Genetics exam 1

What is a gene? How is it related to phenotype?

-Section of DNA that codes information for a gene product. - Contain info for a protein or a noncoding RNA (ncRNA) Phenotype: comes from the gene or the environment - protein or ncRNA performs a function which is one piece of the phenotype. An organism's phenotype (physical traits and behaviors) are established by their inherited genes. Genes are certain segments of DNA that code for the production of proteins and determine distinct traits.

What is satellite DNA?

-Stretches of tandemly repeated DNA sequence -Higher GC content -Satellite DNA is composed of regions of short tandem nucleotide sequences repeated many times. -Most satellite DNA consists of the centromere. -It has a different G/C content than the rest of the genome, it has a slightly different density and migrates differently from the majority of the genome in a centrifugation tube. This creates "satellite" bands around the main DNA band.

population genetics and example

-Study of traits determined by one or a few genes in a large group of individuals -the study of how populations change genetically over time For example, in a population of fifty people where all the blood types are represented, there may be more IA alleles than i alleles. Population genetics is the study of how selective forces change a population through changes in allele and genotypic frequencies.

Quantitative Genetics and examples

-Study of traits that are complex -the study of the genetic basis underlying phenotypic variation among individuals. -Quantitative traits are polygenic; a characteristic, such as height or skin color, that is influenced by two or more genes. Because multiple genes are involved, polygenic traits do not follow the patterns of Mendelian inheritance. Many polygenic traits are also influenced by the environment and are called multifactorial. -Examples of quantitative traits include height, skin colour, weight and blood pressure. There is no single gene for any of these traits, instead it is generally believed that continuous variation in a trait such as blood pressure is partly due to DNA sequence variations at multiple genes.

Describe the end-problem of replication in eukaryotes.

-Unlike bacterial chromosomes, the chromosomes of eukaryotes are linear (rod-shaped), meaning that they have ends. -These ends pose a problem for DNA replication. The DNA at the very end of the chromosome cannot be fully copied in each round of replication, resulting in a slow, gradual shortening of the chromosome.

What subunits make up a histone core? How many subunits are there?

-dsDNA is negatively supercoiled around histone Octomer -Two of each subunit: H2A, H2B, H3, H4 -four subunits

Define gene. Define genome.

-gene is a specific segment of DNA that tells cells how to function. -A genome is the entirety of the genetic material inside an organism. - All the coding and noncoding genetic material of an organism. - 2% is coding and 98% is noncoding The human genome consists of between 20,000 and 25,000 genes.

A protein domain is a part of a protein that is shaped a certain way so that it can perform a specific function. We've discussed three domains for DNA polymerase I. Let's list them below. (Hint: what are the three functions of DNA polymerase I?)

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Label the carbons in the ribose ring.

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Summary of higher level chromatin structure in euks

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What must DNA be able to do?

1. Must contain, in a stable form, the information about an organism's cell structure, function, development, and reproduction. 2. Must be able to be expressed so the information can be used for the above functions. 3. Must replicate accurately so that progeny cells have the same information as the parent cells. 4. Must be capable of change because without change, a population would not have variation. Adaptation and evolution would not occur.

State the 5 subdisciplines of genetics

1. Transmission Genetics 2. Molecular Genetics 3. Genomics 4. Popular Genetics 5. Quantitative Genetics

What two properties dictate supercoiling?

1. Twist - One strand crosses over the other 2. Writhe - Both strands cross over itself As dsDNA is twisted (or is untwisted), bond angles and length constraints cause it to writhe

List the four major steps in transcription.

1. initiation, 2. promoter clearance 3. elongation 4. termination

How is polyadenylation performed as a step in transcription termination?

1. mRNA is cleaved at the polyA cleavage site 2. mRNA is released from the transcription bubble 3. mRNA is polyadenylated

How many base pairs are in a 360 degree turn of the helix?

10

Approximately how many types of these enzymes are present in a cell?

20, one for each amino acid

Calculate the melting temperature for the following dsDNA sequence. For simplicity, only one strand's sequence is given. Assume the second strand is complementary. 5'-ATG-GAC-CCG-ATT-TAT-3'

42 degrees Celsius

Below is a segment of duplex DNA that is in frame and encodes part of a polypeptide: ...5' GGCTATCTGCTT 3'... ...3' CCGATAGACGAA 5'... What is the transcript if the top strand is the coding strand?

5' GGCUAUCUGCUU 3'

What is added to the 5' end of the mRNA? What purpose does it serve? When does this happen?

5' m7G cap is added to the mRNA during transcription Protects RNA from 5' to 3' exonucleases The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein.

Where are the three splice sites of an mRNA intron located?

5' splice site 3' splice site Branch point A (in the middle)

What is the order of mRNA maturation events?

5′ capping, splicing, 3′-end cleavage and polyadenylation, exported from the nucleus

ch 11. Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. a. If the RNA primer consists of eight nucleotides, what is its base sequence? 3′.......GGCTACCTGGATTCA....5′

5′ACCUAAGU-3′

Locate an anticodon and position of an acyl bond (or where it would form during aminoacylation).

A (amino acid site) -binds with anticodon of charged DNA

What are the three tRNA binding sites?

A (aminoacyl), P (peptidyl), E (exit) A (aminoacyl), P (peptidyl), E (exit), sites - tRNA binds here during different stages of polypeptide synthesis mRNA passes through the small subunit Ribosome translocates along the mRNA 5' to 3'

What are gene variants?

A gene variant is a permanent change in the DNA sequence that makes up a gene. This type of genetic change used to be known as a gene mutation, but because changes in DNA do not always cause disease, it is thought that gene variant is a more accurate term. Variants can affect one or more DNA building blocks (nucleotides) in a gene. Change of sequence is due to mutation called polymorphism

What is the relationship between a polypeptide and protein?

A protein can consist of one polypeptide Ex: insulin consists of one polypeptide A protein can consist of two or more polypeptides Ex: hemoglobin protein consists of four polypeptide subunits A protein can consist of polypeptide and a functional RNAs Ex: telomerase consists of polypeptide and snRNA

Describe the nomenclature of tRNA and a charged tRNA.

A tRNA becomes 'charged' when a high energy acyl bond connects it to its cognate amino acid Amino acid added to the 3' end of the tRNA -Uncharged tRNA example: tRNAphe -Charged tRNA example: phe-tRNAphe

What end of the mRNA is the polyA tail added to?

About 250 adenine nucleotides (ATPs) are added to the 3' end of the RNA by PolyA Polymerase -Called the polyA tail

Describe the mechanism of translocation.

Active transport/active movement of sugar (sucrose) at the source into phloem cells causes the water potential of phloem contents to become more negative. Therefore, water flows by osmosis from adjacent cells. This means the hydrostatic pressure in phloem increases which causes mass flow.

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

Define the function and major characteristics of origin replication

An origin of replication is a sequence of DNA at which replication is initiated on a chromosome, plasmid or virus. DNA replication is initiated at the origin of replication, a sequence of DNA found throughout the genome. An enzyme called helicase unzips the DNA double-strand at the origin of replication to form a separation in DNA, a structure known as the replication bubble.

In the recessive condition in humans known as sickle cell anemia, the β-globin polypeptide of hemoglobin is found to be mutated. The wild-type β-globin is a glutamate (glu) the sixth amino acid from the N-terminal, whereas the mutant β-globin has valine at this position. The codon sequence is differs by one base pair. Explain how this amino acid substitution occurred in terms of differences in the DNA and the mRNA.

