism of inheritance does not change allele frequencies
What are two examples of epigenetic phenomena?
X-chromosome inactivation and genomic imprinting
nanotubes
a major form of bacterial communication in nature enables exchange of cellular molecules within and b/t species
Sanger sequencing
a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication - termination of replication occurs every time a dideoxynucleotide shows up
Neutral Mutation
a mutation that has no effect on survival or reproduction
example of specialized transduction
a temperate prophage inserted into a fixed site on the bacterial chromosome. when prophage dna separates from the chromosome, the imperfect separation can carry host genes w/ it
Which of the following is NOT correctly associated? a. Eastern blot — to study the defective proteins in a mixture of proteins b. Northern blot — study of gene expression by detecting mRNA in the sample b. Autoradiography — visualization of radioactive probe binding onto the molecule of question c. Southern blot — detection of a specific DNA sequence in DNA sample d. Western blot — identification of a specific protein in a protein mixture by using antibodies
a. Eastern blot — to study the defective proteins in a mixture of proteins
Which of the following is NOT correctly associated? a. Exonuclease — to create the genome fragments during cDNA library b. Genomic library — a representation of entire genome of an organism c. cDNA library — a representation of coding regions of expressed genes of an organism d. Reverse transcriptase — synthesis of cDNA from mRNA e. DNA ligase — to ligate the genome fragments into the cloning vector
a. Exonuclease — to create the genome fragments during cDNA library
Which of the following are presently involved in DNA fingerprinting for CODIS? a. STRs b. Gel electrophoresis c. RFLPs d. restriction enzymes
a. STRs b. Gel electrophoresis d. restriction enzymes
q^2
aa (recessive)
resistance factors (R factors) carry ___ ___ genes
abx resistance
risk factors that predispose pts to colon cancer?
adverse lifestyle choices - high fat/low-fiber diet, little exercise, smoking, alcohol overuse
Screening for colon and rectal cancer
advised for everyone 50 years and older. - screening programs are capable of detecting cancers at earliest stages while they are curable.
Point mutation
affect a single nucleotide in the DNA sequence. can result from a base substitution
Lynch Syndrome II
all of the features of I are present. additionally, pts have inordinately incr susceptibility to certain extracolonic cancers - endometrial - carcinoma of ovary, gastric, small bowel, pancreas, ureter, renal pelvis, breast
lifetime probability of developing cancer by site in women
all sites is 1/3 breast is 1/8
you can add luminescence to the DNA and visualize light on the DNA fragments to show
all the DNA in the gel
What is cell free DNA?
allows non-invasive testing - also called NIPS (non-invasive prenatal screening)
2 pieces of cleaved insulin
alpha beta connected by disulfide bond
Silent Mutation
alters a base but does not change the amino acid
_____ genomes have both + and - strand characteristics
ambisense
size of coronavirus genome
among the largest RNA genomes 28-33 kb
Deamination - Spontaneous DNA damage
an amino group of C or A is spontaneously lost - C or A without amino groups can't H bond with normal G or T - DNA pol sees deaminated C or A and puts the wrong base
Balanced Gene Expression
an equal amount of each allele being expressed
FISH mapping
an example of physical mapping - gene mapping by fluorescence in situ hybridization of biotin labeled DNA probe for MGO to spread of human metaphase chromosomes
When RFLP analysis is used to search for a human gene, the strategy is to first locate:
any DNA marker co-inherited with the genetic trait of interest
what can viruses infect?
any living cell (even amoeba)
ectopic expression of APC outside of the colorectal epithelial cells induces
apoptosis
example of ambisense RNA viral genome
arenaviridae (lassa virus)
using ___ ___ as vectors allows for large-scale analysis of genomes
artificial chromosomes
why do we gen new flu vax on yearly basis
assortment
lynch syndrome I (HNPCC) inheritance pattern
autosomal dominant
APC interacts w/ a very important cell adhesion/signalling molecule called ___ ___ through a series of binding and down-regulating repeats
b-catenin
Which of the following are integral to the cloning technique? a. An antibiotic resistance gene that can be interrupted by the DNA of interest b. An antibiotic resistance gene to allow growth on antibiotic containing medium c. A gene with an observable phenotype that can be interrupted by the DNA of interest d. The vector (plasmid) should have an origin of replication so that multiple copies can be made
b. An antibiotic resistance gene to allow growth on antibiotic containing medium c. A gene with an observable phenotype that can be interrupted by the DNA of interest d. The vector (plasmid) should have an origin of replication so that multiple copies can be made
For which of the following purposes does the RFLP technique not serve as a useful tool? a. Determination of disease risk b. Gene cloning onto vector c. Localization of genes for genetic disorder d. Paternity testing e. Genome mapping
b. Gene cloning onto vector
In the pharmaceutical industry, the biotechnological techniques are used to produce what? a. T-cells b. Human insulin c. Growth hormones d. Liver cells e. rDNA vaccines
b. Human insulin c. Growth hormones e. rDNA vaccines
What is a short tandem repeat (STR)? a. Microsatelitte composed of a unit of twenty-two nucleotides repeated hundreds of times in a row on the DNA b. Microsatelitte composed of a unit of two nucleotides repeated hundreds of times in a row on the DNA c. Microsatelitte composed of a unit of two hundred nucleotides repeated hundreds of times in a row on the DNA d. Microsatelitte composed of a unit of two hundred twenty-two nucleotides repeated hundreds of times in a row on the DNA e. Microsatelitte composed of a unit of twenty nucleotides repeated hundreds of times in a row on the DNA
b. Microsatelitte composed of a unit of two nucleotides repeated hundreds of times in a row on the DNA
Which of the following two enzymes are needed to construct a cDNA library? a. Reverse transcriptase and Taq polymerase b. Reverse transcriptase and DNA Polymerase c. DNA ligase and Taq polymerase d. Taq polymerase and RNA polymerase
b. Reverse transcriptase and DNA Polymerase
The E. coli bacterium transformed with a recombinant plasmid which was obtained after the insertion of the human insulin gene in the Lac Z gene on that plasmid (Lac Z and Amp resistance genes initially present on the plasmid). Now the research wants to pick a transformed bacterial cell with correctly cloned human insulin gene. For what kind of phenotypic character he should look for when the bacterial cells are grown in a medium containing ampicillin and X-gal in it? a. Metallic blue bacterial colonies b. White bacterial colonies c. Blue bacterial colonies d. Bacterial colonies with any color except white and blue e. Pale blue bacterial colonies
b. White bacterial colonies
sequence repetitions can occur ____ restriction sites
b/t
endospores are produced by which type of bacteria
bacillus clostridium
plasmid vectors can be taken up by which kind of hosts?
