exam 4 Flashcards
which of the following is a palidromic sequece?
A 5' CATTAG 3' B 5' CAATTG 3' C 5'CATTTG3' D 5'GATTTC3' E 5'CATCAT3'
B 5’CAATTG3’
DNA BECASUE IT HAS A _____ CHARGE MOVES TO THE_______ ELECTRODE DURING GEL ELECTROPHORESIS AND _____ DNA MOLECULES MIGRATE THE MOST QUICKY
NEGATIV, POSTITIVE, SMALLER
From the list below selec the sequence of steps for insreing a peice of foreign dna into a plasmid vector inroducing the plasmid into bacteria and verifying that the plasmid and the foreign gene are present
1, transform host cells
2 select for the the lack of plasmid reporter gene 1 function
3 select for the plasmid reporter gene 2 function
4 digest vector and foreign dna with a restriction enzyme which inactivates plasmid reporter gene 1
5 ligate the digested plasmid together with the foreign dna
4,5,1,3,2
our textbook describes a sheep named dolly whats special about dolly
she was the first cloned mammal
what percentage of the human genome codes for protein
less than 5%
the traditional way to study bacteria is to first grom them in the lab its now posile to isolat DNA from environmental samples and study bacteria without having to grow them in the lab what is this new field of study called
metagenomics
which of the following is a technques that can be used to clone mamals
a. mammals cant be cloned B, nuclear transer c. cDNA technology D x......... of eggs e. Microinjection of egg cytoplasm into somatic cells
c cDNA technology
restriction en- zymes
which cut dou- ble-stranded DNA molecules—such as those injected by bac- teriophage—into smaller, noninfectious fragments
These enzymes break the bonds of the DNA backbone between the 3′ hydroxyl group of one nucleotide and the 5′ phosphate group of the next nucleotide. This cutting process is called re- striction digestion.
Why doesn’t a restriction enzyme cut the DNA of the bacte- rial cell that makes it?
One way that the cell protects itself is by modifying the restriction sites on its own DNA. Specific modi- fying enzymes called methylases add methyl (—CH3) groups to certain bases at the restriction sites on the host’s DNA after it has been replicated.
Most virus particles, called viri- ons, are composed of?
only nucleic acid and a few proteins.
negative regulation
the gene is normally transcribed. Binding of a repressor protein prevents transcription.
positive regulation
the gene is normally not transcribed. An activator protein binds to stimulate transcription.
lytic cycle
the infected host cell lyses (bursts), releasing progeny viruses. Once a virus has injected its nucleic acid into a cell, that nucleic acid takes over the host’s synthetic machinery.
In a host cell infected with a virus, the viral genome uses its early genes to shut down host transcription while it replicates itself. Once the viral genome is replicated, its late genes produce capsid proteins that pack- age the genome and other proteins that lyse the host cell.
lysogenic cycle
Some viruses have evolved an ad- vantageous process called lysogeny that postpones the lytic cy- cle. In lysogeny, the viral DNA becomes integrated into the host DNA and becomes a prophage
In the lysogenic cycle, an inactive prophage is integrated into the host DNA where it is replicated during the bacterial life cycle.
The Reproductive Cycle of HIV
This retrovirus enters a host cell via fusion of its envelope with the host’s plasma mem- brane. Reverse transcription of retroviral RNA then produces a DNA provirus—a molecule of complementary DNA that inserts itself into the host’s genome.
inducers
Compounds that, like lactose, stimulate the synthesis of a protein are called inducers
An Inducer Stimulates the Expression of a Gene for an Enzyme It is most efficient for a cell to produce an enzyme only when it is needed. Some enzymes are induced by the presence of the substance they act upon (for example, β-galactosidase is induced by the presence of lactose).
inducible proteins
Proteins that ar made by inducers
constitutive proteins.
whereas proteins that are made all the time at a constant rate are called constitutive proteins. (Think of the constitution of a country, a document that does not change under normal circumstances.)
structural genes
The genes that encode the three enzymes for processing lactose in E. coli are structural genes; they specify the primary structure (the amino acid sequence) of a protein molecule. Structural genes are genes that can be transcribed into mRNA.
operon
A cluster of genes with a single promoter is called an operon, and the operon that encodes the three lactose-metabolizing enzymes in E. coli is called the lac operon.
the operon that encodes the three lactose-metabolizing enzymes in E. coli is called the lac operon.
the lac operon.
