exam 1 chapter 10-14
Which of the following is not consistent with Erwin Chargaff's findings? (A + G) = (C + T) (A + C) = (G + T) A = T (C + G) = (A + T) (A + G) / (C + T) = 1
(C + G) = (A + T)
List three main differences between DNA and RNA.
1. uracil in RNA replaces thymine in DNA 2. Ribose in RNA replaces deoxyribose in DNA 3. RNA often occurs as both single and partially double-stranded forms, whereas DNA most often occurs in double stranded form
Due to the spacing of each nucleotide, each 360 turn of the double helix contains approximately how many base pairs? 5 10 20 None of the above
10
Due to the spacing of each nucleotide, each 360o turn of the double helix contains how many nucleotides? 5 10 20 None of the above
10
What subunits make up a histone core? How many subunits are there? What does H1 do?
2 of each subunit H2A, H2B, H3 and H4 make up the histone core. H1plays an important role in chromatin compaction, transcription regulation, nucleosome spacing and chromosome spacing. H1 function in DNA and chromatin structure stabilization is well studied and established.
In which direction does RNA polymerase move along the template strand during transcription? It moves along the coding strand not the template strand It reads both strands 5'-3' 3'-5'
3'-5'
Which sequence below would have the highest melting temperature? One strand's sequence is often provided in cases such as this one. Assume that each sequence is one strand of a dsDNA sequence and the second strand is complementary. 5'-GCCATTCAT-3' 5'-ATGGGACAT-3' 5'-AGTTAACCG-3' 5'-CCGGGGCCA-3' 5'-ATTTACATT-3'
5'-CCGGGGCCA-3'
How does a deoxyribonucleotide differ from a ribonucleotide?
A deoxyribonucleotide has an H on the 2' carbon, but ribonucleotides have OH on the 2' C.
Define gene
A gene is a section of DNA that codes for a product (protein or RNA).
What is a gene? How is it related to phenotype?
A gene is a section of DNA that codes for a product (protein or RNA).
define genome
A genome is all the coding and non-coding genetic material of an organism
What does it mean that the helix is right-handed?
A helix is right-handed if it turns clockwise.
What is the relationship between a polypeptide and protein? What is a protein subunit?
A polypeptide is a chain of amino acids, but a protein is a folded polypeptide.
The T(m) of dsDNA is influenced by....... The length of the DNA The GC content of the sequence The total number of hydrogen bonds between the base pairs of the sequence A, B, and C None of the above
A,B, and C
The poly(A) tail of mRNA _____. Choose all that are correct. a. is recognized by the translation machinery at the start of translation b. is added to the 3′ end of eukaryotic mRNAs c. helps terminate transcription d. helps prevent degradation of eukaryotic mRNAs
ALL ARE CORRECT
Summarize and compare the properties of DNA polymerase I, II, and III.
All three enzymes share several common properties first none can initiate DNA synthesis on a template but all can elongate an existing DNA strand assuming there is a template strand as shown in the following figure. polymerization of nucleotides occurs in the 5' to the 3' direction where each 5' phosphate is added to the 3' end of the growing poly nucleotide
Why might we predict that the organization of eukaryotic genetic material will be more complex than that of viruses or bacteria?
Although greater DNA Content per cell is associated with eukaryotes one cannot universally equate genomic size with an increase in organismic complexity however single question in another way it is likely that a much higher percentage of the genome of a bacterium is actually involved in phenotype production than in a eukaryote eukaryotes have involve the capacity to obtain and maintain what appear to be large amounts of extra DNA given the larger amount of eukaryotic DNA per cell and the requirement that the DNA be partitioned in an orderly fashion to daughter the cells during cell division certain mechanisms and structures have you vote for packaging in this
What is endonuclease
An endonuclease is an enzyme that cuts off the phophodiester bond within a nucleic acid polymer (in the middle).
What is Exonuclease?
