Chapters 13,14,15 test Flashcards
What was The major achievement of James Watson and Francis Crick?
They made an elegant double-helical model for the 3 dimensional structure of DNA
What make nucleic acids unique in nature?
Their ability to direct their own replication from monomers
What was the key factor in determining the identity of genetic material? why?
Choosing the appropriate organisms to study, like bacteria and viruses because they are simpler
What is transformation? Who first used this term in genetics?
discovered by Frederick Griffith, transformation is a change in genotype and phenotype due to assimilation of external DNA by a cell
What are bacteriophages?
Called phages for short, these are viruses that infect bacteria that are used to study DNA
What is a virus?
An organisms that is basically just DNA(or sometimes RNA) enclosed within a protective coat that must infect other cells and take over their metabolic machinery to reproduce
Who discovered whether viruses used DNA or protein to infect and reprogram other cells and how?
Alfred Hershey and Martha Chase. They did this by tagging phage protein with a radioactive isotope of sulfur and tagging phage DNA with radioactive phosphorus. They found that phage DNA entered the the host cells and protein did not
Why was Hershey and chase’s experiment important and what were their conclusions?
They concluded that DNA injected by the phage must be the molecule carrying genetic information that makes the cells produce new viral DNA and proteins. Their study was important bc it provided powerful evidence that nucleic acids rather than proteins are hereditary material, at least viruses.
How was Erwin Chargaff significant?
He provided further evidence that DNA is the genetic material. He first discovered that the base ratios that compose DNA vary in different species, a diversity that was believed to be absent made DNA a more credible candidate to be genetic material. He also noticed that the number of adenines was close to the number of thymines and the number of guanines almost equaled the number of cytosines. These discoveries resulted in Chargaff’s rules(which are these 2 findings)
What dies antiparallel mean? what part of DNA is this applicable to?
Antiparallel means that they run in opposite directions parallel to each other. This sugar phosphates run in the DNA double helix structure
Why is adenine always paired with thymine and guanine with cytosine?
A and G are purines, nitrogenous bases with 2 rings. C and T are pyrimidines, nitrogenous bases with 1 ring. Purines are about twice as wide as pyrimidines, so purine-purine pairs are too wide and pyrimidine-pyrimidine pairs are 2 narrow to account for the uniform 2nm diameter of a double helix. Furthermore, each base has chemical side-groups that can form H bonds with it’s partner only
What is the model of DNA that Watson and Crick came up with for their hypothesis on DNA replication?
The semiconservative model
What are the origins of replication?
The particular sites where DNA replication begins, these are short patches of DNA having a specific sequence of nucleotides. Proteins that initiate DNA replication attach to the DNA and separate the two strands and opening up a replication bubble
What is a replication fork?
A Y-shaped region where the parental strands of DNA are being unwound
What are helicases?
Enzymes that untwist he double helix at the replication forks, separating the two parental strands and making them available as template strands
What are single-strand binding proteins?
Proteins that bind to the unpaired parental strands after they separate, keeping them from repairing
What is topoisomerase?
A enzyme that helps relieve the strain caused by the untwisting if the double helix that causes tighter twisting and strain ahead of the replication fork
How is DNA replication similar and different bacteria and prokaryotes?
Bacteria have one origin of replication, while eukaryotes have multiple to speed of the process. Both of these processes are similar in that replication proceeds in both directions from each origin
What is a primer?
The short stretch of RNA that is the initial nucleotide chain produced during DNA synthesis.
What is primase? What does it result in?
The enzyme that synthesizes a primer by starting a complementary RNA chain from a single RNA nucleotide, adding RNA nucleotides one at a time, using the parental DNA strand as a template. The completed primer is based paired to the template strand and the new DNA strand will start from the 3’ end of the RNA primer
What are DNA polymerases?
Enzymes that catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain. Most require a primer and a DNA template strand along which complementary DNA nucleotides lines up
What are 2 examples of DNA Polymerase?
DNA Polymerase III and DNA Polymerase I, they play a major role in DNA replication in E. coli.
III: adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides complementary to the parental DNA strand to the growing end of the new DNA strand
What consists of each nucleotide added to a growing DNA strand?