bacteria, viruses, mammalian cells, insect cells
Ti plasmids are found in ____ cells and often infect certain kinds of plants
bacterial
what is the primary reservoir of genetic info within the bacterial cell?
bacterial chromosome
what are gene transfer agents (GTAs)
bacteriophage like particles
process of transduction involves
bacteriophages carry DNA from donor to recipient cell
why must reoviridae with dsRNA have RNAPol in the virus particle?
bc dsRNA can't be translated - cannot be accessed by the ribosome even though have +/-
why does blotting paper need to be put in sealed container
bc it has radioactively labelled DNA nucleotides and needs to hybridize
why do bigger DNA fragments move slower through gel during electrophoresis
bc they have a harder time pushing through it
what enzyme is encoded by the lac Z gene?
beta-galactosidase
how do prokaryotes divide
binary fission
the distinction b/t sporadic vs familial causes & genetic vs environmental predisposing factors has become ___ and should be thought of a ____ contributing to CRC
blurred continuum
function of beta-galactosidase
breaks lactose down to galactose and glucose
a striking example of the genetic differences within a single tissue type is ___ cancer
breast diff cells: luminal A/B, HER2-enriched, basal-like. basal-like looked more like ovarian ca and squamous
in pts w/ FHx HNPCC, when should they begin screening
by age 25 y/o OR 5-10 yrs before the age of the earliest colorectal cancer dx'd in fam even if Asx
Which of the following is NOT correctly associated regarding gene transfer in eukaryotic cells? a. Microinjection ----- Physical method of gene transfer in eukaryotic cells. b. Agrobacterium ----- Natural genetic engineer. c. BAC ----- Transfer platinum particles coated with DNA to the animal cell. d. Ti plasmid ----- Induce crown galls in Agrobacterium tumefaciens infected plants. e. Biolistic particle delivery system ----- Transfer gold or tungsten particles coated with DNA to the host cell.
c. BAC ----- Transfer platinum particles coated with DNA to the animal cell.
Which of the following viral vectors is not used to deliver the rDNA molecule into the defective cells in human gene therapy? a. Adenovirus b. Vaccinia c. Human immunodeficiency virus d. Adeno-associated virus e. Herpes simplex virus
c. Human immunodeficiency virus
A researcher wants to use a molecular technique to find the DNA sequence ATGGGCCAGCT in the genome of mice. He should use the __________ technique with __________ as a probe. a. Western blotting; TACCCGGTCGA b. Gel electrophoresis; ATGGGCCAGCT c. Southern blotting; TACCCGGTCGA d. Southern blotting; ATGGGCCAGCT e. Gel electrophoresis; DNA dye
c. Southern blotting; TACCCGGTCGA
Gene therapy involves which of the following? a. The replacement of defective ribosome with the functional one in an individual's cells to treat a hereditary disease b. The replacement of defective mRNA with the functional one in an individual's cells to treat a hereditary disease c. The replacement of defective gene with the fully functional gene in an individual's cells to treat a hereditary disease d. The replacement of defective rRNA with the functional one in an individual's cells to treat a hereditary disease e. The replacement of defective tRNA with the functional one in an individual's cells to treat a hereditary disease
c. The replacement of defective gene with the fully functional gene in an individual's cells to treat a hereditary disease
____ libraries permit storage of only coding sequences
cDNA
how are euk genes able to be expressed in bacterial cells?
cDNA libraries (complementary DNA libraries)
norwalk virus is caused by
caliciviruses
polymorphism means
can acquire a diff shape/size/change in the genetic code
what is the function of membrane vesicles (MVs)
can transfer abx resistance genes, virulence and metabolic traits
dissimilation plasmids encode enzymes for the ____ of unusual compounds
catabolism (example - oil/toxic spills can be cleaned up by bacteria)
Neural Tube Defects
caused by high levels of AFP
Chromosomal abnormalities
caused by low levels of AFP; can cause downs (trisomy 21) or edwards syndrome (trisomy 18)
Damaging Agent: IR, HU, UV- light, X-rays, anti-tumor agents
causes lesion: inerstrand crosslink double strand breaks Repair process: recombinational repair (HR/NHEJ)
what does it mean for a bacterial cell to be competent?
cell is capable of accepting genetic material through transformation
conjugation is aka
cell sex
cell wall maintains ___ ___
cell shape
some archaea completely lack a
cell wall
what are found in all bacteria
cell/cytoplasmic membrane bacterial chromosome/nucleoid ribosomes cytoplasm
reverse mutation
changes a mutant phenotype back to the wild-type phenotype
What Maternal Blood Screening and what does it measure? (4)
checks your blood to see if your baby may be at risk for some birth defects, like down syndrome from 15-22 weeks of pregnancy - QUAD SCREENING 1) MS-AFP 2) estriol 3) hCG 4) inhibin A
histones bind to ___ DNA
chromosomal
blood supply is full of ___ viruses
circo
WG reveals all genomic mutations as presented w/ the two ____ plots
circos
TT virus is example of ____viridae
circoviridae
prokaryote is one ____ chromosome that is not enclosed by a membrane
circular
molecular ____ allows for many genetically identical copies
cloning
CCR5 Gene
codes for a receptor used by HIV to enter host immune cells - the mutant △CCR5 gene will not allow entry causing an HIV resistance
Which cancer is most common
colon cancer. - by age 70, 50% of population have acquired precancerous adenomas, and 10% progress to malignancy
APC (FAP) is expressed in ___ epithelial cells and concentration incr w/ cell age
colorectal
loss of APC function is likely to play a rate-limiting role in tumor initiation in the
colorectum
what is hereditary nonpolyposis colorectal cancer, HNPCC?
