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127 Cards in this Set

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T to C mutation
transition mutation
G to T
transversion mutation
mutations that change nucleotide sequence but not the amino acid sequence
silent mutation
base substitution resulting in change of an amino acid
missense mutation
base substitutions resulting in a new stop codon
nonsense mutations
The activity of DNA Polymerase that removes incorrectly incorporated nucleotides is called
proofreading repair
Example of a chemical that is a base analog
5-bromouracil
Ultraviolet light primarily damages DNA by forming 1.----- dimers. A defect in the repair mechanism results in a human inherited autosomal 2.----- disease xeroderma pigmentosum.
pyrimidine; recessive
What is the minimum number of single-nucleotide substitutions that would be necessary for the replacement of amino acid methionine with tyrosine?
3
The molecular basis of the fragile-X chromosome has been traced to an 1.----- of the 5'-GGC-3' (repeat) present in the DNA at the site where the breakage takes place.
expansion
Developmental genes are often controlled by 1.----- of gene products, either within cells or across parts of the embryo
gradient
In higher plants differentiation takes place almost continuously throughout life in regions of actively dividing cells called 1.----- in both the vegetative organs and the floral organs.
meristems
Genes that function in the mother that are need for development of the embryo are called 1.----- genes. Mutations in these genes are easy to identify because 2.----- females produce eggs that are unable to support normal embryonic development, whereas homozygous males produce normal sperm.
maternal-effect; homozygous
Describe the two essential functions of cytoplasm in an animal egg.
Storage of molecules to support cleavage divisions and rapid RNA and protein synthesis and Organization of molecules in the cytoplasm to provide positional information
The 1.----- genes determine the principle coordinate axis of the embryo; the anterior-posterior, which defines the front and rear, and the dorsal-ventral axis, which define the top and bottom.
coordinate
The C. elegans lin-12 gene, which controls a number of yes-or-no developmental decisions, codes for a
transmembrane receptor protein
The homeotic genes encode
transcriptional activator proteins
Imprinting is
DNA modification in gametogenesis that effects gene expression in the zygote.
Induction of the morphogenic events in the Drosophilia imaginal disks is initiated by
hormone ecdysone
A cell that is capable of differentiating into a complete organism is called a(n)
Totipotent cell
The carrier DNA molecule used to propagate a desired DNA fragment is called a 1.-----.
vector
study of the genome (all the genes, dna sequences, function and organization)
genomics
studying all the proteins (functions, organization, interactions) in a cell or organism
proteomics
"sticky ends"
asymmetric cleave
"blunt ends"
symmetric cleave
Because many eukaryotic genes contain 1.----- that are present in the primary transcript, but are removed from the mature mRNA, the cDNA sequence is not identical with the genomic DNA.
introns
The backbone of each strand is cleaved by a restriction enzyme, creating a free 3' 1.----- group and a free 5' 2.----- group.
hydroxyl; phosphate
forms a covalent bond between the 3'OH and the 5' P groups
DNA ligase
synthesizes a complimentary DNA strand from a RNA template
Reverse transcriptase
synthesizes a strand of RNA from a DNA template
RNA polymerase
synthesizes a strand of DNA from a DNA template
DNA polymerase
Deliberate alteration of the genome for treatment of disease is called 1.-----.
gene therapy
All are true of what? 1.also called a polylinker 2. Useful vectors always contain MCS 3. contains unique cleavage sites for many different restriction enzymes
true of a multiple cloning site
Plasmids or BACs used for in vitro cloning of foreign DNA fragments are called
vectors
The bacterium used as the model for genetic recombination and engineering in plants is
Agrobacterium tumefaciens
The ability of an introduced DNA fragment to correct a genetic defect in a mutant organism is called a(an)
transformation rescue
At which level are genes regulated?
All levels of transcription, translation etc..
Default state of transcription is "on"
negative regulation
Default state of transcription is "off"
positive regulation
Repressor DNA binding protien keeps transcription OFF, unless inducer present
Inducible transcription
transcription is ON until an active repressor is formed and binds
repressible transcription
Which enzyme cleaves lactose to yield glucose and galactose?
beta-galactosidase
The negative regulator of the lac operon is encoded by the 1.----- gene and the positive regulator of the lac operon is the 2.----- complex.
Lac I; cAMP-CRP
1.----- refers to heritable changes in gene expression that are not due to changes the DNA sequence itself, but to something "in addition to" the DNA sequence, usually either chemical modification of the bases, or protein factors bound with the DNA.
epigenetic
Triggers degradation of RNA transcripts containing homologous sequences.
RNA interference (RNAi)
Heavy methylation is associated with
low transcription rate.
