After Exam 3 Flashcards
Watson and Crick noted that the specific base pairing suggested
A possibly copying mechanism for genetic materiaal
Since the two strands of DNA are complementary each strand acts as
a template for building a new strand in replication
In DNA replication the parent molecule unwinds and ____ are built based on base-pairing rules
2 new daughter strands
Watson and Crick came up with the ____ model
semiconservative
What is the semiconservative model?
When a double helix replicates, each daughter nuclei will have one old strand and one new strand
What were the competing models of the semiconservative one?
Conservative and dispersive
What did Meselson and Stahl accomplish?
They tested the 3 models by interacting old strands with a heavy isotope of nitrogen and new strands were labeled with a lighter isotope.
What did the first replication from meselson and stahl produce?
A band of hybrid DNA eliminating the conservative model.
What did the second replication produce?
Both light and hybrid DNA, eliminating the dispersive model.
Where does DNA Replication begin?
Special sites called origins of replication.
Describe DNA replication
2 strands are separated opening up a replication bubble.
What does the replication bubble consist of?
A replication fork
What is a replication fork?
A y shaped region where new DNA strands are elongating at each end
What is helicase?
Untwists the double helix and separates the template DNA strands at the replication fork
What is the single strand binding protein
Binds to and stabilizes signle stranded DNA until it can be used as a template
What is topoisomerase
corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands
What is rate of elongation in bacteria?
~500 nucleotides/sec
What is the rate of elongationi in human cells?
~50 nucleotides/sec
What is the nucleotide that is added to a growing dna strand?
A nucleoside triphosphate
True or false: the antiparallel structure of the double helix affects replication
True
What end to DNA polymerases add nucleotides to?
free 3’ end of a growing strand
What direction can DNA ONLY elongate in?
5’ to 3’ direction
Along what strand of DNA can DNA polymerase synthesize a complementary strand continuously moving toward the replication fork
The leading strand
How does DNA polymerase elongate the lagging strand?
DNA polymerase must work in the direction away from the replication fork
The lagging strand is synthesized as a series of segments called _____ which are joined together by ______
Okazaki fragments,
DNA ligase
True or false: The DNA replication machine is probably not stationary during the replication process
false
How do DNA polymerases look for and fix mistakes?
They proofread and replace any incorrect nucleotides
What can DNA be damaged by?
chemicals, x-rays, UV light, cigarettes
What is the mismatch repair of DNA
Repair enzymes correct errors in base pairing
What is the nucleotide excision repair?
Enzymes cut out and replace damaged stretches of DNA
What creates problems for the linear DNA of eukaryotic chromosomes?
Limitations of DNA polymerase
What do repeated rounds of replication produce and why?
Shorter DNA molecules with uneven ends, because the machinery provides no way to complete the 5’ ends
What are telomeres?
End nucleotide sequences in eukaryotic chromosomal DNA molecules
What is the function of telomeres?
They pospone erosion of genes near the ends of DNA molecules
True or false: Telomeres prevent the shortening of DNA molecules
False
What would happen if chromosomes of germ cells became shorter in every cell cycle?
Essential genes would eventually be missing from gametes they produce
What is the function of telomerase?
Catalyzes the lengthening of telomeres in germ cells
True or false: There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist
True
The shortening of telomeres is proposed to be connected to
Aging
What is the shortening of telomeres proposed to do?