The lac operon of E. coli is a segment of DNA that includes a promoter, an operator, and the three structural genes that code for lactose-metabolizing enzymes.
What are Two Ways to Regulate a Metabolic Pathway
Feedback from the end product of a metabolic pathway can block enzyme activity (allosteric regulation), or it can stop the transcription of genes that code for the enzymes in the pathway (transcriptional regulation).
operator
The operator is a short stretch of DNA that lies between the pro- moter and the structural genes. It can bind very tightly with regulatory proteins that either acti- vate or repress transcription.
repressor
When the repressor is bound, transcription of the operon is blocked.
regulatory gene
the regulatory gene produces a protein whose sole function is to regulate expression of the other genes; and
• certain DNA sequences (operators and promoters) do not code for proteins, but are binding sites for regulatory or other proteins.
co-repressors
This binding causes the repressor to change shape and bind to the operator, thereby inhibiting transcription.
An example is the operon whose structural genes catalyze the synthesis of the amino acid tryptophan:
inducible system
the substrate of a
metabolic pathway (the inducer) interacts
with a regulatory protein (the repressor), rendering the repressor incapable of bind-
ing to the operator and thus allowing transcription.
repressible systems
the product of a metabolic pathway (the co-repressor) binds to a regulatory protein, which is then able to bind to the operator and block transcription.
catabolite repression,
a system of gene regulation in which the presence of the pre- ferred energy source represses other catabolic pathways
The promoter for the lac operon does not function efficiently in the absence of cAMP, as occurs when glucose levels are high. High glucose levels thus repress the enzymes that metabolize lactose.
the lactose-metabolizing enzymes—is transcribed.
What ways in which a prokaryotic cell can shut off the sup- ply of an unneeded protein.
The cell can:
• downregulate the transcription of mRNA for that protein;
• hydrolyze the mRNA after it is made, thereby preventing
translation;
• prevent translation of the mRNA at the ribosome;
• hydrolyze the protein after it is made; or
• inhibit the function of the protein.
you discover a new gene in the mouse and want to study its function which of the following techniques would you use to make a mouse with reporter gene inseted into the middle of the gene youre studying
A.DNA CHIP B. siRNA C.cDNA D.knockout E.PCR
knockout
which of the following techniques would be best for comparing the genes being expresed in normal cancer cells
A DNA sequencing B. Kockout Technology C. siRNA D. DNA chip Technology E. recumbanint DNA
D. DNA chip technology
Biotechnology is being used to do which of the following
a making insulin b making TPA C improving crops d. making vaccines E all of the above
all of the above
what are restriction enzymes
they cut DNA molecules at specific sequences
they protect bacteria from viral infections
which of the following would be used to join two differnt DNA molecules
DNA ligase
what does the c in cDNA stand for
complementary
which of the following is used to ihibit synthesis of a protein by destroying a specific mRNA molecule
a siRNA b. knockouts c alph protosome ambiones
siRNA
you have 2 clones of a human gene one was made from cDNA the other otained directly from a chromosome
how differnt are they
The cDNA lacks introns
red and white blood cells in adult humans are produces by stem cells in the
bone marrow
which of the following could not be used to regulate the activity of a gene in eukaryotes
A. chromatin structure B. transport to the cytoplasm C mRNA stability D post- transcriptional processing E all of the above could be used to regulate
all of the above can regulate
RNA interference (RNAi) inhibits ?