condition where tendency to develop colorectal cancer is inherited
High frequency transfer or Hfr transfer is a form of
conjugation
transposition onto a _____ plasmid can lead to rapid dissemination of resistance among different bacteria
conjugative
conjugation pictorial w/ explanation
conjugative plasmid in A is donating a strand of its DNA to cell B. transferred DNA either synthesizes a complementary strand and recirculizes as in C and D OR remains in fragments as in E fragments either recombine w/ recipient cell chromosomes as in F or are digested by nucleases in the cytosol
why does the size of plasmids vary?
copy # of plasmids per bacterial cell varies for different plasmids, ranging from 1 to 1000's of copies per cell
SARS, MERS and SARS-CoV-2 are all caused by
coronaviruses
since 1997, STRs have been used in the
courtroom
What is recombination?
crossing over and synapsis allow genetic recombination - occurs in prophase
restriction endonuclease function
cut specifically in the middle of gene so you can tell if the gene of interest that we are inserting is present or not.
What kind of testing is available to detect abnormalities in chromosome structure, protein function, and DNA sequence?
cytogenetic, biochemical, and molecular testing
Which of the following does NOT fall under the category of vectors for gene cloning? a. Yeast artificial chromosome b. Cosmid c. Plasmid d. Cyanobacterium e. Bacterial artificial chromosome
d. Cyanobacterium
Which of the following statements is NOT true regarding reverse genetics? a. Reverse genetics works in the reverse direction to that of the forward genetics b. The gene silencing (RNAi) falls under the category of gene knockdown as its effects are temporary, whereas gene knockout effects are permanent c. Reverse genetics helps to understand the function of a gene by analyzing the phenotypic effects of specifically mutated or silenced gene sequences d. The normal mouse exhibits an obesity model as compared to the knockout mouse under the laboratory conditions e. In reverse genetics, the genes are deleted by gene targeting or gene knockout to determine their phenotypic function
d. The normal mouse exhibits an obesity model as compared to the knockout mouse under the laboratory conditions
Southern blot can be used to learn which of the following? a. The size, its copy number and exact position of tRNA onto the ribosome molecule b. The size, its copy number and exact position of mRNA, tRNA and rRNA molecules onto the ribosome molecule c. The size, its copy number and exact position of mRNA onto the ribosome molecule d. The size, its copy number and exact position of rRNA onto the ribosome molecule e. The size, its copy number and exact position of a cloned gene within the rDNA molecule
d. The size, its copy number and exact position of a cloned gene within the rDNA molecule
HNPCC appears to involve _____ MMR
defective. result in genetic anomalies rapidly accumulate. after ras mutation, accelerated progress through intermediate stages of carcinogenesis are seen (post-Ras mutation)
in knock-out mice, a cloned gene of an unknown function is used to make a mutant that is ____ in that gene
deficient
endospores are resistant to
desiccation, heat, chemicals, radiation
Ultrasonography can be used to
determine the presence of Neural Tube Defects (like spina bifida) as well as chromosomal abnormalities
Norwalk virus causes outbreaks of
diarrheal disease on cruise ships, schools, colleges, prisons, any institutional setting
recombinant DNA is used to create ______ in an organism to establish gene function
differences
there are ____ in DNA seqs b/t patho islands and their host genomes
differences also presence of Tn-like genes to which supports the theory of origin and movement from unrelated bacterial spp
in the new taxonomy with TCGA, ca of nonepithelial origin (neural, muscle, connective tissue) appear the most _____ from epithelial tumors based on virtually all molecular platforms
different arising from basal layer-like cells (C2-squamous-like and C4-BRCA/basal) & those w/ secretary functions subtypes reflect primarily cell of origin
if restriction fragment length increases and the restriction endonuclease is introduced, end up with ___ length of DNA
different length different banding pattern
are eukaryotic cells easy or difficult to transform
difficult
Mutation in imprinting center
directs sex-specific methylation. Translocation can move the genes away from their imprinting center, then those genes can get methylated and turned off
the mutation of APC is ____ in tendency to FAP
dominant
familial adenomatous polyposis (FAP) is an autosomal ___ predisposition to development of multiple adenomatous polyps in the colon and the rectum
dominant also at risk for extracolonic manifestations
What is low MS-AFP indicative of?
down syndome
genome type III is which genome type
dsRNA
The molecular cloning term refers to which of the following? a. The method of replication of one molecule of phospholipid to produce a population of cells with phospholipid molecules b. The method of replication of one molecule of polysaccharide to produce a population of cells with polysaccharide molecules c. The method of replication of one molecule of fatty acid to produce a population of cells with fatty acid molecules d. The method of replication of one molecule of protein to produce a population of cells with protein molecules e. The method of replication of one molecule of DNA to produce a population of cells with identical DNA molecules
e. The method of replication of one molecule of DNA to produce a population of cells with identical DNA molecules
Restriction fragment length polymorphism, or RFLP, exploits which of the following? a. Similarities in heterologous RNA sequences b. Variations in homologous RNA sequences c. Variations in homologous mRNA sequences d. Similarities in heterologous DNA sequences e. Variations in homologous DNA sequences
e. Variations in homologous DNA sequences
lynch syndrome I (HNPCC) age of onset
early age of CRC onset, age 45 y/o
genomic libraries provide ____ access than entire chromosomes do
easier
What can reduce risk of colon cancer?
