100
consequences of alternative splicing
-different effect on translated protein -alter enzymatic activity -change receptor binding ability -change protein localization in the cell
Alternative splicing (eukaryotes)
-different forms of RNA are generated from identical pre-RNA molecules -one gene= several proteins with similar or different function
Which of the following risk are associated with ART?
-ectopic pregnancies -low birth weights -passing on male infertility to sons -early delivery
L1 family
-most common LINE -6400 bp long and repeated up to 100,000 times -Retrotransposons
Memory B cell
A long-lived B cell produced after exposure to an antigen that plays an important role in secondary immunity
Behavioral trait more common in males:
Alcoholism
Cord blood is better for transplants than marrow because
it has not been exposed to pathogens and is less likely to carry antibodies
there are numerous models that are used for biomedical research; however the mouse model is currently the most frequently used. what is the main reason that the mouse emerged as the principal model for studies of human genetic disorders?
mice are amendable to gene targeting via homologous recombination in embryonic stem cells
In positional cloning, the inheritance of a disease, in a pedigree, was linked to the inheritance of
marker sequences produced by restriction enzymes
in positional cloning, the inheritance of a disease, in a pedigree, was linked to the inheritance of:
marker sequences produced by restriction enzymes
In a pedigree analyzed using positional cloning, the inheritance of a disease trait is typically linked to the inheritance of:
marker sequences produced by restriction enzymes.
According to Darwin fitness is a
measure of survival and differential reproduction
Biochemical reactions in the cell are linked together to form
metabolic pathways
PCR
method for amplifying DNA segments using cycles of denaturation, annealing to primers, and DNA polymerase-directed DNA synthesis
Embryo splitting
method of cloning; after in vitro fertilization, early embryonic cells are divided and grown into clones
Nuclear transfer
method of cloning; enucleated eggs are fused with embryonic or adult cells and grown into clones (Dolly the sheep)
Clone-by-clone method
method of genome sequencing; finds the order of clones first, then sequences
Shotgun sequencing
method of genome sequencing; sequences first, then orders them
Positional cloning
method of mapping and cloning genes with no prior information about the gene product or its function
When a woman is artificially inseminated and surrenders the child to the father and his mate, the woman is both the gestational and genetic mother. (T/F)
True
cancer cells
bypass cell cycle checkpoints and divide continuously
Czar Nicholas Romanov II
forensics used to confirm identity of bones of this person and wife and kids
sense mutation
former stop codon becomes sense codon, lengthens polypeptide
BRCA1 protein
found only in the nucleus, is activated when DNA is damaged • Stops DNA replication • Binds to Rap80 protein to identify DNA damage and initiate repair Mutant forms are unable to repair DNA • Mutations accumulate; cell become cancerous
the ELSI program of the HGP is investigating all of the following areas of concern except:
genetic targets for biological warfare agents (investigating protection of personal genetic info; the use of genetic info in reproductive decisions; availablity of and advertizing claims made for genetic testing; and the ethical boundaries for use of genomics and genetic info)
Major histocompatibility complex (MHC)
genes on chromosome 6 that encode recognition molecules that prevent the immune system from attacking a body's own organs and tissues
rDNA
genes that encode rRNA transcripts
Caretaker genes
genes that help maintain the integrity of the genome; for example DNA repair genes
Oncogenes
genes that induce or continue uncontrolled cell proliferation
oncogenes
genes that induce or continue uncontrolled cell proliferation
proto-oncogenes
genes that initiate or maintain cell division may become cancer genes by mutation
Proto-oncogenes
genes that initiate or maintain cell division; may become oncogenes by mutation
Gatekeeper genes
genes that regulate cell growth and passage through the cell cycle; for example, tumor suppressor genes.
The ELSI program of the Human Genome Project is investigating all of the following areas of concern except
genetic targets for biological warfare agents
Societies with the highest number of individuals who are able to produce lactase as adults are those who:
historically maintain dairy herds
The number of protein produced by the human genome is significantly greater than the number of genes it contains. (T/F)
True
Viruses have been determined to be the cause of
a few cancers
A normal ras gene is
a proto-oncogene
About what portion of all couples are affected by infertility
about 1 in 6
What portion of all cases of amyotrophic lateral sclerosis (ALS) are caused by mutations in the SOD1 gene
about 20%
Antibody-mediated immunity
immune reaction mediated by B cells that protects against invading viruses and bacteria using antibodies produced by plasma cells
Natural DNA vectors
plasmids and phages
Human GAA is produced in...
transgenic hamster cells and transgenic female rabbits
chronic idiopathic urticaria
treated with xolair - Dr. Derr has this
T/F - Babies conceived through IVF have a much higher risk of premature birth than babies conceived naturally
true, premature birth is higher in IVF
mutation rate
# of events that produce mutated alleles per locus per generation Mutations are rare events Mutation rates are different for different genes Mutation rates range from approx 1 in 10,000 to 1 in 1,000,000
Monzygotic twins
"Epigenetic differences arise during the lifetime of monozygotic twins" - Mario Fraga 2005
DNA polymerase
"proofreading" activity 3' to 5' exonuclease activity. Important and effective "first line of defense". In eukaryotes, proofreading is done by other enzymes and not the DNA polymerases.
370
# human therapeutic proteins made in plants are currently in development
20,000-25,000
# of human genes
300,000
# of proteins a human can produce
According to Dr. Budowle, it cost how much to place a persons genotype in the CODIS database?
$200-300
X-linked agammaglobulinemia (XLA)
A rare, X-linked recessive trait characterized by the total absence of immunoglobulins and B cells.
Positional cloning
A recombinant DNA-based method of mapping and cloning genes with no prior information about the gene product or its function.
Positional cloning
A recombinant DNA based method of mapping and cloning genes with no prior information about the gene product or its function
Inheritance of molecular markers
A recombinant DNA-based method of mapping and cloning genes with no prior information about the gene product or its function
Positional cloning
A recombinant DNA-based method of mapping and cloning genes with no prior information about the gene product or its function
positional cloning
A recombinant DNA-based method of mapping and cloning genes with no prior information about the gene product or its function. Inheritance of molecular markers is used to track the inheritance of genetic disorders in pedigrees and thus the gene responsible
Intracytoplasmic sperm injection
A treatment to overcome defects in sperm count or mobility; egg is fertilized by micro injection of a single sperm
B cell
A type of lymphocyte that matures in the bone marrow and mediates antibody-directed immunity.
T cell
A type of lymphocyte that undergoes maturation in the thymus and mediates cellular immunity.
B cell
A type of lymphocyte that matures in the bone marrow and mediated antibody directed immunity
T cell
A type of lymphocyte that matures in the thymus and mediates cellular immunity
Centimorgan (cM)
A unit of distance between genes on chromosomes. One centimorgan equals a frequency of 1% crossing over between two genes.
Centimorgan
A unit of distance between genes on a chromosome. One Centimorgan equals a frequency of 1% crossing over between two genes
Centimorgan (cM)
A unit of distance between genes on chromosomes.
Requirements to clone DNA
A way to cut DNA at specific sites A carrier molecule to hold DNA for cloning A place where the DNA can be copied (cloned)
What is needed to clone DNA
A way to cut DNA at specific sites. A carrier molecule to hold DNA for cloning. A place where the DNA can be copied (cloned).
Intracytoplasmic sperm injection (ICSI)
An egg is fertilized by microinjection of a single sperm (for defects in sperm count or motility)
Pompe disease
An inability to make a-glucosidase (GAA) Leads to reduced heart and muscle function Treated by enzyme replacement therapy
Damage to ovaries that causes infertility can likely be dure to any of the following except
homone imbalance (due to surgery, inflammation, autoimmune disease, ovarian cysts)
A predictable effect of genetic drift in a small population is an increase in
homozygosity
Damage to ovaries that causes infertility can likely be due to any of the following except
hormone imbalance
Avery, MacLeod, McCarty experiment
isolate DNA, protein and others, mix with normal bacteria to prove DNA is transforming substance
Which one of the following statemtns about genomic imprinting is FALSE
it can occur in any gene
In what way is Golden Rice improved over normal rice
it contains beta-carotene
in what way is Golden Rice improved over normal rice
it contains beta-carotene and vitamin A
which one of the follwoing statements best summarizes the use of transgenic crops over the last 10 years
it has increased significantly in both industrialized and developing nations
Typically, to grow transgenic plants, the vector with the inserted gene is incorporated into
plant cell that is then cultured to produce a whole plant
typically, to grow transgenic plants, the vector with the inserted gene is incorporated into:
plant cell that is then cultured to produce a whole plant
Mutations that block one reaction in a pathway can
produce mutant phenotypes in several ways
bacteria
produce restriction enzymes to protect themselves from viral infections
RNAP IV and V
produce various small RNAs in plants
Acridine orange
produces frameshift mutations
RNAP II
produces mRNA and small RNAs
RNAP I
produces pre-rRNA
RNAP III
produces tRNAs, rRNA and small RNAs
corn, soybeans, cottonseed and canola oils
products that most commonly contain transgenic ingredients
Friedreich ataxia
progressive and fatal neurogenerative disorder inherited as an autosomal recessive trait
replication errors
proofreading failures, base changes, insertions, deletions
Theodor Boveri
proposed a link between genetics and cancer in the nineteenth century
Antibodies are
protein molecules that represent a class of immunoglobulins
Antibodies are
protein molecules that represent a class of immunoglobulins.
Preimplantation genetic diagnosis (PGD)
removal and genetic analysis of a single cell from a 3 to 5 day old embryo
transposable elements
replicate and translocate over short timescales, diversify and multiple over long timescales, LINES and SINES
small RNAs
snoRNAs, miRNAS, piRAS, regulation of gene activity
nucleosomes form this structure
solenoid
Helper T cells
stimulates production of antibodies by B cells when an antigen is present; stimulates division of B cells and cytotoxic T cells
UAA, UAG, UGA
stop codons
Suppressor T cells
stop immune responses of B cells and other T cells
Adult stem cells can be reprogrammed into induced pluripotent stem cells by
transferring specific genes into their nuclei
DNA profiles use __ to identify individuals with a high degree of accuracy and reliability
variations in the length of short repetitive DNA sequences
A typical lunch for PKU might include
vegetable soup, crackers, fruit cocktail, and formula; not Protein-rich foods such as hamburger, chicken, dairy products cannot be eaten
short tandem repeats
very short (2-6 bp) repeated tandemly, tens of thousands scattered across genome, microsatellites
phage
viral genome that can carry some extra DNA from host cells
mRNA processing
5`capping, 3` polyadenlyation, splicing
DNA>RNA>Proteins>Physiology
Gene expression pathway
Lod method
A probability technique used to determine whether two genes are linked.
alternative splicing
"skip" spots (markers) in genome
silencer
+ activator, decreases transcription rate
Humans have approximately __ genes
20,000
telomeric DNA
6 or 7 base repeating units, hundreds of thousands of units long
Restriction enzymes
Bacterial enzymes that cut DNA at specific sites
Pathogens
Disease causing agents such as viruses, bacteria, fungi and parasites
__ contains increased levels of Vitamin A
Golden Rice
CODIS
In the US, a standard set of 13 STRs, used to prepare a profile
Age
Primary risk factor in cancer
colon polyps
Small clusters of dividing cells on the lining of colon
Mutant genes
The basis of genetic disorders
clastogen
a substance that causes chromosome abnormalities.
mutation
any heritable change in the base sequence of the genetic material
Restriction enzymes
attach to DNA molecules and cut it at specific sites.
Cancer
can be caused by an inherited susceptibility or a sporadic event
conservative
codon change, new AA R group similar to original
legal restrictions on the use of PGD
none
There are more __ in the body than genes
proteins
Germ-line Mutations
-occur in cells that produce gametes -transmitted to future generations - inherited
__ to __ percent of foods in US supermarkets contain some transgenic plant material
60 to 70
Nuclear Transfer
-requires the fusion of enucleated eggs -can produce larger numbers of identical embryos than embryo splitting -has a low success rate -can use cells from an adult donor
Nuclear transfer:
-requires the fusion of enucleated eggs with other cells -can produce larger numbers of identical embryos than embryo splitting -has a high failure rate -can use cells from an adult donor animal
nutritional mutation
- in bacteria and fungi, results in loss of ability to synthesize an amino acid or vitamin
If the frequency of an autosomal recessive trait is 1 in 10,000, how frequent are heterozygotes
1 in 50
One Centimorgan equals a frequency of...
1% crossing over between two genes.
Regulatory proteins
*indirectly or directly assist RNA polymerase* 1. A domain that recognizes the proper regulatory element . 2. A domain that interacts with RNA polymerase or any of its associated proteins. 3. A domain that interacts with proteins at nearby docking sites. 4. A domain that influences chromatin condensation 5. A domain that senses physiological differences in the cell.
enhancer
+ activator, increases transcription rate
Major causes of male infertility
- (37%) varicocele - (25%) Unknown - (10%) semen disorders - (9%) Testicular failure - (7%) other - (6%) Undescended testes - (6%) obstruction
Major causes of female infertility
- (50%) Oviduct blockage, uterine problems, damaged or absent ovaries - (10%) cervical problems - (40%) hormone-related ovulation problems
Inducible enzymes
- Bacteria are nutritional opportunists--they "swim" in their environment, and use the compounds that are available instead of making them. - Bacteria adapt to their environment by producing *these certain enzymes* only when specific substrates are present - An abundance of an end product in the environment represses gene expression
Base replacement
- Chemical compounds similar to nucleotides become incorporated into DNA. - Cause mispairing, and incorrect nucleotides to be incorporated during replication. - 5-BU causes GC-->AT or AT-->GC transitions during replication. - 2-AP (2-amino-purine) is an analog of adenine that mispairs with cytosine.
Mechanisms regulating genomic imprinting
- Differentially Methylated "CpG islands". - Differential active and repressive histone modifications.
mtDNA
-mitochondria has its own DNA -maternally inherited -double stranded closed circular DNA that replicates semi-conservatively -generally do not contain introns -5-10 mtDNA per organelle
Constitutive enzymes
- Enzymes continuously produced regardless of chemical makeup of the environment
Function of CpG methylation
- Genomic stability - Represses retrotransposons - Formation of heterochromatin --> X chromosome inactivation --> Centromere - Controls transcription
Angelman's Syndrome
- Loss of function of maternal UBE3A - *maternal inheritance of deletion* - 1/10,000-1/20,000 - Severe intellectual disability (IQ 30-50) - Ataxia (loss of full control of body movements) - Seizures - Absent speech
Prader-Willi Syndrome
- Loss of paternal derived HBII-85 snoRNA - *paternal inheritance of deletion* - Feeding difficulties - Failure to thrive - Mild developmental delay - Hypotonia (state of low muscle tone/strength) - Severe obesity
Histone Modifications
- N0terminal region of each histone extends beyond the nucleosome, and amino acids in these tails can be covalently modified in several ways - includes addition of acetyl, methyl and phosphate groups - alter the structure of chromatin, making genes on nucleosomes accessible or inaccessible for transcription - *writers*: proteins that add chemical groups - *readers*: proteins that interpret these modifications - *erasers*: proteins that remove these chemical groups
Issues that ELSI focuses on
- Privacy and confidentiality of genetic information - Fairness in the use of genetic information by insurers, employers and others - Discrimination caused by someone's genetic status - Use of genetic information in reproductive decisions
Base Alteration
- Some mutagens (EMS--ethylmethanesulfonate) alter bases, causing mispairing. - Add alkyl groups to positions on all four bases. - Result in GC-->AT transitions. - Intercalating agents 1. Proflavin 2. Acridine orange 3. ICR compounds. - Cause singlenucleotide-pair insertions or deletions
Role of Proteomics
- Understanding gene function and its changing role in development and aging - Identifying proteins that are biomarkers for diseases; used to develop diagnostic tests - Finding proteins for development of drugs to treat diseases and genetic disorders
Gene Regulation
- What allows different types of cells to have different functions even though they all contain the same DNA - Only a fraction of different genes are expressed at a given time during development or at different times in an organism's lifespan. - The differences are caused by differences in cell or tissue-specific gene regulation. Occurs at many levels 1. Adjusting the transcription of DNA into RNA, or translation of RNA into protein. 2. mRNA stability 3. Posttranslational modifications of proteins. *Most regulation occurs at the level of transcription.*
To better understand a genetic disorder several questions must be answered:
- Where is the gene located? - What is the normal function of the protein encoded by this gene? - How does the mutant gene or protein produce the disease phenotype?
point mutation
- a change of one base pair to another - aka *base substitution* Possible outcomes 1. creation of a new triplet that codes for a different amino acid in the protein product (a *missense mutation*) 2. triplet will be changed to a stop codon, resulting in termination of translation of the protein (a *nonsense mutation*) 3. codon is altered but does not result in change in the amino acid that position in the protein (due to degeneracy of the genetic code) (a *silent mutation*)
Epigenetic trait
- a stable, mitotically and meiotically heritable phenotype that results from changes in the pattern of gene expression without alterations of the DNA sequence
HAT complex
- activator binding recruitment of HAT complex causes histones to be acetylated - *transcriptive activation* by allowing attachment of RNA polymerase II
behavioral mutations
- affect behavior patterns of an organism - ex: mating behavior of fruit fly may be impaired if it cannot beat its wings - harder to observe --> defect may be in flight muscles, nerves leading to them, or the brain
regulatory mutations
- affect regulation of gene expression bc mutation is located in regulatory region
DNA methylation
- aka *CpG methylation* - in mammals, takes place after replication and during cell differentiation - *Methyl group added to the #5 carbon of cytosine located 5' to guanine* - almost exclusively on cytosine bases located adjacent to guanine base (a*CpG dinucleotide*) which are clustered in regions called *CpG islands* but can also occur at non-CpG islands - CpG islands are located in and near promoter sequences adjacent to genes - this is a reaction catalyzed by family of enzymes called DNA methyltransferases (DNMTs) - normal process during development (ex: X chromosome inactivation is associated with DNA methylation of these groups) - abnormal patterns of DNA methylation are associated with specific human diseases, including cancer - *Demethylase* is an enzyme that can demethylate these groups
CpG island
- area of DNA with > 200 bp with GC content > 50% and observed CG ratio > 60%
Reprogramming
- at fertilization, mammalian embryo receives maternal and paternal set of chromosomes - maternal set carries female imprints and paternal set contains male imprints - when gamete formation begins in female germ cells, both maternal and paternal imprints are erased and reprogrammed to a female imprint that is transmitted to the next generation through the eggg - opposite for male germ cells Reprogramming occurs at 2 stages 1. erasure by demethylation and reprogramming by remethylation lay down a male or female-specific imprinting pattern in germ cells of the parent 2. large-scale demethylation occurs in embryo sometime before 16-cell stage of development. After implantation, differential genomic remethylation recalibrates which maternal alleles and which paternal alleles will be inactivated *remember, imprinted alleles remain transcriptionally silent in all cells, while genes silenced by epigenetic methylation can be reactivated by external signals*
Maternal behavior
- can have effect on epigenome - ex: mothers that lick and groom and use arch-back nursing in rats saw offspring with differences in CpG methylation, histone acetylation, etc.
Epigenetic Modifications
- covalent modifications imparted onto either DNA or histone proteins. - They mask or expose regulatory elements (enhancers/silencers) and promoters
biochemical mutations
- do not always affect morphological characters, but they affect the function of proteins that can affect the well-being and survival of affected individuals - ex: sickle-cell anemia, hemophilia
conditional mutations
- effect on organism depends on environment in which organism finds itself - ex: temp-sensitive mutations
Maternal nutrition
- effects the epigenome - "Transposable elements: targets for early nutritional effects on epigenetic gene regulation." - RA Waterland 2003
Spontaneous mutations
- happen naturally and randomly and are usually linked to normal biological or chemical processes in the organism.
Epigenetics in imprinting
- imprinting is an epigenetically regulated process in which genes are expressed in a parent-of-origin pattern; that is, certain genes show expression of only the maternal allele or the paternal allele - results in the differential allelic expression of certain genes. This leads to the expression of one allele and repression of the other allele. - caused by differential methylation of CpG-rich regions and methylation of promoter sequences that produce allele-specific imprinting and subsequent gene silencing - once a gene has been impritned, it remains transcriptionally silent during embryogenesis and development - most imprinted genes direct aspects of growth during prenatal development - having only one functional allele makes impritned genes highly susceptible to deleterious effects of mutations
How many proteins can humans produce?
300,000
Recessive mutation
- most loss-of-function mutations - results in wild-type phenotype when present in a diploid organism and the other allele is wild type - in this case, the presence of less than 100 percent of the gene product is sufficient to bring about the wild-type phenotype
lethal mutation
- mutation that adversely affects a gene product that is essential tot he survival of the organism
neutral mutations
- mutation that can occur etiher in a protein-coding region or in any part of the genome, and its effect on the genetic fitness of the organism is negligible.