A sugar attached to a base and 3 phosphate groups
What is dATP and how is it different from ATP?
dATP is the adenine nucleotide used to make DNA. It is different from ATP because its sugar is deoxyribose instead of ribose
What makes the nucleotides used for DNA synthesis chemically reactive?
their triphosphate tails have an unstable cluster of negative charge
What exergonic reaction helps drive the polymerization reaction?
As each monomer joins the growing end of a DNA strand, two phosphate groups are lost as a molecule of pyrophosphate then they undergo hydrolysis to become two inorganic molecules of phosphate
What does a helix being antiparallel affect replication?
Due to the structure, DNA can only add to the free 3’ end of a primer or growing DNA strand, never to the 5’ end. Thus, the new DNA strand can only elongate in the 5’ to 3’ direction
What is the leading strand?
The DNA strand made by the continuous addition of nucleotides to the new complementary strand as the replication fork progresses
How many primers are needed for DNA pol III to synthesize the leading strand?
One
What is the lagging strand?
The template strand elongating away from the replication fork
What are okazaki fragments?
The fragments in which the lagging strand is synthesized discontinuously by.
What is different about primers on the leading and lagging strand?
One primer is required on the leading strand, whereas each okazaki fragment must be primed separately on the lagging strand
What is the role of DNA pol III and I on lagging strands?
DNA pol III forms the okazaki fragment after the RNA primer. DNA pol I replaces the RNA nucleotides of the adjacent primer with DNA nucleotides
What is DNA ligase?
An enzyme that joins the final nucleotide of the replacement DNA from DNA pol I to the first DNA nucleotide of the Okazaki fragment, joining sugar-phosphate backbones of all okazaki fragments into a continuous DNA strand
Why is the railroad track representation if DNA inaccurate?
- The various proteins in DNA replication actually fork a single large complex
- The DNA replication complex may not move along the DNA, it may actually be vice versa
Why is DNA replication so accurate?
During replication, DNA polymerases proofread each nucleotide against its template as soon as it is added to the growing strand. If an error is found, the nucleotide is removed and synthesis is resumed
What is mismatch repair?
When enzymes other than DNA polymerase remove and replace incorrectly paired nucleotides that DNA polymerase missed
What is nuclease?
A DNA cutting enzyme that cuts out a damaged segment of DNA and the resulting gap is filled with nucleotides, using DNA polymerase and DNA ligase
What is nucleotide excision repair?
A DNA repair system involving nuclease and its function
What makes a mismatched nucleotide replication permanent?
replication
How has mutation effected evolution?
A low mutation rate allows evolution and diversity of species we see today. Some mutations are beneficial and are ultimately responsible for the appearance of new species
What is telomerase?
An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells, restoring them to their original length and compensating for the shortening that occurs in replication
How are bacterial and eukaryotic chromosomes different?
Eukaryotic chromosomes consist of one linear DNA molecule associated with a large amount of protein. Bacteria consist mostly of one double stranded circular DNA molecule
How is a nucleoid and a nucleus different?
The nucleoid is not surrounded by membrane and the nucleus is
What is heterochromatin?
Interphase chromatin that is visible as irregular clumps with a light microscope. This is less accessible to the machinery responsible for transcription
What is euchromatin?
Less compacted and more disperse chromatin
What are the 4 most common types of histones in eukaryotes and what do they do?
H2A, H2B, H3 and H4. They are critical for DNA packing
What is a nucleosome?
(10nm) Unfolded chromosome resembling “beads”, the basic unit of DNA packing. These consist of DNA wrapped twice around a protein core composed of two molecule of each histone type and a histone tail extending from the nucleosome
What is a 30-nm fiber?
The next level of packing from nucleosomes/10-nm fibers. A fifth histone, H1, becomes involved at this level. The histone tails of one nucleosome and the DNA linker of another interact, coil, and fold to form a 30nm fiber, this is prevalent in the interphase nucleus
What are looped domains?
(300-nm fiber) The next level from 30 nm fibers. The 30nm fibers form loops called looped domains attached to a chromosome scaffold composed of proteins, making up the 300nm fiber
What is the metaphase chromosome?
The next level of packing from a 300 nm chromosome. The looped domains coil and foil to form a 700nm chromatid. Particular genes always end up located at the same places
What is nucleic acid hybridization?