Answer: Both GAA and GAG code for glutamic acid, while GUU, GUC, GUA, and GUG code for valine. There was an AT-to-TA change in the DNA causing the codon to be GUA or GUG and encode valine.

How is the anticodon related to the mRNA codon?

Anti codon loop contains 3 nucleotides complimentary to mRNA codons

What does it mean when we say dsDNA is antiparallel?

Antiparallel arrangement -Two strands have opposite directionality -Directionality is sometimes referred to as polarity -Like a two-lane highway

A gene normally found in euchromatin is transposed into the centromere. In what way(s) do you expect its expression level to change compared to its wild-type location?

At its wild-type locus, the packing is relatively open and accessible because the gene is in euchromatin. Therefore, gene expression is relatively high. After transposition, the gene expression will be silenced because the centromere is condensed into heterochromatin.

What kind of linkage connects the 5' cap to the mRNA?

Attached to mRNA by a 5'-5' linkage when mRNA is 20-30 nucleotides long

How do bacteria like E. coli package their DNA? a. Using proteins called histones b. By supercoiling the DNA c. By acetylating the DNA d. By methylating the DNA e. All of the above

B. By supercoiling the DNA Rationale Bacteria have to compact their DNA for it to fit inside the cell. Supercoiling, underwinding the DNA so that it folds up on itself, is a way that compacts the DNA yet still allows it to be accessible for transcription and replication. While bacterial DNA is modified (methylated, etc.), the modification does not play a direct role in packing the DNA. Histones are found in eukaryotes, but not E. coli. Proteins are associated with E. coli DNA but these proteins are not histones.

What activity provides D N A pol III the ability to proofread? a. DNA pol III has 5′→3′ exonuclease activity. b. DNA pol III has 3′→5′ exonuclease activity. c. DNA pol III has exonuclease activity in both the 5′→3′ and 3′→5′ directions. d. DNA pol III has polymerase activity in the 5′→3′ and 3′→5′ directions. e. The sliding clamp activity.

B. D N A pol III has 3′→5′ exonuclease activity. Rationale The ability to move "backward" over a newly synthesized strand and remove bases (exonuclease activity) that are mismatched is called proofreading. As D N A pol synthesizes D N A in the 5′→3′ direction, exonuclease activity in the 3′→5′ direction would allow proofreading, like a backspace key on a computer keyboard.

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 GTFs bind to DNA sequences called the core promoter just upstream of the transcription start site (TSS). Once bound, RNA polymerase is positioned at the TSS. This entire complex is called the pre-initiation complex (PIC).

The genetic code is _________, allowing for an amino to be coded by more than one codon. a. unambiguous b. degenerate c. commaless d. universal e. nonoverlapping

B. degenerate Rationale There is redundancy built into the genetic code in that the third base of two codons could differ, but they still indicate the same amino acid. These codons are said to be synonymous. Degeneracy in the code is NOT the same as wobble, although the two phenomena are related.

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 Rationale All known polymerases (both DNA and RNA polymerases) add nucleotides to the 3' end of the new strand. Therefore they have 5' to 3' polymerization activity. No known polymerase has 3' to 5' polymerization activity. DNA polymerases cannot initiate chain synthesis on their own; they need a primer. RNA polymerases do not need a primer. Only DNA polymerase I has 5' exonuclease activity to degrade the RNA primer for Okazaki fragment resolution.

What enzyme will replace the RNA primers found in the newly synthesized strand? a. DNA pol III b. DNA pol II c. DNA pol I d. Primase e. ligase

C. DNA pol I Rationale While D N A pol III performs the bulk of D N A synthesis, D N A pol I has the special 5′→3′ exonuclease activity which allows it to remove R N A primers.

Satellite DNA ____________. a. Is found outside of the nucleus b. Is a term used to describe very small chromosomes c. Is a form of repetitive DNA d. Is less subject to breakage than other chromosome regions e. Is only found in telomeres

C. Is a form of repetitive DNA Rationale Satellite DNA is composed of regions of short tandem nucleotide sequences repeated many times. Most satellite DNA consists of the centromere. It has a different G/C content than the rest of the genome, it has a slightly different density and migrates differently from the majority of the genome in a centrifugation tube. This creates "satellite" bands around the main DNA band.

Where does DNA polymerase I start its synthesis of DNA? (e.g. What is the 'primer' for DNA polymerase I?) a. RNA synthesized by primase b. DNA synthesized by primase c. Okazaki fragment d. It doesn't need a primer

C. Okazaki fragment Rationale DNA polymerase I is involved in Okazaki fragment resolution. It degrades the RNA primer ahead of it as it synthesizes new DNA, thus replacing the RNA primer. Primase synthesizes an RNA primer, which is used by DNA polymerase III. All known DNA polymerases require a primer, but RNA polymerases do not.

Is there any role for an RNA polymerase in DNA replication? a. No, only DNA polymerases function in DNA replication. b. Yes, in order to synthesize mRNA. c. Yes, to generate primers. d. Yes, to synthesize RNA that will bind to and keep the two DNA strands unwound. e. Yes, in eukaryotes an RNA polymerase functions in telomere maintenance.

C. Yes, to generate primers. Rationale Primase is a specialized R N A polymerase. It synthesizes short R N A primers from a D N A template that allow the formation of small, double-stranded D N A-R N A hybrid regions during replication. These regions permit the initiation of D N A replication by D N A polymerase.

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 Rationale The peptidyl transferase, the enzyme that joins two amino acids together in the ribosome, is a rRNA. Because it's an RNA that has catalytic activity, it is known as a ribozyme. There are many types of ribozymes (RNAs with catalytic activity) in nature.

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 Rationale The genetic material does not necessarily need to directly influence the development of traits. The central dogma states that DNA is transcribed to mRNA, which is translated to protein, thereby influencing traits. Because the system uses RNA and protein as its functional units, DNA does not directly influence traits.

Describe the centromere. What is its function?

Centromeres -tandemly repeated sequence -satellite DNA -Spindle fibers are attached during mitosis and meiosis -Important for disjunction of chromosomes -Not always in middle of chromosome -plays a key role in helping the cell divide up its DNA during division (mitosis and meiosis). -Specifically, it is the region where the cell's spindle fibers attach.

What is meant by aminoacylation?

Charging of tRNA also called aminoacylation Aminoacylation is catalyzed by an enzyme called tRNA synthetase -Each tRNA synthetase recognizes its cognate amino acid and tRNA -Example: leucyl-tRNA synthetase binds to leucine and tRNAleu but not other amino acids and tRNAs - those each have their own synthetases

What is chromatin?

Chromatin = DNA + associated protein in the nucleus Each chromosome exists as chromatin -Each chromosome is precisely positioned into its territory within the nucleus -How DNA is arranged and positioned plays a large role in gene expression regulation

What are codon usage bias and wobble?

Codon usage bias - the tendency for an organism to use a certain codon for an amino acid more than others -Advantageous for fast-growing organisms. Why? Wobble - Third base pairing between tRNA anticodon and codon doesn't follow complementary base pairing rules -More than one codon can be recognized by the same tRNA Advantageous. Why?

What did Franklin's results show?