An exonuclease has the ability to move "backwards" over a newly synthesized strand and remove bases at the end of a nucleic acid polymer.
How do bacteria like E. coli package their DNA? Using proteins called histones By supercoiling the DNA By acetylating the DNA By methylating the DNA All of the above
By supercoiling the DNA
Define C-value. What is the C-value paradox? Define haploid versus diploid. What is a karyotype?
C-value is the amount of haploid DNA in base pairs in an organism. The C-value paradox is that an increased C-value (base pairs) does not mean increased complexity. Haploid: contains one set of chromosomes (n) Diploid: contains two sets of chromosomes (2n) Karyotype: The chromosomal complement of a cell or individual. An arrangement of metaphase chromosomes in a sequence according to length and centromere position.
Apply Chargaff's rule.
Chargaff's rule is that A:T and C:G ratios are always close to 1. But comparing (A+T) and (C+G) would differ among different species.
What is chromatin? What kind of proteins interact with DNA? What does it mean when we say histones are highly conserved?
Chromatin is DNA and its associated proteins in the nucleus. The four core histones (H2A, H2B, H3 and H4), which are responsible for folding DNA into nucleosomes, Highly conserved: There are very few differences among the amino acid sequences of the histone proteins of different species. It doesn't change much throughout evolution.
In humans, the phenylalanine hydroxylase gene is 90,000 (90 k b) bases long, yet the mRNA is only 2,400 (2.4 k b). What explains this difference? a. R N A editing b. Removal of exons in the final m R N A c. Loss of stability without a 5′ cap d. Presence of introns in D N A e. Code for poly A tail that is removed in m R N A
D- Presence of introns in DNA
What does the term "processivity" mean in the context of DNA replication? a. that the DNA polymerase has completed its self-assembly into a holoenzyme b. that the DNA polymerase has completed one round of DNA replication c. that DNA polymerase is replicating bidirectionally d. the length of DNA that is replicated by d. DNA polymerase before it detaches from the template e. the ability of DNA polymerase to move "backward" for proofreading.
D. the length of DNA that is replicated by DNA polymerase before it detaches from the template
What enzyme will replace the RNA primers found in the newly synthesized strand? DNA pol III DNA pol II DNA pol I Primase ligase
DNA Pol I
What is the purpose of DNA? What must it be able to do?
DNA contains genetic material and it must be able to replicate and become
Describe the organization of DNA in E. coli. Where is it found? E coli modify their DNA, but does this contribute to packing?
DNA in E. coli is covalently closed circularly, double stranded DNA. They are found in the nucleoid.
Where is DNA found in a eukaryote?
DNA is found in the nucleus.
What activity provides DNA pol III the ability to proofread? DNA pol III has 5′→3′ exonuclease activity. DNA pol III has 3′→5′ exonuclease activity. DNA pol III has exonuclease activity in both the 5′→3′ and 3′→5′ directions. DNA pol III has polymerase activity in the 5′→3′ and 3′→5′ directions. The sliding clamp activity.
DNA pol III has 3′→5′ exonuclease activity.
The genetic code is _________, allowing for an amino to be coded by more than one codon. unambiguous degenerate commaless universal nonoverlapping
Degenerate
What are the two types of nucleic acids?
Deoxyribonucleic acid and ribonucleic acid
What is the difference between DNA polymerase III and I in terms of their activities during DNA replication?
Dna polymerase III: adds nucleotides ONLY in the 5' to 3' direction. A protein sliding clamp holds polymerase III onto DNA template, and it syntehsizes from the RNA primer in the leading and lagging strand. Adds dNTP to the 3' of the growing strand. Moves along the template strand in 3' to 5' direction. Dna polymerase I: replaces the RNA primer with dNTPs using its polymerase activity. Digests primer ahead of it using its 5' to 3' exonuclease activity.
What does the chromatin of an interphase cell look like versus a metaphase cell?