The base pairing of one strand of nucleic acid to a complementary sequence on another strand
What are plasmids?
small circular DNA molecules that replicate separately from the bacterial chromosome
What is recombinant DNA?
A DNA molecule formed when segments of DNA from 2 different sources-often different species-are combined in a test tube
What is gene cloning?
The production of multiple copies of a single gene
What is the most common way to clone DNA in a laboratory?
Using E. coli plasmids to make a recombinant bacterium
What are restriction enzymes?
Enzymes that cut DNA molecules at a limited number of specific locations. They protect bacteria by cutting up foreign DNA from other organisms or phages
What is a restriction site?
A specific, short DNA sequence that a restriction enzyme recognize where it cuts the DNA
How is the DNA of a bacterial cell protected from its own restriction enzymes?
The addition of methyl groups to adenines and cytosines within the sequences recognized by the enzymes
What are restriction fragments?
The fragments made when a restriction enzyme cuts DNA. All copies of an identical DNA molecule yield the same fragments
What is gel electrophoresis?
A technique used to see restriction fragments. This technique separates a mixture of segments by length.
What is a sticky end?
The single stranded end of a restriction fragment that can formed H-bonded base pairs with complementary sticky ends on any other DNA molecules cut by the same enzyme, which are temporary but can be made permanent by DNA ligase
What is a cloning vector?
The two DNA molecules joined in gene cloning. A DNA molecule that can carry foreign DNA into a host cell and replicate there. It often is a bacterial plasmid that has ine copy of a restriction site recognized by a particular restriction enzyme selected by the researcher and purchased
What is a polymerase chain reaction?
(PCR) A technique used to copy a specific DNA sample quickly
What are the parts of a PCR cycle?
- Denaturation: heat briefly to separate DNA strands
- Annealing: Cool to allow primers to form H bonds with ends of target sequence
- Extension: DNA polymerase adds nucleotides to the 3’ end of each primer
What is DNA sequencing?
Using the principle of complementary base pairing to determine a gene’s complete nucleotide sequence
What link phenotype and genotype?
Proteins
What is gene expression?
The process by which DNA directs the synthesis of proteins
What is the bridge between DNA and protein synthesis?
nucleic acid RNA, DNA undergoes transcription and translation
What is transcription?
The synthesis of RNA using information in the DNA
What is messenger RNA?
(mRNA), RNA with a transcript of the gene’s protein building instructions. Comes from a template of DNA in which it gets its sequence from
What is translation?
Synthesis of a polypeptide using mRNA. The cell translates the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide
What are the sites of translation?
ribosomes
How does the flow of genetic information differ in transcription and translation in bacteria and eukaryotes?
Since bacteria dont have nuclei, their DNA is not separated by nuclear membranes from ribosomes and other protein synthesizing equipment. This allows translation to begin while transcription is still in progress
Where does transcription occur?
the nucleus
What is pre-mRNA?
RNA in eukaryotic cells that has yet to be modified in mRNA
What is a primary transcript?
The initial RNA transcript from any gene, including RNA that is not synthesized into protein
What is a triplet code?
the genetic information for a polypeptide chain written in DNA as a series of nonoverlapping, 3 nucleotide words
What is the template strand?
The DNA strand that gets transcribed and provides a pattern or template for the sequence of nucleotides in an RNA transcript
how are DNA an RNA strands related
they are complementary bc of base pairing, not identical
How is mRNA similar and different than the pairs that form during DNA replication?
They have the same base pairs except for U/T and mRNA has ribose instead of deoxyribose
What are codons?
mRNA nucleotide triplets, they go in the 5’ to 3’ direction. Can also be DNA triplets in the nontemplate strand. The are complementary to the template strand
What are the functions of codons? what does AUG do?
Codons initiate, stop and code for amino acids. AUG codes for an amino acid and serves as a start codon
What are reading frames?
Reading the symbols of nucleotides in the correct groupings
What is RNA polymerase?
An enzyme that pries two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand
How are DNA and RNA polymerase different?
Similar: can go in the 5’ to 3’ direction
Different: RNA polymerase doesnt need a primwr, DNA polymerase does
What is a promoter and a terminator?
A promoter is the DNA sequence where the RNA attaches for transcription. In bacteria, the terminator is the sequence that signals the end of transcription
What is a transcription unit?