Epimutations
- mutations in imprinted genes can arise by dysfunctional epigenetic changes
gene mutations
- mutations occurring primarily in the base-pair sequence of DNA within individual genes - different than mutations in large regions of chromosomes (chromosomal mutations) - cell can defend itself from such mutations using various mechanisms of DNA repair - the extent to which a mutation changes the characteristics of an organism depends on which type of cell suffers the mutation and degree to which the mutation alters the function of a gene product or a gene-regulatory region
null mutations
- mutations that result in complete loss of function
Mutagens
- natural or artificial agents that induce mutations. - Different mutagens have different mutational specificities for types and sites. 1. Base replacement: changes the base itself. 2. Base alteration: causes the base to mispair with another base. 3. Base damage: makes the base unable to pair
Somatic mutations
- occur in any cell except germ cells and are not heritable.
Germ-line mutaitons
- occur in gametes and are inherited.
loss-of-function mutation
- one that reduces or eleminates the function of the gene product - any type of mutation, from a point mutation to deletion of the entire gene, may lead to loss of functions
Disadvantages of adult stem cells
- rare and difficult to isolate - only limited developmental potential - can only be used to treat a relatively small number of diseases - more difficult to grow and reprogram
Epigenome
- refers to pattern of epigenetic modifications present in a cell at a given time. - cell-type specific and changes throughout the life cycle in response to environmental cues - an organism has one genome, which can be modified in diverse cell types at different times to produce many epigenomes - can be transmitted to daughter cells by mitosis and future generations by meiosis
Induced mutations
- result from the influence of an extraneous factor, either natural or artificial.
mutation hot spots
- some DNA sequences that appear to be highly susceptible to mutation
Dominant mutation
- some loss-of-function mutations - results in a mutant phenotype in a diploid organism, even when the wild-type allele is also present - Dominant mutations can have 2 different types of effects 1. Haploinsuffiency (occurs when single wild-type copy of gene does not produce enough gene product to bring about a wild-type phenotype) 2. Dominant gain-of-function mutation (results in gene product with enhanced, negative, or new functions)
Epigenetics
- study of the ways in which chemical modifications to DNA and histones after cell- and tissue-specific patterns of gene expression - emerging field of Epigenetics is providing us with molecular basis for understanding how heritable changes other than those in DNA sequence can influence phenotypic variation - (ex: monozygotic twins that have identical genotypes but often have different phenotypes)
Histone code
- sum of complex patterns and interactions of histone modifications that alter chromatin organization and gene expression - combinations of these changes allow differentiated cells to carry out cell-specific patterns of gene transcription and to respond to external signals that modify these patterns without any changes in DNA sequence
frameshift mutation
- the *insertion* or *deletion* of a nucleotide causes all the subsequent three-letter codons to be changed - will occur when any number of bases are added or deleted, except in multiples of 3, which would reestablish the initial frame of reading
mutation rate
- the likelihood that a gene will undergo a mutation in a single generation or in forming a single gamete
visible mutations
- those that affect morphological trait and therefore are most easily observed -
HDAC complex
- with repressor and HDAC complex, histones are deacetylated - *transcriptive repression*
Retrotransposons
-move around genome via "molecular copy and paste" -copy themselves and then paste copies into the genome in different locations -first copies themselves to RNA -then RNA is copied to DNA by reverse transcriptase and inserted back into the genome
Somatic Mutations
-occur in cells of the body that do not form gametes -Is not transmitted to future generations
Yeast Centromeric DNA region 2
-100 base pairs -extremely A/T rich
Yeast Centromeric DNA region 3
-11 base pairs -well conserved -most critical for function
Alu Family
-200 to 300 bp long -interspersed throughout genome, both in and between genes -present in about 5% of the genome
Yeast Centromeric DNA region 1
-9 base pairs -well conserved
Where in the human body can you find T cells?
-Bone marrow -Thymus glands -Blood -Spleen
Chromatin
-Complex of DNA, RNA, histones and non-histone proteins that make up uncoiled chromosomes characteristic of the interphase nucleus
Heterochromatin
-DNA remains condensed -generally genetically inactive due to lack of genes/transcription repression -centromeres/telomeres -repetitive DNA is typically found here
Repetitive Transposed Sequences
-DNA segment that translocates to other sites of the genome
Euchromatin
-DNA that becomes uncoiled -gene rich regions -usually have more unique sequences -contains genes that are going to be needed soon, so it replicates before heterochromatin
10,000 fold
-DNA undergoes extensive coiling and folding after replication to make more room. What is the fold histone compaction?
Which of the following risks are associated with ART (Assisted Reproductive Technology)?
-Ectopic pregnancies -Low birth weights -Passing on male infertility to sons
Who is Louise Brown and why is she important in the field of genetics?
-First person to be born via in vitro fertilization -her birth confirmed ART was a possibility and can be used to ID early on genetic diseases
Nanopore technology:
-Is the fourth generation sequencing method -Depends on a single molecule sequencing without amplification -It is still under development -Can scan a whole genome in 15 minutes with very low cost
LINE
-Long Interspersed Elements
Three types of nucleotide substitutions
-Missense -Sense -Nonsense
RNAi
-RNA interference is a powerful research tool -can create single gene defects without creating heritable mutations (doesn't change DNA, it just changes gene expression) -highly specific, relatively inexpensive, rapid gene function analysis. Systematically knocks out function of individual genes -Can be useful in gene therapy for silencing disease genes
SINE
-Short Interspersed Elements -Alu Family
What is the value of having transgenic mice with the human gene for Huntington's Disease?
-The mice can be sacrificed and their brains examined to learn about the early stages of the disease. -The mice can be used to screen possible anti-HD drugs -The mice are much more numerous and available for study than human patients
Role of proteomics
-Understanding gene function and its changing role in development and aging -Identifying proteins that are biomarkers for diseases; used to develop diagnostic tests -Finding proteins for development of drugs to treat diseases and genetic disorders
Short RNA molecules
-about 21 bp long -regulate gene expression in cytoplasm -repress translation of mRNA -degrade mRNA
Cloned libraries contain all the DNA fragments of:
-all the genes expressed in a certain cell type -a specific chromosome of a species -the entire genome of a species
Cloned libraries contain all the DNA fragments of:
-all the genes expressed in a certain cell type -the entire genome of a species -the specific chromosome of a species
Bacterial Chromosomes
-always double stranded and circular DNA -compacted into nucleoids
Viral Chromosomes
-can be either DNA or DNA -can single or double stranded -can be circular or linear
Sporadic cancer
-cancer caused by accumulation of a number of mutations in somatic cells -mutation occurs in a single somatic cell -additional mutations accumulate
alphoid family
-common in centromeric regions in humans -170 bp in tandem arrays up to a million bases
histones
-contain positvely charged amino acids that are attracted to negatively charged DNA. These proteins help package and order DNA into nucleosomes.
alternative splicing changes
-development -apoptosis -axon/axon connection in CNS
Proteins are (2)
-essential components of all biological structures and processes -the end product of gene expression
BLAST
-finds region of similarity between biological sequences -compares nucleotide/protein sequences data bases and calculates statistical significance
Postranscriptional gene silencing (PTGS)
-gene specific double strand RNA processed by Dicer -Dicer has double stranded RNAse activity that cuts RNA into 21 nucleotide intervals -products RNAi (short interfering RNA) -RNA unwinds into sense and anti-sense single strands -antisense strands combines with RISC protein complex -recognizes, binds, and cleaves mRNA
Regulation of Gene expression (eukaryotes)
-greater genetic info -many chromosomes -have nuclei -large # of genes -DNA complex (in billions) with histones/proteins in chromatin -open/closed configuration -expression regulation
Satellite DNA
-identified in a cesium chloride gradient -determined to be highly repetitive via reassociation kinetics -highly repetitive= satellite DNA
alternative splicing
-increases # of proteins that can be made from a gene -protein diversity can exceed gene # by several folds -common in vertebraes/humans (30-60% of human genes use alternative splicing) -25,000 genes produce 250,000-1 million proteins -mutations affecting regulation of splicing= basis for several human disorders
Inherited cancer syndromes
-inherited mutant genes cause a predisposition to cancer -mutations carried in all cells in a heterozygous state -the normal allele is lost in the cancer cell
Garrod & Bateson Experiments
-involves alkaptonura (acid accumulates in cells/tissues and is excreted in the urine to give urine a black color) -Homogentistic acid can be deposited in joints and give a benign arthritic condition -autosomal recessive -increase dietary protein or phenylalanine/tyrosine intake
Embryo splitting:
-is a means of cloning animal embryos -mimics the way that identical twins are produced naturally -requires in vitro fertilization -is a technology that could improve the production of domestic animals
Ultraviolet light:
-is mutagenic -is a type of non-ionizing radiation -causes DNA strand breaks -causes mutations which can be repaired
Regulation of gene expression (prokaryotes)
-less genetic info -'one' chromosome -no nuclei -fewer gene #s -DNA simple -no open/closed configuration -no expression regulation
Short Tandem Repeats
-microsatellites -repeated sequences consisting of di-, tri-, tetra-, and pentanucleotides -CA is the most common human microsatellite -may actually influence gene regulation
Embryo splitting
-mimics the way identical twins produce naturally -requires in vitro fertilization -is a means of cloning animals -could improve the production of domestic animals
Embryo splitting:
-mimics the way the identical twins and triplets are produced naturally -requires in vitro fertilization -is a means of cloning animal embryos -is a technology that could improve the production of domestic animals
Variable Number Tandem Repeats (VNTRs)
-mini satellites -no assigned function -repeating sequence may be 15-100 bp long -found within and between genes -been used for forensic matters
Centromeric DNA
-minimum region of the centromere that supports chromosomal segregation (includes kinetochore in eukaryotes) -Divided into three regions in yeast -more complex in eukaryotes
microRNA (miRNA)
-short RNA molecules; 20-25 bp long; single stranded -derived from longer RNA molecules, forms a hairpin, and is cleaved by Dicer -miRNA binds with internal or 3' untranslated region of mRNA -BLOCKS translation or targets RNA for degradation
SSR locator
-simple sequence repeats -ex: using microsatellites to tell it what sequences to look for
What factors influence mutation rate?
-size of the gene (larger=higher mutation rates) -nucleotide sequence (nucleotide repeats associated with higher mutation rates) -Spontaneous chemical changes (C/G more likely to mutate than A/T)
Accurate measurement of mutation rates depends on what factors?
-the frequency at which heritable changes in DNA occur -the rate at which mutations are detected and repaired by cells -whether the mutation results in a recognizable phenotype
Transgenic mice with the human gene for Huntington's Disease
-the mice can be sacrificed and their brains examined to learn about early stages of the disease -mice can be used to screen possible drugs -mice are much more numerous and available
Risks of ART
-threefold increase in ectopic pregnancies -multiple births -increased risk of low birth weight -increased risk of transmitting genetic defects to male children in ISCI
Eukaryote gene expression
-transcription is spatially and temporally separated from translation -transcripts are processed -mRNA hlaf life is much longer than pros -multicellular, different cell types= difference genes in active tissues
Prokaryote gene expression
-transcription/translation occur in the same place and at the same time -no need to transcripts to be processed -mRNA decays immediately after transcription stops -simple system!
acetylation
-type of chromatin remodeling -acetylates histones to open up the chromatin structure -occurs via histone acetyltransferase (HAT)
methylation
-type of chromatin remodeling -methylates the amino acid (lys & arg) of the histones -occurs via methyltransferases -associated with gene activation
phosphorylation
-type of chromatin remolding -phosphorylates amino acids (lys & arg) of histone proteins -occurs via kinase enzymes -phosphate group gets added to OH group on amino acids
Two main properties of cancer
-uncontrolled cell division -ability of these cells to metastasize
No software
-use Kraemer based method to figure the genome size, then plot the coverage of all sequence contigs -repeats will be present in much higher copt number and have higher depths of coverage
Repeat Masker Software
-use an annotated repeat library for a given species to find and mask repeats for the same species -can also be used across species, if species of interest has no repeat library
DNA profiles
-variations in short tandem repeats produce the banding pattern -the pattern is unique for all except twins -the bands are derived from variations in restriction cutting sites of DNA
In DNA profiles:
-variations in short tandem repeats produce the banding pattern. -ideally, the pattern is unique for all individuals except identical twins. -the bands are derived from restriction cutting sites of DNA.
Three Things Required for DNA Cloning
1) a way to cut DNA at specific sites 2) carrier molecule to hold DNA 3) a host cell where the DNA can be copied
A genetic map is made in these two steps
1. Finding linkage between two genes 2. Measuring how frequently crossing-over takes place between them
3 steps in FAP associate colon cancer
1. Mutation in the APC (Adenomatous Polyposis Coli) gene on chromosome 5 2. Mutation of one copy of the k-ras proto-oncogene in a polyp cell transforms the polyp into an adenoma; mutations in both alleles of any of several downstream genes, including DCC (Deleted in Colorectal Cancer), leads to formation of late-stage adenomas 3. Mutations in both alleles of the p53 gene on chromosome 17 cause the late-stage adenoma to become cancerous
Two unique properties of stem cells
1. They renew their numbers by cell division 2. Can form many or most of the different cell types in the body
3 steps in FAP colon cancer
1. mutation in APC gene on chromosome 5 2. mutation of one copy of k-ras photo-oncogene transforms polyp into adenoma; mutation in both alleles of several downstream genes(DCC) leads to late stage adenomas 3. mutations in both alleles of p53 on chromosome 17 cause late stage adenoma and become cancerous
3 major epigenetic mechanisms
1. reversible modification of DNA by addition or removal of methyl groups 2. Chromatin remodeling by addition or removal of chemical groups to histone proteins 3. regulation of gene expression by non-coding RNA molecules
steps of PCR
1.DNA is heated to break the hydrogen bonds between the two polynucleotide strands. Two single-stranded DNA molecules serve as templates 2. Short nucleotide sequences (primers for DNA replication) are mixed with the DNA and bind to complementary regions on single-stranded DNA. Takes place at lower temperature. Primers are 20-30 nucleotides long, synthesized in the laboratory 3.The enzyme Taq polymerase is added to synthesize a complementary DNA strand. Taq is a DNA polymerase from a bacterium found in hot springs. These three steps make up one PCR cycle
DNA profiles are used in more than __ criminal cases per year.
10,000
if meiotic non-disjunction occurs during meiosis 1 what percentage of the gametes would you expect to have an abnormal karyotype?
100%
centromeric DNA
120-600 BP repeating units, tens of thousands of units long
In the US, about __ percent of all couples are infertile
13
variable number of tandem repeats
15-100 bp units repeated tandemly, thousands scattered across genome, minisatellites
The first successful in vitro fertilization was carried out in __
1981
An Enzymatic Reaction
2 substrate molecules, substrates contacting active site of enzyme, substrates briefly bind tightly to enzyme active site, product molecule, enzyme unchanged by the reaction
mRNAs are processed in many ways so 20,000 to 30,000 genes can produce __ proteins
300,000
The number of genes in the human genome is estimated to be between
20,000 and 25,000
The number of genes in the human genome is estimated to be between:
20,000 to 25,000
number of genes in the human genome
20,000-25,000
The number of genes in the human genome is estimated to be between:
20000 and 25000
the number of genes in the human genome is estimated between:
20000 and 25000
There is a family with a rare genetic condition that causes teeth to turn black. In an attempt to map this gene, it was noted that in families with the black teeth trait, black teeth segregated together with type B blood in 38 out of 50 cases. In 12 cases they separated in the offspring. The map distance between the black teeth and blood type genes is therefore:
24 cM
in the pedigree above (both parents are carriers, male son affected, 3 other daughters unaffected) what are the chances that another child will be born with the same disease as the male proband?
25% (autosomal recessive)
A lod score of __ or higher are taken as establishing linkage.
3
IVF is estimated to be a $__-billion-per-year industry
3
Lod scores over __ are linked
3
The human genome contains over ___ ___ nucleotides
3 billion
average annual radiation exposure in US
360 mrem
How much radiation is an average US person exposed to per year?
360 mrem/year
Requirements of genetic material
4 C's code copy control change
Since 1981, more than __ hospitals and clinics have opened for IVF
40
What dose of rem can cause somatic mutations?
5,000 mrem
deletions and insertions account for
5-10% of known mutations
in the pedigree above what are the chances that the mother of the proband with have another child with the same disease as the proband? (generation I male carrier --> gen II male carrier --> gen III female carrier --> gen IV male affected)
50%
Only about __ percent of our __ billion nucleotides of DNA encode protein coding genetic information, much of the rest codes for ___ ___
5; 3 ; regulatory information
Using positional cloning, the FRDA gene was mapped to chromosome __, then isolated, cloned and sequenced
9
Infertility
A complex problem and has many causes, including physical and physiological problems with gamete formation and hormonal imbalances
B. a proto-oncogene
A normal ras gene is: A. a tumor suppressor gene B. a proto-oncogene C. a gene for DNA repair D. an oncogene E. a gene with microsatellites
frameshift mutations
A number of bases (other than multiples of three) are added to or removed from DNA, causing a shift in the codon reading frame
Severe combined immunodeficiency disease (SCID)
A collection of genetic disorders in which affected individuals have no immune response; both the cellmediated and antibody-mediated responses are missing.
Map-based sequencing
A method of genome sequencing that begins with genetic and physical maps; clones are sequenced after they have been placed in order.
Whole genome sequencing
A method of genome sequencing that selects clones at random from a genomic library and, after sequencing them, assembles the genome sequence by using software analysis.
2N+1 (N is number of loci, assume 2 alleles per locus)
phenotypic classes
Linkage
A condition in which two or more genes do not show independent assortment. Rather, they tend to be inherited together. Such genes are located on the same chromosome. When the degree of recombination between linked genes is measured, the distance between them can be determined.
Vp
phenotypic variance
Copy number variation (CNV)
A DNA segment at least 1,000 base pairs long with a variable copy number in the genome.
Copy number variant
A DNA segment at least 1000 base pairs long with a variable copy number in the genome
Linkage
A condition in which two or more genes do not show independent assortment. Rather they tend to be inherited together. Such genes are located on the same chromosome. When the degree of recombination between linked genes is measured, the distance between them can be determined
Linkage
A condition in which two or more genes do not show independent assortment. Rather, they tend to be inherited together. Such genes are located on the same chromosome. When the degree of recombination between the linked genes is measured, the distance between them can be determined.
Hemolytic disease of the newborn (HDN)
A condition of immunological incompatibility between mother and fetus that occurs when the mother is Rh− and the fetus is Rh+.
X linked agammaglobulinemia
A rare X linked recessive trait characterized by the total absence of immunoglobulins and B cells
Restriction enzyme
A bacterial enzyme that cuts DNA at specific sites
Restriction enzyme
A bacterial enzyme that cuts DNA at specific sites.
neutral mutation
A base-pair change with a change in the amino acid sequence but with no change in the function of the protein.
Bipolar disorder
A behavioral disorder characterized by mood swings that vary between manic activity and depression.
Schizophrenia
A behavioral disorder characterized by disordered thought processes and withdrawal from reality. Genetic and environmental factors are involved in this disease.
Schizophrenia
A behavioral disorder characterized by disordered thought processes and withdrawal from reality. Genetic and environmental factors are involved in this disease
Bipolar disorder
A behavioral disorder characterized by mood swings than vary between manic activity and depression
Pharmacogenomics
A branch of genetics concerned with the identification of protein variants that underlie differences in the response to drugs.
Structural genomics
A branch of genomics that generates three dimensional structure of proteins from their amino acid sequences.
Structural genomics
A branch of genomics that generates three-dimensional structure of proteins from their amino acid sequences
Signal transduction
A cellular molecular pathway by which an external signal is converted into a functional response.
Signal transduction
A cellular molecular pathway by which an external signal is converted to a functional response
missense mutation
A change in an mRNA codon resulting in an amino acid replacement
Complement system
A chemical defense system that kills microorganisms directly, supplements the inflammatory response, and works with (complements) the immune system.
Complement system
A chemical defense system that kills microorganisms directly, supplements the inflammatory response, and works with the immune system
Histamine
A chemical signal produced by mast cells that triggers dilation of blood vessels.
Neurotransmitter
A chemical that transmits a nerve impulse from one neuron to another
Antibody
A class of proteins produced by B cells that bind to foreign molecules (antigens) and inactivate them.
Yeast artificial chromosome
A cloning vector that has telomeres and a centromere that can accommodate large DNA inserts and uses the eukaryote yeast as a host cell
Yeast artificial chromosome (YAC)
A cloning vector that has telomeres and a centromere that can accommodate large DNA inserts and uses the eukaryote yeast as a host cell.