eating fresh fruit, veggies, and grains, maintaining proper weight, exercise, reduce exposure to toxins and tobacco
viruses caused by filoviridae
ebola virus marburg virus unusual filamentous particles
shotgun method of transforming euk cells
electrical charged cells are bombarded with gold/tungsten particles coated in DNA and hope cells uptake the DNA
how to separate fragments of DNA
electrophoresis
women at risk for HNPCC should have yearly _____ screening
endometrial
sporulation means
endospore formation
plasmids often code for proteins that
enhance pathogenicity of a bacterium
men and women at risk for HNPCC need exams of the
entire colon
naked virus lacks
env
capsid may be surrounded by an ___ of lipid membranes and proteins
envelope
Phenotypes can be affected by...?
environment. ex: siamese cats and rabbits produce a temperature-sensitive version of tyrosinase. - If the temp is BELOW 33°, tyrosinase is active = dark pigment. - If the temp is ABOVE 33°, tyrosinase is inactive = no pigment.
function of RdRp
enz that can copy the RNA genome neg strand to +mRNA
Which of the following is an intercalating agent?
ethidium bromide
are archaea evolutionary closer to euk or bacteria
euk
circoviruses infect who?
everyone! they are in our blood at most times in our lives
mutations of what region of BRCA2 are associated w/ greater risk of ovarian ca and lower risk of breast ca than are mutations outside of this region
exon 11 containing OCCR, 8 BRC repeats
mature mRNA encodes for only the ___ portions of the protein
expressed
membrane vesicles (MVs) are AKA
extracellular vesicles (EVs) or exosomes
what is the F plasmid
fertility plasmid. allows for cell sex/conjugation
e coli and gonococci use ___ to adhere to epithelial cells
fibriae
amphitrichous flagellar arrangement
flagella at both poles of the cell
polar flagellar arrangement
flagella attached at 1 or both ends of the cell
peritrichous flagellar arrangement
flagella dispersed randomly over the cell surface
direct repeats (DRs) in host DNA ____ a transposable element
flank allows uptake of sticky ends
Intercalating Agents - Induced DNA Damage
flat, multi-ringed molecules tightly wedge themselves between the bases of DNA and distort the 3D structure -used for ethidium bromide to visualize DNA during centrifugation or gel electrophoresis
how do radioactive probe (ssDNA) hybridize with the DNA on the blotting paper?
float around and look for partner strands of denatured DNA fragments in the gel to bind with
how is a recombined plasmid formed?
foreign DNA wants to anneal to the bacterial plasmid once introduced OR could potentially not recombine
slime layer surface coating
forms loosely around the cell protects cell from loss of water nutrients
plasmids are found in most ____ and in some ___
found in most bacteria in some fungi
DNA fingerprinting compares the ___ ____ of DNA
fragment lengths
We can determine from various populations?
frequency and distribution ex: in some countries, there are higher incidences of variant gene
gene therapy is the process of using ____ ____ to replace defective genes
genetic engineering
Crossing over and synapsis allow
genetic recombination
the -ssRNA ___ is used to make +RNA
genome
NP mRNA is translated to form a protein to which participates in
genome replication
what are the only RNA genome viruses?
genome type III (dsRNA)
HBV viral genome
genome type VII gapped dsDNA genomes
DNA microarray is used for ____-wide analysis in breast ca
genome-wide
what tells a virus which cell to infect, when to replicate, how to kill host cell and avoid immune system?
genomic material of the virus
how to trick bacteria into taking only exons
get a DNA copy of the mature mRNA (cDNA) using RT
Recombinant Frequencies
give relative map distances - missed double crossovers will end up calculating shorter recombination frequencies
What is recombination frequency (Genetic Map)?
gives an estimate to how far apart 2 genes are on chromosomes
how is HBV gapped dsDNA repaired in host?
goes to nucleus cell enz repair it take off protein and little piece of RNA dsDNA transcribed to mRNA, translated into proteins, becomes part of virus particle
Which proteins allow HIV into the cell?
gp120 and gp41
Which hormones are made by the placenta?
hCG, Inhibin A, and estriol (which goes to liver)
Loci that are far apart:
have a higher recombination rate than loci that are close together.
Bacteria
have no nuclei and no membrane bound organelles.
hereditary breast ca has genetic _____
heterogeneity
the overall grade of both BRCA1 & 2 breast ca was significantly ____ than that of the controls.
higher
women with Lynch Syndrome have a much ____ chance of developing colon, endometrial, ovarian cancer than the general pop
higher
applications of genomic revolution in breast ca
histological subtypes - IDC, ILC (invasive ductal and lobular ca) main findings - white outstanding challenges - blue
prokaryotes have no
histones organelles
What occurs in Meiosis I?
homologous chromosomes pair and align on the meiotic spindle - paternal and maternal homologous exchange homologous segments crossover creating new daughter chromosomes
Prophase I of Meiosis
homologous chromosomes pair up and form tetrads, crossing over occurs - if no crossing over occurs, we end up with parental gametes - if crossing over occurs, we end up recombinant gametes
transposition does not need ____ _____
homologous recombo which requires high similarity b/w resident and incoming DNA
conjugation is a form of ____ gene transfer
horizontal
transduction is a form of ____ gene transfer
horizontal
transformation is a form of _____ gene transfer
horizontal
pathogenicity islands have the ability to make their ___ pathogenic
hosts they contain multiple genes coordinated to create a new trait in the bacterium
what is meant by viral flexibility
how many mistakes can be made, bypass host immune system or antiviral rxs, no proofreading, frequent mutation
What is hCG?
human chorionic gonadotropin, a hormone made in the placenta
what do you do after you have copy of DNA on piece of blotting paper
hybridize it with probes incubated w/ radioactive nucleic acids and then rinsed
WES and TS identify ___ of mutations and ____ reflect the stark differences b/t the two genomic landscapes
id only a fraction of mutations do not necessarily reflect
how would you have differences in fragment lengths in DNA?