During interphase: the chromatin is not as uniform, there are regions that are more and less tightly packed M phase: two sister chromatids and are more tightly packed
Define euchromatin versus heterochromatin. Which is more likely to have repetitive DNA sequences? Which is more likely to have higher gene expression? Why?
Euchromatin is open and accessible to transcription machinery, therefore expressed (arranged to be accessible). Heterochromatin is packed tightly; closed and silenced (pushed up against cell wall). Heterochromatin is more likely to have repetitive DNA sequences since it has centromeres and telomeres. Euchromatin is more likely to have higher gene expression because it's accessible to transcription machinery.
What are some other differences between prokaryotic and eukaryotic replication? Describe the end-problem of replication in eukaryotes.
Eukaryotes have many origins of replication per chromosome, have telomeres that need to be extended, have DNA polymerase delta, immediately after replication DNA is wound around histones, and Okazaki processing involves a flap. The end problem is that the last few nucleotides cannot be synthesized because of the RNA small stretches of DNA at the 3′ ends of chromosomes cannot be copied because these stretches are not covered by Okazaki fragments. It is solved by locating highly repeated DNA sequence at the end, or telomeres, of each linear chromosome. In humans and other vertebrate organisms, the sequence of nucleotides in telomeres is TTAGGG 100s of times.
State the 5 subdisciplines of genetics and give an example of each.
Ex. mendel's peas and fruit flies Molecular genetics- The structure and function of genes Ex. DNA molecule at molecular level Population genetics- Study of the frequency of traits and how frequencies change from generation to generation of a population Ex. Genomics- Analysis of genomes. Sequencing DNA and RNA using bioinformatics Ex. Quantitative genetics- (study of complex traits) How the genes and the environment influence phenotypic expression. Ex.
What is fidelity? What is proofreading? How do these terms relate to exonuclease activity?
Fidelity is the accuracy in adding base pairs (how many times polymerase incorporates the wrong noncomplementary base) Its proofreading activity increases its fidelity. Proofreading is removing newly made nucleotide base incorporation errors from the primer terminus before further primer extension. Proofreading is a source of spontaneous mutation. These relate to exonuclease activity because if there is error, proofreading will catch it and use exonuclease activity to fix it.
What did Franklin's results show?
Franklin's results showed that DNA is helical, snf 3.4 nm is 360 degrees (full turn) and 0.34 nanometers is the space between bases. About 10 base pairs per turn.
What are gene variants?
Gene variant is a stretch of DNA with different polymorphism.
What is Rho-dependent termination
Hairpin structure in RNA that causes RNA polymerase to stall. Rho (helicase) unwinds the RNA-DNA duplex.
Provide a comprehensive definition of heterochromatin and list as many examples as you can.
Heterochromatin is a chromosomal material that stains deeply and remains condensed when other parts of chromosomes such as eukaromatin are otherwise pale and decondensed. heterochromatic regions replicate late in S phase and are relatively inactive in a genetic sense either because there are few genes present or because the genes present are repressed. telomeres and the areas adjacent to centromeres are composed of heterochromatin
DNA polymerase _____ has 5' to 3' and 3' to 5' exonuclease activity. A-I B-III
I
Satellite DNA ________ - Is found outside of the nucleus - Is a term used to describe very small chromosomes - Is a form of repetitive DNA - Is less subject to breakage than other chromosome regions - Is only found in telomeres
Is a form of repetitive DNA
What can you conclude about the genetic material for German measles given its nucleic acid analysis A + G / U + C ratio of 1.13? Choose all that apply. Its genetic material is DNA Its genetic material is RNA Its genetic material is double stranded Its genetic material is single stranded
It genetic material is RNA Its genetic material is single stranded
If a circular piece of DNA has 100 helical turns, and is underwound by 2 turns, it will negatively supercoil by two twists. What do you predict would happen if you overwound it by 2 turns? - It will positively supercoil 2 twists. - It will negatively supercoil 2 twists. - It will stay in relaxed circle. - Only short piece of D N A can supercoil. - You cannot overwind D N A; it would break.