Acquired immunodeficiency syndrome (AIDS)
A collection of disorders that develop as a result of infection with the human immunodeficiency virus (HIV)
genomic library
A collection of clones that contains all the genetic information in an individual
Acquired immunodeficiency disease
A collection of disorders that develop as a result of infection with HIV
Severe combined immunodeficiency disease
A collection of genetic disorders in which affected individuals have no immune response; both cell mediated and antibody mediated immune responses are missing
Hemolytic disease of the newborn
A condition of immunological incompatibility between mother and fetus that occurs when the mother is Rh- and the fetus is Rh+ To prevent this, mother given Rh- antibody after birth of first child if that child is Rh+
Genetic map
A diagram of a chromosome showing the order of genes and the distance between them based on recombination frequencies (centimorgans).
Physical map
A diagram of a chromosome showing the order of genes and the distance between them measured in base pairs.
Genetic map
A diagram of a chromosome showing the order of genes and the distance between them based on recombination frequencies (centimorgans)
Genetic Map
A diagram of a chromosome showing the order of genes and the distance between them based on recombination frequencies (centimorgans).
Physical map
A diagram of a chromosome showing the order of genes and the distance between them measures in base pairs
What is a proto-oncogene?
A gene that regulates cell division
Genetically modified organisms (GMOs)
A general term used to refer to transgenic plants or animals created by recombinant DNA techniques.
Clone-by-clone method
A genomic library (a collection of clones) is developed Physical maps are prepared Clones are organized into overlapping groups DNA cut with restriction enzymes Each clone is sequenced and software assembles sequence from the libraries
Clone-by-Clone Method
A genomic library (a collection of clones) is developed. Physical maps are prepared. Clones are organized into overlapping groups. DNA cut with restriction enzymes. Each clone is sequenced and software assembles sequence from the libraries.
B. Is a surrogate that provides for the development of the embryo after conception
A gestational mother: A. Is genetically related to the fetus B. Is a surrogate that provides for the development of the embryo after conception C. Is one who has undergone tubal ligation D. Provides the normal female gamete for a normal sperm E. None fo these
Alzheimer disease (AD)
A heterogeneous condition associated with the development of brain lesions, personality changes, and degeneration of intellect. Genetic forms are associated with genes on chromosomes 14, 19, and 21.
Alzheimer disease
A heterogeneous condition associated with development of brain lesions, personality changes, and degeneration of intellect. Genetic forms are associated with genes on chromosomes 14, 19 and 21
probe
A labeled nucleic acid used to identify a complementary region in a clone or genome
Probe
A labeled nucleic acid used to identify a complementary region in a clone or genome.
Probe
A labeled nucleus acid used to identify a complementary region in a clone or genome
Which of the following best sums up the current stat of knowledge about the genes that influence susceptibility to alcoholism
A large number of candidate genes has been identified but none has been shown to be influential
Membrane attack complex
A large, cylindrical multi protein that embeds itself in the plasma membrane of an invading microorganisms and creates a pore through which fluids can flow, eventually bursting the microorganism
Membrane-attack complex (MAC)
A large, cylindrical multiprotein that embeds itself in the plasma membrane of an invading microorganism and creates a pore through which fluids can flow, eventually bursting the microorganism.
Memory B cells
A long lived B cell produced after exposure to an antigen that plays an important role in secondary immunity
Helper T cell
A lymphocyte that stimulates the production of antibodies by B cells when an antigen is present and stimulates division of B cells and cytotoxic T cells.
Helper T cells
A lymphocyte that stimulates the production of antibodies by B cells when an antigen is present and stimulates division of B cells and cytotoxic T cells
retinoblastoma
A malignant tumor of the eye arising in retinoblasts (embryonic retinal cells that disappear at about 2 years of age)
Retinoblastoma
A malignant tumor of the eye arising in retinoblasts (embryonic retinal cells that disappear at about 2 years of age). Because mature retinal cells do not transform into tumors, this is a tumor that usually occurs only in children.
Retinoblastoma
A malignant tumor of the eye arising in retinoblasts. Usually occurs only in children caused by mutation in tumor suppressor gene
Polymerase chain reaction (PCR)
A method for amplifying DNA segments using cycles of denaturation, annealing to primers, and DNA polymerase-directed DNA synthesis.
Southern blot
A method for transfering DNA fragments from gel to a membrane filter, developed by Edwin Southern for use in hybridization experiments
Southern blot
A method for transferring DNA fragments from a gel to a membrane filter, developed by Edwin Southern for use in hybridization experiments.
Polymerase chain reaction
A method of amplifying DNA segments using cycles of denaturation, annealing to primers, and DNA polymerase directed DNA synthesis. faster and easier than conventional cloning
Map based sequencing
A method of genome sequencing that begins with genetic and physical maps; clones are sequenced after they have been placed in order.
Whole genome sequencing
A method of genome sequencing that selects clones at random from a genomic library and after sequencing them, assembles the genome sequence by using software analysis
Phenylalanine Metabolism and PKU
A mutation in a gene encoding the enzyme that controls the first step in the conversion of phenylalanine to tyrosine causes phenylketonuria (PKU)
Cancer stem cells
A new cancer model states that some cancers have stem cells. A small population of cells in the tumor whose continuous division drives the growth of the tumor May offer a new more specific approach to therapy
transgenic Bt crops have been genetically modified to:
produce an insecticide
Cancer has a genetic component
A predisposition to more than 50 forms of cancer are inherited to one degree or another Most chemicals that cause cancer are also mutagens Some viruses carry genes that promote cancer Specific chromosomal changes are found in certain cancers Mutations are the ultimate cause of cancer
What Happens When Women With PKU Have Children?
A pregnant woman with PKU who eats a normal diet will have high levels of phenylalanine in her blood Excess phenylalanine has a minimal affect on the mother because her nervous system has already developed Phenylalanine crosses the placenta and damages the the developing nervous system of the fetus, no matter what its genotype is
Vaccine
A preparation containing dead or weakened pathogens that elicits an immune response when injected into the body.
Vaccine
A preparation containing dead or weakened pathogens that elicits an immune response when injected into the body
Lod method
A probability technique used to determine whether two genes are linked.
Lod method
A probability technique used to determine whether two genes are linked
In vitro fertilization (IVF)
A procedure in which gametes are collected and fertilized in a dish in the laboratory; the resulting zygote is implanted in the uterus for development.
In vitro fertilization
A procedure in which gametes are collected and fertilized in a dish in the lab; the resulting zygote is implanted in the uterus for development
Genetic counseling
A process of communication that deals with the occurrence or risk of a genetic disorder in a family
metastasis
A process by which cells detach from the primary tumor and move to other sites in the body, forming new malignant tumors
Metastasis
A process by which cells detach from the primary tumor and move to other sites, forming new malignant tumors in the body
Metastasis
A process by which cells detach from the primary tumor and move to other sites, forming new malignant tumors in the body.
Genetic counseling
A process of communication that deals with the occurrence or risk of a genetic disorder in a family
Friedreich ataxia
A progressive and fatal neurodegenerative disorder inherited as an autosomal recessive trait with symptoms appearing between puberty and the age of 25.
Friedreich ataxia
A progressive and fatal neurodegenerative disorder inherited as an autosomal recessive trait Symptoms appear between puberty and age 25
Friedreich ataxia
A progressive and fatal neurodegenerative disorder inherited as an autosomal recessive trait with symptoms appearing between puberty and the age of 25
millirem
A rem is equal to 1,000 millirems
HIV
A retrovirus that selectively infects and kills the T4 helper cells of the immune system
Assisted reproductive technologies (ART)
A series of methods used to help infertile couples have children
DNA microarray
A series of short nucleotide sequences placed on a solid support (such as glass) that have several different uses, such as detection of mutant genes or differences in the pattern of gene expression in normal and cancerous cells.
DNA microarray
A series of short nucleotide sequences placed on a solid support (such as glass) that have several uses such as detection of mutant genes or differences in the pattern of gene expression in normal and cancerous cells
Recombinant DNA technology
A series of techniques in which DNA fragments from an organism are linked to self replicating vectors to create recombinant DNA molecules which are replicated or cloned in a host cell
Recombinant DNA technology
A series of techniques in which DNA fragments from an organism are linked to self-replicating vectors to create recombinant DNA molecules, which are replicated or cloned in a host cell.
Major histocompatibility complex (MHC)
A set of genes on chromosome 6 that encodes recognition molecules that prevent the immune system from attacking a body's own organs and tissues.
Major histocompatibility complex
A set of genes on chromosome 6 that encodes recognition molecules that prevent the immune system from attacking a body's own organs and tissues. human leukocyte antigen system.
Halotype
A set of genetic markers located close together on a single chromosome or chromosome region.
Haplotype
A set of genetic markers located close together on a single chromosome or chromosome region.
Haplotype
A set of genetic markers located close together on a single chromosome or chromosome region
Anaphylaxis
A severe allergic response in which histamine is released into the circulatory system.
Anaphylaxis
A severe allergic response in which histamine is released into the circulatory system
Exome sequencing
A strategy of sequencing only the coding regions of a genome
carcinogen
A substance capable of inducing cancer in an organism.
DNA sequencing
A technique for determining the nucleotide sequence of a DNA molecule
DNA sequencing
A technique for determining the nucleotide sequence of a DNA molecule.
trinucleotide repeats
A three base-pair repeating sequence
trinucleotide repeats
A three base-pair repeating sequence (example: CGGCGGCGGCGG)
Intracytoplasmic sperm injection (ICSI)
A treatment to overcome defects in sperm count or motility; an egg is fertilized by microinjection of a single sperm.
Transgenic Bt crops have been genetically modified to:
produce an insecticide.
Base-pair substitutions or point mutations
A-T to G-C
B cells
produce circulating antibodies.
DNA profiles based on
variations in the copy number of DNA sequences
primary structure
AA sequence of polypeptide chain
The drug Gleevec is most closely associated with which of the following molecules?
ATP
epigenetics and cancer
Abnormal DNA methylation is associate with many types of cancers Epigenetic changes to DNA can alter gene expression and contribute to cancer
philidelphia chromosome
Abnormal chromosome produced by translocation between the long arms of chromosomes 9 and 22 • Linked to chronic myelogenous leukemia (CML)
How many genes do humans have?
About 20,000
$200-$300
According to Dr. Budowle, it cost how much to place a person genotype in the CODIS database?
polar AA
Asn, Cys, Gly, Gln, Ser, Thr, Tyr
Induced pluripotent stem (iPS) cells
Adult cells that can be reprogrammed (induced) by gene transfer to form cells with most of the developmental potential of embryonic stem cells. Because of this developmental potential, such cells are pluripotent.
Induced pluripotent stem cells
Adult cells that can be reprogrammed (induced) by gene transfer to form cells with most of the developmental potential of embryonic stem cells. Because of this, such cells are pluripotent
embryo splitting
After in vitro fertilization, early embryonic cells are divided and grown into clones
non-polar AA
Ala, Ile, Leu, Met, Phe, Pro, Trp, Val
Which one of the following risks is increased by ART?
All of these 1. ectopic pregnancies 2. low birth weights 3. Multiple births 4. passing on male infertility to sons
The MHC complex is a set of genes that
All of these 1. encodes cell regognition molecules 2. is located on chromosome 6 3. Produces molecules to which antigens must attach in order to activate cell-mediated immunity 4. prevents the immune system from attacking the body's own tissues
Which of the following are now routinely frozen for future use
All of these 1. sperm 2. eggs 3. embryos
Which one of the following is NOT an assumption underlying the Hardy Weinberg model of alleles in a population
All of these are assumptions underlying the Hardy Weinberg model: 1. The population must be large 2. Mating is random with respect to the alleles 3. All genotypes from the alleles confer equal ability to survive and reproduce 4. Other factors that change allele frequency, such as mutation and migration, are absent or rare enough to be ignored
The mutant huntingtin protein that results in Huntington disease
All of these: 1. Causes a decrease in production of another protein 2. Leads to degeneration of cells in the brain's striatum 3. Is toxic to brain cells 4. Leads to degeneration of cells in the brain's striatum and is toxic to brain cells only
Which of the following disorders with a behavioral phenotype alters the visible structures of teh brain
All of these: 1. HD 2. Charcot-Marie-Tooth Disease 3. Alzheimers
Alfred Knudson hypothesis
Also multiple-hit hypothesis. Cancer is the result of accumulated mutations to a cells DNA
Those who carry one or two copies of a specific allele of the APOE gene are at increased risk of developing
Alzheimer disease
Essential amino acids
Amino acids that cannot be synthesized in the body and must be supplied in the diet
Gamete intrafallopian transfer (GIFT)
An ART procedure in which gametes are collected and placed into a woman's oviduct for fertilization.
Zygote intrafallopian transfer (ZIFT)
An ART procedure in which gametes are collected, fertilization takes place in vitro, and the resulting zygote (fertilized egg) is transferred to a woman's oviduct
Gamete intrafallopian transfer
An ART procedure in which gametes are collected and placed into a woman's oviduct for fertilization
Zygote intrafallopian transfer
An ART procedure in which gametes are collected, fertilization takes place in vitro, and the resulting zygote is transferred into a woman's oviduct
Philadelphia chromosome
An abnormal chromosome produced by translocation of parts of the long arms of chromosomes 9 and 22.
Philadelphia chromosome
An abnormal chromosome produced by translocation of parts of the long arms of chromosomes 9 and 22. in chronic myelogenous leukemia
teratogen
An agent that increases the incidence of congenital malformations.
mutagen
An agent, either chemical or physical, that is capable of inducing mutations.
Huntington disease (HD)
An autosomal dominant disorder associated with progressive neural degeneration and dementia. Adult onset is followed by death 10 to 15 years after symptoms appear.
Huntington disease
An autosomal dominant disorder associated with progressive neural degeneration and dementia. Adult onset is followed by death 10 to 15 years after symptoms appear. single gene disorder.
Hereditary nonpolyposis colon cancer
An autosomal dominant trait associated with genomic instability of microsatelite DNA sequences and a form of colon cancer
Hereditary nonpolyposis colon cancer (HNPCC)
An autosomal dominant trait associated with genomic instability of microsatellite DNA sequences and a form of colon cancer
Hereditary nonpolyposis colon cancer (HNPCC)
An autosomal dominant trait associated with genomic instability of microsatellite DNA sequences and a form of colon cancer.
Familial adenomatous polyposis (FAP)
An autosomal dominant trait resulting in the development of polyps and benign growths in the colon • Polyps often develop into malignant growths and cause cancer of the colon and/or rectum
Familial adenomatous polyposis (FAP)
An autosomal dominant trait resulting in the development of polyps and benign growths in the colon Polyps often develop into malignant growths and cause cancer of the colon and/or rectum
Familial adenomatous polyposis
An autosomal dominant trait resulting in the development of polyps and benign growths in the colon. Often develop into malignant growths and cause cancer in the colon and/or rectum
Familial adenomatous polyposis (FAP)
An autosomal dominant trait resulting in the development of polyps and benign growths in the colon. Polyps often develop into malignant growths and cause cancer of the colon and/or rectum.
Phenylketonuria (PKU)
An autosomal recessive disorder of phenylalanine metabolism that results in mental retardation if untreated; The phenotype is caused by the build-up of phenylalanine levels and the products of secondary reactions
Transgenic organism
An organism that has received a gene from another species by means of recombinant DNA technology
Annotation
Analysis of genomic nucleotide sequence data to identify protein-coding genes, non-protein-coding genes, their regulatory sequences and functions
Pharmacogenomics
Analyzes genes and proteins for therapeutic use
Pharmacogenomics
Analyzes genes and proteins to identify targets for therapeutic drugs
polar acidic (- charge)
Asp, Glu
Stages of antibody mediated immune response
Antigen detection. B cells bind to antigens and become antigen-presenting cells (APCs) Activation of helper T cells. Activated helper T cells identify and activate specific B cells Antibody production by B cells. Activated B cells form two types of daughter cells: effector cells and memory B cells
Allergens
Antigens that provoke an inappropriate immune response.
Allergens
Antigens that provoke an inappropriate immune response
Bacterial plasmids
Are circular
A haplotype is a set of SNPs which
Are closely linked and therefore inherited together
polar basic (+ charge)
Arg, His, Lys
Which of the following is the oldest in the hominoid lineage
Australopithescines
Circulating antibodies are produced by
B cells
intercalating agents
Chemicals that insert themselves into DNA Produce frameshift mutations
Which one of the following is typically attacked by the antibody-mediated response, not the cell-mediated.
Bacterial cells
restriction enzymes
Bacterial enzymes that cut DNA at specific sites
B. are circular
Bacterial plasmids: A. carry larger DNA fragments than YACs B. are circular C. cannot replicate unless incorporated into the main chromosome D. A and B E. All of the above
_________ is the use of recombinant DNA technology to produces commodities of services.
Biotechnology
According to the current theory of antibody formation
Gene recombination accompanies B cell maturation
sporadic cancer
Cancer caused by accumulation of a number of mutations in somatic cells Mutation occurs in a single somatic cell
Multipotent
Can develop into a limited number of mature cells
The polymerase chain reaction:
Can provide sufficient DNA for analysis from a small sample of biological material at the scene of a crime AND requires a heat-resistant polymerase
What condition has been the target of over half the gene therapy trials performed so far?
Cancer
cancer is a decendant from a single cell
Cancer cells are clonal descendants from one mutant cell The cell accumulates specific mutations over a long period of time Cancer cells escape control of the cell cycle continually divide Mutations continue to accumulate Cancer cells can be either non-invasive (benign) or invasive and spread to other sites (metastatic)
Prebiotics
Carbohydrate based diet supplements that promote the growth and metabolic activity of certain beneficial bacteria
mutagens
Chemicals that cause mutations
5000 mrem can
Cause somatic mutations Increase susceptibility to cancer
missense mutation
Cause the substitution of one amino acid for another in a protein
Beckwith-Wiedemann syndrome (BWS)
Caused by abnormal patterns of imprinting that in turn are caused by improper epigenetic modifications of certain genes located in clusters on chromosome 11
Embryonic stem cells
Cells in the inner cell mass of early embryos that will form all the cells, tissues, and organs of the adult. Because of their ability to form so many different cell types, these cells are called pluripotent cells
Embryonic stem cells (ESCs)
Cells in the inner cell mass of early embryos that will form all the cells, tissues, and organs of the adult. Because of their ability to form so many different cell types, these cells are called pluripotent cells
Embryonic stem cells (ESCs)
Cells in the inner cell mass of early embryos that will form all the cells, tissues, and organs of the adult. Because of their ability to form so many different cell types, these cells are called pluripotent.
Stem cells
Cells with two properties: the ability to replicate themselves, and the ability to form a variety of cell types in the body.
Stem cells
Cells with two properties; the ability to replicate themselves, and the ability to form a variety of cell types in the body
Xenotransplants
Cells, tissues or organs that are transplanted from one species to another
Xenotransplants
Cells, tissues, or organs that are transplanted from one species to another.
nonsense mutations
Change an amino acid specifying a codon to one of three termination codons
sense mutation
Change of a (stop) codon, i.e., UAG, UAA, or UGA to one that codes for an amino acid.
nonsense mutation
Change to a chain-terminating (stop) codon, i.e., UAG, UAA, or UGA
intercalating agents
Chemicals that insert themselves into DNA generally produce frameshift mutations by distorting the double helix, resulting in addition or deletion of a base pair during DNA replication Example: Acridine orange inserts into DNA and produces mutations
core promoter element and enhancer elements
Cis-acting elements that regulate initiation of transcription by RNAP II
When a phagocytic cell engulfs and destroys a bacterium, it displays some of the partially digested bacterial proteins on its surface, attached to
Class II MHC proteins
D. all of these
Cloned libraries contain all the DNA fragments of: A. all the genes expressed in a certain cell type B. the entire genome of a species C. a specific chromosome of a species D. all of these E. none of these
B. all derived from a single ancestor
Clones are: A. identical in phenotype but not necessarily in genotype B. all derived from a single ancestor C. offspring of a genetically pure ancestor D. only produced by recombinant DNA methods E. carriers of genetic information derived from gene insertions
yeast artificial chromosome (YAC)
Cloning vector with telomeres and a centromere Carries DNA fragments up to 1 million bases long Uses the eukaryote yeast as a host cell
Comparative genomics
Compares the genomes of different species to look for clues to the evolutionary history of genes or a species.