if crossing over and uneven during meiosis, sequence reads the same so could be frequent
how to test if bacteria picked up a gene of interest when the gene of interest has ampicillin resistant abx gene & beta-galactosidase enzyme?
if the bacteria picked up the plasmid, the it will have ampicillin resistance and will grow on medium with ampicillin. It will also metabolize and turn blue (phenotypic presentation) in the presence of X-gal (sugar metabolized by beta-galactosidase enzyme)
southern blot involves DNA-probe hybridization with the DNA of interest to label it and show
if the sequences of interest are in the DNA library
what would cause a banding pattern with bands far from one another
if translocation event occurs - small piece of DNA/RFLP ends up on complementary chromosome or non-sis chromatid during crossing over - restriction fragment length may increase
What is the Hardy-Weinberg Principle?
in a population at equilibrium, allelic and genotypic frequencies in that population will remain constant from generation to generation.
X-Inactivation
in females, impacts gene expression dependent on sex. different from gene imprinting because gene imprinting only affects genes- doesn't matter which parent it comes from. - one chromosome is chosen to be inactivated (dosage compensation) and condenses up, it becomes epigenetically modified so that we have a DNA methylation or histone modification - females are mosaic - barr body= heterochromic masses seen during interphase
in HNPCC, the phenotype results from ____ of one of four MMR genes, namely:
inactivation 1. MSH2 2. MLH1 3. PMS1 4. PMS2
What if genes are really far apart? What do they exhibit?
independent assortment
viruses caused by orthomyxoviridae
influenza virus causes annual outbreaks of respiratory disease in millions
example of segmented -ssRNA viruses
influenza viruses have 8 -ssRNA segments
FAP arises from mutations in APC gene on chromosome 5 which is meant to ____ cell growth
inhibit
initiation/progression of FAP
initiation - fast progression - normal
initiation/progression of HNPCC
initiation - normal progression - fast
once the gene is opened up with the restriction endonuclease, you can ___ the foreign DNA
insert
example of using bacterial cells to produce human genes
insulin
In metabolic pathways, what kind of enzymes are present?
interdependence of enzymes
all transposable elements contain ___ ___ at the ends of elements and a transposase gene
inverted repeats (IRs)
molecular cloning involves
isolation of gene of interest, insertion of gene into bacterial genome, amplification of the DNA in transformed cells by reproduction in the plasmid/bacterial chromosome
What do test crosses involve?
it involves crossing an unknown with a homozygous recessive to reveal an unknown genotype. - it uses a homozygous recessive crossed with unknown genotype to find out genotype.
what happens when HBV (gapped dsDNA) enters the host cell?
it must be repaired. gapped dsDNA -> dsDNA occurs in the nucleus, cell enz repair it
how can you tell that the DNA of interest has been inserted into the bacterial plasmid on the plant?
it will develop a tumor
____ genes shift from one part of the genome to another, such as b/w DNA molecules NOT CELLS
jumping genes (Tns, TEs)
diff b/t STR and RFLPs
just two letters repeated over and over --RFLPs are long.
although introns are not expressed in euk genome, bacterial ____ the machinery to clip out introns
lack
viruses lack the ___ and ____ for synthesizing proteins
lack enzymes & machinery
flaviviridae ____ a poly A tail at 3' end
lacks
picornaviridae ____ a cap at 5' end
lacks. instead have small viral protein (VPG)
example banding pattern of STRs on gel
lane 1 is reference (DNA found at scene) other lanes are compared to reference piece lane 7 person did crime
Chromosomal mutations
large segments of chromosomes are deleted, inverted, moved, duplicated
artificial chromosomes are used to store ____ fragments than bacterial plasmids
larger
viruses caused by arenaviridae
lassa virus causes hemorrhagic fever - largely in Africa
plasmids are much ___ effective in eukaryotes
less
What other risk factors predispose patients to colon cancer?
lifestyle choices like: high fat, low fiber diet, little exercise, smoking and alcohol overuse = sporadic colon cancer
proteins needed by viruses come from the ____ bc they are unable to carry proteins/ribosomes themselves due to small size
living host cell
there are several ____ penetrance mutations that contribute to CRC in an additive way - involving interactions b/t genes & environmental factors
low penetrance
what are membrane vesicles (MVs)
lumen containing spheres of lipid bilayers derived from cell surface
why can't HBV viral DNA be made into mRNA when it enters the cell
mRNA can only be made from dsDNA among the DNA viruses. mRNA cannot be made from gapped DNA or ssDNA.
Unbalanced Gene Expression
main reason for imbalance - can be random - can occur if one gene is not expressed at the same rate as the other genes
would have to use ___ different RFLPs to get a DNA fingerprint
many
The Goldilocks Principle
many genetics disorders involve changes in the amount of gene product.
Positional cloning refers to:
mapping a gene to a chromosomal region and then identifying and cloning a genomic copy of the gene from the region
viruses caused by paramyxoviridae
measles virus mumps virus important childhood infections
Genetic Mapping
measure genetic distance between 2 genes or DNA markers, based on the frequency of recombination events, which is a measure of how close 2 genes or DNA markers are to each other. - also called DNA Linkage Analysis - the degree to which 2 genes/DNA markers travel together (segregate) on chromosomes is a measurement of their genetic distance, and how closely they are linked together
Physical Mapping
measures physical distance between DNA fragments are measured. This is used to assign DNA fragments to specific chromosomes. - provides most accurate map distance
viruses lack a ____ system & therefore must obtain energy from host cells
metabolic
Imprinting is thought to be caused by:
methylation of a region of a chromosome surrounding a gene
Prader-Willi Syndrome
microdeletion on chromosome 15 from father. Mother's gene is expressed. - paternal segment is deleted, undeleted maternal chromosome remains - Treatment: Diet modification for obesity, behavioral therapy, SSRI for OCD, Growth hormone therapy - 70% paternal deletion - 20-30% maternal from uniparental disomy
Angelmann's Syndrome
microdeletion on chromosome 15 from mother. Father's gene is expressed. - maternal segment is deleted, undeleted paternal chromosome remains - Treatment: EEG for treatment of seizures, physical and speech therapy, special education - 70% maternal deletion - 7% paternal (from uniparental disomy)
____ instability serves as a useful marker of mutator phenotype characteristic of HNPCC and some sporadic tumors
microsatellite
how do euk cells divide
mitosis
instead of defining cancers according to their tissues of origin, TCGA (new system) considers
molecular subtypes
capsule surface coatings
more tightly bound to a cell than a slime layer denser and thicker than slime layer
what freq of colon cancers occur sporadically or in cluster in susceptible families?