Concluded that DNA 1. is helical 2. has distinct periodicities along the helix 3.4 nm = 360o turn 0.34 nm = space between bases About 10 base pairs per turn

What makes centromeres and telomeres constitutive heterochromatin?

Constitutive heterochromatin -Present in all cells at the same position on the chromosome -Typically repetitive DNA -Examples: centromeres and telomeres

What is an example of dispersed-repeated DNA?

Could be dispersed Examples: transposons, rRNA genes

What is meant by charging of the tRNA?

Covalent linkage of an amino acid to the appropriate tRNA molecule. attaching correct amino acids to specific tRNA according to genetic code

What differentiates type 1 versus type 2 of the Topoisomerase protein enzymes ?

Cuts DNA, introduce positive or negative twist in the DNA, then reseals the DNA Type I: nicks one strand Type II: nicks both strands

What is the name of the nucleotide that's incorporated into DNA?

Cytosine? DNA is made up of four building blocks called nucleotides: Pyrimidine: thymine (T) and cytosine (C) - One ring Purine: guanine (G) adenine (A) - two rings

In which direction does RNA polymerase move along the template strand during transcription? a. It moves along the coding strand not the template strand b. It reads both strands c. 5' to 3' d. 3' to 5'

D. 3' to 5' RNA polymerase moves along the template strand of DNA and assembles the ribonucleotides of the RNA according to complementary base pairing rules.

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. a. 5'-GCCATTCAT-3' b. 5'-ATGGGACAT-3' c. 5'-AGTTAACCG-3' d. 5'-CCGGGGCCA-3' e. 5'-ATTTACATT-3'

D. 5'-CCGGGGCCA-3' Rationale Because all the molecules are the same length, we just need to consider GC content. Since this answer has the highest GC content, then it has the highest melting temperature.

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 Introns make up the bulk of the phenylalanine hydroxylase gene in humans. After transcription, the introns are removed and the exons spliced together.

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 DNA polymerase before it detaches from the template e. the ability of DNA polymerase to move "backward" for proofreading.

D. the length of D N A that is replicated by DNA polymerase before it detaches from the template Rationale The sliding clamp allows for DNA polymerase to remain associated to the DNA template for longer than it normally should, thus increasing the processivity of DNA polymerase.

Human insulin can be made by E. coli containing the human gene that codes for insulin. This is an example of the code being a. unambiguous b. degenerate c. commaless d. universal e. nonoverlapping

D. universal Rationale The same genetic code is used in all organisms. In other words, a specific codon that codes for an amino acid on one species would code for that same amino acid in another species. The universality of the code is a tool used in genetic engineering of transgenic organisms (putting a gene from one species into another species).

What are the two types of nucleic acids?

DNA - deoxyribonucleic acid -no hydroxyl at 2' carbon RNA - ribonucleic acid -hydroxyl at 2' carbon -All known prokaryotes, eukaryotes, and a few viruses have dsDNA as the genetic material -Many viruses have RNA as their genetic material

What are telomeres?

DNA at the tips of chromosomes Reverse transcriptase -Synthesizes DNA from an RNA template -Human telomerase is called hTERT

How do fidelity and proofreading relate to exonuclease activity?

DNA polymerase (DNAP) is a type of enzyme that is responsible for forming new copies of DNA, in the form of nucleic acid molecules. -DNAP I and III have exonuclease activity -like a backspace key -DNAP removes incorrect 3' base, inserts correct base, and continues synthesizing It is estimated that proofreading improves the fidelity by a 2-3 orders of magnitude. The primer with the incorrect terminal nucleotide has to be moved to exonuclease active site, and after removal of the wrong nucleotide must be transferred back to polymerase active site.

State the central dogma of molecular biology.

DNA->RNA->protein DNA is transcribed into mRNA which is then translated into Protein.

Differentiate dispersed versus tandemly-repeated DNA sequences.

Dispersed repeats are segments of DNA that occur multiple times at more or less random positions in the genome. -They are typically transposable elements, large segments that encode a protein responsible for the moving of the segment from one site to another. Most tandem repeats are small segments of DNA repeated one after another. -Often heterochromatin -For example, the trinucleotide CAG repeated hundreds of times is responsible for active Huntington Disease in humans.

Identify the parts of a 10 nm fiber.

Double helix wound around histone core (H2A, H2B, H3,H4) to form a chain of nucleosomes known as the 20 nm fiber Beads on a string -dsDNA -Histone -writhe -nucleosome -linker DNA

What protein is functioning at the point marked with the large arrow? a. DNA ligase b. helicase c. gyrase d. DNA polymerase I e. DNA polymerase III

E. DNA polymerase III Rationale Replication is performed by D N A polymerases. This must be Pol III, as we see synthesis of both leading and lagging strands.

What is meant by a polycistronic versus a monocistronic RNA?

E. coli mRNA are polycistronic -One mRNA contains the sequence information from several genes -One mRNA encodes several proteins -Allows for tight regulation of protein synthesis for proteins that are in the same pathway Eukaryotes are monocistronic -one gene and one protein

Define euchromatin versus heterochromatin.

Euchromatin - open and accessible to the transcription machinery, therefore expressed Heterochromatin - Packed tight; closed and silenced

Different mutations in the same protein can cause different effects

Example: CFTR is mutated in cystic fibrosis

What makes a Barr body facultative heterochromatin?

Facultative heterochromatin -Can vary between cell type, developmental stage, or even between homologous chromosomes -Euchromatin becomes heterochromatin under certain conditions -Example: one of the two X chromosomes in XX mammals (wild-type genetic female) is deactivated to form a Barr body

Describe the structure of tRNA.

Folded into a cloverleaf structure Fits nicely into the ribosome sites Each has an anticodon 3 nt sequence that complementary base pairs with the mRNA codon

Define haploid versus diploid.

Haploid cells contain only one set of Chromosomes (n). Diploid, as the name indicates, contains two sets of chromosomes (2n). Haploid cells are formed by the process of meiosis. Diploid cells undergo mitosis.

Define euchromatin versus heterochromatin on a picture

Heterochromatin- tightly packed euchromatin- loosely packed

How is the 30 nm fiber formed?

Histone H1 condenses nucleosome of 10 nm fiber to form 30 nm fiber

What kind of proteins interact with DNA?

Histones (eukaryotes) -help pack DNA into chromatin -highly conserved Non histone proteins (prokaryotes) -various functions (replication, repair, transcription, recombination, etc.) -may or may not be highly conserved

Human genome vs individual genome

Human genome - wild type arrangement of genes (reference) individual genome- Considers specific alleles

ch 11: An alien organism was investigated. When DNA replication was studied, a unique feature was apparent: No Okazaki fragments were observed. Create a model of DNA that is consistent with this observation.

If the DNA contained parallel strands in the double helix and the polymerase would be able to accommodate such parallel strands, there would be continuous synthesis and no Okazaki fragments. Several other possibilities exist. If the DNA were replicated as single strands, the synthesis could begin at the free ends and there would be no need for Okazaki fragments.

How is PCR different from DNA replication in the cell?

In contrast to cellular DNA replication, which amplifies all of a cell's DNA during a replication cycle, PCR does targeted amplification to replicate only a segment of DNA bounded by the two primers that determine where DNA polymerase begins replication.