Comparative genomics
Compares genomes of different species for clues to the evolutionary history of genes or a species
Comparative genomics
Compares the genomes of different species to look for clues to the evolutionary history of genes or a species
Usually, the first procedure a genetic counselor performs for a client is
Constructing a pedigree
Humans produce more different polypeptides that we have different genes. That excess is mainly the result of
Cutting and splicing of pre-mRNA in several different ways
Which of the following are more common among white people than among black or Asian people
Cystic Fibrosis and phenylketonuria
50%
What percent does social behavior contribute to cancer cases in the US?
nucleosome
DNA and core of histone proteins, basic unit chromatin structure
To sequence a small amount of DNA, (Sanger method)
DNA bases (A, T, C, G) are tagged with a radioisotope or a fluorescent tag used to synthesize DNA. The products are separated by size
Why DNA cloning is important
DNA clones are used to find genes, map them, and transfer them between species. Cloning technology is used to find carriers of genetic disorders, perform gene therapy, and create disease-resistant plants.
indirect evidence of DNA as genetic material
DNA content per cell constant within species DNA content per gamete is half of diploid DNA not "turn over" in non-dividing cells Mutagens alter DNA (or RNA) structure Mutagenic properties of UV irradiation
complementary DNA (cDNA) library
DNA copies of mRNA (reverse transcriptase)
cloned libraries contain
DNA fragments of all genes in a certain cell type, the entire genome of a species, and a specific chromosome of a species
recombinant DNA
DNA from different sources that has been combined to form a new DNA molecule
steps in the process of cloning
DNA is cut with a restriction enzyme. Fragments produced end in specific sequences Fragments are mixed with vector molecules cut by the same enzyme. DNA ligase joins recombinant DNA molecules Plasmid vectors with inserted DNA fragments are transferred into bacterial cells. Recombinant plasmids replicate and produce many clones of the recombinant DNA molecule Colonies carrying cloned recombinant DNA molecules are identified, collected, and grown. Host cells are broken open and recombinant plasmids are extracted
Denaturation
DNA is heated to break the hydrogen bonds between the two polynucleotide strands
3`-5` 5`-3`
DNA is read in what direction? RNA is built in what direction?
DNA repair systems
DNA polymerase has proofreading function 2nd system recognizes and repaires UV light damage (thymine dimers)
Two breast cancer genes, BRCA1 and BRCA2, function in the process of _______.
DNA repair
Some mutations in __ ___ ___ can destabilize the genome
DNA repair genes
Microsatellites
DNA sequences, 2 to 9 nucleotides long, that are repeated thousands of times and located on many chromosomes
The application of recombinant DNA technology to forensic cases requires all of the following except
DNA sequencing
the application of recombinant DNA technology to forensic cases requires all of the following except:
DNA sequencing (requires cloning of DNA, establishment of DNA profiles, and STR analysis)
two times
DNA wound how many times around nucleosome core
Plasma cells
Daughter cells of B cells, which synthesize and secrete 2,000 to 20,000 antibody molecules per second into the bloodstream.
Effector cells
Daughter cells of B cells, which synthesize and secrete 2,000 to 20,000 antibody molecules per second into the bloodstream
Plasma cells
Daughter cells of B cells, which synthesize and secrete 2000 to 20000 antibody molecules per second into the bloodstream
The trend towards increased mobility of the world populations will probably lead to:
Decreased allele frequency differences among populations
Angleman Syndrome
Deletion of long arm of chromosome 15 on maternal copy Severe mental retardation, uncontrollable puppet-like movements and seizures of laughter.
Prader-Willi syndrome
Deletion of long arm of chromosome 15 on paternal copy Obesity, uncontrollable appetite and mental retardation.
The correct order of PCR steps is:
Denaturation, annealing, DNA synthesis
Structural genomics
Derives 3-D structures for proteins
Structural genomics
Derives three-dimensional structures for proteins
DNA fingerprint
Detection of variations in minisatellites used to identify individuals
DNA fingerprint
Detection of variations in minisatellites used to identify individuals.
DMR
Differentially Methylated Region - CpG island - Promoter --> Sense or antisense (*?*) - Regulates imprinting of one gene - Methylated on only one parental chromosome (differential) - Typically represses the expression of the methylated allele
genomic imprinting disorders
Disorders due to imprinting of chromosome 15 • Prader-Willi syndrome (PWS): deletion on the paternal copy • Angelman syndrome (AS): deletion on the maternal copy
ID of dominant mutation
Dominant mutations are easiest to detect; they are expressed in the heterozygous condition Sudden appearance of a dominant mutation in a family can be observed in a single generation Accurate pedigree information can be used to identify the individual in whom a mutation arose
Shotgun sequencing (done by who)
Done by a private company operated by Dr. Craig Ventor.
What transgenic animal, other than mice, has been used to model human neurodegenerative diseases
Drosophila
embryonic stem cells can be used to generate a knock out and knock in mouse models of human genetic diseases. why unique properties do ES cells possess that allow them to be used to generate genetic models?
ES cells facilitate homologous recombination and are capable of differentiating into germ cells
Risks are associated with ART?
Ectopic pregnancy, low birth weight, passing on male infertility
In gel electrophoresis, what causes the DNA fragments to migrate?
Electrical charge
E. all of these
Embryo splitting: A. mimics the way that identical twins and triplets are produced naturally B. requires in vitro C. is a means of cloning animal embryos D. is a technology that could improve the production of domestic animals E. all of these
Inner Cell Mass
Embryonic stem cells are harvested from a part of the blastocyst stage embryo called the ____________.
polymerases
build new DNA strand, nucleotide by nucleotide, by catalysis of 5` phosphate to 3` OH phosphodiester bond
nuclear transfer (cell fusion)
Enucleated eggs are fused with embryonic or adult cells and grown into clones Dolly the sheep
Nuclear transfer (cell fusion)
Enucleated eggs are fused with embryonic or adult cells and grown into clones. Dolly the sheep cloned this way.
epigenome
Epigenetic state of a cell Can change multiple times over the lifespan of the cell, depending on the environment
Phenylalanine is an _____ _____ ____ and the starting point for a network of metabolic reactions
Essential amino acids
Enhancement gene therapy and germ-line gene therapy are not currently in use because of
Ethical concerns
Nail-Patella syndrome and ABO blood type
Example of linkage
It is currently illegal to offer genome sequencing and analysis services to the public without being specifically licensed to do so. (T/F)
False
Myelogenous leukemia is caused by a mutant tumor-suppressing gene. (T/F)
False
(T/F) Adult cells cannot be used as the source of nuclei for cloning animals.
False
(T/F) For a number of different reasons, gene therapy has not yet cured any patients of their genetic disorder.
False
(T/F) The Human Genome Project took much longer to complete and cost more than was originally anticipated.
False
For a number of different reasons, gene therapy has not yet cured any patients of their genetic disorder. (T/F)
False
The Human Genome Project took much longer to complete and cost more than was originally anticipated. (T/F)
False
The FOXP2 gene encodes a protein involved in aggressive behavior. (T/F)
False - it has to do with language
The genetic model of colon cancer states that development of colo-rectal cancer requires only one key mutation. (T/F)
False - it requires 6+ mutations
Schizophrenia has been shown to be a single gene disorder. (T/F)
False - it's a multifactorial or polygenic disorder
(T/F) Two genes have a lod score of 6.1. This means that the two genes are most likely on different chromosomes.
False. A lod score of 3 of more indicates two genes are close together on a chromosome.
(T/F) Sickle cell anemia is caused by a nonsense mutation.
False. Caused by a missense mutation.
(T/F) The difference between the GIFT and ZIFT procedures is where in the woman's body the implantation occurs.
False. In GIFT, you are injecting individual gametes (sperm and egg) into the fallopian tubes, whereas in ZIFT you are injecting a fertilized zygote into the fallopian tubes.
(T/F) An RNA polymerase is used in most polymerase chain reactions.
False. Only used in RNA chain reactions.
Two pathways to colon cancer related to genetic predispositions
Familial adenomatous polyposis (FAP) • Hereditary nonpolyposis colon cancer (HNPCC)
The increased blood flow to an infected area that occurs during inflammation is caused by cells releasing
histamine
J. Watson and later F. Collins
Federally funded and lead clone-by-clone method
Construction of a genetic map
Finding linkage between two genes Measuring how frequently crossing-over takes place between them
A. naturally occurring radiation
For the average person in the US, the largest source of radiation exposure is: A. naturally occurring radiation B. nuclear wastes and power plants C. x-rays D. consumer products E. computer and television screens
Germ-line gene therapy
Gene transfer to gametes or the cells that produce them. Transfers a gene to all cells in the next generation, including germ cells.
Chapter 15
Gene Mutation, DNA repair, and Transposition
In which of the following does fertilization take place within a woman's body
GIFT
In Huntington's syndrome a CAG expansion of the coding sequence adds additional glutamine amino acids to the protein sequence. What type of mutation do you consider this to be?
Gain of function
Gamete intrafallopian transfer (GIFT)
Gametes are collected and placed into a woman's oviduct
Enhancement gene therapy
Gene transfer to enhance traits such as intelligence and athletic ability rather than to treat a genetic disorder.
Enhancement gene therapy
Gene transfer to enhance traits such as intelligence and athletic ability rather than treat a genetic disorder
Germ line gene therapy
Gene transfer to gametes or the cells that produce them. Transfers a gene to all cells in the next generation, including germ cells
Somatic gene therapy
Gene transfer to somatic target cells to correct a genetic disorder.
Somatic gene therapy
Gene transfer to somatic target cells to correct a genetic disorder. only gene therapy actually in use today
Genetically modified organisms
General term used to refer to transgenic plants or animals created by recombinant DNA techniques
Tumor suppressor genes
Genes encoding proteins that suppress cell division act at control points in the cell cycle deletion or inactivation causes cells to divide continuously
tumor suppressor genes
Genes encoding proteins that suppress cell division and regulate the cell cycle • These gene products act at control points in the cell cycle, at G1/S or G2/M • Deletion or inactivation of these products cause cells to divide continuously
tumor suppressor genes
Genes encoding proteins that suppress cell division and regulate the cell cycle Deletion or inactivation of these products cause cells to divide continuously
Tumor-suppressor genes
Genes encoding proteins that suppress cell division.
Linkage
Genes located on the same chromosome tend to be inherited together
caretaker genes
Genes that help maintain the integrity of the genome; for example, DNA repair genes
Oncogenes
Genes that induce or continue uncontrolled cell proliferation
oncogenes
Genes that induce or continue uncontrolled cell proliferation
Oncogenes
Genes that induce or continue uncontrolled cell proliferation.
proto-oncogenes
Genes that initiate or maintain cell division May become cancer genes (oncogenes) by mutation
gatekeeper genes
Genes that regulate cell growth and passage through the cell cycle; for example, tumor suppressor genes
Clones
Genetically identical molecules, cells, or organisms all derived from a single ancestor
clones
Genetically identical molecules, cells, or organisms all derived from a single ancestor
Clones
Genetically identical molecules, cells, or organisms, all derived from a single ancestor.
Shotgun cloning
Genomic library prepared No genetic or physical maps are created Restriction enzymes are used to cut DNA, and overlapping fragments are created Clones selected at random from each library and sequenced Assembler software programs organize information into genomic sequences
Shotgun Cloning
Genomic library prepared. No genetic or physical maps are created. Restriction enzymes are used to cut DNA, and overlapping fragments are created. Clones selected at random from each library and sequenced. Assembler software programs organize information into genomic sequences.
Charles Steward
Grew carrots by cloning in the lab. first undifferentiated ball of cells(callus) then in soul become full carrots.
Helper T Cells
HIV targets _______ cells for infection.
E. the proportion of all genotypes will remain the same
Hardy and Weinberg mathematically prove that as time goes by in a non-evolving population: A. dominant alleles will increase to a 3:1 ratio B. heterozygotes will usually increase C. recessive genes will gradually increase since they hide in the heterozygotes D. the frequency of homozygotes will increase E. the proportion of all genotypes will remain the same
...the proportion of all genotypes will remain constant
Hardy and Weinberg mathematically proved that as time goes by in a population...
HIV targets ___ cells for infection
Helper T cells
In the immune response, which cell type activates B cells for antibody production
Helper T cells
Lactose Intolerance is a Genetic Variation
Human milk is around 7% lactose The enzyme lactase is required for the breakdown of lactose for energy Levels of lactase drop off during middle to late childhood Lactose intolerance is not a genetic disorder but a genetic variation that results in very low lactase levels affects millions of adults worldwide
basic properties of cancer result from the inability of cancer cells to repair damage to DNA including
High rates of mutation, chromosomal abnormalities, and genomic instability
Instead of finding and mapping disease genes one by one, the ___ was initiated to sequence all the DNA in the human genome and to use this information to identify all the genes in the genome
Human Genome Project (HGP)
In the PCR technique, what bonds are broken when DNA is heated?
Hydrogen
Skin grafts between identical twins are more successful than grafts between more unrelated individuals. Why?
Identical twins have identical HLA alleles
Cell-mediated immunity
Immune reaction mediated by T cells directed against body cells that have been infected by viruses or bacteria.
Cell mediated immunity
Immune reaction mediated by T cells directed against body cells that have been infected by viruses or bacteria
Antibody-mediated immunity
Immune reaction that protects against invading viruses and bacteria using antibodies produced by plasma cells.
Antibody mediated immunity
Immune reaction that protects against invading viruses and bacteria using antibodies produced by plasma cells
Proteins link genes and phenotype
Impact cell structure, metabolic reactions, hormonal responses, cell-to-cell signaling systems, and the immune system
Genomic imprinting reversible
Imprinting is an epigenetic change • Involving reversible changes due to reversible methylation of DNA and gene function without affecting the nucleotide sequence • Methylation causes gene silencing In each generation, the previous imprinting is erased and the gene is reimprinted • During gamete formation or early development
D. all of these
In DNA profiles: A. variations in STRs produce the banding pattern B. ideally, the pattern is unique for all individuals except identical twins C. the bands are derived from variation in restriction cutting sites of enzyme D. all of these E. none of these
Loss of heterozygosity (LOH)
In a cell, the loss of normal function in one allele of a gene where the other allele is already inactivated by mutation.
Loss of heterozygosity
In a cell, the loss of normal function in one allele of a gene where the other gene is already inactivated by mutation
E. a single amino acid is altered
In a missense mutation: A. a nucleotide is added to the DNA B. all the amino acids beyond the mutation point are changed C. the protein is always completely nonfunctional D. a nucleotide is deleted from the DNA E. a single amino acid is altered
D. marker sequences produced by restriction enzymes
In a pedigree analyzed using positional cloning, the inheritance of a disease trait is typically linked to the inheritance of: A. gene families B. a specific blood type C. other diseases or conditions D. marker sequences produced by restriction enzymes E. all of these
Genomic library
In recombinant DNA terminology, a collection of clones that contain all the genetic information in an individual
Genomic library
In recombinant DNA terminology, a collection of clones that contains all the genetic information in an individual.
average exposure of radiation
In the US, the average person is exposed to about 360 mrem/year, 81% of which is from natural background sources A dose of 5,000 mrem can cause somatic mutations and increase susceptibility to cancer
allelic expansion
Increase in gene size caused by an increase in the number of trinucleotide sequences • Potential for expansion is a characteristic of a specific allele
allelic expansion
Increase in gene size caused by an increase in the number of trinucleotide sequences
familial retinoblastoma
Individuals inherit one mutant copy of RB1 gene • 85% to 95% chance of developing the disease
A gestational mother
Is a surrogate that provides for the development of the embryo after conception
molecular markers
Inheritance of these is used to track the inheritance of genetic disorders in pedigrees and thus the gene responsible
Fragile X syndrome
Inherited from of mental retardation Defect on X-chromosome Responsible gene, FMR1, fragile X mental retardation 1, normally contains 6-52 CGG repeats Mutant alleles carry more than 230 repeats
inherited cancer
Inherited genes cause a predisposition to cancer Mutations are carried in all cells
inherited cancer syndromes
Inherited mutant genes cause a predisposition to cancer • Mutations are carried in all cells in a heterozygous state • The normal allele is lost in the cancer cell (loss of heterozygosity)
B. the male is infertile
Intracytoplasmic sperm injection is used in couples in which: A. the female is approaching menopause B. the male is infertile C. the female has very irregular ovulation D. the source of sperm is a sperm bank E. the female has blocked oviducts
nucleotide substitutions
Involve replacing one or more nucleotides in a DNA molecule with other nucleotides
Antigens
Molecules usually carried or produced by viruses, microorganisms, or cells that initiate antibody production.
Drosophila melanogaster is a commonly used model system used to study human genetic disease. the GAL4-UAS system in Drosophila is a particularly useful tool because:
It allows tissues or cell specific expression of gene of interest
Which of the following best described the use of transgenic crops over the last 10 yrs?
It has increased significantly in both industrialized and developing countries
Which one of the following statements best summarizes the use of transgenic crops over the last 10 years
It has increased significantly in both industrialized and developing nations
Antigens
Molecules usually carried or produced by viruses, microorganisms, or cells that initiate antibody production
sex linked recessive mutations
It is even more difficult to determine the origin of a sex-linked recessive mutation • Generally will only appear in males in a family tree ex. hemophilia
ID of recessive mutations
It is more difficult to detect a recessive mutation • Can be detected only in the homozygous condition It is extremely difficult to identify the origin of a recessive mutation
Which of the following statements is correct concerning the current regulation of genetically modified foods by the FDA?
Labeling of genetically modified foods is not required
H1, H2A, H2B, H3, H4
histones associated with nucleosome, but H1 not in core
Mutations in genes encoding enzymes can affect the metabolic pathways of other biological molecules, including
carbohydrates
Probiotics
Living microorganisms that colonize the large intestine and confer health benefits on the recipient
Which of the following is a pair of agents that both puncture the membranes of foreign bacteria
MAC and cytotoxic T cells
A and O
Most common blood types
Skin cancer
Most common form of cancer in US - half of all cases
E. coli
Most common host cell for cloning
sex-linked recessive mutation
Most difficult mutation to determine the origin of Generally will only appear in males in a family tree
Blood type
One of the classes into which blood can be separated based on the presence or absence of certain antigens
MZ twin concordance values are less than 100 percent in both bipolar disorder and schizophrenia. This suggests that these disorders are
Multifactorial
base analogs
Mutagenic chemicals (purine or pyrimidine) that structurally resemble nucleotides and are incorporated into DNA or RNA during synthesis
What is the source of all genetic variation in humans and other organisms?
Mutation
frameshift mutations
Mutational events in which a number of bases (other than multiples of three) are added to or removed from DNA, causing a shift in the codon reading frame
What is the ultimate cause of cancer?
Mutations
BRAC1 and BRAC2 genes
Mutations in BRAC1 and BRAC2 genes can predispose women to breast and ovarian cancer
sense mutations
Mutations in a single nucleotide can change a termination codon into one that codes for an amino acid, producing elongated proteins Example: Stop codon UAA in alpha globin can mutate to CAA
sense mutations
Mutations in a single nucleotide can change a termination codon into one that codes for an amino acid, producing elongated proteins
sporadic retinoblastoma
Mutations of both copies of RB1 gene occur in a single cell • Occurs with a frequency of approximately 1 in 15,000
missense mutations
Mutations that cause the substitution of one amino acid for another in a protein Example: The GAG codon in hemoglobin can mutate to GUG, AAG, or GCG
nonsense mutations
Mutations that change an amino acid specifying a codon to one of three termination codons Example: A UAU codon in beta globin can mutate to a stop codon UAA
Nucleotide substitutions
Mutations that involve replacing one or more nucleotides in a DNA molecule with other nucleotides this causes Hb variants
recombinant DNA technology
Techniques in which DNA fragments are linked to self-replicating vectors to create recombinant DNA molecules which are replicated in a host cell
Are there any legal restrictions on the use of PGD (Preimplantation Genetic Diagnosis)?
No
genomic disorders (i.e. duplications or deletions) are described as large mutation that often arise due to genome architecture. the molecular event that causes most deletions and duplications is due to _________ during meiosis.
Non-allele homologous recombination (during prophase I of meiosis the parental chromosomes swap sections that have high sequence similarity but are not alleles)
Which of the following statements about retinoblastoma offers support for the idea that multiple mutations are needed in cancer?
Non-inherited cases involve one eye and occur later in life
Proto-oncogenes
Normal genes that initiate or maintain cell division and that may become cancer genes (oncogenes) by mutation
Proto-oncogenes
Normal genes that initiate or maintain cell division and that may become cancer genes (oncogenes) by mutation.
repairing DNA damage
Not all mutations cause permanent genetic damage Cells have enzyme systems that repair DNA • Correct errors in replication • Repair damage caused by environmental agents such as ultraviolet light, radiation, and chemicals
E. none of these
Nuclear transfer: A. does not require the fusion of enucleated eggs with other cells B. can not produce larger numbers of identical embryos than embryo splitting C. has a fairly high success rate D. can not use cells from an adult donor animal, must use embryonic cells E. none of these
silent mutations
Nucleotide change but the same amino acid inserted in the protein.