mRNA
why do eukaryotes usualy have many copies of the rRNA fenes
Eukaryotas need to make lots of rRNA
many eukaryotes have regions called enhancers what is an enhancer
a dna sequence far from the promoter whare a specific protein can bind to active transcription
a cell is found that contains two BARR bodies the cell has
Three X chromosmes
many organisms have DNA sequences that can move from place to place in their genome what are these DNA sequences called
transposons
Tropomyosin is a muscle protein that we studied in class the and is differnt in smooth muscle than skeletal muscle becasue
of alternative splicing
what sequence qacounts for over 10% do the human genome
Alu
which statement about gene transcription in eukaryotes is not ture
A. regulatory proteins can bind far from the promoter
b transcription factors are required
C genes are usually transcribed in groups called operons
genes are usualy transcribed in groups called operons
how many differnt kinds of RNA polymerase are found in prokaryotic cells
1
how many differnt kinds of RNA polymerase are found in eukaryotic cells
3
RNA polymerase that produces mRNA molecules in eukaryotic cells is
RNA polymerase II
Adenosine is binding to an Adenosine receptor on a nerve cell in the brain what is the result
reduction in brain activity
cell differentiation in mammals is usually not reversible
true
what is the result when homologous chromosomes brak at differnt positions and exchange segments
translocation
G ptoyeins have binding sites for
GTP GDP and G protein linked receptors
what kind of receptor does caffeine bind to
Adenosine
when caffeine binds to this receptor it acts as an
antagonist
odar signal receptors involves all of the following except
G proteins
Inon Channel
cAMP
Nitric oxide
G protein linked receptor
nitric oxide
the acetylcholine receptor in vertebrate skeletal muscle is best described as
an ion channel receptor
a chemical binds to the insulin receptor and provents insulin from binding this chemical is called
an insulin antagonsit
a molecule that binds to a receptor is called a
ligand
what does nicotine bind to
acetylcholine receptor
steroid hormones usually bind to
a cytoplamic receptor
signals to distant cells are called
hormones
why is nitroglycerin an effective drug for treating angina
nitroglycerin releases nitric oxide which acts as
the traditional way to study bacteria is to first from them in the lab it is now possible to isolate DNA From enviromental samples and study the bacteria with out having to grow them in the lab what is this called
metagenomics
which of the following is a technique that can be used to clone mammals
cDNA Technology
ips cells (a kind of stem cell) can be made from skin cells what adcantage to iPS cells have over embryonic stem cells ?
no embryos are destroyed in the production of iPS cells
iPS will not provoke an inverse response
after a dog dies its owner has the dog cloned using the same technology developed to clone sheep which of the following is true
the cloned dog is genetically identical to the dog that died
the cloned dog will be sterile and unable to reproduce
most eukaryotic genes have their own promoter
true
most human genes do not have introns
false
regulation of transcription is the most important step in regulating gene activity in both prokaryots and eukaryotes
true
many eukaryotic genes are members of gene familes which of the following processes could have produced the gene family?
abnormal (unequal) crossing over
the function of the promoter is to tell RNA polymerase
where to stat transcribing the DNA
which strand of DNA to read
we learned about a repetitive secuence called ALa what kind of sequence is ALa
Sine
WHAt is THID
it binds to the tata box in eukaryotes
fetal hemolglobin structure is alpha2 beta2
false
fetal hemogolobin has a higher effinity for oxygen than adult hemoglobin
true
recognition sequence—
the sequence recognized by RNA polymerase.
TATA box
The second, closer to the transcription initiation site, is the TATA box (so called because it is rich in AT base pairs), where DNA be- gins to denature so that the template strand can be exposed.
The Initiation of Transcription in Eukaryotes
Apart from TFIID, which binds to the TATA box, each transcription factor in this transcriptio
complex has binding sites only for the other proteins in the complex, and does not bind directly to DNA. B, E, F, and H are transcription factors.
What happens when the TFIID (“TF” stands for transcription factor) binds to the TATA box
Binding of TFIID changes both its own shape and that of the DNA, presenting a new surface that attracts the binding of other transcription factors to form a transcription complex
How can a single gene code for more than one protein?
alternative splicing can be a deliberate mechanism for gen- erating a family of different proteins with different activities and functions from a single genes
Pre-mRNA can be spliced differently in differ- ent tissues, resulting in different proteins
What is X chromosome inactivation and how does it occur?
An X chromosome is compacted to make a small dense structure called a Barr body. Most of the genes on the Barr body are inactive meaning that they ar not transcribed sometimes this process is called lyonization
How are eukaryotic genomes different from prokaryotic genomes?
• Eukaryotic genomes are larger than those of prokaryotes, and they have more protein-coding genes.
.• Eukaryotic genomes have more regulatory se- quences—and many more regulatory pro- teins—than prokaryotic genomes.
.• Much of eukaryotic DNA is noncoding. Distrib- uted throughout many eukaryotic genomes are various kinds of DNA sequences that are not transcribed into mRNA, most notably introns and gene control sequences.
.• Eukaryotes have multiple chromosomes. The genomic “encyclopedia” of a eukaryote is separated into multiple “volumes.”