It will positively supercoil 2 twist
Who is the best at genetics ever
Jamie
Describe the molecular composition and arrangement of the components in the nucleosome.
Nucleosome's are optometric structures containing two molecules of each of the four core histones: H2A H2B H3 H4. each octometer consist of two tetramers (H2A)2*(H2B)2 and (H3)2*(H4)2. between the nucleosomes and complexed with linker DNA is histone H1. A 147 base pair sequence of DNA wraps around the nucleosome in a left handed helix that completes about 1.7 turns
What are the differences between prokaryotic and eukaryotic transcription?
PROKARYOTES: - 1 type of RNA polymerase - Transcription and translation processes are near each other Polycistronic mRNA (several proteins encoded in one mRNA) - Limited RNA processing - Intrinsic and rho-dependent termination EUKARYOTES: - 3 types of RNA polymaerase (I, II, III) Transcription and translation processes are temporally and spatially separated by nuclear envelope - Monocistronic mRNA (one protein encoded in one mRNA) mRNA is processed (capped, polyadenylated, and spliced) before being exported from nucleus) - Poly-a-dependent termination
What are the three major groups of a nucleotide? What does the phosphodiester bond do?
Phosphate group, ribose sugar, and a base.
How is polyadenylation performed as a step in transcription termination? What end of the mRNA is the polyA tail added to? What adds the polyA tail? What is the purpose of the polyA tail?
Polyadnylation is done by adding about 250 adenine nucleotides to the 3' end of RNA by polyA polymerase. It is coated with protein and is necessary to protect the 3' of mRNA to 3' exonucleases.
Why isn't primase added to a PCR? a. Primers for Taq polymerase are added to the reaction b.RNA gets quickly degraded c. Taq polymerase doesn't need a primer d. Primase doesn't work at the high temperatures found during PCR
Primers for Taq polymerase are added to the reaction
What is processivity with respect to replication?
Processivity is how many base pairs polymerase adds before it falls off (sliding clamp increases its processivity)
Good job Jamie youre doing such a good job studying
Proud of you
What kinds of RNA do eukaryotic RNA polymerase I, II, and III transcribe?
RNA polymerase I: rRNA (in nucleolus eukaryotes) RNA pol II: mRNA and snRNA (in nucleoplasm eukaryotes) RNA pol III: tRNA (in nucleoplasm eukaryotes)
List the four major steps in transcription.
RNA polymerase is positioned at the transcription start site DNA is locally denatured (form transcription bubble) One strand is the exact copy of RNA Other strand is template strand RNA polymerase assembles NTPs complementary to template strand No primer needed Add NTPs 5' to 3' (to 3' of growing strand) DNA duplex reforms behind the bubble
During which phase of the cell cycle does replication occur?
Replication occurs during the S phase of the cell cycle.
What is satellite DNA? Name the satellite DNA that is often used as genetic markers. What can they be used for? What do their acronyms stand for?
Satellite DNA is a form of repetitive DNA. The satellite DNA that is often used for genetic markers is micro satellite DNA.
What are telomeres? Where are they located and what do they consist of? Describe the activity of telomerase? What kind of enzyme is telomerase? What purpose does its snRNA serve?
Telomerase is responsible for helping maintain chromosome size, contains its own RNA template, is a reverse transcriptase, and extends one strand of the telomere.
What makes centromeres and telomeres constitutive heterochromatin? What makes a Barr body facultative heterochromatin?
Telomeres and centromeres are constitutive heterochromatin because they contain repetitive DNA. Heterochromatin consists of constitutive heterochromatin that is usually not transcribed and remains condensed. Facultative heterochromatin, like Barr bodies, is formed when certain genes are silenced.