Minisatellites
Nucleotide sequences 14 to 100 base pairs long organized into clusters of varying lengths; used in the construction of DNA fingerprints
Minisatellite
Nucleotide sequences 14 to 100 base pairs long, organized into clusters of varying lengths, on many different chromosomes; used in the construction of DNA fingerprints
Minisatellite
Nucleotide sequences 14 to 100 base pairs long, organized into clusters of varying lengths, on many different chromosomes; used in the construction of DNA fingerprints.
Which of the following blood types are safe to transfuse to O blood type?
O
somatic mutations
Occur in cells of the body that do not form gametes Are not transmitted to future generations
Somatic Mutations
Occur in cells of the body that do not form gametes • Is not transmitted to future generations
germ-line mutation
Occur in cells that produce gametes Transmitted to future generations-inherited
Germ-line Mutations
Occur in cells that produce gametes • Transmitted to future generations - inherited
Proto-oncogenes to oncogenes
Oncogenes are permanently switched on protooncogenes that cause uncontrolled cell division • A single base change can produce an altered gene product • Mutations can increase the number of copies of a normal gene
Blood type
One of the classes into which blood can be separated on the basis of the presence or absence of certain antigens.
A. Transfer of herbicide resistance to weeds
One of the concerns with the use of genetically-engineered, herbicide resistant crops is ______. A. Transfer of herbicide resistance to weeds B. Decreased yield C. Potential allergic reaction D. The expense of using herbicides E. Loss of genetic diversity
Lod scores for three genes are obtained: for genes A and B the score is 4.2' for genes A and C it is 2.5; for genes B and C it is 2.1. The conclusion would be that
Only A and B are linked
Lod scores for three genes are obtained: for genes A and B the score is 4:2; for genes A and C it is 2:5; and for genes B and C it is 2:1. The conclusion would be that
Only A and B are linked
Anticipation
Onset of a genetic disorder at earlier ages and with increasing severity in successive generations • Due to increasing number of repeats with successive generations more repeats = earlier onset
anticipation
Onset of a genetic disorder at earlier ages and with increasing severity in successive generations Due to growing number of trinucleotide repeats
Open vs. Closed configuration of chromatin
Open: - DNA is unmethylated and histones are acetylated - Genes can be transcribed Closed - DNA is methylated at CpG islands - histones are deacetylated - genes can not be transcribed
Other Metabolic Disorders in the Phenylalanine Pathway
Others include defects of certain thyroid hormones and the build-up of another compound, homogentisic acid (Alkaptonuria).
Flame retardants
PBDEs(Polybrominated diphenyl ethers) , is chemically related to contaminants known to cause cancer and other health problems in humans PBDE levels in blood serum and milk are 10 to 100 times greater in the US than in Europe; a 6-fold increase between 1985 and 2002
60%-70%
Percentage of foods in US supermarkets that contain some transgenic plant material
epigenetic trait
Phenotype that is produced by epigenetic changes to DNA
Why would it be easy to measure allele frequencies in a codominant allele system
Phenotypes are equivalent to genotypes
Adult stem cells
Stem cells recovered from bone marrow and other organs of adults. These cells can differentiate to form a limited number of adult cells, and are called multipotent cells.
Lack of the enzyme alpha-glucosidase (GAA) is the biochemical cause of
Pompe disease
Theodor Boveri
Proposed link between genetics and cancer in 19th century 4 lines of evidence 1. predisposition to more than 50 forms of cancer inherited to one degree or another 2. most chemicals that cause cancer cause mutations 3. some viruses carry genes that promote and maintain the growth of cancer in infected cells 4. Specific chromosomal changes are found in certain forms of cancer, especially leukemia
HNPCC cont
Proteins encoded by MSH2 and MLH1 genes repair errors (DNA mismatch repair protein 2) made during DNA replication When these genes are inactivated by mutation, microsatellite mutation rates increase, promoting mutations in other genes
transition mutations
Purine to purine or pyrimidine to pyrimidine change
transversion mutations
Purine/pyrimidine or pyrimidine/purine
components of HIV
RNA molecules (genetic material) The enzyme reverse transcriptase. Transcribes HIV RNA into a DNA molecule which is inserted into a human chromosome T cells make viral RNA and proteins A protein coat. Encloses the other two components
background radiation
Radiation in the environment that contributes to radiation exposure
background radiation
Radiation in the environment that contributes to radiation exposure
ionizing radiation
Radiation that produces ions during interaction with other matter, including molecules in cells
ionizing radiation
Radiation that produces ions during interaction with other matter, including molecules in cells
Suppressor T cells
Stop immune responses of B cells, other T cells
Ras continued
Ras is the name given to a family of related proteins found inside cells. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells (cellular signal transduction). Ras is the prototypical member of the Ras superfamily of proteins, which are all related in 3D structure and regulate diverse cell behaviours. The name 'Ras' is an abbreviation of 'Rat sarcoma', reflecting the way the first members of the protein family were discovered.
Transgenic
Refers to the transfer of genes between species by recombinant DNA technology, transgenic organisms have received such a gene
Transgenic
Refers to transfer of genes between species by recombinant DNA technology; these organisms have recieved such a gene
Chapter 16
Regulation of Gene Expression in Prokaryotes
Preimplantation genetic diagnosis (PGD)
Removal and genetic analysis of a single cell from a 3- to 5-day-old embryo. Used to select embryos free of genetic disorders for implantation and development
Preimplantation genetic diagnosis
Removal and genetic analysis of a single cell from a 3-5 day old embryo. Used to select embryos free of genetic disorders for implantation and development. Used to select siblings who are suitable tissue or organ donors for other members of family.
Effect of 5-bromuracil
Replaces thymine; causes insertion of G rather than A; results in a A/T to G/C mutation
photolyase
Requires light energy (320-370 nm, blue light) Does not remove any nucleotides Repairs dimer formation by splitting the T=T bonds.
C. Are the same on both strands if read 5' to 3'
Restriction sites typically A. Begin with G B. Are 6 base pairs long C. Are the same on both strands if read 5' to 3' D. A and B are correct E. A and C are correct
Incompatibility in the Rh blood system can result in hemolytic disease of the newborn. The following combination poses the greatest risk
Rh negative mother, Rh positive fetus
Incompatibility in the Rh blood system can result in hemolytic disease of the newborn. The following combination poses the greatest risk:
Rh negative mother, Rh positive fetus
DNA profile
STR pattern used to identify individuals
genetic imprinting
Selective expression of a gene depending on whether it is inherited from the mother or the father
Vectors
Self replicating DNA molecules that are used to transfer foreign DNA segments between host cells
Vectors
Self-replicating DNA molecules that are used to transfer foreign DNA segmentsbetween host cells.
vectors
Self-replicating DNA molecules used to transfer foreign DNA segments between host cells
Genomics and cancer
Sequencing cancer genomes has allowed the identification of additional cancerassociated genes
repair system disorders
Several genetic disorders, including xeroderma pigmentosum, are caused by mutations in genes that repair DNA
Griffith experiment
Something from dead bacteria taken up by live bacteria, it transforms one bacteria into another. *Transforming factor*
Short tandem repeat
Short nucleotide sequences 2 to 9 base pairs long found throughout the genome that are organized into clusters of varying lengths; used in the construction of DNA profiles
Short tandem repeat (STR)
Short nucleotide sequences 2 to 9 base pairs long found throughout the genome that are organized into clusters of varying lengths; used in the construction of DNA profiles.
Short tandem repeats (STRs)
Short nucleotide sequences 2 to 9 base pairs long organized into clusters of varying lengths
Short tandem repeat (STR)
Short nucleotide sequences 2 to 9 base pairs long organized into clusters of varying lengths--Microsattelites
What types of DNA sequences provide the basis for DNA profiles?
Short tandem repeats
Antisense oligonucleotides
Short, single stranded DNA or RNA molecule synthesized to be complementary to a sequence of interest
The allele for glucose-6-phosphate dehydrogenase (G6PD) deficiency has been selected for by the same mechanism as the allele for
Sickle Cell Anemia
Adult stem cells
Stem cells recovered from bone marrow and other organs of adults. These cells can differentiate to form a limited number of adult cells and are called multipotent cells
Adult Stem Cells
Stem cells recovered from bone marrow and other organs of adults. These cells can differentiate to form a limited number of adult cells and are called multipotent cells.
Several factors influence mutation rate
Size of the gene: Larger genes have higher mutation rates • Nucleotide sequence: Presence of nucleotide repeats are associated with higher mutation rates • Spontaneous chemical changes: C/G base pairs are more likely to mutate than A/T pairs
Because identical twins have identical HLA alleles
Skin grafts between identical twins are more successful than grafts between more unrelated individuals. Why?
lifestyle factors and contribution to cancer
Smoking: 85% of lung cancer in men and 75% in women are related to smoking Sunlight and skin cancer Some viral infections lead to cancer: HPV and cervical cancer Radiation Occupational exposure to some chemicals poses a cancer risk to workers in a number of industries
chromosome rearrangements
Some cancers, such as chronic myelogenous leukemia, are caused by translocation events, creating hybrid genes that activate cell division • Philadelphia chromosome Other forms of cancer are also associated with specific chromosomal abnormalities • Myeloblastic leukemia, Burkitt's lymphoma, multiple myeloma
chemical mods of bases
Some chemical mutagens directly modify the bases in DNA, changing one base to another Example: Nitrous acid changes cytosine into uracil, resulting in a G/C to A/T mutation
Chemicals Can Cause Mutations
Some chemicals cause nucleotide substitutions or change the number of nucleotides in DNA Other chemicals structurally change the bases in DNA, causing a base pair change after replication Chemicals that cause mutations are called mutagens
Mutant Gene Products
Some genes encode proteins that act as growth hormones, receptors, and growth factors Mutated genes can produce abnormal or non-functional proteins that produce changes in phenotypes
Which of the following types of species inhabit an area that would most likely experience genetic drift
Species that live on high mountain peaks
which of the following are now routinely frozen for future use
Sperm, eggs, embyro
mutations occur
Spontaneously as a result of errors in DNA replication or By exposure to environmental factors such as radiation or chemicals
Annotation makes use of all of the following except
Start codons
Colon cancer
Study of colon cancer provides insight into the number and order of steps involved in transforming normal cells into cancer cells Colon cancer starts as a benign tumor that later becomes malignant • Six or more mutations required to initiate cancer
Proteomics
Study of expressed proteins in a cell at a specific time under a particular set of circumstances
Before biotechnology, human proteins used in treatment of diseases were
Substituted for by similar animal proteins and harvested from blood or cadavers only
Risks associated with prenatal testing include:
infection, hemorrhage, fetal injury, and spontaneous abortion.
The quick response of the immune system to a second infection is due to
T and B memory cells
Killer T cells
T cells that destroy body cells infected by bacteria. These cells can also attack and kill cancer cells and cells of transplanted organs.
Killer T cells
T cells that destroy body cells infected by bacteria. These cells can also attack and kill cancer cells and cells of transplanted organs
false
T/F RNA polymerase requires a primer
true
T/F genes can overlap but codons can't
true
T/F: an increased susceptibility to cancer can be inherited
false
T/F: cancer can be inherited
false
T/F: cancer is not a genetic disease
Inflammatory response
The body's reaction to invading microorganisms, a nonspecific active defense mechanism that the body employs to resist infection.
Open reading frame (ORF)
The codons in a gene that encode the amino acids of the gene product.
Pluripotent
The ability of a stem cell to form any fetal or adult cell type
Pluripotent
The ability of a stem cell to form any fetal or adult cell type.
Which of the following have a memory component?
The adaptive immune response
methylation
The addition of a methyl group to a DNA base or a protein Occurs almost exclusively on cytosine bases adjacent to a guanine base (a CpG sequence)
Annotation
The analysis of genomic nucleotide sequence data to identify the protein coding genes, the nonprotein coding genes, their regulatory sequences, and their function(s).
Annotation
The analysis of genomic nucleotide sequence data to identify the protein coding genes, the non protein coding genes, their regulatory sequences, and their functions
In DNA profiles:
The bands are derived from variation in restriction cutting sites of DNA; Ideally, the pattern is unique for all individuals except identical twins; variations in short tandem repeats produce the banding pattern
Inflammatory response
The body's reaction to invading microorganisms, a nonspecific active defense mechanism that the body employs to resist infection
Microbiome
The genomes of all the microbial organisms that live on or in the human body
The government sponsored Human Genome Project used:
The clone-by-clone method
Open reading frame
The codons in a gene that encode the amino acids of the gene product
Assisted reproductive technologies (ART)
The collection of techniques used to help infertile couples have children.
Assisted reproductive technologies
The collection of techniques used to help infertile couples have children
Inborn error of metabolism
The concept advanced by Archibald Garrod that many genetic traits result from alterations in biochemical pathways. We now use the term mutation.
Cancer
The condition has been the target is over half the gene therapy trials performed so far?
What were the results of the DNA profiling of the remains of the last czar of Russia and his family?
The czar and all of his family were accounted for in the remains
gene poor regions
The dark bands on chromosomes
Exon skipping
The directed removal of exons during mRNA processing to restore the reading frame of the mature mRNA to make a shortened, but functional protein
B. Clone-by clone method
The government sponsored HGP used: A. Annotation B. Clone-by clone method C. Shotgun Cloning D. None of these E. Both B and C
A. they are single stranded
The ends of DNA molecules cut by restriction enzymes are "sticky" because: A. they are single stranded B. the enzymes coat them with protective complex polysaccharides C. unless a second enzyme is added, the fragments stick to the restriction enzymes D. all DNA ends are sticky E. none of the above
E. portion of the genome that encodes proteins
The exome refers to: A. entire genome B. guanine based genes C. portion of the genome that contains regulatory sequences D. portion of the genome that contains introns E. portion of the genome that encodes proteins
Immunogloubins
The five classes of proteins to which antibodies belong (ADEGM)
Immunoglobulins (Ig)
The five classes of proteins to which antibodies belong.
accurate measurement of mutation rates depends on several factors
The frequency at which heritable changes in DNA occur • The rate at which mutations are detected and repaired by cells • Whether the mutation results in a recognizable phenotype
mutation rate factors
The frequency at which heritable changes in DNA occur The rate at which mutations are detected and repaired by cells Whether the mutation results in a recognizable phenotype
pedigree analysis, linkage analysis, and twin studies
The genetics of human behavioral traits may be studied by
Epistasis
The interaction of two or more non-allelic genes to control a single phenotype.
Epistasis
The interaction of two or more non-allelic genes to control a single phenotype
Synapse
The junction between two nerve cells where nerve impulses are transmitted and received
Biotechnology
The use of recombinant DNA technology to produce commercial goods and services.
Intracytoplasmic sperm injection is used by couples in which:
The male is infertile.
what is the value of having transgenic mice with the human gene for huntingtons disease (HD)
The mice can be sacrificed and their brains examined to learn about the early stages of the disease; the mice can be used to screen possible anti-HD drugs; the mice are much more numerous and available for study than human patients; the mice can be used to screen possible anti-HD drugs and are much more numberous and avaible for study than human patients
Biotechnology
The use of recombinant DNA technology to produce commercial goods and services. Its use has produced unresolved ethical issues.
Mutation rates can only be measured for dominant alleles under certain conditions
The mutant phenotype must never be produced by recessive alleles • The mutant phenotype must always be fully expressed and completely penetrant • Paternity must be clearly established • The phenotype must never be produced by nongenetic agents • The phenotype must be produced by mutation of only a single gene
rate measurement conditions (dominant)
The mutant phenotype must never be produced by recessive alleles The mutant phenotype must always be fully expressed and completely penetrant Paternity must be clearly established The phenotype must never be produced by nongenetic agents The phenotype must be produced by mutation of only a single gene
Which of the following best describes the effect of cancer-causing mutations on the cell cycle?
The mutations cause cells to bypass checkpoints in the cycle
Which of the following best describes the effect of cancer-causing mutations on the cell cycle?
The mutations increase the speed of the cycle.
mutation rates
The number of events that produce mutated alleles per locus per generation
20,000 and 30,000
The number of genes in the human genome is estimated to be between ______ and ______.
DNA profile
The pattern of STR allele frequencies used to identify individuals
DNA profile
The pattern of STR allele frequencies used to identify individuals. used in law enforcement, conservation and the study of human populations. Based on variation in the copy number of DNA sequences.
A. Can provide sufficient DNA for analysis from a small sample of biological material at the scene of a crime and requires a heat resistant polymerase
The polymerase chain reaction: A. Can provide sufficient DNA for analysis from a small sample of biological material at the scene of a crime and requires a heat resistant polymerase B. Uses a restriction enzyme C. Uses a restriction enzyme and can provide sufficient DNA for analysis from a small sample of biological material at the scene of the crime D. Can not provide sufficient DNA for analysis from a small sample of biological material at the scene of the crime E. Requires a heat-resistant ligase
Shotgun
The private attempt to sequence the human genome, coordinated by Celera Corporation, used a method called _______ cloning.
Radiation
The process by which electromagnetic energy travels through space or a medium such as air Radiation causes biological damage • Ionized molecules can cause mutation in DNA • Free radicals (H+, OH- ) produced by hydrolysis can cause mutations in DNA • If mutations are not repaired, cell death or cancer can occur
radiation
The process by which electromagnetic energy travels through space or a medium such as air
Cloning
The production of identical copies of molecules, cells, or organisms from a single ancestor
cloning
The production of identical copies of molecules, cells, or organisms from a single ancestor
T and B memory cells
The quick response of the immune system to a second infection is due to
Lod score
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.
Lod score
The ratio of probabilities that two genes are linked to the probability that they are not linked, expressed as a log10 Scores of 3 or more means that the odds are 1,000 to 1 or greater in favor of linkage
Lod score
The ratio of probabilities that two genes are linked to the probability that they are not linked, expressed as a log10. Scores of 3 or higher are taken as establishing linkage
promoter
The regulatory region located at the beginning of a gene Chemical modifications (e.g. methylation) can make it available (or unavailable for transcription)
Multipotent
The restricted ability of a stem cell to form only one or a few different cell types
Multipotent
The restricted ability of a stem cell to form only one or a few different cell types.
mutations occur spontaneously by
The result of errors in DNA replication or The result of structural shifts in nucleotide bases
Genome
The set of DNA sequences carried by an individual.
Genome
The set of DNA sequences carried by an individual
The gene pool is best defined as
The set of genetic information carried by a population
Proteome
The set of proteins present in a cell at a specific time under a specific set of environmental conditions.
Proteome
The set of proteins present in a cell at a specific time under a specific set of environmental conditions
Substrate
The specific compound acted on by an enzyme
Product
The specific compound that results from enzymatic action
epigenetics
The study of chemical modifications of DNA and its associated proteins that: Alter gene expression Without changing the nucleotide sequence of the DNA
epidemiology
The study of factors that control the presence, absence, or frequency of a disease • Provides statistical correlation between the environment and diseases such as cancer many cancers are environmentally induced
Epidemiology
The study of factors that control the presence, absence, or frequency of a disease. Provides statistical correlation between the environment and diseases such as cancer.
Proteomics
The study of the proteome, the set of expressed proteins present in a cell.
Genomics
The study of the organization, function, and evolution of genomes
Genomics
The study of the organization, function, and evolution of genomes
Proteomics
The study of the proteome, the set of expressed proteins present in a cell
Metabolism
The sum of all biochemical reactions by which cells convert and utilize energy
Genetic screening
The systematic search for members of a population with certain genotypes
Gene therapy
The transfer of cloned genes into somatic cells as a means of treating a genetic disorder. Procedure in which normal genes are transplanted into humans carrying defective copies, as a means of treating genetic diseases.
Gene therapy
The transfer of cloned genes into somatic cells as a means of treating a genetic disorder. Procedure in which normal genes are transplanted into humans carrying defective copies, as a means of treating genetic diseases
Transgenic
The transfer of genes between species
mutations are
The ultimate source of all genetic variation in humans and other organisms
Pharmacogenomics
The use of biotechnology to identify genetic variations that influence an individual's response to therapeutic drugs as a means of improving drug therapy
Bioinformatics
The use of computers and software to acquire, store, analyze, and visualize the information from genomics.