The helix-turn-helix and zinc finger are structural motifs found in
DNA binding proteins.
low free tryptophan resulting in termination of transcripti
Attenuation
mRNA leader sequence able to change its conformation when triggered by direct binding of a small molecule (SAM)
Riboswitches
expressed constitutively at low levels
Housekeeping genes
function irrespective of orientation, bind with transcriptional activators to control/activate transcription
Enhancers
short nucleotide sequences are targets for DNA binding proteins trigger complex protein assemble to block transcription
Silencers
means by which enhancers activate transcription, physical interactions between regions of DNA
DNA looping
In prokaryotes, mRNA molecules commonly contain coding sequences for several different polypeptide chains; such a molecule is called a 1.-----.
polycistronic mRNA
The excision of the introns and joining of the exons constitutes 1.-----.
RNA splicing
What is true of the promoter sequence of E. coli as discussed in class:
(1.) consensus sequences are located 35 and 10 nucleotides upstream from the transcription start site (2). the -10 consensus sequence is termed the TATA box.( 3.) promotors affects the RNA polymerase binding strength which in turn affects gene expression
Which amino acid has a free amino group?
Met
Which amino acid has a free carboxyl group?
Gin
The carboxyl group of what amino acid formed a peptide bond with the amino end of His?
Trp
Which amino acid was added last?
Gin
All true of RNA
(1) . RNA has a hydroxyl group at the 2' carbon (2) In RNA uracil is used in the place of thymine (3) RNA polymerase is able to initiate chain growth without a primer.
True of RNA processing
It may be autocatalytic
All are true
(1) DNA polymerase has proof-reading activity (2) The 3' end of mRNA corresponds to the carboxyl terminus of the protein. (3) Inverted repeats are characteristic of many termination sites of RNA synthesis.
provides coding sequence of bases that determines the amino acid sequence
Messenger RNA
where protein synthesis occurs, move along mRNA and align amino acids forming peptide bonds
Ribosome
adaptor molecule attached to a specific amino acid and having a specific anticodon
Transfer RNA
enzymes that attaches each tRNA to its specific amino acid
Aminoacyl-tRNA synthetases
The anticodon of one tRNA can bind with several codons.
True
In eukaryotes, the enzyme responsible for transcribing all protein-coding genes is
RNA polymerase 2
DNA transferred by bacteriophage from cell to cell
transduction
cell acquires genes from DNA in surrounding media
transformation
DNA transferred from bacterial donor cell to recipient cell by contact
conjugation
Cotransformtion of two genes at a frequency substantially 1.----- than the product of the single-gene transformations implies that the two genes are close together in the bacterial chromosome.
greater
Because the F factor can exist either separate from the chromosome or incorporated into it, it qualifies as an 1.----- ; a genetic element that can exist free in the cell or as a segment of DNA integrated in to the chomosome.
episome
The integrated phage DNA is called the 1.-----, and the bacterial cell carrying the integrated phage DNA is called the 2.-----.
prophage; lysogen
In E.coli, the 1.----- plasmid can mobilize the chromosome for transfer to another cell in the process of conjugation.
fertility
A leu+ strain carring a cloned copy of leu on a plasmid is an example of
partial diploidy
In time-of-entry mapping, the use of compounds to inhibit the growth of donor cells is called
counterselection
What are the 2 principle mechanisms restricting the developmental potential of cells within a lineage?
Autonomous development and intercellular signaling
4. In C. elegans, describe how the lin-3 gene controls the fate of other cells in the development of the vulva
The important role of the lin-3 gene product is suggested by the opposite phenotypes of loss-of-function and gain-of-function alleles. Loss of LIN-3 results in the complete absense of vulval development, where overexpression of LIN-3 results in excess vulval induction. LIN-3 is a typical example of an interacting molecule, or ligand, that binds with an EGF- type transmembrane receptor.
5. What type of genes have homeoboxes? How do they work?
Homeotic genes. They are transcriptional activators of other genes. Most HOX genes contain more than one copy of characteristic of a sequence of about about 180 nucleotides (homeoboxes) that are found in key genes concerned with development of embryonic segmentation in organisms. Homeobox sequences are found in exons and code for a protein-folding domain that includes a helix-turn-helix DNA binding motif.
Why are missense mutations less likely to result in proteins lacking normal function than frame shift mutations?
Missense changes only one amino acid into another, while frameshift will change an amino acid and every amino acid downstream from the site of the mutation.
8. What is a base analog and why are some mutagenic?
A molecule similar enough to a purine or pyrimidine base to substitute for the normal bases, resulting in abnormal base pairing. A key feature of mutagenic base analogs is that they form base pairs with more than one other base. This can cause mutations during the next round of replication, when the replication machinery tries to pair a new base with the incorporated mutagen. For instance, 5-bromo-deoxyuridine (5BU) exists in two different forms. One mimics thymine and therefore pairs with adenine during replication, while the other mimics cytosine and therefore pairs with guanine. In its thymine-mimicking form, 5BU can be incorporated across from an adenine. If it then converts to its cytosine-like form, during the next round of replication, it will cause a gua-nine to enter the opposite strand, rather than the correct adenine.