DNA and RNA are chemically very similar but are distinguished, in large part, by the presence of a group in RNA and a group in DNA. Why do you suppose that both DNA and RNA have groups and we do not typically find nucleic acids within cells that have groups?
The 3' - OH group is critical for both DNA and RNA because it is involved in the phosphodiester bonds that link together deoxy nucleotides or nucleotides into the long polymers that function as informational molecules of nucleic acid with a 3' - H group would be unable to form phosphodiester bonds and nurse would be unable to form polymers
Where is the base attached to the ribose? Where is the phosphate attached to the ribose? Be able to recognize the bases. Which bases are purines and which are pyrimidines? Which bases belong in DNA versus RNA? How many H bonds are between the complementary base pairs?
The base is attached to the ribose at the 1' Carbon. The phosphate is attached to the ribose at the 5' Carbon. Purines: Adenine and Guanine, Pyrimidines: Cytosine, Thymine, and Uracil. A,G,C,T are in DNA but U is in RNA instead of T. C and G have 3 hydrogen bonds but A and T have 2 hydrogen bonds.
What is the chromosomal theory of inheritance?
The chromosomal theory of inheritance states that genes for phenotypes are carried on chromosomes.
Describe the "end-replication problem" in eukaryotes. How is it resolved?
The end replication problem refers to the difficulties posed in replicating the ends of linear eukaryotic chromosomes. once primers are removed from a 5' ends a gap remains which cannot be filled. this shortens the chromosome with each round of replication potentially leading to deletion of gene coding regions. the action of telomerase lengthens the telomere which is then made double-stranded except for the end through conventional DNA synthesis
Where is the glycosidic bond? Label the carbons in the ribose ring.
The glycosidic bond is between the sugar and base. Starts from the right labeled as the 1 Carbon, then the bottom right is 2, bottom left is 3, top left is 4, and on top of that is 5.
Identify the major and minor grooves. Why do proteins tend to interact with the major groove?
The major groove is where the backbones are far apart and the minor groove is where they are closer together. Proteins tend to interact with the major groove because there is more area to interact with.
What is melting temperature and how is it calculated? Be able to use the 2+4 Rule of Thumb.
The melting temperature is ___ and is calculated by the 2+4 Rule of Thumb. Which means 2(A+T) + 4(C+G).
How does chromatin packing contribute to the level of gene expression?
The more tightly packed chromatin is, (heterochromatin) the less likely it will be expressed but the more loosely it is packed (euchromatin) it is more open and accessible to transcription.
What is the name of the nucleotide that's incorporated into DNA? How many phosphate groups does it have? How many of these phosphate groups actually end up in DNA? What overall charge does the phosphate give DNA?
The nucleotide in DNA
Is the phosphodiester backbone (sugar-phosphate backbone) covalently bonded?
The phosphodiester backbone is covalently bonded.
Describe the centromere. What is its function?
The telomere is constitutive heterochromatin, tandemly repeated DNA at the ends of linear chromosomes. The number of repeats is dependent on species and age. It's important for stability of chromosomes Ex. like the plastic cap on shoe laces.
Describe the various characteristics of the Watson-Crick double-helix model for DNA.
There are 2 polynucleotide chains, each formed by phosphodiester linkages between the five carbon sugars and the phosphates
How many base pairs are in a 360 degree turn of the helix?
There are ten base pairs in 360 degree turn of the helix.
How many molecules of DNA make up one chromosome?
Two molecules of DNA make up one chromosome.
Human insulin can be made by E. coli containing the human gene that codes for insulin. This is an example of the code being unambiguous degenerate commaless universal nonoverlapping
Universal
What evidence did Watson and Crick have at their disposal in 1953? What was their approach in arriving at the structure of DNA?
Watson and Crick knew the chemical structure of each nitrogenous base end of each nucleotide they also have available the x-ray diffraction information of Asberry Franklin and Wilkins and the base ratio information of chargraph the approach wants to construct a simple model
How are RNA molecules able to take on so many different structures? Why are these structures noteworthy?