most
sx of HNPCC
most pts develop polyps and cancer of the colon and rectum w/o sx. however, sx can occur - hematochezia - diarrhea not related to diet/flu - chronic constipation - cramping of abdomen - persistent decr size of stool - frequent distention of abdomen - weight loss - fatigue should NOT wait for sx to develop
although STRs are useful, b/c we have sequenced the genome, may move towards
move more towards DNA sequencing
is PCR faster or slower than molecular cloning
much faster
What adds to accuracy of genetic map?
multiple loci
what does it mean to be a strict intracellular parasite
must reproduce inside host cell (virus)
Frameshift mutation
mutation that shifts the "reading" frame of the genetic code by inserting or deleting a base (nucleotide)
What can influence genotypic frequencies?
mutation, migration, and selection with non-random union of gametes
new horizontal gene transfer is done by
nanotubes
findings suggest that breast cancer due to BRCA1 has a different ___ _____ compared to BRCA2 or apparent sporadic ca.
natural history may have implications for screening/management
amniocentesis
needle puncture of the amniotic sac to withdraw amniotic fluid for analysis
after translation of viral proteins has been complete, the proteins go on to produce ____ viral particles
new
how do some individuals w/ HNPCC not have an affected parent?
new mutation/newly altered gene. they can then pass to their children
are circoviruses harmful
no
can individuals who have not inherited the HNPCC gene pass it to their children?
no
can viruses make energy/ATP?
no
do Mycoplasmas contain peptidoglycan in cell wall?
no
do archaea have peptidoglycan?
no
do viruses have free AAs or sugars
no
Is it easy to make a genetic map out of human genome?
no - difficult because there are so many genes. The X-chromsome alone has over 1000 known genes mapped.
function of - strand RNA
no function except to be a template for synthesis of more + strands
can early p53 mutation by itself cause carcinoma?
no, KO p53 -/- mice appear viable but highly susceptible to tumors. tumors not induced until other somatic mutations occur, p53 then removes one of last barriers to full blown carcinoma
if the lac Z gene is non-functional, then the beta-galactosidase enzyme is
non-functional
What is prenatal screening?
non-invasive and often used to identify the need for more invasive prenatal diagnosis techniques -measurements of analytes, proteins, and hormones in maternal serum
specificity of shotgun transformation method
non-specific although successful
_____ means that cancer can occur when only small # polyps present
nonpolyposis
are cells able to copy an RNA molecule into another RNA?
nope
can non-pathogenic bacteria have pathogenicity islands?
nope
____ blotting is used for detecting mRNA
northern
Polygenic Inheritance
not all traits fit Mendel's expected ratios 1) each trait is specified by a single gene 2) 2 alternative alleles 3) gene production acts independently 4) no environmental effects *Skin color and height are continuously varying traits because they are influenced by multiple genes *means that we have multiple genes involved in the expression of this trait
after blotting, the nitrocellulose paper contains a
nucleic acid print
combination of capsid + the genome is referred to as
nucleocapsid
What is the repair pathway that plays a major role in repair of thymine dimers?
nucleotide excision repair
when the plasmid is introduced to the plant cells, the plasmid can make its way into the ____ to infect the plant
nucleus
what is the obligatory 1st step when ambisense RNA viral genomes do when they enter host cell?
obligatory 1st step is genome is replicated to form mRNA from the 3'. called NP mRNA catalyzed by RNAPol in viral particle
participating bacteria in a single transduction even must be
of the same species b/v bacteriophages are very specific in the cell type that they will infect
Pleiotropic Inheritance
often one gene has more than one effect, which may skew ratios if one is lethal - albinism, PKA, marphan syndrome
how do you view DNA libraries once made?
once DNA has been cloned, can use it to probe for similar genes and other organisms
how common is colon cancer?
one of the common forms of disease. 50% pop has pre-cancerous adenomas at age 70 and 10% progress to malignancy
Insertion Mutation
one single base is inserted, which changes the whole reading frame so everything downstream gets changed - more damaging as it causes many missense mutations
when are structural proteins of virus made
only when virus is ready for assembly. timing is encoded by viral genome
cell wall withstands strong ____ pressure
osmotic pressures
sometimes, ___ cancers other than CRC can occur in families w/ HNPCC
other - uterus - ovary - stomach - urinary tract - small bowel - bile duct
The Hardy-Weinberg Equations
p+q=1 p^2+2pq+q^2=1
Which Hardy-Weinberg equation represents the genotype frequencies in a population?
p2 + 2pq + q2 = 1
final stages that lead to invasive carcinoma appear to involve ___ mutation, which eliminates the key protections against anomalous DNA replication
p53
euk have ___/___ chromosomes surrounded by a nuclear membrane
paired/several
example of non-segmented -ssRNA viruses
paramyxoviruses (measles, mumps, rabies)
which virus causes fifth disease?
parvovirus. rash/fever illness
cats and dogs are commonly infected with animal ___viruses and they have vax for them
parvoviruses
What is a gene pool?
people with the same allele; twice the number of individuals sampled for autosomes
bacteria contains _____ in cell walls
peptidoglycan
Test cross reveals
phenotypic recombinants
hybridization of radioactively labelled nucleic acids with those in the gel are able to be visualized b/c
photographic film laid over the filter and exposed only in areas that contain radioactivity (autoradiography)
crossing over involves
physical exchange of genetic material that accompanies phenotypic recombination; chromosomes physically swap pieces and can be seen under the microscope.
transduction is the case of the ___ DNA
piggyback
how do tumors grow in plant cells infected by Ti plasmids?
plant cells replicate to allow the tumor to grow
mechanism of action of Ti plasmid in plant
plasmid is transferred to the plant and induces a tumor.