Protect cells from cancerous growth by limiting the number of cell divisions
The _____is a double stranded, circular DNA molecule associated with a ____ amount of protein
bacterial chromosome, small
_____ have linear DNA molecules associated with a ____ amount of proteins
Eukaryotic chromosomes, large
____ is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells
Chromatin
____ are proteins responsible for the first level of DNA packing in chromatin
Histones
DNA winds around histones to form nucleosome “beads” called
Nucleosomes
Interactions between nucleosomes cause the thin fiber to coil or fold into this
thicker fiber, 30nm fiber
The 30 nm forms looped domains that
attach to proteins (300 nm fiber)
Arrange in size from smallest to largest:
scaffolded domains, double helix, metaphase chromosome, nucleosome, 30nm fiber
double helix nucleosome 30 nm fiber scaffolded domains metaphase chromosome
Most chromatin is loosely packed in the nucleus during interphase and condenses prior to
mitosis
what is euchromatin
loosely packed chromatin
What is heterochromatin
highly condensed chromatin
Dense packing of the heterochromatin makes it difficult for the cell to express ____ coded in regions of ___ and ____
genetic information
centromeres
telomeres
____ are not highly condensed by still occupy specific ____ regions in nucleus
interphase chromosomes
restricted
What is gel electrophoresis
Indirect method of rapidly analyzing and comparing genomes
What is the function and name of the PCR
Polymerase chain reaction
can produce many copies of a specific target segment of DNA
What are the three steps that bring about a chain reaction and what does it produce?
Heating, cooling, replication
produces exponentially growing population of identifcal DNA molecules
Taq DNA polymerase do not have to add
fresh DNA polymerase
The PCR can amplify DNA from
all organisms, fetal cells, and fossils
Once a gene is cloned, complementary base pairing can be exploited to determine
The gene’s complete nucleotide sequence called DNA Sequencing
Define gene expression
Process by which DNA directs protein synthesis
Define transciption
The synthesis of RNA under the direction of DNA
Produces messenger RNA (mRNA)
Define Translation
actual synthesis of a polypeptide which occurs under the direction of mRNA
Occurs in ribosomes
How many nucleotide bases and amino acids are there in DNA
20 amino acids
4 nucleotide bases
What is a triplet code?
A series of nonoverlapping, 3 nucleotide words
The genetic code consists of __ codons and ___ stop codons
64
3
What are the 3 stop codons?
UAA
UGA
UAG
RNA synthesis is catalyzed by
RNA Polymerase
RNA polymerase pries ____ apart and hooks ____ together
DNA strands
RNA nucleotides
RNA synthesis follows the same base pairing rules as DNA except
uracil substitutes for thymine
What is the promoter
The DNA sequence where RNA polymerase attaches
What is the transcription Unit
The stretch of DNA that is transcribed
What happens during initiation
After RNA polymerase binds to the promoter, the DNA strands unwind and the polymerase initiates RNA synthesis at the start point on the template strand
What happens during elongation
Polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5’—>3’. During transcription, the DNA strands reform a double helix
What happens during termination
Eventuall the RNA transcript is released and the polymerase detaches from the DNA
During initiation, ___ signal the initiation of RNA synthesis
promoters
What is the function of the TA TA box
A promoter crucial in forming the initiation comples in eukaryotes
What is the function of transcription factors
To mediate the binding of RNA polymerase and initiation of transcription
What is the transcription initiation complex
Completed assembly of TF’s and RNA polymerase II bound to a promoter
Describe elongation of the RNA strand
As RNA polymerase moves along the DNA, it untwists the double helix 10-20 bases at a time
What end does RNA polymerase add nucleotides to?