How is okazaki processing done in prokaryotes versus eukaryotes?

In prokaryotic cells -polymerase III is the major replicative polymerase, functioning in the synthesis both of the leading strand of DNA and of Okazaki fragments by the extension of RNA primers. -Polymerase I then removes RNA primers and fills the gaps between Okazaki fragments. -has 3' and 5' exonuclease activity -Gap closed by ligase In eukaryotic cells -polymerase δ fills the gaps between Okazaki fragments following primer removal. -has 3' exonuclease activity -displaces RNA primer to form a flap which is then cut off by Flap endonuclease -Gap closed by ligase

What is the role of the general transcription factors?

Initiation in eukaryotes

What is the difference between intrinsic and rho-dependent termination?

Intrinsic termination -Hairpin structure in RNA causes RNA polymerase to stall -RNA-DNA duplex dissociates due to a weak dissociation between the RNA and DNA Rho-dependent termination -Hairpin structure in RNA causes RNA polymerase to stall -Rho (helicase) unwinds the RNA-DNA duplex

Name a segment of a gene that is transcribed but not translated.

Intron, 5' UTR, 3' UTR

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? a.It will positively supercoil 2 twists. b. It will negatively supercoil 2 twists. c. It will stay in relaxed circle. d. Only short piece of D N A can supercoil. e. You cannot overwind D N A; it would break.

It will positively supercoil 2 twists. Rationale This question has you thinking about the shape of DNA; supercoiling can occur from either under- or over- winding the helix. However, if you underwind, you would induce twists in one direction ("negative"), but if you overwind, it would twist in the opposite direction ("positive"). While negative supercoils are most common, positive supercoils are sometimes observed during DNA replication or transcription.

How does chromatin packing contribute to the level of gene expression?

Less uniform, but still highly organized within the nucleus Packed tightly → closed → lower levels of transcription Packed loosely → open → higher levels of transcription

Name the satellite DNA that is often used as genetic markers. What can they be used for? What do their acronyms stand for?

Microsatellites or Single Sequence Repeats (SSRs) -are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. -widely used for DNA profiling, also known as "genetic fingerprinting", of crime stains (in forensics) and of tissues (in transplant patients). -They are also widely used in kinship analysis (most commonly in paternity testing).

Below is a segment of duplex DNA that is in frame and encodes part of a polypeptide: ...5' GGCTATCTGCTT 3'... ...3' CCGATAGACGAA 5'... What is the polypeptide sequence if the top strand is the coding strand?

N- gly - try - leu - leu - C

Human obesity is determined by a number of interacting genetic and environmental factors. Insights into how specific genes function to regulate body fat content have come from studies of mutant mice who display an obese phenotype. A comparison of the DNA sequence of the wild-type and mutant alleles has revealed a single base pair change between them. The mutation causes an alteration of the first base at the 5' end of the first intron, so that a G-C base pair has been mutated to a T-A base pair. A longer transcript is found in the mutant mice than in the wild-type mice. Why is a longer transcript found in the mutant mice?

Notice that the mutation is in the first base pair of the intron. It is a splice-site mutation, which disrupts splicing of the mRNA. Thus the resulting transcript is much longer than in the wild-type mouse.

Which is more likely to have repetitive DNA sequences?

Often heterochromatin -Repeated several to millions of times in the genome -Could be dispersed -Examples: transposons, rRNA genes -Could be tandemly repeated -Examples: satellite DNA of telomeres and centromeres

Define the function and major characteristics of okazaki fragment replication

Okazaki fragments are short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA. It is essential as it allows for the synthesis of both the daughter strands required for cell division.

Identify the 5' and 3' ends of DNA strands and of a nucleotide.

On DNA: Antiparallel arrangement -Two strands have opposite directionality -Directionality is sometimes referred to as polarity -Like a two-lane highway 5' to 3' on left strand 3' to 5' on right strand

ch 14: 14.1 In 1962, F. Chapeville and others reported an experiment in which they isolated radioactive They then removed the sulfur group from the cysteine, creating When was added to a synthetic mRNA calling for cysteine, but not alanine, a polypeptide chain was synthesized containing alanine. What can you conclude from this experiment? in picture full

One can conclude that the amino acid is not involved in recognition of the codon.

What is a polysome?

One mRNA is being translated by many ribosomes at any given time Both prokaryotes and eukaryotes

How is dNTP changed once its added to DNA?

Only one out of the three phosphates ends up in DNA

Be able to use the genetic code if given a DNA or mRNA sequence.

Open reading frame - the codons of an mRNA that are read sequentially to specify amino acids in the resulting polypeptide (includes start and stop codons) mRNA read 5' to 3'

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 EUKARYOTES -3 different types (classes) of RNA polymerase -Txn and tln are temporally and spatially separate -Monocistronic mRNA (one protein encoded in one mRNA) -mRNA is processed (capped, polyadenylated, and spliced) before being exported from the nucleus

What does the chromatin of an interphase cell look like versus a metaphase cell?

Packing along the chromosomes is less uniform during interphase

New sequencing technologies have been developed to quickly sequence entire genomes. Currently, it is possible to sequence an entire human genome for $1000 in a few hours. (We'll talk about how this sequencing is done later in the semester.) Still, the genome of the single-celled Ameoba proteus might present a challenge since it has nearly 100 times the C value of the human genome. If we sequenced its genome, do you expect we would identify about 100-fold more genes than the human genome? Why or why not? If not, what do you expect we would learn about its genome?

Paradoxically, there is no simple relationship between haploid DNA content of a cell and an organism's complexity. The genome of A. proteus is unlikely to have 100-fold more genes than have been found in the human genome. However, there is a general increase in gene number with complexity, so we expect humans to have more genes than does a single-celled organism such as an amoeba. Increases in genome size are driven more by repetitive DNA content than by gene number. Therefore, the amoeba genome likely has a great deal more repetitive DNA than does the human genome. If we sequenced its genome, we would discover what types of repetitive DNA sequences it has and how they were organized relative to location of genes.

What adds the polyA tail?

PolyA Polymerase

What is the purpose of the polyA tail?

PolyA tail is coated with protein Necessary for translation Protects 3' end of mRNA from 3' exonucleases that would otherwise degrade it

What is the difference between DNA polymerase III and I in terms of their activities during DNA replication?

Polymerase III adds nucleotides ONLY in the 5' to 3' direction -Sliding clamp holds polymerase on the DNA template -Polymerase III synthesizes from the RNA primer for both the leading and lagging strands -Adds dNTPs to the 3' end of the growing strand -Moves along the template strand in the 3' to 5' direction Polymerase I replaces the RNA primer with dNTPs using its polymerase activity -Digests primer ahead of it using its 5' to 3' exonuclease activity -DNA ligase seals the nick between adjacent fragments We'll draw this out together in class!

What is the difference between relaxed and supercoiled DNA?

Positive supercoiling - positive (more) twist is added "overwound" Found ahead of the transcription or replication bubbles and in thermophilic organisms Negative supercoiling - negative (less) twist is added "unwound" Most DNA in cells is negatively supercoiled

Most genes encode proteins. What exactly is a protein, structurally speaking? List some functions of proteins.