What’s the size of the human genome?How many genes are in the human genome
The human genome contains approximately 3.2 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of all our cells. Each chromosome contains hundreds to thousands of genes, which carry the instructions for making proteins.
What are gene families?
A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions
pseudogenes
Non functional genes which result from mutations that cause a loss of function rather than an enhanced or new function. The DNA sequence of a pseudogene may not differ greatly from that of other family members. I
Highly repetitive sequences
are short (less than 100 bp) se- quences that are repeated thousands of times in tandem (side-by- side) arrangements in the genome. They are not transcribed. Their proportion in eukaryotic genomes varies, from 10 percent in humans to about half the genome in some species of fruit flies.
Moderately repetitive sequences
are repeated 10–1000 times in the eukaryotic genome. These sequences include the genes that are transcribed to produce tRNAs and rRNAs, which are used in protein synthesis.
TRANSPOSONS
Apart from the RNA genes, most moderately repetitive sequences are not stably integrated into the genome. Instead, these sequences can move from place to place, and are thus called transposable elements or transposons. Transposons make up over 40 percent of the human genome and about 50 per- cent of the maize genome, although the percentage is smaller (3–10 percent) in many other eukaryotes.
What are restriction enzymes? What’s prevents them from cutting up the host DNA?
Some bacteria defend themselves against such invasions by producing restriction en- zymes (also known as restriction endonucleases), which cut dou- ble-stranded DNA molecules—such as those injected by bac- teriophage—into smaller, noninfectious fragments (Figure 15.7). These enzymes break the bonds of the DNA backbone between the 3′ hydroxyl group of one nucleotide and the 5′ phosphate group of the next nucleotide. This cutting process is called re- striction digestion.
One way that the cell protects itself is by modifying the restriction sites on its own DNA. Specific modi- fying enzymes called methylases add methyl (—CH3) groups to certain bases at the restriction sites on the host’s DNA after it has been replicate
Know the structure/replication of HIV
HIV is an enveloped virus; it is enclosed within a phos- pholipid membrane derived from its host cell. Proteins in the membrane are involved in infection of new host cells, which HIV enters by direct fusion of the viral envelope with the host plasma membrane.
proteome
The proteome is the sum total of the proteins produced by an organism, and it is more complex than its genome.
Two methods are commonly used to analyze the proteome:• Because of their unique amino acid compositions (primary structures), most proteins have unique combinations of electric charge and size. On the basis of these two proper- ties, they can be separated by two-dimensional gel elec- trophoresis. Thus isolated, individual proteins can be ana- lyzed, sequenced, and studied (Figure 17.17B).• Mass spectrometry uses electromagnets to identify proteins by the masses of their atoms and displays them as peaks on a graph.
where does transcription begin
at the promoter
ribosomes are composed of
a few proteins and four rRNA molecules
which of the following is a technique used to separate DNA molecules of differnt sizes
electrophoresis
viruses are obligate intracellular parasites
true
bacteriophage are bacteria that eat other bacteria
False
what is the genetic material of viruses
DNA single or double or rna single or doubel
why do people need to get Vaccinated against influenza every year
the influenza virus changes from year to year
hiv is a
retrovirus
a virus enters a bacteria cell and inserts a copy of its genetic material into the host
the lysogenic cycle
the simplest virsuses are composed of which of the folowing
capsid proteins and nucleic acid
what enzymes produce the genetic material inside HIV
reverse transcriptase
bacteriophage lambda infects a cell and makes lots of cl protein and little cro proteins what happens
a lysogenic cycle
what is a signal sequance
it indicates where a protein should go
which of the following statments about HIV is False
a. HIV has a high mutation rate
b. Infection by HIV results in the destruction of helper T cells
c. Reverse transcriptase, protease, and integrase are required for HIV replication
d. HIV is surrounded by an envelope containing glycoproteins
e. Reverse transcriptase uses RNA as a template to synthesize DNA in the nucleus
reverse transcriptase usses RNA as a template to syntesize DNA in the nucleus
influenza virus does not contain a viral envelope
true
what does HIV stand for
human immunodificiency virus
what is recombinant DNA
a DNA molecule made in the lab using atleast two differnt sources of DNA
what is restriction enzymes