Bioinformatics
The use of computers and software to acquire, store, analyze and visualize the information from genomics
Bioinformatics
The use of computers and software to acquire, store, analyze, and visualize genomic information
enhancement gene therapy
The use of growth hormones produced by recombinant DNA technology to stimulate the growth of short children who have no genetic disorder is an example of
Genetic testing
The use of methods to determine if someone has a genetic disorder, will develop one, or is a carrier
Biotechnology
The use of recombinant DNA technology to produce commercial goods and services -Is an outgrowth of recombinant DNA technology -Makes use of transgenic organisms -Has generated unresolved ethical issues
type and location of mutation within a gene are important
The wide range of mutations in some genetic disorders leads to wide variation in clinical symptoms • Depending on the mutation, symptoms can range from very mild to very severe More than 1,600 different mutations have been discovered in the CFTR gene • Some people carry two different mutations
The main disadvantage of using transgenic plant cells to produce human proteins is
The yields of the proteins are often low
What is the strong objection many people have to the use of embryonic stem cells
The zygote or embryo used is considered a human life that is destroyed
In Sanger's DNA sequencing method, all of these are TRUE about ddNTPs:
There is no 3' hydroxyl group There is no phosphodiester bond ddNTPs will stop the DNA synthesis (false: ddNTPs works without Taq polymerase)
The ends of DNA molecules cut by restriction enzymes are "sticky" because:
They are all single-stranded
The ends of DNA molecules cut by restriction enzymes are "sticky" because:
They are single-stranded.
clone-by-clone method
This is the method used by US Government sponsored researchers.
Which of the following couples would NOT ordinarily be encouraged to seek genetic counseling?
Those who plan to raise large families
The following ordinarily be encouraged to seek genetic counseling?
Those with a child who has an inherited disorder or birth defect Those who are first cousins Those who have had babies who died in infancy or before birth Those whose occupations may pose a risk to pregnancy (Those who plan to raise large families would not)
Risks of ART
Threefold increase in ectopic pregnancies. Multiple births(35% in IVF). Increased risk of low birth weight. Increased risk of transmitting genetic defects to male children.
Most single gene defects that affect human behavior do so
Through their action on the structure, development, or function of the nervous system
ELSI (Ethical, Legal, and Social Implications)
To deal with the impact of genomic information on society, the HGP set up this program to ensure that genetic information would be safeguarded, not used in discriminatory ways. It works to develop policy guidelines for the use of genomic information
Cancer genome atlas
To employ large scale genome sequencing of cancer cells to catalog genetic changes and identify new genes
Since sons adopted by alcoholic men show a rate of alcoholism more like that of their biological father, there is an argument for the role of genetic factors in this disease. (T/F)
True
One of the concerns with the use of genetically-engineered, herbicide-resistant crops is
Transfer of herbicide resistance to weeds
Transition vs. Transversion
Transition: if a pyrimidine replaces a pyrimidine or a purine replaces a purine Transversion: if a purine replaces a pyrimidine, or vice versa
Enzyme replacement therapy
Treatment of a genetic disorder by providing a missing enzyme encoded by the mutant allele responsible for the disorder.
Enzyme replacement therapy
Treatment of a genetic disorder by providing a missing enzyme encoded by the mutant allele responsible for the disorder. Usually by IV infusion, provides enzyme to someone in whom the enzyme is missing or non functional
(T/F) About 40 percent of the human genes so far identified have a known function.
True
(T/F) According to the FBI, you can request to have your DNA profile removed from the CODIS database if you are not found guilty of a crime.
True
(T/F) Babies conceived through IVF (In Vitro Fertilization) have a much higher risk of premature birth than babies conceived naturally.
True
(T/F) Based on the information from the human genome project, genes appear to be unevenly distributed along chromosomes.
True
(T/F) Chemicals that insert themselves in DNA can cause frameshift mutations.
True
(T/F) DNA is split into single strands during the polymerase chain reaction.
True
(T/F) It is possible to have a mutation in a gene that produces no change whatever in the protein coded for by that gene.
True
(T/F) The number of proteins produced by the human genome is significantly greater than the number of genes it contains.
True
About 40 percent of the human genes so far identified have a known function. (T/F)
True
Adult cells can be used as the source of nuclei for cloning animals. (T/F)
True
Animal genes cannot function in plants. (T/F)
True
At some point in the procedure, DNA is split into single strands during the polymerase chain reaction. (T/F)
True
Babies conceived through IVF have a much higher risk of premature birth than babies conceived naturally. (T/F)
True
False
True or False: About 40% of the human genes so far identified have a known function
True
True or False: According to the FBI, you can request to have your DNA profile removed from the CODIS database if you are found not guilty of the crime.
False - DNA polymerase
True or False: An RNA polymerase is used in most polymerase chain reactions
True
True or False: Based on information from the HGP, genes appear to be unevenly distributed along the chromosome
True
True or False: Chemicals that insert themselves in DNA can cause frameshift mutation
True
True or False: DNA is split into single strands during the polymerase chain reaction
False
True or False: For a number of different reasons, gene therapy has not yet cured any patients of their genetic disorder
True
True or False: It is possible to have a mutation in a gene that produces no change whatever in the protein coded for by that gene
False Missense mutation
True or False: Sickle cell anemia is caused by a nonsense mutation
False
True or False: The HGP took much longer to complete and cost more than was originally anticipated
False GIFT - eggs and sperm placed in the oviduct ZIFT - IVF zygote placed in the oviduct
True or False: The difference between GIFT and ZIFT procedures is where in the woman's body the implantation occurs
False Over 3 and they are on the same one
True or False: Two genes have a lod score of 6.1. This means that the two genes are most likely on different chromosomes
False
True or False: adult cells cannot be used as the source of nuclei for cloning animals
True
True or False: babies conceived through IVF have a much higher risk of premature birth than babies conceived naturally
True
True or False: the number of proteins produced by the human genome is significantly greater than the number of genes it contains
These types of evidence have linked bipolar disorder to genes:
Twin studies Adoption studies Association studies Studies involving degrees of relatedness (not biochemical studies)
DNA repair
Two breast cancer genes, BRAC1 and BRAC2, function in the process of ___________.
E. none of these
Ultraviolet light: A. is not mutagenic B. is a type of ionizing radiation C. causes chromosome breaks D. causes mutations which cannot be repaired E. none of these
characteristics of cancer
Uncontrolled cell division The ability of cancer cells to spread to other parts of the body
Cancer is a complex disease characterized by two main properties:
Uncontrolled cell division • The ability of these cells to spread to other sites in the body (metastasis) Each year, more than one million new cancer cases are diagnosed and approximately 500,000 people will die from the disease
role of proteomics
Understanding gene function and its changing role in development and aging Identifying proteins that are biomarkers for diseases; used to develop diagnostic tests Finding proteins for development of drugs to treat diseases and genetic disorders
T-cell receptors (TCRs)
Unique proteins on the surface of T cells that bind to specific proteins on the surface of cells infected with viruses, bacteria, or intracellular parasites.
T cell receptors
Unique proteins on the surface of T cells that bind to specific proteins on the surface of cells infected with viruses, bacteria, or intracellular parasites
centimorgan (cM)
Unit of distance between genes on chromosomes Equals a value of 1% crossing-over between two genes
Rem
Unit of radiation exposure used to measure radiation damage in humans • The amount of ionizing radiation that has the same effect as a standard amount of x-rays
Rem
Unit of radiation exposure used to measure radiation damage in humans The amount of ionizing radiation that has the same effect as a standard amount of x-rays
male breast cancer
Very rare Approximately 2,000 cases per year Men who inherit mutant BRCA1 or BRCA2 have an 80-fold elevated risk
Oncotype DX assay
Used to help decide on more personalized treatment of breast cancer -analyzes how a cancer is likely to behave/respond to treatment and chance or recurrence
spontaneous mutation
Usually a low level of genetic changes that occur through time. These changes may be due to transposable elements, DNA replication errors and naturally occurring mutagens or natural radiation.
h^2
Va/(Va+Ve)
Methods for transferring cloned genes into human cells
Viral vectors(most widely used) Chemical methods used to transfer genes across cell membranes Physical methods such as microinjection or fusion of cells with vesicles carrying cloned DNA
C. A few cancers
Viruses have been determined to be the cause of: A. No cancers B. Most cancers C. A few cancers D. About half of cancers E. All cancers
Dolly the sheep
Was cloned by using nuclear transfer method. Was cloned by using cell fusion method. Got most of her genetic materials from the donor sheep. Got mitochondrial info from another sheep.
A. Xeroderma pigmentosum
We have evidence that DNA repair in humans is under genetic control from which genetic disease? A. Xeroderma pigmentosum B. fragile-X syndrome C. PKU D. Sickle cell anemia E. none of these
E. all of these
What is the value of having transgenic mice with the human gene for Huntington's Disease? A. The mice can be sacrificed and their brains examined to learn about the early stages of the disease B. the mice can be used to screen possible anti-HD drugs C. The mice are much more numerous and available for study than human patients D. the mice can be used to screen possible anti-HD drugs and are much more numerous and available for study than human patients E. all of these
E. none of these
What legal restrictions on the use of PDG are in place in the US? A. it cannot be used for screening embryos to be tissue donors B. it cannot be used for sex selection C. it can only be used to prevent implantation if the disease diagnosed has a 100% chance of occurring with the genotype revealed D. it has been banned across the board E. none of these
genomic imprinting
When expression of a gene depends on whether it is inherited from the mother or the father • Also known as genetic or parental imprinting
E. All of these
Where in the human body can you find T cells? A. Bone marrow B. Thymus glands C. Blood D. Spleen E. All of these
The key difference between the map-based and whole genome methods of sequencing is
Whether the clones are sequenced before or after their order/place in the genome has been determined
DNA ligase
Which enzyme is responsible for covalently linking DNA strands together?
D. all of these
Which of the following are risks associated with ART? A. ectopic pregnancies B. low birth weights C. passing on male infertility to sons D. all of these
B. mutations cause the cell to bypass checkpoints in the cell
Which of the following best describes the effect of cancer-causing mutations on the cell cycle? A. mutations increase speed of the cycle B. mutations cause the cell to bypass checkpoints in the cell C. mutations interfere with S stage of the cycle D. mutations eliminate one or more stages E. none of these
A. the adaptive immune response
Which of the following has a memory component? A. the adaptive immune response B. more than one of these C. the physical barrier response D. the inflammatory response E. the innate immune response
Lymphocytes
White blood cells that originate in bone marrow and mediate the immune response.
Lymphocytes
White blood cells that originate in the bone marrow and mediate the immune response
How did Dolly the Sheep get her name?
Wilmut the scientist who cloned her said "she came from a mammary gland cell and there wasn't a more impressive pair of glands than Dolly Parton's"
Umbilical cord blood contains stem cells used to treat...
XLP and other immune disorders
Evidence that DNA repair in humans is under genetic control from which genetic disease?
Xeroderma pigmentosum
Antibody
Y-shaped protein molecules produced by B cells that bind to foreign molecules (antigens) and inactivate them
Biotechnology
___________ is the use of recombinant DNA technology to produce commodities or services
PKU can be Treated with
a Diet Low in Phenylalanine
Complement system
a chemical defense system of 20-30 proteins that kill microorganisms directly, supplements the inflammatory response, and works with (complements) the immune system; activate MACs
Histamine
a chemical signal produced by mast cells that triggers dilation of blood vessels
Physical map
a diagram of a chromosome showing the order of genes and the distance between them measured in base pairs
Alzheimer disease is most likely
a disorder caused by mutations at any of three loci
Viruses are the cause of
a few cancers
Viruses have been determined to be the cause of:
a few cancers
Repoxygen
a form of gene therapy which results in increased synthesis and release of erythropoietin, may be impossible to detect
the primary difference between a forward genetic screen and reverse genetics is that:
a forward genetic screen involves the investigation of a particular phenotype
Genetically modified organisms (GMOs)
a general term used to refer to transgenic plants or animals created by recombinant DNA techniques
(EPO)
a hormone that increases production of red blood cells to enhance athletic performance
Probe
a labeled nucleic acid sequence used to identify a complementary region in a clone or genome by hybridization
Memory cells
a long-lived B cell produced after primary exposure to an antigen that plays an important role in secondary immunity
genetically-engineering herbicide resistant crops can lead to
a loss of genetic diversity
Huntington disease is
a model of a single gene defect affecting behavior
Population frequencies for STRs are multiplied together to produce
a probability that a person will have that combination
Genetic counseling
a process of communication that deals with the occurrence or risk that a genetic disorder will occur in a family
A normal ras gene is:
a proto-oncogene
Ras gene
a proto-oncogene
Assisted Reproductive Technologies (ART)
a series of methods used to help infertile couples have children
Recombinant DNA Technology
a series of techniques in which DNA fragments are linked to self-replicating vectors to create recombinant DNA molecules, which are replicated in host cells
The gene pool is best defined as
a set of genetic information carried by members of a population.
missense mutation
a single amino acid is altered
In a missense mutation:
a single amino acid is altered.
genetic diseases are often caused by: (types of mutations)
a single base mutation or small insertion/deletion that affects the function of a particular gene (genomic disease most often caused by large mutations resulting from genome architecture)
To be effective as a force of changing genetic diversity, drift requires
a small, isolated population.
B cell
a type of lymphocyte that matures in the bone marrow and mediates antibody-directed immunity
T cell
a type of lymphocyte that undergoes maturation in the thymus and mediates cellular immunity
The only successful gene therapy has been in ...
a very few cases of severe combined immunodeficiency disease (SCID)
Tertiary structure
folding of secondary polypeptide in coils, sheets, cylinders
Philadelphia chromosome
abnormal chromosome produced by translocation between the long arms of chromosomes 9 and 22; linked to chronic myelogenous leukemia (CML)
about what portion of all couples are affected by infertility
about 1 in 6
Induced pluripotent stem cells
adult cells reprogrammed by gene transfer. Similar to embryonic stem cells
Induced pluripotent stem cells (iPs)
adult cells reprogrammed by gene transfer. They behave similar to embryonic stem cells.
Induced pluripotent stem cells
adult cells reprogrammed by gene transfer; behave similar to embryonic stem cells
Autosomal dominant mutations typically:
affect both a parent and an offspring (affected ind. will have aff. parent & affects both sexes equally)
leading risk factor for cancer
age
Familial adenomatous polyposis (FAP)
autosomal dominant trait resulting in the development of polyps and benign growths in the colon; polyps often develop into malignant growths and cause cancer of the colon
in the pedigree below, the proband is homozygous for a disease causing mutation. genetic testing shows that both parents are carriers for it. what type of mutation likely causes the disease in the proband? (both parents are carriers, male son affected, 3 other daughters unaffected)
autosomal recessive mutation
inherited cancer susceptibility
higher risk for cancer than general population
Clones
all derived from a single ancestor
Clones are:
all derived from a single ancestor
Clones are:
all derived from a single ancestor.
What is the value of having transgenic mice with the human gene for HD
all of these
Once a gene has been cloned it can be used for
all of these 1. disease diagnosis 2. detecting heterozygotes in the population 3. making biosynthetic products for commercial use
Which one of the following is a role of proteomics in research
all of these 1. understanding gene function 2. identifying proteins that are markers for disease 3. understanding how genes function in development and aging 4. finding proteins that are targets for drugs to treat diseases
In DNA profiles
all of these are true 1. the bands are derived from variation in restriction cutting sites of DNA 2. Ideally, the pattern is unique for all individuals except identical twins 3. Variations in short tandem repeats produce the banding pattern
The closely linked group of HLA genes on each chromosome number 6 can be accurately described as
all of these: 1. haplotype 2. codominant gene system 3. gene complex 4. antigen-coding gene cluster
pre-mRNA processing
alternative splicing
PCR
amplifies specific DNA segments billions of times
Intracytoplasmic sperm injection (ICSI)
an egg is fertilized by microinjection of a single sperm; used for defects in sperm count or motility
Transgenic organism
an organism that has received a gene from another species by means of recombinant DNA technology
Annotation
analysis of genomic nucleotide sequence data to identify protein-coding genes, non-protein-coding genes, their regulatory sequences and functions
Pharmacogenetics
analyzes genes and proteins to identify targets for therapeutic drugs
Huntingtons disease is an autosomal dominant disorder affecting motor coordination and cognitive function. trinucleotide expansion of CAG repeats in the HD gene causes Huntingtons. Often times the symptoms associated with the disease arise earlier in life and become more severe in affected individuals as the mutation is inherited. This phenomenon is known as:
anticipation
Galactosemia is an ________ _______ disorder with a frequency of 1 in ______ births
autosomal recessive; 57,000 births
Hereditary nonpolyposis colon cancers (HNPCC)
are casued by mutations in DNA reprair genes AND increases mutation rates in microsatellite regions
Bacterial plasmids
are circular
Bacterial plasmids:
are circular
a haplotype is a set of SNPs which
are closely linked and therefore inherited together
Complement proteins
are involved in defending the body against microorganisms
Complement proteins:
are involved in defending the body against microorganisms
The phenotypes of many human behavioral problems
are not well-characterized and defined
Restriction sites typically:
are the same on both strands if read 5' to 3'
Restriction sites
are the same on both strands of read 5' to 3'
The other species whose DNA was sequenced in the Human Genome Project were species that
are used in experimental genetics
the other species whose DNA was sequenced in the HGP were species that
are used in experimental genetics
Crossover frequencies
are used to construct genetic maps, giving the order and distance between genes on the chromosome
H3
arginine rich
H4
arginine rich
mutation
as a detectable and heritable change in genetic material that is not caused by genetic recombination.
in pedigree analysis, it is easiest to identify the individual most likely to be the source of the mutation is the mutation is
autosomal dominant
Hereditary nonpolyposis colon cancer (HNPCC)
autosomal dominant trait associated with genomic instability of microsatellite DNA sequences and a form of colon cancer
alternate frataxin location
bacteria and mitochondria
Parts of the frataxin protein matched sequences found in...
bacteria and related to a mitochondrial gene
Which one of the following is typically attacked by the antibody-mediated response, not the cell-mediated response?
bacterial cells
sequences are read from the
bottom
Mutant genes are the
basis of genetic disorders
tRNA
between mRNA and ribosome, brings AA to ribosome in order specified by mRNA clover leaf pattern
The function of T cell receptors (TCRs) is to
bind to proteins on the surface of infected cells
The Rhes protein, thought to be important in Huntington disease
binds only to the mutant form of HH
telomerase
binds to distal end of DNA, adds repeat DNA to protect against progressive shortening (due to lagging strands NOT NORMALLY FOUND IN ADULTS (embryonic, fetal and cancer cells)
Several types of evidence have linked bipolar disorder to genes. Which one of the following is NOT one of these types of evidence
biochemical studies
Techniques used in cloning DNA
biochemistry, genetics and molecular biology
Nonobstructive axospermia (lack of sperm production) can be caused by all of the following except
blockage of the epididymis
nonobstructive azoospermia (lack of sperm production) can be caused by all of the following except
blockage of the epididymus (can be caused by use of anabolic steriods, injury to the testes, hormonal imbalances, undescended testes)
Inflammatory response
body's reaction to invading microorganisms; nonspecific active defense mechanism that resists infection
Location of T-cells
bone marrow, thymus glands, blood, spleen
concordance
both twins exhibit same measurement for a trait
Sperm, eggs, and embryos
can be frozen for future use.
enhancer elements
can be upstream or downstream from promoters
In Hardy-Weinberg calculations, the value q^2
can be used to determine the frequency of the homozygous recessive genotypes.
PCR
can provide sufficient DNA for analysis from a small sample of biologcial material at the scene of a crime and requires heat-resistant Taq polymerase
The polymerase chain reaction:
can provide sufficient DNA for analysis from a small sample of biological material at the scene of a crime and requires heat-resistant polymerase.