Possible answer A protein is composed of one or more polypeptides, each of which is composed of a folded, linear chain of amino acids. Proteins function in many different ways, including as enzymes to catalyze biochemical reactions, as structural molecules (cytoskeleton), as receptors (at a neuron's surface, for example, for neurotransmitters), as transporters (like the protein that transports sugars across a membrane), as ion channels, and regulatory molecules like transcription factors. All of these proteins are encoded in the organism's genome.

Why do you think codon usage bias and wobble are advantageous for a fast growing organism?

Possible answer Without these phenomena, the cell would need to make a different tRNA for each codon. For example, if all six of the synonymous leucine (leu) codons were used by a cell, it would need to make six different tRNAleu. Instead, the cells can save energy by making fewer types of tRNAleu.

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 Rationale Oligonucleotides are the primers added to a PCR. Oligonucleotides are single stranded DNA molecules of about 20 base pairs that act as the initiation site for Taq polymerase.

What are the major differences between prokaryotic and eukaryotic translation?

Prokaryotes Has ribosome binding sequence Happens cotranscriptionally Linear translation Eukaryotes Start codon near Kozak sequence Happens only after processing and transport from the nucleus is complete Closed-loop translation

Which bases belong in DNA versus RNA?

Pyrimidine: cytosine (C)-DNA , Uracil (U)-RNA

Be able to recognize the bases. Which bases are purines and which are pyrimidines?

Pyrimidine: thymine (T), cytosine (C)-DNA , Uracil (U)-RNA - One ring Purine: guanine (G) adenine (A) - two rings

What kinds of RNA do eukaryotic RNA polymerase I, II, and III transcribe?

RNA polymerase I - rRNA RNA polymerase II - mRNA and snRNA RNA polymerase III - tRNA Each are recruited to their genes by dedicated transcription factors

How does the snRNA of these subunits recognize the splice sites?

RNA subunits base pair with RNA sequences called splice sites within the intron

What kind of enzyme is telomerase?

RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template.

How are these properties related to code degeneracy?

Redundant/degenerate -more than one codon occurs for each amino acid -Third nt is often different -These codons are synonymous

What purpose does its snRNA serve?

Regulate gene expression and slice introns Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts.

Define the function and major characteristics of replication bubble

Replication bubble is a structure formed by the separation of two DNA strands by the helicase enzymes. The formation of a replication bubble leads to the formation of a replication fork which initiates replication.

Define the function and major characteristics of replication fork

Replication fork is a two line fork or prong-like structure that is formed in the replication bubble. the formation of a replication fork initiates replication.

How does a deoxyribonucleotide differ from a ribonucleotide?

Ribonucleotides contain only purines; deoxyribonucleotides contain only pyrimidines. Ribonucleotides have a hydroxyl group bonded to their 3' carbon; deoxyribonucleotides have an H at the same location. In ribonucleotides the sugar is a pentose; deoxyribonucleotides have a hexose.

Why are these structures noteworthy?

Secondary structure and protein interactions are important for -recognition of mRNA versus all of the other types of RNA in the cell -ncRNA (noncoding RNA) function

The sigma subunit of bacterial RNA polymerase _____. Circle all that are true. a. binds to a bacterial gene's promoter b. is composed of both polypeptide and RNA molecules c. is required for RNA polymerization d. is required for termination of transcription e. is required for ribosomal binding f. is part of the holoenzyme and not the core enzyme

Sigma does bind to the promoter, thereby recruiting RNA polymerase to the transcription start site of the gene. It is only composed of protein. It is not required for RNA polymerization. In fact, it dissociates from the core enzyme once elongation begins. It is also not required for termination. It participates in transcription, not translation, so it is not required for ribosome binding. The holoenzyme of E. coli RNA polymerase includes the core enzyme plus sigma. The RNA polymerase core enzyme consists of the the subunits REQUIRED for polymerization.

ch 12 26: At the end of the short arm of human chromosome 16 (16p), several genes associated with disease are present, including thalassemia and polycystic kidney disease. When that region of chromosome 16 was sequenced, gene-coding regions were found to be very close to the telomere-associated sequences. Could there be a possible link between the location of these genes and the presence of the telomere-associated sequences? What further information concerning the disease genes would be useful in your analysis?

Since both genes mentioned in the problem are near the telomeric heterochromatin, they may be subject to silencing due to the position effect. It is also possible that erosion of the end of the chromosome is related to each disease. Examination of the gene by in situ hybridization and molecular cloning indicates that thalassemia involves a terminal deletion in the distal portion of 16p.

What is spliced in the splicing of mRNA?

Splicing (removal) of introns

E coli modify their DNA, but does this contribute to packing?

Supercoiling allows for DNA to fit inside the cell

In prokaryotes, how does RNA polymerase find the TSS?

TSS= Transcription start site -Sigma (part of RNA polymerase holoenzyme) binds to promoter sequences -Positions RNA polymerase core enzyme on the DNA template strand at the transcription start site -RNA polymerase starts synthesizing RNA -Sigma dissociates from the core enzyme after transcription starts To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and begin transcribing.

Describe the activity of telomerase?

Telomerase adds telomere repeats -Because eukaryotic chromosomes are linear, they possess a "telomere problem," where one daughter helix (built with the 3′→5′ lagging strand) would be shortened after each round of replication by the length of the primer. -To prevent this shortening, the enzyme telomerase lengthens the 5′→3′ strand by reverse transcription, using a built-in RNA as template and guide. -Now this helix's length can be maintained in the usual manner by DNA replication.

How might the activity of telomerase be different in nondividing cells versus cancer cells?

Telomerase is active during development and in cells that continue to divide, such as stem cells. It is silenced in cells that have ceased to divide, such as terminally differentiated cells. If cancer is uncontrolled cell division, then telomerase activity would need to be turned back on in cancer cells, otherwise the cells would exhibit shortening of the chromosomes. One of the hallmarks of many cancers is the reactivation of telomerase, allowing the cells to proliferate when they shouldn't.

Where are telomeres located and what do they consist of?

Telomerase is made up of protein and snRNA (small-nuclear RNA) -snRNA is used as a template for DNA synthesis -Protein is an enzyme that synthesizes DNA against the snRNA according to complementary base pairing rules

Describe the telomere. What is its function?

Telomeres -Tandemly repeated DNA sequence -at the ends of linear chromosomes Ex: TTAGGGTTAGGGTTAGGG -number of repeats depends on spores + age (cell divisions) -short tandem repeats (STR) -Important for protection of chromosome ends -protect genome from nucleolytic degradation, unnecessary recombination, repair, and interchromosomal fusion. -Telomeres therefore play a vital role in preserving the information in our genome.

ch 10: 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 deoxynucleotides or nucleotides into the long polymers that function as informational molecules. A nucleic acid with a 3' H group would be unable to form phosphodiester bonds and thus would be unable to form polymers.

How many H bonds are between the complementary base pairs?

The Adenine - Thymine base pair is held together by 2 hydrogen bonds Guanine - Cytosine base pair is held together by 3 hydrogen bonds.

How do amino acid R groups contribute to protein structure?

The R groups along the polypeptide determine how it will fold and thus function -Each amino acid has unique features governed by its R group -Although some amino acids may look similar, small changes in the amino acid sequence (mutations in DNA) can have drastic effects on the protein structure and phenotype

What is melting temperature and how is it calculated? Be able to use the 2+4 Rule of Thumb.