____ are independent, self-replicating, circular units of dsDNA
plasmids
many bacteria possess small independently replicating extrachromosomal nucleic acid molecules such as
plasmids and bacteriophages
process of conjugation
plasmids transferred from one bacterium to another
picornaviridae causes
polio
Errors of DNA polymerase - Spontaneous DNA damage
polymerases and proofreading/repair enzymes are not perfect. Some major causes include: strand slippage = repeats cause abnormal loop (DNA pol copies the same thing twice) and defective proofreading
prokaryote comes from the Greek words for ____
prenucleus
bacterial chromosome is the ___ reservoir of genetic info within the cell
primary
Most types of DNA damage can be fixed...
prior to DNA rep except: transposons and retroviruses
archaea cell plan
prokaryotes
ribosomes is the site of _____ synthesis
protein
ribosomes are made of ____ and _RNA
protein and rRNA
what is a capsid
protein coat surrounding a virus
archaea cell walls made of
proteins or polysaccharides
lynch syndrome I (HNPCC) localization of colon cancer
proximal colonic predilection to CRC, 70% proximal to the splenic flexure
how is HNPCC inherited?
pts w/ HNPCC have 50% chance of passing the HNPCC gene to each of their children. The gene can be passed on even if parent has had surgery to remove the colon.
viruses caused by rhabdoviridae
rabies virus zoonotic infection
generalized transduction
random fragments of disintegrating host DNA is packaged into a phage during assembly. any gene from the bacterium can be transmitted
HNPCC is characterized by ___ progression of cancer w/o massive accumulation of precancerous cells
rapid
why do we have a new strain of flu that causes global pandemic
reassorted strain
what is the F+ cell?
recipient of the donor F plasmid
____ DNA techniques can be used to construct vax
recombinant
Linked genes always exhibit:
recombination frequencies of less than 50%
Genetic Maps are based on
recombination frequencies; the relative distance between 2 genes on the same chromosome based on recombination frequency - percent recombination can be used to generate a map
What is theta?
recombination frequency between 2 genes. - used in genetic mapping and pedigrees
is molecular cloning a fast or slow process
relatively slow
rotaviruses are examples of _____ family
reoviridae gastroenteritis
+RNA is _____ to make -ssRNA copies to get incorporated into virus particles
replicated
____ enz are used to cut around STRs before run through a gel
restriction
how do Ti plasmids and restriction endonucleases work together
restriction endonuclease cut genes of interest and stick genes to the Ti plasmid
which enz is used to cut up DNA
restriction endonucleases
RFLP stands for
restriction fragment length polymorphisms
knockout mice are an example of ___ genetics
reverse
___ ____ makes a complementary DNA copy of mature mRNA
reverse transcriptase
in HNPCC, CRC occurs primary on the ___ side of the colon
right
human pathogens of togaviridae
rubella, Eastern equine encephalitis virus
what pathogenic bacterial species have patho islands
s aureus e coli h pylori v cholerae salmonella spp. yersinia spp.
plasmids are ___-replicating circular pieces of DNA
self
goal of virus
self propagate/reproduce
conjugation requires cell-to-cell contact via
sex pili
conjugative plasmid carries genes for __ ___ and ___ of the plasmid
sex pili and transfer of the plasmid
STR stands for
short tandem repeats
large number of mutations identified by WGS permit mutation ____ detection
signature
each bacterial cell contains a ____ fragment. All cells together are the DNA library
single
monotrichous flagellar arrangement
single flagellum
during electrophoresis, fragments are separated by ___ as they move through the gels.
size
Continuously Variant Trait
skin color, height is an example SKIN: there is a continuous spectrum of color that could be obtained depending on how many alleles are displayed for pigment; multiple genes have continuous effects HEIGHT: on a continuum!
plasmids are ideal vectors for which sized DNA?
small
lophotrichous flagellar arrangement
small bunches or tufts
Gene Mutations
small changes in DNA sequence, one or few nucleotides
process of transformation
small fragments of soluble DNA from the surrounding environment are accepted by a bacterial cell
___ DNA fragments move faster through gel during electrophoresis
smaller
only virus that was eradicated
smallpox soon to be polio
APC dominant mutation tendency to FAP w/ low freq of advance to adenoma suggests that 1st step is
somatic mutation to which affects the WT allele mutation alone not induce hyperplasia
genome type VII
some viruses have DNA genomes (vs retroviral) with a diff configuration of separate Baltimore class. gapped dsDNA genomes
What is an ultrasound?
sonogram that uses sound waves to show a picture of your baby in utero.