What condition has been the target of over half the gene therapy trials performed so far
cancer
what condition has been the target for over hald the gene therapy trials performed so far
cancer
Knudson hypothesis
cancer is the result of accumulated mutations to a cell's DNA
The most common disease attempted to be treated in gene therapy trials
cancer, cardiovascular, monogenic
Hereditary nonpolyposis colon cancer (HNPCC)
caused by DNA repair defects An autosomal dominant trait associated with genomic instability of microsatellite DNA sequences and a form of colon cancer Mutations in MSH2 or MLH1 genes destabilize the genome, generating a cascade of mutations in DNA microsatellites • Microsatellites are DNA sequences, 2 to 9 nucleotides long, that are repeated thousands of times and located on many chromosomes • Clusters are called simple sequence repeats (SSRs) or short tandem repeats (STRs)
Pluripotent
cell types that can form many different mature cell types
Effect of Nitrous acid
changes cytosine into uracil, resulting in a G/C to A/T mutation
Histamine
chemical signal produced by mast cells that triggers dilation of blood vessels and increased blood flow to the area
Intercalating agents
chemicals that insert themselves into DNA; produce frameshift mutations
transcriptional regulation
chromatin structure (DNA methylation, alters DNA shape) transcription rate (TATA box, CAAT box, GC boxes)
plasmid
circular extra-chromosomal DNA molecule in bacteria
enhancers and silences
cis-acting elements not in the promoter, bind activator proteins that are produced or imported into the cell under certain conditions
function H1
clamp to keep DNA tight on core nucleosome
uses for PCR
clinical diagnosis, forensics, conservation DNA does not have to be purified and can be present in small amounts
Blackrose II
cloned milk cow. average gives 3.9 gal/day, she gave 11.5 gal/day
non-conservative
codon change, new AA different from original
Open reading frame
codons in a gene that encode the AAs of the gene product
Library
collection of cloned DNA sequences from one source
complex traits
collective term for multifactorial traits for which relative contributions of genes and environment are not well understood
genomic instability
common in cancer cells changes in number and structure of chromosomes
Comparative genomics
compares genomes of different species for clues to the evolutionary history of genes or a species
chromosome specific library
complete genome for a specific chromosome
cystic fibrosis is a common disease affecting approximately 1 in 2,500 individuals. affected ind. inherit the mutation from both parents but often the mutations presenting the ind are located at diff sites within the CFTR gene. This is referred to as a:
complex heterozygote (both alleles mutated but with different mutations-- for a person to be a complex heterozygote there must be allelic heterogeneity at that particular locus)
constitutive gene expression
constantly transcribing "housekeeping genes"
often large animal models are used to study human genetic diseases instead of a mouse model. this often happens when the mouse model of the disease:
does not mirror (or recapitulate) the human condition
Adaptive immune response
contains an immunological memory component, is a specific response, develops more slowly
genomic library
contains complete genome of an organism
Golden rice
contains increased levels of vitamin A
quantitative variation
continuous series of overlapping physical traits (height, skin color)
positive control
control of gene expression where default is OFF, regulators stimulate
negative control
control of gene expression where default is ON, regulators repress
core promoter element
controls where RNAP II binds to DNA and begins copying DNA to RNA
usually, the first procedure a genetic counselow performs for a client is
contructing a pedigree
What type of mutation has been associated with risk of developing autism, schizophrenia, and bipolar disorder
copy number variant
Common transgenic food products
corn, soybeans, cottonseed and canola oils
Products made from these ingredients most often contain transgenic ingredients
corn, soybeans, cottonseed and canola oils
ionizing radiation
creates oxygen free radicals and other ions, they react with bases
humans produce more different polypeptides than we have different genes. That excess is mainly the result of
cutting and splicing of pre-mRNA in several different ways
solenoid structures form this structure
cylindrical fiber
cancer heritability pattern
dominant
Effector cells
daughter cells of B cells, which synthesize and secrete 2,000 to 20,000 antibody molecules per second into the bloodstream
in the pedigree below a disease causing mutation is detected in the male pro band but the mutation isn't present in either parent or any of the siblings. What type of mutation would explain the disease in the proband? (By definition this would be a ________ mutation)
de novo mutation
nucleases
degrade DNA nucleotide by nucleotide, breaking 5` phosphate to 3` OH phosphodiester bond
Structural genomics
derives three-dimensional structures for proteins
DNA fingerprint
detection of variations of minisatellites used to identify individuals
allelic heterogeneity refers to:
different mutant alleles of a gene that are capable of causing the same disease
cystic fibrosis
different types of mutations
endonuclease
digest in middle of nucleic acid strand, cut single (nickase) or double strand
exonuclease
digest only free ends of nucleic acid strands single or double strand
once a gene has been cloned it can be used for:
disease diagnosis; detecting heterozygotes in the population; making biosynthetic products for commercial use
Pathogens
disease-causing agents
Down syndrome
disorder associated with high rates of cancer. this predisposition may result from presence of initial mutation or genetic imbalance that moves cells closer to a cancerous state.
effect of transposable elements
disrupts normal gene function, create new genetic functions, move parts of coding genes to create new coding genes
The phenotype in many human behavioral traits are
due to minor genes with no single gene having a major effect and due to environmental interaction and several genes only
sickle cell anemia
due to specific single nucleotide substituation
multicopy DNA
duplicated genes, gene families, pseudogenes
dominant mutations
easiest mutations to detect They are expressed in the heterozygous condition
none or minimal
effect of mutation in non-coding, non-transcribed regions, synonymous codon changes, intron mutations
moderate to serious
effect of non synonymous codon changes
definite serious
effect of premature stop codon created, normal stop codon eliminated, change in reading frame, multiple copies of repeat sequences inserted
Callus
embryo, clump of undifferentiated cells
Annotation is a process done to find all genes that
encode any RNA or protein product
Annotation is a process done to find all genes that:
encode any RNA or protein product
annotation is a process done to find all genes that
encode any RNA or protein product
microRNA
endogenous single stranded RNA
plasmid pBR322
engineered to carry two antibiotic-resistance genes with restriction sites, one for tetracycline, one for ampicillin
The most common cause of low sperm count is
enlarged veins in the testes
the most common cause of low sperm count is
enlarged veins in the testis
in the pedigree below the female proband has a rare neurological disorder. none of her siblings are affected. what type of mutation or molecular defect likely caused this disease? (no one else in family affected except one of the IDENTICAL twin girls)
epigenetic defect
millirem
equal to 1,000 millirems
enhancment gene therapy and germline therapy are not currently in use because of
ethical concerns
termination
everything falls off
Enzymes are proteins that
facilitate biochemical reactions in the cells
in addition to carrying out the biological process to be studied, a good model organism for genetic analysis must:
faithfully mirror some aspects of the human condition (it must: be easy 2 grow, short generation time, produce abundant progeny, be readily mutagenized and crossed, and ^^)
T/F - RNA polymerase is used in most polymerase chain reactions
false, DNA polymerase is used to copy sections of DNA. DNA polymerase involves the use of heating and cooling DNA to make template strands which interacts with primers and Taq polymerase
T/F - Adult cells cannot be used as the source of nuclei for cloning animals
false, Dolly the sheep showed nuclear transfer with fusion, also direct transfer of nucleus of mice into egg
T/F - The difference between GIFT and ZIFT procedures is where it occurs in the woman's body
false, GIFT (gamete intrafallopian transfer), and ZIFT (zygote intrafallopian transfer)
T/F- two genes have a lod score of 6.1. This means that the two genes are most likely on different chromosomes
false, a Lod score of 3 or higher indicates linkage; lod is the ratio of probabilites that two genes are linked to probability that they're not linked
T/F - Sickle cell anemia is caused by a nonsense mutation
false, changes Glu to Val, nonsense- mutations that change an amino acid specifying a codon to one of the three termination codons
T/F- Gene therapy has not yet cured any patients of their genetic disorder
false, it worked for a few genetic freaks...
For PKU, a formula is prepared from enzymatically digested proteins (or synthetic mixtures of amino acids),
fats, carbohydrates, and vitamin and mineral supplements
Infants with PKU develop normally before birth, then develop neurological damage when
fed a normal diet containing protein
Louise Brown
first human born by IVF - 1978
Immunoglobulins (Ig)
five classes of proteins to which antibodies belong, each with unique structure, size, and function
Embryonic stem cells
from the inner cell mass of early embryos
Embryonic stem cells
from the inner cell mass of early embryos; pluripotent
Helper T cells
function as an "on" switch for antibody production.
dominant
gain of function mutations are
In vitro fertilization (IVF)
gametes are collected and fertilized in a dish; the resulting zygote is impanted in the uterus
Gamete intrafallopian transfer (GIFT)
gametes are collected and placed into a woman's oviduct
DNA microarrays are used for
gene expression, SNPs detection, alternative splicing detection, fusion genes detection. (Does not use Transcriptome sequencing RNA-Seq)
Clusters of genes are separated by
gene poor bands
The bands on chromosomes correspond to
gene poor regions
the bands on chromosomes correspond to
gene poor regions
Enhancement gene therapy
gene transfer to enhance traits such as intelligence and athletic ability rather than to treat a genetic disorder; not currently allowed
Germ-line gene therapy
gene transfer to gametes or the cells that produce them; transfers a gene to all cells in the next generation; not currently allowed
Garrod experiment
genes control metabolic pathways
Tumor suppressor genes
genes encoding proteins that suppress cell division and regulate the cell cycle; these gene products act at control points in the cell cycle (G1/S or G2/M)
Linkage
genes located on the same chromosome that tend to be inherited together
Clones
genetically identical molecules, cells, or organisms all derived from a single ancestor
the cancer genome atlas
genome squencing of cancer to catalog genetic changes and identify new genes brain, lung, and ovarian cancer
in in rare circumstances a single mutation (e.g. a large deletion) can lead to 2 entirely different human diseases. This rare phenomenon can be explained by:
genomic imprinting
in the pedigree below a heterozygous mutation in gene X believed to be responsible for causing a disease in the male proband (IV generation). the mutation however is present in the mother, grandfather, and great grandfather. what type of inheritance pattern would permit this to be penetrant in the male proband but not his mother, grandfather or great grandfather? (generation I male carrier --> gen II male carrier --> gen III female carrier --> gen IV male affected)
genomic imprinting
We share __ our genes with the fruit fly and more than __ with mice
half; 90%
Nuclear transfer:
has a fairly low success rate
DNA synthesis (in PCR)
heat-stable enzyme Taq polymerase is added to synthesize a complementary DNA strand
HIV targets
helper T cells
specific population in a specific environment with regard to variation in a specific trait
heritability restrictions
narrow sense heritability
heritability that only considers contribution of additive effects of genes to variation of the phenotype
hRNA
heterogenous nuclear RNA, eukaryotes only
high h^2
high proportion of variation in the phenotype is explain by genetic differences among individuals
often times a disease causing mutation will simply reduce the activity or function of the protein for which it encodes. This type of mutation is called a _______________.
hypomorph (if it completely abolishes function its null, both are loss-of-function mutations)
Cell-mediated immunity
immune reaction mediated by T cells directed against body cells that have been infected by viruses or bacteria
somatic mutation
in a body cell, passed from cell generation to cell generation, not passed to offspring, some harmful, most not
satellite DNA
in heterochromatin of centromeric regions, higher AT content, highly repetitive, short DNA sequences
autosomal monosomies have not been described in humans because they are not compatible with life (i.e. the fetus is lost during gestation). Turner's syndrome however, is a sex chromosomal monosomy (45,X) and the symptoms associated with it are often not that severe. Why is this the case?
in the normal state, only 1 X chromosome per cell is active (XY in males, and X inactivation in females) so having only 1 X in females is tolerated to some degree
Pompe disease
inability to make GAA
gain of function mutations lead to
inappropriate expression levels, turns proto-oncogene into oncogene
Mutation as a force in genetic diversity serves to
increase genetic diversity
dizygotic twins
independent fertilization, shares half their genes
ultraviolet light
induces dimerization between adjacent thymine bases in existing DNA
size of the gene, base sequence, environmental conditions
influences on mutation rate
initiation
initial unwinding, attachment of components of replication fork
stages DNA replication
initiation, elongation, termination
Embryonic stem cells are harvested from a part of the blastocyst stage embryo called the ________.
inner cell mass
acridine dyes
intercalate themselves between bases, warp DNA, DNA polymerase misreads and inserts extra base
Genomics relies on
interconnected databases and software to analyze sequenced genomes and identify genes
the effect of cancer-causing mutations on the cell cycle
interference with the S-stage of the cycle
Dr. Mullis
invented polymerase chain reaction
Huntington's disease
is a model of a single gene defect affecting behavior.
Intracytoplasmic sperm injection
is used by couple in which the female is approaching menopause.
A mutation occurs that changes C to a T in DNA such that in the mRNA transcribed from this place of DNA a UGG codon is changed to UGA. This mutation
is a substitution mutation AND is a nonsense mutation
A gestational mother
is a surrogate that provides for the development of the embryo after conception.
A gestational mother:
is a surrogate that provides for the development of the embryo after conception.
a gestational mother
is a surrogate that provides for the development of the embryp after conception
UV light
is not mutagenic, is not ionizing radiation, doesn't cause chromosome breakage, doesn't cause irreparable damage; causes molecular lesion in which chemical bonds form between thymine bases -thymine dimers
Operation of sperm banks in the USA
is regulated by the US Food and Drug Administration (FDA)
single stranded binding proteins
keep single DNA strands from reannealing after helicase dissociates them NOT ENZYMES
Hershey and Chase experiment
label DNA on procedure, protein coat on second procedure of phages, see what enters cell, it was DNA
Galactosemia is a genetic disorder caused by
lack of an enzyme in sugar metabolism
Membrane-attack complexes (MACs)
large, cylindrical multiprotein complexes that embed in the invading microorganism's plasma membrane and create pores, eventually bursting the microorganism
translocations/hybrid genes can lead to
leukemia Many proto-oncogenes are located at or close to the breakpoints of chromosomal translocations involved with specific forms of leukemia In CML, the C-ABL gene (chromosome 9) is moved next to the BCR gene (chromosome 22) • The hybrid gene encodes an abnormal protein that signals CML cells to divide
photoreactivation
light repair
Rb1 gene
located on chromosome 13 The tumor-suppressing protein pRB (Retinblastoma protein) controls the G1/S transition in the cell cycle • Regulates the activity of an important protein called E2F (a transciption factor) • Without pRB, cell division is uncontrolled
LINEs
long interspersed elements, huge (multiple families) in human genome, self replicating and translocating
lncRNAs
long, non-coding RNAs, few functions
deamination
loss of amino group, C>U, read as A. A>H read as G
the molecular mechanisms causing genetic and genomic diseases are diverse; however most disease causing mutations are often the result of ______________ in genes
loss of function mutations (also have written in my notes most genetic mutations aren't inherited)
recessive
loss of function mutations are
depurination
loss of purine ring, insertion of random nucleotide at replication
genomic architecture can predispose individuals of various ethnic backgrounds to recurrent deletions or duplications. recurrent genomic rearrangements are typically caused by _________ that flank the deleted or duplicated region.
low copy repeats (cell notices the repeats and thinks they are a mistake --> tries to correct itself --> mutation)
A PKU diet must contain phenylalanine levels high enough for normal development, but
low enough to prevent mental retardation and should be maintained for life
low h^2
low proportion of variation in the phenotype is explain by genetic differences
H1
lysine rich
Societies with the highest number of individuals who are able to produce lactase are those who
maintain dairy herds
intracytoplasmic sperm injection is used by couples in which
male is infertile
animal and insect models systems can be used to study human genetic diseases. The main reason that these models can be used to study human diseases is because...? (looking for the best answer)
many genes are conserved among species so there function can be studied in model systems (think about how he has said genetic mechanisms are the same in most organisms-- not much variation in genomes)
In a pedigree analyzed using positional cloning, the inheritance of a disease trait is typically linked to the inheritance of
marker sequences produced by restriction enzymes
Metastasis is a term for what characteristic of cancer
migration of tumor cells to other parts of the body
proofreading
mismatched base pairs create bulge, DNA polymerase recognizes this and inserts the correct nucleotide
Researchers found frataxin in __ and determined its structure, but its specific function is still unknown
mitochondria
oxidative damage
modifies bases in different ways
alkylating agents
modify bases to create base analogs in position, changes for next round of replication
Inheritance of __ __ is used to track the inheritance of genetic disorders in pedigrees and thus the gene responsible
molecular markers
Antigens
molecules that initiate antibody production, carried or produced or microorganisms
elongation
more unwinding, removal RNA primers, add new bases (leaded and lagging), rewinding
E. coli
most common host bacterial cell
based on the most recent stats in the OMIM database, there are more genomic disorders associated with deletions than with duplications. If deletions and duplications are reciprocal events, why aren't there similar numbers of diseases caused by two types of chromosomal rearrangements
most genes associated with genomic disorders are dosage sensitive, so deletions will have a larger impact on the gene with regards to its expression levels than duplications.
copy
must be capable of being replicated accurately and passed from one cell generation to the next
control
must be expressible in molecular forms other than itself than can direct biologic processes
code
must contain (store) biologically useful information and maintain it in a stable manner
change
must possess properties that enable new variation to arise (AKA mutation)
Base analogs
mutagenic chemicals (purine or pyrimidine) that structurally resemble nucleotides and are incorporated into DNA or RNA during synthesis
Steps of FAP
mutation in APC on chromosome 5 --> mutation of k-ras transforming polyp into adenoma --> mutations in DCC leads to formation of late-stage adenomas --> mutations in both alleles of p53 on chromosome 17 cause late-stage adenoma to become cancerous
germ line mutation
mutation in germ cell or germ cell precursor, can be passed to subsequent generations
retinoblastoma
mutation of a tumor suppressor gene A malignant tumor of the eye arising in retinoblasts (embryonic retinal cells that normally disappear at about 2 years of age) • Because mature retinal cells do not transform into tumors, this tumor usually occurs only in children • Associated with a deletion in the long arm of chromosome 13 • The responsible gene, Rb, is located on chromosome 13
Frameshift mutations
mutational events in which a number of bases (other than multiples of three) are added or removed from DNA, causing a shift in the codon reading frame
induced mutations
mutations above background rate, brought about by intentional or unintentional application of specific agents
recessive mutations
mutations detected only in the homozygous condition It is extremely difficult to identify the origin
HNPCC is a DNA repair defect
mutations in MSH2 or MLH1 genes destabilize genome creating a cascade of mutations in DNA microsattelites. Proteins encoded by MSH2 and MLH1 genes repair errors in DNA replication.
Sense mutations
mutations in a single nucleotide can change a termination codon into one that codes for an amino acid, producing elongated proteins
locus heterogeneity referes to:
mutations in different genes that result in the same clinical disease
spontaneous mutation
mutations occurring at a natural background rate
Missense mutations
mutations that cause the substitution of one amino acid for another in a protein
Nonsense mutations
mutations that change an amino acid specifying a codon to one of three termination codons
Nucleotide substitutions
mutations that involve replacing one or more nucleotides in a DNA molecule with other nucleotides
the largest source of radiation exposure for the average person in the U.S.
naturally occurring radiation
For the average person in the US, the largest source of radiation exposure is:
naturally occurring radiation.
missense mutation
new codon specifies different AA, can be conservative or non conservative
nonsense mutation
new codon specifies premature stop
silent mutation
new codon specifies same AA
topoisomerases
nick DNA during unwinding, relieve torsion stress, then reseal the nick
which one of the following mutagens acts b chemically modifying the structure of bases in DNA
nitrous acid
sporadic cancer
no inherited risk above general population rate of cancer (most cancers are this)
down syndrome is caused by trisomy 21 (i.e. 3 copies of chromosome 21). This happens because of ____________ during meiosis
non-disjunction
What legal restrictions on the use of PGD are in place in the US
none of these
ultraviolet light causes
none of these
the use of growth hormone produced by recombinant DNA technology to stimulate the growth of short children who have no genetic disorder is an example of
none of these (NOT somatic gene therapy, germ-line therapy, enhancment therapy; therapuetic therapy
Which of the following usually first appears during childhood
none of these: 1. Alzheimers 2. HD 3. Schizophrenia 4. Bipolar disorder
The use of growth hormone produced by recombinant DNA technology to stimulate the growth of short children who have no genetic disorder is an example of
none of these: 1. somatic gene therapy 2. germ-line therapy 3. enhancement gene therapy 4. therapeutic cloning
proto-oncogenes
normal cellular genes that appropriately promote cell growth and division activities (developmental stages)
Short tandem repeats used
now used routinely instead of minisatellites, and DNA profile has replaced the term DNA fingerprint
solenoid
nucleosomes form this structure
the most direct effect of a mutation is on
nucleotide sequence
Minisatellities
nucleotide sequences 14 to 100 base pairs long organized into clusters of varying lengths; used in the construction of DNA fingerprints
6 or more
number of mutations required to initiate colon cancer
polymorphism
occurrence of multiple allelic forms at a locus at high frequencies
Transgenic plants
often referred to as either genetically modified organisms (GMOs) or genetically modified (GM) plants
Twin Studies
often used to study polygenic traits in behavioral genetics
in genes associated with trinucleotide expansion repeat disorders (Huntington's, fragile X, etc) the pre-mutation allele is often more prone to expansions than the normal allele. Why is this?
once the repeat is expanded (past a certain threshold number) it becomes more susceptible to further expansions during DNA synthesis
Beadle and Tatum experiment
one gene one enzyme
Which one of the follwoing statemaents about the BRCA1 gene for breast cancer is false
one mutated copy of BRCA1 is sufficient to cause cancer
micro injection of fertilized eggs
one way to transfer genes into mammals
photo-reactivation repair
only in presence of visible light, photolyase recognizes pyrimidine dimers, in blue light it fixes it
Y linked disorders affect:
only males
Anticipation
onset of a genetic disorder at earlier ages and with increasing severity in successive generations; due to increasing number of trinucleotide repeats with successive generations
helicases
open up (unwind) DNA double helix
Research has shown that particular copy number variations (CNVs) are related to the odds of success in
organ transplants
Homo erectus:
originated in Africa but migrated outward
many genes are conserved from yeast to higher vertebrates and carry out similar functions in a wide range of organisms. A gene that is conserved between two different species is called a/an:
ortholog (genes in diff species that evolved from common ancestral gene by speciation)
Beta globin is a component of hemoglobin, a quaternary protein that transports
oxygen from the lungs to cells and tissues of the body
Criteria used to determine when a mutation has occurred?
pattern of inheritance, phenotype, biochemistry, degrees of lethality
The genetics of human behavioral traits may be studied by
pedigree analysis, genome analysis, and twin studies
components nucleic acids
pentose sugar, phosphate group, nitrogenous bases
13%
percent of couples that are infertile in US
60%
percentage of human genes with known function
5%
percentage of nucleotides of DNA that encode genetic information
5%
percentage of our 3 billion nucleotides of DNA encode genetic information
90%
percentage of shared genes between humans and mice
Codominant allele system
phenotypes are equal to genotypes so it is easy to measure allele frequencies.