The Tm 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 Rationale The Tm of dsDNA is the temperature at which half of the dsDNA in a sample is denatured (melted) to form ssDNA. The melting of DNA involves breaking the hydrogen bonds holding the base pairs of DNA together. The more hydrogen bonds present between the two strands, the more heat energy required to break those bonds. Because there are three hydrogen bonds between Gs and Cs (versus two for As and Ts), a sequence with a higher GC content would require more heat to melt it compared to a sequence with higher AT content. Also, longer dsDNA molecules have more hydrogen bonds than relatively shorter dsDNA molecules. - 2(A+T) + 4(G+C)

What is meant by polypeptide Quaternary structure?

The aggregate of polypeptide chains that make up a multi subunit protein. Shown is hemoglobin, which consist of two a polypeptide chains, two B polypeptide chains, and four heme groups

Define C-value.

The amount of haploid DNA in base pairs in an organism

Where is the base and phosphate attached to the ribose ?

The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position.

If the template strand of DNA is involved in transcription and the coding strand is not, then why is the coding strand called the coding strand?

The coding strand (also known as the sense strand) encodes the protein product. The template strand (also known as the antisense strand) is the template for RNA polymerase to use.

What is meant by polypeptide Secondary structure?

The folding and twisting of a single polypeptide chain into a variety chain (a- helix)

ch 10: Describe the various characteristics of the Watson-Crick double-helix model for DNA.

The following are characteristics of the Watson-Crick double-helix model for DNA: There are two polynucleotide chains, each formed by phosphodiester linkages between the five-carbon sugars and the phosphates. Bases are stacked 0.34 nm (3.4 angstroms) apart and in a plectonic, antiparallel manner. There is one complete turn for each 3.4 nm, which constitutes 10 bases per turn. Hydrogen bonds hold the two polynucleotide chains together. There are two hydrogen bonds forming the A-T pair and three forming the G-C pair. The double helix exists as a twisted structure, approximately 20 angstroms in diameter, with a topography of major and minor grooves. The hydrophobic bases are located in the center of the molecule; the hydrophilic phosphodiester backbone is on the outside.

What does H1 do in the nucleosome?

The linker histone H1 binds to the entry/exit sites of DNA on the surface of the nucleosomal core particle and completes the nucleosome. It influences the nucleosomal repeat length and is required to stabilize higher-order chromatin structures.

What happens when one R group is switched out for another R group, as would happen in mutation?

The new amino acid would not form the same interactions with hydrophobic vs hydrophilic R groups, and the protein's shape would likely be affected.

What overall charge does the phosphate give DNA?

The phosphate group gives DNA (and RNA) a net negative charge and is the reason DNA is a nucleic acid

What does it mean that the helix is right-handed?

The right handed DNA helix is β conformation. If a clockwise screwing motion moves the helix away from the observer, then it is called a right-handed helix; if anticlockwise and towards the observer, then it is a left-handed helix.

What is meant by polypeptide primary structure?

The sequence of amino acids dictates a protein's structure (STRUCTURE=FUNCTION) The sequence of amino acids in a polypeptide chain

Autosomal dominant dyskeratosis congenita is a multisystemic disorder resulting from defective telomeres. Clinical features are variable and include bone marrow failure, pulmonary and liver fibrosis (high amounts of scar tissue, such as collagen fibers), and premature graying of the hair. Several genes have been associated with the disorder. Why would a loss-of-function mutation in the gene encoding an snRNA (small nuclear RNA) cause dyskeratosis congenita? How might one loss-of-function mutant allele cause the disease, making it a dominant disorder?

The small-nuclear RNA component of hTERT is used as a template for reverse transcription. A portion of the snRNA base pairs with a repeat, then the enzyme adds DNA nucleotides using complementary base pairing rules against the remaining portion of the snRNA. If the snRNA cannot base pair, the process of extending the telomeres cannot be initiated, causing progressive shortening of the telomeres and cell death. If an individual with the disease has one mutant and one wild-type allele, then they likely are making half the amount of wild-type gene product and so although the can add some telomere repeats, the process is impaired in the heterozygous affected individual, making it a dominant disorder. Because of the important function of hTERT, have two loss-of-function mutant alleles (and therefore no wild-type gene product) would likely be lethal.

What is meant by polypeptide Tertiary structure?

The specific three dimensional folding of a polypeptide chain Shown is the B polypeptide chain of hemoglobin

ch 10: 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?

The structure of deoxyadenylic acid is given below and in the text. Linkages among the three components require the removal of water

ch 14: 14.3 HbS results from the substitution of valine for glutamic acid at the number 6 position in the B chain of human hemoglobin. HbC is the result of a change at the same position in the B chain, but in this case lysine replaces glutamic acid. Return to the genetic code table (Figure 13.7) and determine whether single-nucleotide changes can account for these mutations. Then view Figure 14.16 and examine the R groups in the amino acids glutamic acid, valine, and lysine. Describe the chemical differences between the three amino acids. Predict how the changes might alter the structure of the molecule and lead to altered hemoglobin function.

There are two codons for glutamic acid: GAA and GAG. With two of the codons for valine being GUA and GUG, a single base change from glutamic acid's GAA or GAG could cause the Glu--> Val switch. Likewise, single base changes to lysine's AAA or AAG could also cause a Glu--> Val switch. The normal glutamic acid is a negatively charged amino acid, whereas valine carries no net charge and lysine is positively charged. Given these significant charge changes, one would predict some, if not considerable, influence on protein structure and function. Such changes could stem from internal changes in folding (tertiary and/or quaternary structure) or from interactions with other molecules in the RBC, especially other hemoglobin molecules.

What would happen if the splice sites are mutated?

This change can disrupt RNA splicing resulting in the loss of exons or the inclusion of introns and an altered protein-coding sequence.

ch 10: List three main differences between DNA and RNA.

Three main differences between RNA and DNA are the following: (1) Uracil in RNA replaces thymine in DNA. (2) Ribose in RNA replaces deoxyribose in DNA. (3) RNA often occurs as both single-stranded and partially double-stranded forms, whereas DNA most often occurs in a double-stranded form.

What family of enzymes controls supercoiling?

Topoisomerase's -Highly conserved family of proteins -Cuts DNA, introduce positive or negative twist in the DNA, then reseals the DNA

What are the properties of the genetic code?

Triplet code - each mRNA codon consists of 3 nucleotides Continuous - the mRNA is read 3 nts at a time without skipping any Nonoverlapping- the mRNA is read in successive groups of 3 nts Universal - all known organisms (even E.T.) have the same genetic language -Ex: Round-up resistant plants, human insulin production in bacteria Redundant/degenerate -more than one codon occurs for each amino acid -Third nt is often different -These codons are synonymous Unambiguous - One codon specifies only one amino acid Has a start and stop signal - Call for the beginning and end of translation -AUG = methionine (met) -UAG, UAA, UGA = stop = nonsense (versus a sense codon)

Following replication, two DNA plasmids are catenated. Which type of topoisomerase would free the two molecules from each other?

Type 2

In an interphase eukaryotic cell's nucleus, two chromosomes are being positioned into their territories. One chromosome needs to pass through the other. What type of topoisomerase is involved in this process?

Type 2

ch 11. Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. b. In the intact RNA primer, which nucleotide has a free terminus? 3′.......GGCTACCTGGATTCA....5′

U

What is the subunit of RNA?