The stretch of DNA that is transcribed into an RNA molecule
What are the stages of transcription?
- Initiation: After RNA polymerase bonds to the promoter, DNA strands unwind, polymerase initiates RNA synthesis at the start point of template strand
- Elongation: polymerase moves downstream, unwinding DNA and elongating the RNA transcript 5’ to 3’ , DNA strands reform a double helix after
- Termination: Eventually, the RNA transcript is released and polymerase detaches from DNA
what are transcription factors?
A collection of proteins that mediate the binding of RNA polymerase and the initiation in eukaryotes
What is the transcription initiation complex?
The collection of transcription factors and RNA polymerase II bond to the promoter
What is a TATA box?
A very important DNA sequence in a promoter
What end of the RNA gets nucleotides added to it?
the 3’ end
How is termination if transcription different in bacteria and eukaryotes?
Bacteria: Polymerase hits terminator sequence in DNA and detaches
Eukaryotes: RNA polymerase II transcribes a polyadenylatiom sequence, then about 10-35 nucleotides downstream from there, proteins cut the transcript from the RNA polymerase releasing pre-mRNA
What is RNA processing?
In eukaryotic nuclei, enzymes modify pre-mRNA before the genetic messages are dispatched to the cytoplasm. Both ends of the primary transcript are altered. Sometimes parts of the pre-mRNA are cut out and the remaining parts are spliced together, the results produce and mRNA molecule ready for translation
What is a 5’ and a poly-A tail? What functions do they share?
A 5’ cap is a modified form of guanine added to the 5’ end after transcription of the first 20-40 nucleotides. A poly-A tail is 50-250 A nucleotides added to the 3’ end.
They both
- Facilitate transport of mature mRNA from the nucleus
- Protect mRNA from degradation by hydrolytic enzymes
- They help ribosomes attach to the 5’ end of the mRNA once in the cytoplasm
What is RNA splicing?
Cutting and pasting of regions of RNA
What are introns and exons?
Introns: Segments of intervening sequences between coding regions. These are cut out in the nucleus after pre-mRNA is transcribed
Exons: Coding regions that are usually expressed
What is alternative RNA splicing and why is this used?
Alternative RNA splicing is when different sections of pre-mRNA are treated like introns and exons, therefore many more types of polypeptides can be produced than the number of genes
What is a spliceosome and its function?
A large complex of proteins and small RNAs(that catalyze the process) that remove the introns by bonding to several short nucleotide sequences along the intron, including key sequences at the end. The intron is released and rapidly degraded
What are ribozymes?
RNA molecules that function as enzymes
What is transfer RNA?
(tRNA) The translator that transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide of a Ribosome
What is an anticodon?
the nucleotide triplet that base-pairs to a specific mRNA codon
What is the structure of a tRNA codon?
tRNA is a series of about 80 nucleotides with and anticodon at one and at an amino acid attachment at the other end
How is tRNA made in eukaryotes?
It is transcribed from DNA templates in the nucleus, then travels to the cytoplasm
how is tRNA similar in bacteria and eukaryotes?
Each tRNA molecule is used repeatedly, picking up its designated amino acid in the cytosol, depositing onto a polypeptide chain then leaves the ribosome to pick up an amino acid
What are aminoacyl-tRNA synthetases?
A family of related enzymes responsible for the correct matching of tRNA to amino acids
What is wobble?
The flexible base pairing of codons and anticodons
What is required for the accurate translation of genetic messages?
- A tRNA that binds to an mRNA molecule must carry the right amino acid and no other(aminoacyl-tRNA synthetases)
- Pairing a tRNA anticodon to the right mRNA codon(wobble)
What are ribosomes made up of?
A large and small subunit each consisting of proteins and one or more rRNAs
How are ribosomes similar and different in bacteria and eukaryotes? Where are ribosomes synthesized in the eukaryotes?
In eukaryotes, the subunits are made and the rRNA genes are transcribed in the nucleus. This is then exported to the cytoplasm.
Similarities: Large and small subunits join to form a functioning ribosome only when they attach to an mRNA molecule.
Differences: rRNAs are 3 molecules in bacteria and 4 in eukaryotes. Eukaryotic ribosomes are slightly larger
What are p sites, a sites and e sites?