The 3’ end as it continues along the double helix
Transcription progresses at a rate of ___ in eukaryotes
40 nucleotides/sec
True or false: A gene can be transcribed simultaneously by several RNA polymerases
True
True or false: The mechanisms of termination are not different in prokaryotes and eukaryotes
False
Describe termination in bacteria
The polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification
Describe termination in eukaryotes
RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10-35 nucleotides past this polyadenylation sequence
Enzymes in the eukaryotic nucleus modify____ before the genetic messages are dispatched to the cytoplasm
Pre-mRNA
During RNA processing:
- both ends of primary RNA transcript are usually altered
- usually some interior parts of the molecule are cut out and the other parts spliced together
Describe the modification of the 5’ end of the pre-mRNA molecule
It receives a modified nucleotide cap
Describe the modified 3’ end
It gets a poly A tail
What are the functions of the modifications to the pre-mRNA molecule
- Facilitate export of mRNA
- Protect mRNA from hydrolytic enzymes
- Help ribosomes attach to the 5’ end
True or false: Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions
True
What are introns
non coding regions, intervening sequences
What are exons
expressed, usually translated into amino acid sequences
RNA splicing removes ____ and joins ____ creating an mRNA molecule with a continuous coding sequence
introns, exons
What is the structure and function of spliceosomes
To recognize the splice states
consist of nuclear snRNPs and a variety of proteins
What are ribozymes
catalytic RNA molecules that function as enzymes and can splice RNA
The discovery of ribozymes rendered what belief obsolete
the belief that all biological catalysts were proteins
Some genes encode more than one kind of ____ depending on which segments are treated as exons during RNA splicing
polypeptide
What are the variations in polypeptide codings called
alternative RNA splicing
Because of alternative splicing, the number of different proteins an organism can produce is much ____ than its number of genes
Greater
Proteins have a modular architecture consisting of
discrete structural and functional regions called domains
In many cases ___ code for the ___ in a protein
different exons
different domains
A cell translates a ____ into the protein with the help of tRNA
mRNA message
tRNA carry what two things, one on each end
specific amino acid, an anticodon
The anticodon base pairs with a
complementary codon on mRNA
A tRNA molecule consists of a single RNA strand that is only about ___ nucleotides long
8-
A tRNA is ___ into one plane to reveal its base pairing
flattened
Because of ____ tRNA twists and folds into a 3-D l shaped structure
Hydrogen bonds
What two steps does accurate translation require
A correct match between tRNA and an amino acid done by the enzyme aminoacyl-tRNA synthetase
A correct match between the tRNA anticodon and mRNA codon
Ribosomes facilitate ____ in protein synthesis
specific coupling of tRNA anticodons with mRNA codons
What are the 3 binding sites for tRNA in a ribosome
A, P, and E sites
What does the A site do
holds the tRNA that carries the next amino acid to be added to the chain
What does the P site do?
Holds the tRNA that carries the growing polypeptide chain
What does the E site do
Is the exit site, where discharged tRNA’s leave the ribosome
When does a tRNA fit into a binding site
When its anticodon base pairs with an mRNA codon
What does the P site hold
The tRNA attached to the growing polypeptide
What does the A site hold
tRNA carrying the next amino acid to be added to the polypeptide chain
The initiation xtage of translation brings together
mRNA
tRNA with the first amino acid
2 ribosomal subunits
Termination of Translation occurs when
a sstop codon in the mRNA reaches the A site of the ribosome
The A site accepts a protein called a
release factor
What does the release factor do?
causes the addition of water molecule instead of an amino acid
What does the reaction of the release factor cause
It releases the polypeptide and the translation assembly then comes apart
A number of ribosomes can translate a single mRNA simultaneously, forming a
Polyribosome
What do polyribosomes do?
Enable a cell to make many copies of a polypeptide very quickly
During and after synthesis a polypeptide chain spontaneously ____ into its 3D shape
coils and folds
True or false: often translation is not sufficient to make a functional protein
True
Proteins may require ____ modifications
post translational
Completed proteins are ____ in the cell
Targeted to specific sites
Protein synthesis begins in the
cytosol
Synthesis finishes in the ___ unless the polypeptide signals the ribosome to attach to the ER
cytosol
Polypeptides destined for the ER or for secretion are marked by a
signal peptide
A ____ binds to the signal peptide
Signal-recognition particle SRP
What are mutations
Changes to the genetic material of a cell or virus
Spontaneous mutations can occur during
DNA replication, recombination, or repair
___ are physical or chemical agents that can cause mutations
Mutagens
What are point mutations
chemical changes in just one base pair of a gene
What do point mutations lead to
production of an abnormal protein
Point mutations are divided into 2 general categories
Nucleotide pair substitutions
one or more nucleotide pair insertions or deletions
What are silent mutations
Have no effect on the amino acid produced by a codon because of redundancy in the genetic code
What are missense mutations
Still code for an amino acid but not necessarily the right amino acid
What are nonsense mutations
Change an amino acid codon into a stop codon nearly always leading to a nonfunctional protein
What does a nucleotide pair substitution do
replaces one nucleotide and its partner with another pair of nucleotides
What are insertions and deletions
Additions or losses of nucleotide pairs in a gene
Insertions and deletions have a ___ on the resulting protein more often than ___ do
disastrous
substitutions
Insertions or deletion of nucleotides may alter the ___ producing a ____
reading frame
frameshift mutation
Prokaryotic cells __ a nuclear envelope allowing translation to begin while transscription progresses
Lack
In a eukaryotic cell: the nuclear envelope ____ and extensive RNA processing occurs in the ____
separates transcription from translation
nucleus
A gene is
discrete unit of inheritance
specific nucleotide sequence in a chromosome
dna sequence that codes for a specific polypeptide chain
Define gene
a region of DNA that can be expressed to produce a final functional product either a polypeptide or an RNA molecule
DNA—-> RNA—>
protein
Prokaryotes and eukaryotes alter gene expression in response to their
changing environment
In multicellular eukaryotes, genexpression regulates ____ and is responbsible for differences in ____
development
cell types
Bacteria regulate _____ gene expression
their own
Why do bacteria regulate their own gene expression?