Circulating antibodies are produced by
plasma cells
Activated B cells divide rapidly to produce
plasma cells and memory cells
multifactorial traits
polygenic traits that also have significant influence from the environment
Ve
portion of Vp due to environmental (non-genetic) effects
Va
portion of genetic variance due to additive effect of alleles
The exome refers to the:
portion of the genome that encodes proteins.
age
primary risk factor for cancer
Annealing
primers are mixed with the DNA and bind to complementary regions on single-stranded DNA; low temps
C. Venter
privately funded shotgun cloning
Analysis of DNA profiles combines
probability theory, statistics, and population genetics to estimate how frequently an allele combination is found in a population
Transgenic Bt crops have been genetically modified to
produce an insecticide
Antibodies
proteins produced by B cells that bind to specific foreign molecules (antigens) and inactivate them
Ras genes
proto-oncogenes that regulate cell division A mutation in the ras gene converts it to an oncogene that continually signals cell division
Meslsohn and Stahl experiment
proves semi-conservative method DNA replication by measuring mass of DNA of bacteria at different generations
Background radiation
radiation in the environment that contributes to radiation exposure
Ionizing Radiation
radiation that produces ions during interaction with other matter, including molecules in cells
B and AB
rarest blood types
In 1949, James Neel identified sickle cell anemia as a ________ _______ disease caused by a mutation in the gene encoding beta globin
recessively inherited
restriction endonucleases
recognize and cut DNA at specific nucleotide sequences
restriction endonuclease
recognize and cut specific DNA sequences, most are palindromes
base excision repair
recognize, remove and replace damaged nucleotides individually
nucleotide excision repair
recognize, remove and replace damaged nucleotides regionally
mismatch repair
recognizes mismatches overlooked by DNA polymerase, in prokaryotes recognizes methylation
Adult stem cells
recovered from bone marrow or other organs
Adult stem cells
recovered from bone marrow or other organs; multipotent
in the development of a model organism, the process of inducing a loss of function mutation in a particular gene to study its function is known as:
reverse genetics
rRNA
ribosomal RNA
repetitive DNA
satellite, centromeric and telomeric DNA
ligases
seal DNA breaks by restoring 5` phosphate to 3` OH bond joins Okazaki fragments
Cytotoxic "killer" T cells
secrete perforin to destroy infected body cells
Vectors
self-replicating DNA molecules used to transfer foreign DNA segments between host cells (commonly plasmids)
Sanger DNA sequencing method
sequence a small amount of DNA DNA bases (A, T, C, G) are tagged with a radioisotope used to synthesize DNA. The products are separated by size
Transcriptome
set of all RNA molecules produced by a cell or an organism; doesn't require hybridization
secondary structure
shape of polypeptide molecule
SINEs
short interspersed elements (multiple families), not self replicating, rely on LINE machinery to replicate and translocate
Short tandem repeats (STRs)
short nucleotide sequences 2 to 9 base pairs long organized into clusters of varying lengths; microsatellites
What types of DNA sequences provide the basis for DNA profiles
short tandem repeats
What types of FNA sequences provide the basis for DNA profiles
short tandem repeats
The private attempt to sequence the human genome, coordinated by Celera Corporation, used a method called ______ cloning.
shotgun
Many human behavioral traits
show genetic heterogeneity with the same phenotype resulting from different genes
monozygotic twins
single fertilization, genetically identical
mutation rate affectors
size of gene nucleotide sequence spontaneous chemical changes
the mutation rate of a gene is influenced by
size of the gene and number of GC pairs versus AT pairs
3 defenses against infection
skin, inflammation, and the immune response
H2A/H2B
slightly lysine rich
Colon Polyps
small clusters of dividing cells on the lining of colon
siRNAs
small interfering RNAs, exogenous double stranded RNA, processed by DICER and RISC
To be effective as a force changing genetic diversity, drift requires
small, isolated population
intrauterine insemination
sperm injected into uterus
sources of mutation
spontaneous or exposure
annotation makes use of all of the follwoing except
start codons (makes use of seqences present in all gene promoters; sequences marking splice sites between introns and exons; sequences marking the add position for the poly-A tail; and ORFs)
base analogs
structurally similar to normal bases, linked to deoxyribose to form unnatural nucleotides
Proteomics
study of expressed proteins in a cell at a specific time under a particular set of circumstances
Before biotechnology, human proteins used in treatment of diseases were:
substituted for by similar animal proteins and harvested from blood or cadavers only
proteome
sum of all proteins produced by all cell types oer all developmental stages
transcriptome
sum of all transcripts produced by all cell types over all developmental stages
According to Darwin, fitness is a measure of
survival and differential reproduction
Gleevec
targeted cancer therapy; blocks the BCR-Abl oncogene in CML
Herceptin
targeted cancer therapy; blocks the HER2 receptor on certain breast cancers
tautomeric shifts
tautomers of normal bases make anomalous base pairing, insert different nucleotide at replication
DNA sequencing
technique for determining the nucleotide sequence of a fragment of DNA
mRNA
template for protein synthesis in prokaryotes it is the initial transcript in eukarytoes it is not the initial transcript
In Hardy-Weinberg calculations, the value 2pq can be used to directly determine
the frequency of heterozygous genotypes and the chance that a zygote will carry unlike combinations of alleles
HIV targets ________for infection.
the helper T cells
autoimmune disease
the immune system attacks and kills cells and tissues of the body
In positional cloning, the inheritance of a disease in a pedigree was linked to
the inheritance of marker sequences produced by restriction enzymes.
Gene therapy involves
the introduction of a normal gene into an individual carrying a mutant copy.
recombinant DNA molecules
transferred into host cells; cloned copies are produced as the host cells grow and divide
Epidemiology
that study of factors that control the presence, absence, or frequency of a disease
The first demonstration of gene linkage in humans was an analysis that showed
that the genes for hemophilia and color blindness are both on the X chromosome
the first demonstration of gene linkage in humans was an analysis that showed
that the genes from hemophilia and color blindness are both on the X-chromosome
Pluripotent
the ability of a stem cell to form any fetal or adult cell type
Which of the following have a memory component?
the adaptive immune response.
The government sponsored Human Genome Project used:
the clone-by-clone method
The government sponsored Human Genome project used:
the clone-by-clone method
The governmnet sponsored Human Genome Project used
the clone-by-clone method
In the Sanger's DNA method, each of the four nucleotides are distinguished from the others by:
the color of the fluorescent dye attached to it.
in some instances a person can have a disease that is similar to a mitochondrial disorder, but no mutation is present in the mitochondrial genome. How can this be?
the disease is caused by a mutation in the nuclear genome that encodes a protein used by the mitochondria (so this isn't mito mutation bc mitochondrial mutations HAVE to be mutations on mitochondrial DNA)
When the degree of recombination between linked genes is measured
the distance between them can be determined
The B blood type allele frequency in Europe forms a gradient, with the highest frequency in
the east
RFLP
variation in the length of DNA fragments produced by a restriction endonuclease
The main disadvantage to using plant cells has been...
the low yields of transgenic protein
Intracytoplasmic sperm injection is used by couples in which
the male is infertile
Intracytoplasmic sperm injection is used by couples in which:
the male is infertile
intracytoplasmic sperm injection is used by couples in which
the male is infertile
In the cloning procedure for plants, the "callus" is
the mass of undifferentiated cells grown from each single cell.
in some situations an X linked disorder (e.g. rett syndrome) is present in girls and not boys. how can this be?
the mutation is lethal in boys
Which of the following best describes the effect of cancer causing mutation on the cell cycle
the mutations cause the cell to bypass checkpoints in the cycle
Mutation rate
the number of events that produce mutated alleles per locus per generation
oligogenic diseases differ from monogenic disease by...?
the number of mutated genes needed to cause the disease
imprinted diseases are unique as the penetrance of the disease is dependent on:
the parent of origin
Exome
the portion of the genome that encodes proteins
Lod score
the probabilities that two genes are linked to the probability they are not linked, expressed as log10. Scores of 3 or more mean they are linked
Radiation
the process by which electromagnetic energy travels through space or a medium such as air
To sequence an entire genome
the process is automated; each base is labeled with a different fluorescent dye which can be read in a single lane by a scanner linked to a computer
Hardy and Weinberg mathematically proved that as time goes by in a population
the proportion of all genotypes will remain constant
Hardy and Weinberg mathematically proved that as time goes by in a non-evolveing population
the proportion of all genotypes will remain the same
Hardy and Weinberg mathematically proved that as time goes by in a non-evolving population:
the proportion of all genotypes will remain the same.
Lod score
the ratio of probabilities that two genes are linked to the probability that they are not linked, expressed as log10. Scores of 3 or more means that the odds are 1,000 to 1 or greater in favor of linkage
fragile X syndrome is caused by expanded CGG repeats in the promoter of the FMRI gene. it is a unique disorder because the repeats are in the promoter region and not in the coding regions (i.e. exons). By what mechanism do you think that the repeats in the promoter region cause fragile X syndrome
the repeats cause the cell to methylate the promoter thus silencing the expression of the FMR1 gene (true epigenetic disorder bc the actual genome isn't the problem-- epigenetic methylation is problem)
genome
the set of DNA sequences carried by an individual
in a missense mutation
the single amino acid is altered
Synaptic cleft
the small gap, measured in nanometers, between neurons across which nerve impulses are transferred
Genomics
the study of the organization, function, and evolution of genomes
A chemical compound can be the product of one reaction and
the substrate for the next reaction
Gene therapy
the transfer of cloned genes into somatic cells as a means of treating a genetic disorder
Biotechnology
the use of DNA technology to produce commercial goods and services
Bioinformatics
the use of computers and software to acquire, store, analyze, and visualize genomic information
what is the strong objection many people have to the use of embyronic stem cells
the zygote or embryo used is considered a human life that is destroyed
ends of DNA molecules cut by restriction enzymes are sticky becuase
they are single stranded
Which of the following couples would NOT ordinarily be encouraged to seek genetic counseling
those who plan to raise large families
Which of the following couples would NOT ordinarily be encouraged to seek genetic counseling
those who plan to raise large families (would seek those with a child who has an inherited disorder or borth defect; those who are first cousins; those who have had babies who died in infancy or before birth; those whose occupations may pose a risk to pregnancy)
codon
three nucleotide base sequence
anticodon
three nucleotide sequence in tRNA that is complimentary to codon of mRNA
Screening newborns for PKU
through blood drawn from foot since 1960s
heritable
trait can be passed down, has genetic basis
polygenic traits
traits with variation controlled by two or more genes, AKA quantitative traits
transcription factors
trans acting polypeptides that bind specific DNA sequences
TATA box, CAAT box, GC boxes
trans-acting proteins attract RNA polymerase, causes start of transcription
repressible gene expression
transcription ceases in presence of end product of the metabolic pathway in which gene participates (AKA negative feedback)
inducible gene expression
transcription occurs in presence of an exogenous substance
One of the concerns with the use of genetically-engineered, herbicide-resistant crops is:
transfer of herbicide resistance to weeds.
adult stem cells can be reprogrammed into induced pluripotent stem cells by
transfering specific genes into their nuclei
which of the gollowing is NOT used in gene therapy to transfer cloned DNA into human cells
transformation (is used retrovirus; fusion of cells with DNA-containing vesicles; microinjection; chemical means to get the DNA through the cell membrane)
Which of the following is NOT used in gene therapy to transfer cloned DNA into human cells
transformations
Which animals produce human GAA to treat Pompe disease?
transgenic female rabbits; transgenic hamster cells
T/F - The number of proteins produced by the human genome is significantly greater than the number of genes it contains
true
T/F - about 40 percent of human genes so far have been identified and have a know function
true, 40% human genes and function identified
T/F- DNA is split into single strands during PCR
true, breaking of the H-bonds in DNA splits in PCR during the heating process
T/F - Chemicals that insert themselves in DNA can cause frameshift mutations
true, chemicals resembling base pairs, called intercalating agents, insert themsleves into DNA, distorting the double helix; replication in this region can result in deletions or insertions of basepairs (frameshift)
T/F - Based on information from the Human Genome Project, genes appear to be unevenly distributed along chromosomes
true, genes are unevenly distributed along chromosome
T/F - It is possible to have a mutation in a gene that produces no change whatsoever in the protein encoded by that gene
true, no change in amino acid can result from a nucleotide stubstitution
It has been suggested that the allele for Tay Sachs disease may confer some protection against
tuberculosis
discordance
twins do not exhibit same measurement for a trait
Watson and Crick Model
two anti-parallel strands with bases inside, complimentary base pairing (AT, GC), molecular interactions lead to right handed helix
Diet and behavior
two major factors in cancer prevention
Reprogrammed (iPS) cell lines are being used to study all of the following except
type 1 diabetes
mutations
ultimate source of all genetic variation in humans and other organisms
heritability
underlying causes of variation
which one of the following is a role of proteonomics in research
understanding gene function; identifying proteins that are markers for disease; understanding how genes function in development and aging; and finding proteins that are targets for drugs to treat disease
single copy DNA
unique genes
T-cell receptors (TCR)
unique proteins on the surface of T cells that bind to specific proteins on the surface of cells infected with viruses, bacteria, or intracellular parasites
Centimorgan (cM)
unit of distance between genes on chromosomes
Rem
unit of radiation exposure used to measure radiation damage in humans
gene
unit of transcription
target therapies
use drugs that selectively block the activity of specific oncogenes • Gleevec blocks the BCR-Abl oncogene in CML • Herceptin blocks the HER2 receptor on certain breast cancers
DNA profiles
use variations in the length of short repetitive DNA sequences to identify individuals with a high degree of accuracy and reliability
plasmids
used as vectors for cloning DNA
Lod method
used to construct genetic maps, giving the order and distance between genes on the chromosome
crossover frequencies
used to construct genetic maps, giving the order and distance between genes on the chromosome
Southern blot
uses gel electrophoresis to separate DNA fragments; radioactive probes identify blotted bands
observation of mutations
using criteria such as pattern of inheritance, phenotype, biochemistry, and degrees of lethality
5`-3`
what direction DNA polymerase adds bases
DNA condensation
what makes DNA inaccessible to enzymes necessary for gene expression and replication
Gametic Phenotypic Value
what the gamete will contribute to the zygote phenotype
Which one of the following common crops is NOT one of the major sources of transgenic ingredients
wheat
Genomic imprinting
when expression of a gene depends on whether it is inherited from the mother or the father
nucleus
where DNA and RNA found
cytoplasm
where RNA and protein synthesis occurs
research, agriculture and medicine
where cloned plants and animals are used
anti-sense strand
where does RNA polymerase bind? (sense or anti-sense)
in the pedigree below the male proband is affected with a severe neurodevelopment disorder. genetic testing shows that the sister mom and grand mom are carriers but unaffected. what is the most likely inheritance pattern of the disease causing mutation in the proband?
x-linked (probably x linked recessive because females are carriers)
DNA repair in humans is under genetic control as proof of which disease
xeroderma pigmentosum
We have evidence that DNA repair in humans is under genetic control for which genetic disease?
xeroderma pigmentosum
Genetic counseling
• A process of communication that deals with the occurrence or risk that a genetic disorder will occur in a family
Galactosemia
• A heritable trait associated with the inability to metabolize the sugar galactose • Defect is in the gene encoding the enzyme GALT (Galactose-1-phosphate uridyl transferase) • If left untreated, high levels of galactose-1-phosphate accumulate, causing cataracts and mental retardation • Dietary treatment does not prevent long-term complications
Clone-by-clone method AKA Map-based sequencing
• A method of genome sequencing that begins with genetic and physical maps • Uses clones from a genomic library that have been arranged to cover an entire chromosome • After the order of clones is known, they are sequenced
Shotgun sequencing method AKA Whole genome sequencing
• A method of genome sequencing that selects clones at random from a genomic library • After the clones are sequenced, assembly software organizes them into the genomic sequence
Friedreich ataxia
• A progressive and fatal neurodegenerative disorder inherited as an autosomal recessive trait • Symptoms appear between puberty and age 25
Pompe disease
• An inability to make α-glucosidase (GAA) • Leads to reduced heart and muscle function • Treated by enzyme replacement therapy
sporadic cancer
• Cancer caused by accumulation of a number of mutations in somatic cells • Mutation occurs in a single somatic cell • Additional mutation accumulate
Open reading frame (ORF)
• Codons in a gene that encode the amino acids of the gene product • Control sequences (CAAT, CCAAT) at the beginning of genes; splice sites between exons and introns; poly-A tail at the end
In vitro fertilization (IVF)
• Gametes are collected and fertilized in a dish • The resulting zygote is implanted in the uterus
Germ-line gene therapy
• Gene transfer to gametes or the cells that produce them • Transfers a gene to all cells in the next generation, including germ cells - not yet in use mainly due to unresolved ethical issues
Use of ART raises unresolved ethical issues
• Health risks to both parents and their offspring resulting from ART • Use of preimplantation genetic diagnosis to select siblings who are suitable tissue or organ donors for other members of the family
Producing induced pluripotent stem cells from individuals with these genetic diseases provides a way to study cells of the individual
• Huntington's disease • Gaucher disease • Type I juvenile diabetes
Advantages of the use of transgenic plants
• Lower costs • Easier to grow
Counselors help people understand
• Medical facts, diagnosis, and treatment • How heredity contributes to the disorder and risk of having children with the disorder • Alternatives for dealing with the risk of recurrence • Ways to adjust to the disorder
base analogs
• Mutagenic chemicals (purine or pyrimidine) that structurally resemble nucleotides and are incorporated into DNA or RNA during synthesis Example: 5-bromouracil can replace thymine • Causes insertion of G rather than A • Results in a A/T to G/C mutation
Types of genetic testing and screening
• Newborn screening • Carrier testing - done on family members • Pre-natal testing • Pre-symptomatic or predictive testing
Preimplantation genetic diagnosis (PGD)
• Removal and genetic analysis of a single cell from a 3- to 5-day old embryo • Used to select embryos free of genetic disorders for implantation and development • Has been used to select embryos tissue-matched to siblings with Fanconi anemia or leukemia to serve as transplant donors
Proteomics
• Study of expressed proteins in a cell at a specific time under a particular set of circumstances
Two strategies for genome sequencing
• The map-based or clone-by-clone method • The whole genome or "shotgun" method
Somatic gene therapy
• The only form of gene therapy used to date • Gene transfer to somatic target cells • Involves a single target tissue treating only one person • Done to correct a genetic disorder, using established ethical and medical guidelines
Gene therapy
• The transfer of cloned genes into somatic cells as a means of treating a genetic disorder
Biotechnology
• The use of DNA technology to produce commercial goods and services • Is an outgrowth of recombinant DNA technology • Makes use of transgenic organisms • Has generated unresolved ethical issues
Risks of ART
• Threefold increase in ectopic pregnancies • Multiple births (35% in IVF) • Increased risk of low birth weight • Increased risk of transmitting genetic defects to male children (in ICSI)
Huntington Disease Mice
• Used to study the progressive destruction of brain structures in early disease stages • Used to link changes in brain structure with changes in behavior • Used to screen drugs to improve symptoms or reverse brain damage
Methods for transferring cloned genes into human cells
• Viral vectors • Chemical methods used to transfer genes across cell membranes • Physical methods such as microinjection or fusion of cells with vesicles carrying cloned DNA
Counseling is recommended for
• Women who are or may be pregnant after age 35 • Couples who have a child with a genetic defect • Couples seeking information about genetic defects that are common in their ethnic group • Couples who are close blood relatives • Individuals at risk through jobs or lifestyle • Women who have had multiple miscarriages • Those concerned that they may have an inherited disorder or birth defect
Enhancement gene therapy
•Gene transfer to enhance traits such as intelligence and athletic ability rather than to treat a genetic disorder - not yet in use mainly due to unresolved ethical issues