P: Holds tRNA carrying the growing polypeptide chain
A: holds tRNA carrying the next amino acid to be added to the chain
E: the exit site for discharged tRNAs
How is initiation of translation similar and different in bacteria and eukaryotes?
Different: In bacteria a small subunit binds to tRNA and mRNA in either order. In eukaryotes, the tRNA binds to the 5’ cap and moves downstream
Similar: Start codon signals start of translation
Initiation of translation
A small ribosomal subunit binds mRNA to initiator tRNA. This is completed by the attachment of the large ribosomal subunit. Initiation factor protein bring everything together. Initiator tRNA sits in P site, A site is ready for the next tRNA
Elongation(translation)
Amino acids are added one by one to the polypeptide chain. Involves elongation factor proteins. rRNA of large ribosomal subunit catalyzes the formation of a peptide bond between amino acids
Termination of translation
Final stage, a stop codon reaches the A site of a ribosome, a release factors bonds to the stop codon in the A site breaking the bond between the polypeptide and tRNA in the P site releasing the polypeptide through the exit tunnel
Where is GTP required in translation?
Initiation: To form initiation complex
Elongation: Codon recognition(increases efficiency and accuracy), translocation
Termination: breakdown of translation assembly
What happens to a polypeptide after translation?
It undergoes folding, coiling and modifications. Modifications include cleaving, chemical modifications, and combining with other chains
What is a signal peptide?
A signal that makes the free ribosome attach to the ER during translation
What is a signal-recognition particle?
A protein-RNA complex that recognizes the signal peptide. Escorts the ribosome to ER membrane receptors
What are polyribosomes?
Strings of ribosomes that translate a strand of RNA at the same time to produce copies of the same polypeptide quickly
What are missense mutations?
Nucleotide substitution point mutations that change one amino acid to another
What is a nonsense mutation?
A point mutation that changes a codon for an amino acid into a stop codon. Almost always lead to nonfunctional proteins
What is a frameshift mutation?
An insertion or deletion mutation that isnt a multiple of 3. This causes the codons to be improperly grouped
What are mutagens?
Physical and chemical agents that interact with DNA in a way that causes mutations
What is an operator?
A segment of DNA that acts as a switch, located within the promoter or in between the promoter and enzyme coding genes. It controls the access if RNA polymerase to these genes
What is an operon?
The promoter, operator, and genes they control
What is a repressor?
A protein that switches on operon off by bonding to the operator and preventing the attachment of RNA polymerase. Can be active or inactive
What is a regulatory gene?
The gene that produces a repressor
What is a corepressor?
A molecule that cooperates with a repressor to turn an operon off(tryptophan)
What are repressible and inducible operons?
Repressible: Usually on but can be repressed when a molecule bonds to a regulatory protein
Inducible: Usually off but can be stimulated when a molecule bonds to a regulatory protein
What is an inducer?
A molecule that bonds to the repressor and inactivates it
What is the difference between positive and negative gene regulation?
Positive: Regulatory protein interacts directly with the genome to switch transcription on, and vice versa for negative
What is an activator?
a protein that binds to DNA and stimulates transcription of a gene
How do repressors and activators act as on/off switches and volume control?
Repressors determine if a gene transcribes at all and an activator determines the rate at which a gene transcribes
What is differential gene expression?
the expression of different genes by cells with the same genome
What is a common control point for gene expression in all organisms?
transcription
What is DNA methylation?
The process of enzymes methylating DNA bases. Effects are heritabke
What is epigenetic inheritance?
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequenfe
What are control elements?
segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for transcription factor proteins
What are enhancers?
groupings of distal control elements(binding sites)
How can enhancers influence transcription?
Activator proteins bind to the distal control elements. Then a DNA bending protein bends the DNA and brings the activators/enhancers/distal control elements closer to the promoter. The activators bind to mediator proteins and transcription factors, forming an active transcription initiation complex on the promoter
How can transcription factors function as repressors?
- Bind directly to a control element, blocking activator binding or turning off transcription when activators are bound
- Block the binding of activators to proteins that allow the activators to bind to DNA
How do activators and repressors influence transcription indirectly?
by affecting chromatin structure by recruiting proteins
In which cells can RNA splicing occur?
Eukaryotic cells
Where can nucleotide sequences that determine mRNA lifespan be found?
Most commonly at the 3’ end of the UTR