are used to cut DNA into fragments and then splice them together in new combinations
sticky ends
some restriction enzymes recognize palindromic DNA sequences
some make straight cuts some make staggerd cuts resulting in overhangs or sticky ends
sticky ends can bind by base pairing to other sticky ends
fragments from differnt sources can be joined
then ligase catalyzes formation of covalent bonds between adjacent nucleotides at fragment ends
Reporter genes
selectable markers or reporter genes :
genes whoses expression is easly observed
ex. antibiotic resistance
flourescence
WHAT IS Cdna AND HOW IS IT MADE
smaller libraries can be made from complementary DNA(cDNA)
mRNA is extracted from cells then cDNA is produced by complementary base pairing catalyzed by reverse transcriptase
cDNA library is a snapshot of the transcription patern of the cell
cDNA libraries are used to compare gene expression in differnt tissues at differnt stages of development
what are knockouts and why are they useful
genes can also be studied by inactivating them (eg transposon mutagenesis) to define the minimal genome
in animals this is called a knockout experiment
homologus recombination can knock out a specific gene
what are antisense RNA
translation of mRNA can be blocked by complementory micro RNAs- antisense RNA
Antisense RNA can be synthesized and added to cells to prevent translation the effects of the missing proteins can then be determined
what are RNAi
interference RNA (RNAi( is a natural mechanism that blocks translation
short dounle stranded RNA is unwound and binds to complementary mRNA by a protein complex which also catalyzes the breakdown of the mRNA
small interfering RNA (siRNA) can be synthesized in the lab to inhibit gene expression
concerns over biotechnoloy
genetic manipulation is an unnatural interference with nature
genetically alterd food are unsafe to eat
genetically altered cropplants are dangerous to the environment
what is signal transduction
all cells process information from the environment
the information can be a chemical or physical stimulus such as light
a signal tansduction pathway is the sequence of events that leas to a cells response
what are autocrine signals
signals that affect the cells that made them
what are paracine signals
signals that affect nerby cells
hormones
travel to distant cells usually via the circulatory system
juxtacrine signals
affect only adacent cells
what are the properties of receptors and ligands
proteins that have a very specific binding site for chemical signal molecules or ligands
abonding the ligands causes the receptor to change shape the binding is reversible
antagonist
inhibitors that bind to receptor proteins and prevents the apropriate ligand has an advers affect
agonists
Drugs that mimic or potentiate
the effect of a neurotransmitter are called agonists
WHERE are receptors located
receptors can be located in the cytoplasm or in the cell membrane
intracellular receptors: small or non polar ligands can diffuse across the cell membrane
membrane receptors: large or polor ligands bind to the cell membrane receptors
what are the differnt types of plasma membrane receptors
ion channels: channel proteins tthat allows ions to enter or leave a cell
protein kinase receptors: some receptors become protine kinase they catalyze phosphorylation of themselves and or other proteins
g protein-lnked receptors
ligand binding changes the shape of the cytoplasmic region which binds to a G protein
acetylcholine
the receptor on a muscle cell is a gated ion channel
insulin receptor
phosphorylates itself and other insulin response substrates which initiates insertion of glucose transporters into the plasma membrane
cAMP… how is it made? what does it do?
is produced from ATP by the enzyme adenylyl cyclase which is activated via a G protein-linked Epinephrine receptor
binding one epinephrine molecule leads to production of many cAMP
the cAMP molecules activate many enzyme targets
what are g Protein linked receptors and how do they work
ligand binding changes the shape of the cytoplasmic region which binds to a g protein
g protein: Mobile membrane protein with three subunits they bind GDP and GTP
what is NO
niyric oxide gas is a second messenger between acetylcholene and the relaxation of smooth mmuscle in blood vessels allowing more bloodflow
how do nitroglycerin and sidenafil affect NO signalling
nitroglycerin, a drug that has been used
for over a century to treat angina, the chest pain caused by insufficient
blood flow to the heart. Nitroglycerin releases NO, which
results in relaxation of the blood vessels and increased blood flow
The drug sildenafil (Viagra) was developed to treat angina via
the NO signal transduction pathway, but was only modestly useful
for that purpose. However, men taking it reported more pronounced
penile erections. During sexual stimulation, NO acts
as a signal causing an increase in cGMP and a subsequent relaxation
of the smooth muscles surrounding the arteries in the corpus
cavernosum of the peni