What is the subunit of RNA? α (two copies), β, β' and ω subunits
3'....... GGCTACCTGGATTCA..... 5' a. If the RNA primer consists of eight nucleotides, what is its base sequence? b. If the RNA primer consists of eight nucleotides, what is its base sequence?
a. 5'- ACCUAAGU-3' b. U.
Define and indicate the significance of (a) Okazaki fragments, (b) DNA ligase, and (c) primer RNA during DNA replication.
a. Okazaki figments are relatively short (1000 to 2000 bases in bacteria) DNA fragments that are synthesized in a discontinuous fashion on the lagging strand template during DNA replication b. DNA ligase is required to form phosphodiester linkage in nicks, which are generated when DNA polymerase I removes RNA primer and meets newly synthesized DNA ahead of it. c. Primer RNA is formed my primase to serve as an initiation point for the production of DNA strands on a DNA template
What is semi-conservative?
after replication, each product contains one parental strand and one nascent strand.
What is the role of eukaryotic general transcription factors? a. They bind to enhancers and silencers to fine tune transcription b. They bind to the core promoter to recruit RNA polymerase to the correct nucleotide c. They are DNA sequences called cis-regulatory elements d. They regulate the length of the mRNA e. They are part of the RNA polymerase holoenzyme
b. They bind to the core promoter to recruit RNA polymerase to the correct nucleotide
All known DNA polymerases _____. a. can initiate DNA chain synthesis b. have 5' to 3' polymerization activity c. have 5' exonuclease activity d. have 3' to 5' polymerization activity e. All of the above
b. have 5' to 3' polymerization activity
The peptidyl transferase _____. a. is a polypeptide subunit of the small ribosomal subunit b. is not found in eukaryotes c. is a function of an rRNA in the large ribosomal subunit d. catalyzes the reaction that joins a tRNA to its amino acid e. is active during initiation of translation
c. Is a function of an rRNA in the large ribosomal subunit
The chromosomal theory of inheritance _____. a. describes how chromosomes can be altered by mutation b. was proposed because the behavior of chromosomes in mitosis is similar to that of genes during gamete formation c. is that genes for phenotypic traits are carried on chromosomes d. does not apply to haploid organisms
c. is that genes for phenotypic traits are carried on chromosomes
Any molecule that serves as the genetic material must have the following characteristics except _____. a. the ability to be replicated b. the ability to store information c. the ability to directly influence the development of traits d. the ability to express stored information e. the potential to be changed via mutation
c. the ability to directly influence the development of traits
Identify the 5' and 3' ends of DNA strands and of a nucleotide. What does it mean when we say dsDNA is antiparallel?
dsDNA is antiparallel because the strands run from 5' to 3' and the complementary strand runs 3' to 5' respectively,
What is Intrinsic termination
is hairpin structure in RNA that causes RNA polymerase to stall. RNA-DNA duplex dissociates due to a weak dissociation between the RNA and DNA.
Draw the chemical structure of the three components of a nucleotide, and then link the three together. What atoms are removed from the structures when the linkages are formed?
linkages among the three components require the removal of water
what is Semi-discontinuous?
refers to DNA being replicated continuously on the leading strand yet discontinuously on lagging strand.
State the central dogma of molecular biology.
the central dogma states that DNA is transcribed to mRNA, which is translated to protein, thereby influencing traits. (The central dogma of molecular biology is genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.)
The genetic code is _________, meaning that one codon indicates only one amino acid. unambiguous degenerate commaless universal nonoverlapping
unambiguous
Is there any role for an RNA polymerase in DNA replication? No, only DNA polymerases function in DNA replication. Yes, in order to synthesize mRNA. Yes, to generate primers. Yes, to synthesize RNA that will bind to and keep the two DNA strands unwound. Yes, in eukaryotes an RNA polymerase functions in telomere maintenance.
yes, to generate primers