Uracil* (I think)

Three models of how DNA was replicated

Watson and Crick's model of DNA allowed for replication, and thus transfer of genetic information There were 3 models of how DNA was replicated Conservative - two strands either remain together or pair again after replication Semiconservative - after replication, each product contains one parental strand and one nascent strand Dispersive - parental strands are cleaved into dsDNA segments and reassembled with interspersed nascent segments

Can one gene mutation can change a protein's function, changing phenotype

Yes Example: the β subunit of hemoglobin protein is mutated in sickle cell disease

Replication is bidirectional. Does that mean each fork has both a leading and lagging strand?

Yes because DNA replication is semi- discontinuous

Is a 5' exonuclease ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

a

The sliding clamp is...

a circle that holds DNA polymerase in place during strand extension -Increases processivity

What are the three major groups of a nucleotide?

a nitrogenous base, a pentose, and one or more phosphate groups. The nitrogenous bases are derivatives of two parent heterocyclic compounds, purine and pyrimidine.

What is a protein subunit?

a polypeptide chain or single protein molecule that assembles with others to form a protein complex. Large assemblies of proteins such as viruses often use a small number of types of protein subunits as building blocks.

Is a 3' exonuclease ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

a,b

Is a 5' to 3' polymerase ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

a,b,c

DNA polymerase _____ has 5' to 3' and 3' to 5' exonuclease activity. a. I b. III

a. I DNA polymerase I has both of these activities. It uses its 5' exonuclease activity to degrade the RNA primer during Okazaki processing and its 3' exonuclease activity to fix its mistakes.

What enzyme performs this reaction?

aminoacetyl tRNA synthetase

What molecule is the peptidyl transferase and where is it located?

an aminoacyltransferase as well as the primary enzymatic function of the ribosome, which forms peptide bonds between adjacent amino acids using tRNAs during the translation process of protein biosynthesis. Large ribosomal subunit

13.3 The following represent deoxyribonucleotide sequences in the template strand of DNA: a. For each strand, determine the mRNA sequence that would be derived from transcription. b. Using Figure 13.7, determine the amino acid sequence that is encoded by these mRNAs. c. For sequence 1, what is the sequence of the coding DNA strand?

answer on next

ch 14: Many antibiotics are effective as drugs to fight off bacterial infections because they inhibit protein synthesis in bacterial cells. Using the information provided in the following table that highlights several antibiotics and their mode of action, discuss which phase of translation is inhibited: initiation, elongation, or termination. What other components of the translational machinery could be targeted to inhibit bacterial protein synthesis?

answer on next

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. a. Its genetic material is DNA b. Its genetic material is RNA c. Its genetic material is double stranded d. Its genetic material is single stranded

b. Its genetic material is RNA d. Its genetic material is single stranded Rationale The nucleic acid sequence contains uracil, therefore its RNA. The ratio of the bases is different from 1.0 and therefore the sequence is single stranded. Many viruses have ssRNA genomes.

Identify the major and minor grooves. Why do proteins tend to interact with the major groove?

because it exposes more functional groups that identify a base pair.

Why do they result in many polypeptides being produced from one mRNA molecule?

before the formation of a polypeptide is completed by one ribosome, another ribosome binds to the recognition sequence and then starts with translation again. Thus, more than one polypeptide formation occurs together from a single mRNA strand.

Synthesizes RNA ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

c

This photomicrograph is most likely of... a. bacterial DNA b. 30nm fiber c. 10 nm fiber d. mitochondrial DNA

c. 10 nm fiber Rationale The "beads on a string" appearance is characteristic of histone association with the DNA and the 10nm fiber. As histone complexes are only present in the eukaryotic nucleus, this image must be from a eukaryote. Like bacteria, mitochondria do not have histones.

Name a segment of a transcript that is neither transcribed nor translated.

cap, ponAtail

What complex catalyzes splicing?

catalyzed by the spliceosome, a large RNA-protein complex composed of five small nuclear ribonucleoproteins (snRNPs).

How is PCR similar to DNA replication in the cell?

cells replicate their DNA before they divide, and in doing so, double the amount of the cell's DNA. PCR essentially mimics cellular DNA replication in the test tube by repeatedly copying the target DNA over and over, to produce large quantities of the desired DNA.

Any two nucleic acid fragments will spontaneously hybridize if they encounter each other as long as they are ________________ and ________________.

complementary and antiparallel.

Relieves supercoiling ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

d

What is dNTP?

deoxynucleotide triphosphate

Prevents reassociation of the complementary base pairs ______ a. DNA polymerase I b. DNA polymerase III c. Primase d. Topoisomerase e. Single stranded binding protein f. None of these

e

Telomerase _____. a. contains its own RNA template b. is a reverse transcriptase c. extends one strand of the telomere d. is responsible for helping to maintain chromosome size e. all of the above

e. all of the above Rationale Because eukaryotic chromosomes are linear, they possess a "telomere problem," where one daughter helix (built with the 3′→5′ lagging strand) would be shortened after each round of replication by the length of the primer. To prevent this shortening, the enzyme telomerase lengthens the 5′→3′ strand by reverse transcription, using a built-in RNA as template and guide. Now this helix's length can be maintained in the usual manner by DNA replication.

Which is more likely to have higher gene expression? Why?

euchromatin the nucleosomes in euchromatin are much more widely spaced, which allows for easier access of different protein complexes to the DNA strand and thus increased gene transcription.

Name a segment of a gene that is transcribed and translated.

exons

What is the difference between an exonuclease versus an endonuclease?

exonuclease - enzyme that cuts phosphodiester bond within a nucleic acid sequence - in the middle endonuclease - enzyme that cuts off the last nucleotide of a nucleic acid - at the end - can be 5' or 3' depending on which end it cuts

Where is the glycosidic bond?

glycosidic bond exists in the DNA molecule between sugar and nitrogen base. The glycosidic bond is formed by the nitrogen-carbon linkage between the 9' nitrogen of purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the sugar group. Sugar present in DNA is deoxyribose.

What is processivity with respect to replication?

how many base pairs polymerase adds before it falls off -Sliding clamp increases its processivity

Considering the structure of double-stranded DNA, _______________ bonds hold one complementary strand to the other.

hydrogen bonds

What are some other differences between prokaryotic and eukaryotic replication?

image

What is the C-value paradox?

increased C-value does not mean increased complexity ex: Ameba- 290 billion base pairs of dna Humans- 3 billion base pairs of dna Humans are still more complex

Define the function and major characteristics of bidirectional replication

involves replicating DNA in two directions at the same time which results in a leading strand and a lagging strand. In linear DNA replication, bidirectional replication is more efficient as it not only goes in both directions (two replication forks --> replication bubble) instead of just one, but you also have multiple replication bubbles throughout the DNA that will merge together, speeding up the process.

What is fidelity?

its accuracy in adding base pairs -how many times polymerase incorporates the wrong (noncomplementary) base -Its proofreading activity increases its fidelity

What does the phosphodiester bond do?

joins 3' carbon of one nucleotide to 5' carbon of another nucleotide, use free carbon on end to define polarity of strand and is usually written as 5'-3'

What molecules are involved in translation?

mRNA, charged (aminoacylated) tRNA, rRNA (small+big subunits), tRNA synthetase, riboenzyme

What are slicesomes made of?

made of subunits consisting of both RNA and protein

Describe the structure of the ribosome.

made out of RNA and proteins, and each ribosome consists of two separate RNA-protein complexes, known as the small and large subunits. The large subunit sits on top of the small subunit, with an RNA template sandwiched between the two.