9. Scientists at a company have just developed a new cleaning agent. Before the company goes further in developing the product they want to determine if it could be carcinogenic. Describe in some detail the initial test you would recommend they perform.
The Ames test uses strains of Salmonella that have been altered to make them more susceptible to mutation than normal Salmonella. To perform the test, the altered Salmonella strains are combined in a test tube with the chemical of interest. Because Salmonella bacteria lack the enzymes that animals use to metabolize chemicals, animal liver enzymes are often added to the test tube. That way, the test is able to detect what might happen if the chemical entered a human body. The Salmonella are then transferred to a petri dish to grow for one or two days. The altered Salmonella used for the test require the amino acid histidine to grow, and a positive result in the test is indicated when, in response to mutation, the Salmonella no longer require histidine to grow.
12. Most mutagens are also carcinogens, and most carcinogens are also mutagens. Explain why this is the case
A mutagen is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level. As many mutations cause cancer, mutagens are typically also carcinogens.
17. Identify 4 factors that can contribute to phenotype variation.
Genotypic variation, Environmental variation, variation due to genotype-by-environment interaction, variation due to genotype-by-environment association.
18. What is the cause of inbreeding depression?
Harmful effects on traits such as yield of grain and egg production. Comes from rare harmful recessive alleles becoming homozygous because of inbreeding
Circular DNA molecules, which replicate independently of the chromosome are called
plasmids
The process by which a bacterial DNA fragment is transferred from one bacterial cell to another by a phage particle is known as
transduction
DNA element that encodes a site-specific recombinase as well as a recognition region that allows other sequences with similar recognition regions to be incorporated by recombination is called
Integron
A mutant microorganism unable to synthesize an essential compound but able to grow if that compound is supplied exogenously is called a
Auxotroph
In a mating between Hfr and F- cells, the Hfr donor
remains Hfr
Phage DNA integrated into the chromosome is called a(n)
prophage
In E. coli, the plasmid that can mobilize the chromosome for transfer to another cell in the process of conjugation is called
F factor
The transferred marker that is selected by the growth conditions is called a
Selected
How long does it take under usual conditions for an entire bacterial chromosome to be transferred during conjugation?
100 min
E. coli cell that contains F factor integrated into bacterial chromosome is called a(n)
Hfr
In polypeptide Arg-Pro-Ser, what amino acid has a free carboxyl group?
Pro
A nucleotide substitution that creates a stop codon and results in premature chain termination during translation, is called a
Nonsense
The enzymatic synthesis of an RNA molecule complementary to one strand of the DNA is called
transcription
RNA splicing takes place in nuclear particles, composed of protein and several specialized small RNA molecules, known as
spliceosomes
In prokaryotes, mRNA molecules commonly contain coding sequences for several different polypeptide chains; such a molecule is called a
polycistronic
The excision of the introns and the joining of the exons constitutes
RNA splicing
The genetic code is degenerate because
Some amino acids are coded by more than one codon
A consensus sequence is a sequence of bases determined by
majority rule
Genetic evidence for a triplet code came from
three-base deletions and insertions
The model of protein evolution through the combination of different exons is called the
Exon shuffle model
How many proteins are bound to the trp operon when tryptophan and glucose are present?
1
The lactose operator is an essential site for
repression
Transcriptional cosuppression in Drosophila, is associated with the
Polycomb group of transcriptional silencer proteins
In S.cerevisiae, the genetic basis of mating-type interconversion is
DNA rearrangement
Heavy methylation is associated with
Low transcription rate
The production of the lac repressor is
constitutive
A regulatory base sequence in eukaryotic cells that increases the rate of transcription of nearby genes regardless of orientation is called a(n)
enhancer
The development of the mammalian immune system involves
Programmed DNA rearangements
How does the lac repressor prevent transcription of lac operon?
By binding to the operator, which makes the promoter inaccessible to RNA polymerase
The type of gene expression, which is constant and independent of on/off regulatory control is called
Constitutive
The cloning site containg unique cleavage sites for many different restriction enzymes is called a(an)
Polylinker
The procedure used to determine experimentally the physical limits of a gene is called
Transformation resque
A DNA molecule has 28 occurrences of the sequence 5'-GGCC-3' along one strand. How many times does the same sequence occur along the other strand?
28
A number of restriction enzymes cleave both DNA strands at the center of symmetry, forming
Blunt ends
You digested a linear DNA molecule with the restriction enzyme and got 3 fragments. How many restriction sites does this DNA have for this particular endonuclease?
2
Deliberate alteration of the genome for treatment of disease is called
gene therapy
Term for the double-stranded DNA produced by reverse transcriptase is
cDNA
DNA produced by reverse transcriptase11. ________________________Use of a transgenic organism
12
n gene-targeting experiments, the replacement of the wildtype gene in the genome with the completely unfunctional gene results in a (n)
knockout mutation
Loss of b-galactosidase activity is often used to detect
recombinant vectors