____ blotting is good tech for identifying DNA in nitrocellulose gel
southern
pathogenicity island
special class of mobile genetic elements containing groups of coordinately controlled virulence genes - often w/ ISs, DR sequence, etc. at their ends
specialized transduction
specific bacterial genes are packaged inside a phage and transferred into a recipient cell
What is high MS-AFP indicative of?
spina bifida
is circoviridae ss or ds DNA virus
ssDNA
is parvovirus ss or ds DNA or RNA?
ssDNA
DNA will ___ to gold/tungsten particles and can be fired at high velocity into cells
stick
what kind of parasites are viruses
strict, intracellular
Transition (base pairs)
substitution of a purine for a purine or a pyrimidine with a pyrimidine - can be corrected through nucleotide excision repair (NER)
Transversion (base pairs)
substitution of a pyrimidine for a purine or a purine with a pyrimidine - can be corrected through nucleotide excision repair (NER)
Depurination - Spontaneous DNA damage
sugar-base bond is spontaneously broken - base is lost (usually purines) and nucleotide is left empty called apurinic site - common
APC acts as a tumor ___ gene.
suppressor loss of function mutation causes develop 100-1000s of adenomas leaving high risk of progression to malignancy
what is the purpose of knocking out genes
take away the gene and look for its function based on what's lacking
TS stands for targeted seq
targeted seq
How do we measure genetic variation in a population?
the Hardy-Weinberg Principle
Population Genetics
the basis of the hardy-weinberg law; the study of genetic variation in populations
what does TCGA stand for
the cancer genome atlas
why is early dx of HNPCC important?
the chance of cure is much higher
Because of meiotic crossing over...
the copy of a chromosome inherited by the boy in generation III is actually a mosaic of parts of all four of the grandparental copies of that chromosome.
What do Lod scores measure?
the likelihood of linkage between genes
The closer two genes are together...?
the more likely they are to segregate together, and less chance at recombination
How can we determine if loci are linked?
theta is 0.5 for unlinked loci
Which of the following statements is true about linked genes?
they co-segregate together
what is the point of genomic libraries
to store the genome and fragments so we can sequence it or figure out what some genes of the genome do
what can Ti plasmids be used for
to transmit info and see that the info (DNA of interest) was transmitted
plasmids allow for ___ of DNA b/t cells
transfer
horizontal gene transfer (HGT)
transfer of genes b/t cells of the same generation results in organisms acquiring new genes that did not come directly from the parent organisms
Vertical Gene Transfer
transfer of genes from an organism to its offspring
vertical gene transfer
transfer of genes from an organism to its offspring
TEs stands for
transposable elements
____ recognizes the IRs and cleaves at both ends of the TE, releasing it from the original site
transposase
resistance genes may be duplicated and inserted from one plasmid to another or from the plasmid to the chromosome via
transposition
Tns stands for
transposons
Lower than normal estriol, AFP, hCG, and inhibin A means the baby has
trisomy 18 aka Edward's Syndrome
Where is hCG elevated?
trisomy 21
eukaryote comes from Greek words for
true nucleus
what is a sex pilus
tube that allows for transfer of genetic material to neighboring cell
what is Ti plasmid
tumor inducing plasmid
BRCA are ___ ____ genes
tumor suppressor
BRCA1 and BRCA2 are both ___ ____
tumor suppressors
___ heritable genes predispose towards colon cancer
two
how many bacteria are required for alpha and beta insulin chains
two
persons at risk for HNPCC usually have FHx of __ successive generations of colon cancer or at least one gen of colon cancer and one gen w/ polyps
two
there are ___ kinds of viruses in general with negative stranded RNA genomes
two 1. segmented genome 2. non-segmented genome
Detection of Linkage and measurement of genetic distance
two loci that are really far apart on the same chromosome or on different chromosomes are unlinked and the ratio of recombinant individuals to non-recombinant individuals is 50:50
how is HNPCC dx'd?
two tests 1. colonoscopy (preferred) 2. barium enema 3. cologuard
mRNA of coronaviridae
typical cap at 5' end polyadenylated tail at 3' end
Three-point Crosses
used to avoid miscalculations - clear up distance issues
What is prenatal diagnosis?
used to diagnose any genetic anomaly especially during IVF pregnancies
RT uses _____ to make ____
uses mRNA (mature) to make cDNA
DNA fingerprinting identifies genomes using ____ and more recently ____ & ____ ____
using RFLPs more recently STRs & gel electrophoresis
how are RFLPs and STRs identified
using gel electrophoresis
host range of plasmids
variable
the _____ of individuals w/ HNPCC develop cancer
vast majority
size of circoviruses
very small, 1.7-2.2 kb don't encode for many proteins
How to determine total number of alleles in the population?
via observed phenotypic frequencies
Human Mitochondria
via oxidative phosphorylation, this organelle produces ATP (E source used in metabolism)
why is human parvovirus B19 potentially lethal for pts with anemia?
virus has affinity for RBC precursors and lyse cells.
what do you do after allowing for hybridization of radioactive probe with DNA fragments?
wash off extra probe visualize
____ blot is used for detecting proteins by using Abs
western
Setting Phase in a Pedigree
what is the chromosomal relationship of the polymorphic alleles to the disease alleles - if the polymorphic allele is on the same homolog as the disease gene, then it is coupled in cis - if the polymorphic allele is on the opposite homolog as the disease gene, then it is repulsion - Several polymorphic alleles in cis closely linked to each other = haplotype
when is using artificial chromosomes as vectors in host-vector systems beneficial?
when cloning larger pieces of DNA ex. sequence whole human genome would need larger storage area for genetic info
germination means
when endospore returns to vegetative state
when are endospores produced
when nutrients are depleted
WES stands for
whole exome seq
WGS stands for
whole genome seq
transduction occurs in a _________ range of bacteria
wide
Tns/TEs are ____ among cells and viruses
widespread
the transposition process can be harmful if insertion occurs where?
within and disrupts a functional gene.
first artificial chromosomes as vectors were made in
yeast YACs - yeast artificial chromosomes
human pathogens of flaviviridae
yellow fever, west nile, HCV
do euk have organelles?
yes
do euk have polysaccharide cell walls
yes when present - WITHOUT peptidoglycan
does -ssRNA virus carry RdRp in the particle?
yes. these genomes have evolved to include RNAPol in the virus particle
viruses with +ssRNA can be translated as soon as they get into the cell, meaning:
you don't need to have a polymerase inside the viral particle, ready to go when virus infects a cell after uncoating
best resolution for an optimal microscope is
~0.2 microns 200 nm