Natural selection has favored bacteria that produce only the products needed by that cell
How do bacteria excersise this metabolic control?
Adjusting activity of metabolic enzymes
Regulating genes that encode metabolic enzymes
Describe the regulation of tryptophan synthesis
An abundance of trp can inhibit the activity of the first enzyme in the pathway (feedback inhibition) a rapid response and repress expression of the genes for all the enzymes needed for the pathway, a longer-term response
In bacteria, genes are often clustered into
operons
What are operons made up of?
An operator (on/off switch)
a promoter
genes for metabolic enzymes
An operon can be switched off by a protein called a
repressor
Where does the repressor bind?
Only to the operon
A repressible operon is one that is usually
On
Binding of a repressor to the operator ____ transscription
Shuts off
The ____ is a repressible operon
trp operon
Repressible enzymes usually function in _____
anabolic pathways
What is a corepressor
A small molecule that cooperates with a repressor to switch an operon off
An inducible operon is one that is usually
Off
A molecule (inducer) inactivates the repressor and _____ transcription
Turns on
The lac operon is a ____ operon
Inducible
Inducible enzymes usually function in _____
Catabolic pathways
Regulation of the ______ involves negative control of genes because operons are switched off by the active form of the repressor
trp and lac operons
Some operons are also subject to ____ through a stimulatory activator protein such as CAP
positive control
The lac operon is under dual control: negative control by the lac ____ ; positive control by ____
repressor
CAP
What is positive control
When glucose is scarce, the lac operon is activated by the binding of CAP
When glucose levels increase, CAP ____ the lac operon turning it off
Detaches from
A mutation that makes the regulatory gene of an inducible operon non functional would result in
Continuous transcription of the operon’s genes
What are the two features of eukaryotic genomes that are a major information-processing challenge?
- typical euk. genome is much larger than that of a prokaryotic cell
- cell specialization limits the expression of many genes to specific cells
Almost all the cells in an organism are genetically
Identical
Differences between cell types result from
Differential gene expression
What is differential gene expression
The expression of different genes by cells with the same genome
Errors in gene expression can lead to
diseases (cancer)
Muscle cells differ from nerve cells mainly because
They express different genes
What is the most important control point of gene expression
Transcription
Genes within hightly packed heterochromatin are usually _____
not expressed
Chemical modifications to histones and DNA of chromatin influence both______ and ______
Chromatin structure
Gene expression
What is histone acetylation
Acetyl groups are attached to a positively charged lysines in histone tails
Histone acetylation seems to loosen chromatin structure thereby _____ the initiation of transcription
promoting
What is DNA methylation
The addition of methyl groups to certain bases in DNA is accociated with reduced transcription in some species
DNA methylation can cause ______ of genes in cellular differentiation
long term inactivation
What is the epigenetic inheritance?