The anticodon for this tRNA indicates the amino acid phenylanine What would be the name of this molecule if it was mischarged with methionine (met)?

met- tRNA ^phe

What other gene products exist besides protein?

noncoding RNA

How many molecules of DNA make up one chromosome?

one single very long, linear DNA molecule.

How many of these phosphate groups actually end up in DNA?

only one phosphate is incorporated into a strand of DNA. - Deoxynucleoside diphosphate (dNDP)

The anticodon for this tRNA indicates the amino acid phenylanine What's the name of the charged form of this tRNA?

phe- tRNA ^phe

The anticodon for this tRNA indicates the amino acid phenylanine What protein has aminoacylated this tRNA?

phenylalanyl- tRNA synthelase

What goes into the PCR tube?

primers, free nucleotides, and an enzyme called DNA polymerase

Which strand does RNA polymerase 'read' and in what direction?

reads the template DNA strand in the 3' to 5' direction.

What are the subunits of this complex called?

snRNP small nuclear ribonucleoproteins

Genomics

study of whole genomes, including genes and their functions -Coding and noncoding sequence in individuals DNA -Sequencing of RNA/DNA -Comparison of genome sequences in the same or different species Genomics includes the scientific study of complex diseases such as heart disease, asthma, diabetes, and cancer because these diseases are typically caused more by a combination of genetic and environmental factors than by individual genes.

In what direction does RNA polymerase synthesize the transcript?

synthesizes the RNA strand in the 5' to 3' direction,

The anticodon for this tRNA indicates the amino acid phenylanine What's the name of the uncharged form of this tRNA?

tRNA ^phe

Name a gene or gene product that is transcribed but not translated.

tRNA, rRNA, snRNA

What is the difference between the core and holoenzyme?

the core is enzymes lacking the sigma factor, the holoenzyme is enzymes comprising the sigma factor.

Define the function and major characteristics of semi-discontinuous replication

the leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously by the formation of Okazaki fragments.

What is the difference between the coding strand and template strand?

the mRNA is complementary to the template (or antisense) strand and an exact copy of the coding (or sense) strand, except thymines are replaced with uracils. The coding strand determines the correct nucleotide sequence of mRNA. The template strand acts as a base for mRNA transcription.

What is proofreading?

the removal of non-complementary nucleotides incorporated during DNA replication -Incorporation of about 1 base in every 1 million bases is incorrect -source of spontaneous mutation -DNAP I and III have exonuclease activity -like a backspace key -DNAP removes incorrect 3' base, inserts correct base, and continues synthesizing

Transmission genetics (Mendelian genetics) and example

the study of how traits are passed from parent to offspring Ex: autosomal dominant or autosomal recessive x-linked dominant or X-linked recessive

Molecular genetics and example

the study of the structure and function of chromosomes and genes. -How does gene expression work? - What are the effects of mutation? ex. only one single amino acid difference between haemoglobin chains of chimps and humans -The different techniques employed in molecular genetics include amplification, polymerase chain reaction, DNA cloning, DNA isolation, mRNA isolation

Define the function and major characteristics of semi-conservative replication

the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. -This results in two DNA molecules with one original strand and one new strand. -beneficial to DNA repair. -During replication, the new strand of DNA adjusts to the modifications made on the template strand.

What does it mean when we say histones are highly conserved?

there are very few differences among the amino acid sequences of the histone proteins of different species. -essentially remains unchanged

How many phosphate groups does it have?

three Adenine nucleotides have the typical structure of nucleotides including the purine base adenine attached to a five-carbon sugar and one to three phosphate groups.

True or false? DNA polymerase δ has exonuclease activity.

true- has proofreading ability

The genetic code is _________, meaning that one codon indicates only one amino acid. a. unambiguous b. degenerate c. commaless d. universal e. nonoverlapping

unambiguous Rationale Each codon only appears once the genetic code. Each codon only indicates one amino acid.

Is the phosphodiester backbone (sugar-phosphate backbone) covalently bonded?

yes

What are the three major steps of PCR that allows for amplification of a DNA sequence of interest?

(1) denaturation of the template into single strands (2) annealing of primers to each original strand for new strand synthesis (3) extension of the new DNA strands from the primers.

ch 13: Recent observations indicate that alternative splicing is a common way for eukaryotes to expand their repertoire of gene functions. Studies indicate that approximately 50 percent of human genes exhibit alternative splicing and approximately 15 percent of disease-causing mutations involve aberrant alternative splicing. Different tissues show remarkably different frequencies of alternative splicing, with the brain accounting for approximately 18 percent of such events a. Define alternative splicing and speculate on the evolutionary strategy alternative splicing offers to organisms. b. Why might some tissues engage in more alternative splicing than others?

(a,b) Alternative splicing occurs when pre-mRNAs are spliced in more than one way to yield various combinations of exons in the final mRNA product. Upon translation of a group of alternatively spliced mRNAs, a series of related proteins, called isoforms, are produced. It is likely that alternative splicing provided an evolutionary advantage since a variety of functionally related proteins from one original source gene can be made in a particular tissue. In other words, varieties of similar proteins can be produced by alternative splicing rather than by independent evolution.

What is the purpose of DNA?

- The molecule inside cells that contains the genetic information responsible for the development and function of an organism. DNA molecules allow this information to be passed from one generation to the next.

What is a karyotype?

- an individual's complete set of chromosomes. The term also refers to a laboratory-produced image of a person's chromosomes isolated from an individual cell and arranged in numerical order. A karyotype may be used to look for abnormalities in chromosome number or structure.

How are RNA molecules able to take on so many different structures?

-Ability to base pair allows for sequence-dependent secondary structures, including helical structures -RNA helix properties are different than DNA helix -Bases can be modified -Coated with associated protein

Where is DNA in E. coli found?

-Chromosome and may contain plasmids -Found in the nucleoid (no nucleus) -Horizontal gene transfer - bacteria can acquire genetic material from the environment (versus a parent cell) -example: antibiotic resistance gene material such as plasmids

Describe the organization of DNA in E. coli. (prokaryotes)

-Double stranded (dsDNA) -Circular -permeabilized plasma membrane (holes poked in it)

Apply Chargaff's rule.

-Erwin Chargaff used spectrophotometry to measure the amounts of different bases in the DNA from different species -A:T and G:C always was ~1, even though the amounts of total AT and total GC could differ among species 30% pyrimidine and 70% purine

What makes up the PIC?

-GTFs recruit RNA polymerase to form the preinitiation complex (PIC) -RNAP cannot locate a gene on its own -Recruitment of polymerase by GTFs is increased by activators bound to enhancer sequences

What do general transcription factors bind to?

-General transcription factors bind to the core promoter -GTFs are named according to the polymerase with which they interact -Ex: TFIIA

What is the chromosomal theory of inheritance?

-Genes for phenotypic traits are carried on chromosome. aka: Genes are carried from parents to offspring on chromosomes

Where is DNA found in eukaryotes?

-Linear chromosomes found in nucleus -Circular chromosomes found in mitochondria and chloroplasts -Wound around histones (negatively supercoiled)