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
Associtated with most eukaryotic genes are multiple ____
Control elements
What are control elements
Segments of noncoding DNA that help regulate transcription by binding certain proteins
To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called
Transcription factors
What are proximal control elements
Located close to the promoter
What are distal control elements
Groups of which are called enhancers, may be far away from a gene or even in an intron
What is an activator
Specific transcription factor, a protein that binds to an enhancer and stimulates transcription of a gene
What is repressor
Specific transcription facotr, inhibit expression of a gene
Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a ___ and ____
promoter and control elements
Transcription alone ____ account for gene expression
does not
The lifespan of mRNA molecules in th cytoplasm is a key to determining
protein synthesis
Eukaryotic mRNA is more ____ than prokaryotic mRNA
long lived
What are differentiated cells?
All have a complete genome, and potential to express all of an organism’s genes
What is a totipotent cell?
One that can generate a complete new organism
Differentiated plant cells have the ability to develop into
A whole new organism
What is nuclear transplantation
Involves replacing nuclei of egg cells with nuclei from differentiated cells
In most transplantation studies only a ____ of cloned embryos developed normally to birth
small percentage
Dolly’s death indicated her cells were not as healthy as those of a normal sheep, possibly reflecting
Incomplete programming of the original transplanted nucleus
Many epigenetic changes such as acetylation of histones or methylation of DNA must be ______
Reversed
Embryonic stem cells
Can give rise to specific types of differentiated
Adult stem cells
Generate replacements for nondividing differentiated cells
How are adult stem cells unlike embryonic stem cells?
They are partway along the road to differentiation
_____ and placenta provide another source of stem cells
Umbillical cord blood
Therapeutic cloning
Produces embryonic stem cells
Human therapeutic cloning
Cloning of embryos for the production of embryonic stem cells for medical use
Transformed cells from Skin cells to ES cells are called
iPS cells
iPS cells can be used to
treat some diseases and to replace nonfunctional tissues
Genes that normally regulate cell growth and division include
Genes for growth factors
Their receptors
Intracellular molecules of signaling pathways
What are oncogenes
Cancer causing genes
What are proto oncogenes
Normal cellular genes that code for proteins that stimulate normal cell growth and division
What are tumor suppressor genes
Help prevent uncontrolled cell growth
What are the functions of tumor supressor proteins
Repair damaged DNA
Control Cell adhesion
Inhibit cell cycle in the cell-signaling pathway
Many human cancers involve mutations in
Ras (proto oncogene—>oncogene)
p53 (tumor suppressor)
A virus ma promote cancer by:
donating an oncogene to the cell
disrupt a tumor suppressor gene
convert a proto oncogene to an oncogene
Viruses seem to play a role in ___% of human cancer cases worldride
15
What are genomics?
The study of whole sets of genes and their interactions
What is bioinformatics
Application of computational methods to the storage and analysis of biological data
What is the Human Genome Project
Mapping of the human genome
Whole genome shotgun approach
skips genetic physical mapping and sequences random DNA fragments directly
What was Griffith’s experiment
Injected pnemonia into mice and discovered a “transformed” strain of bacteria that was lethal. R and HS= +
S and R&HS= -
What were the hershey chase experiments
Confirmed DNA was a genetic material, showed bacteriophages DNA enters the host bacterial cell, but most of their protein does not
What was Chargoff’s experiments
Contributed to two rules to the double helix structure of DNA:
- # G= # C and #A=#T
- Relative amounts of G,C,A,T bases vary from one species to another
What was franklin’s experiments
Did x-rays of DNA which led to discovery of DNA double helix
Describe chromatin packing
DNA wraps around histones forming a nucleosome, the building block. Nucleosomes looped around till densly packed chromosomes.
DNA polymerase vs RNA polymerase
DNA: Synthesizes DNA, require a primer, has a base T, double stranded, continuous till work done, faster, cannot initiate new strand
RNA: synthesizes RNA, does not require a primer, capable of initiating a new strand, has base U, single stranded, RNA polymerase continues to a stop cycle, slower
Describe Trp Operon
repressible, negativ control, anabolic pathways, corepressor needed
Describe lac operon
Inducible, negative control and positive control, catabolic pathways, inactive repressor and active repressor needed
