Biology 192 Unit 1

You have a drug that blocks the activity of ligase. Describe what effect this drug would have on replication of the leading strand.

"No effect." (there would be an effect because the topoisomerase will unwind the strand and it will eventually need to be glued by the ligase

What is 'proofreading' in the context of DNA replication? Why is this important?

DNA polymerase has the ability to review its work to ensure proper complementary bases were added and repair damage caused by radiation and toxins.

What would happen to transcription if the enzyme helicase was not present?

DNA replication/transcription could not occur. Cells would stop dividing and many other important biological processes would come to a halt.

What is DNA and what is a genome?

Deoxyribonucleic acid; a genome is the complete set of DNA that makes up a cell or organism.

10 Features of specific features of the structure of DNA.

Double stranded, each strand is made up of repeating nucleotide subunit; nucleotides contain a phosphate group, sugar, and base; strands oriented anti-parallel; double helix structure; complementary base pair rules: purine pairs with pyrimidine; Adenine (purine) pairs with Thymine (pyrimidine), Guanine (purine) with Cytosine (pyrimidine); A and T have 2 hydrogen bonds, while G and C have 3 hydrogen bonds.

How does the sequence of nucleotides in mRNA code for the sequence of amino acids in a protein? Why is the RNA code for the amino acids called a 'triplet code'?

Each configuration of 3 nucleotides (codons) results in a particular anticodon with an amino acid. Excluding the three terminator codons UGA, UAA, and UAG. They are called triplets because the tRNA reads them in a frame of three at a time.

What are two ways in which a eukaryotic cell uses to speed up DNA Replication?

Enzymes can work on both strands at once and there are many origins of replication, antiparallel.

True or False: At the end of DNA Replication, there are 2 identical strands of DNA.

False: Should be 2 identical DNA molecules.

True or False: The Origin of Replication only occurs twice on the DNA molecule, one on each strand.

False: Should be Origin of Replication occurs many times.

True or False: Topoisomerase prevents reannealing of DNA during replication

False: Topoisomerase unwinds DNA.

Where does the cell get amino acids?

Food eaten, old proteins recycled, cell can manufacture non-essential amino acids. Essential amino acids need to come from our food.

What insights into DNA structure did Watson and Crick derive from the findings of Chargaff and of Franklin?

Franklin determined that the sugar-phosphate backbone was on the outside of the helix, forcing the bases to be on the inside, DNA = 2nm. Chargaff determined that the A%=T% and G%=C%.

Why is gene regulation generally important to cells?

Gene regulation helps organisms respond to environmental changes.

What are the 3 major functions of DNA in the cell?

Genetic instructions for making more DNA, instructions for making proteins, information passed from parent to offspring.

How can a mutation in DNA lead to a genetic disease?

If the DNA is mutated then the RNA and the subsequent protein will all be mutated. Any DNA replicated will also have this mutation.

What happens if a particular step of transcription is prevented/stopped? What are the effects on the cell? The body?

If you stop at initiation no pre-mRNA will be created. If you stop at elongation, the pre-mRNA may be truncated or wrongly transcribed. If you stop at termination then elongation will continue until the strand just falls off and it will probably have excess nucleotides. If the process stops at any point before termination, the protein will not be created.

Where in the cell does DNA transcription occur? What are the key stages of the process? What happens at each stage?

In the nucleus. Initiation begins when the RNA polymerase binds to the promoter site. The DNA is unwinded, the hydrogen bonds are taken apart and RNA polymerase starts to lay free RNA nucleotides from 5' to 3'. Then, during elongation, the polymerase continues to synthesize the RNA strand by momentarily hydrogen bonding to the DNA to add nucleotides and then break that bond to let the RNA sequence go. Once the RNA polymerase reaches the terminator sequence, the polymerase will detach from the DNA and release the pre-mRNA.

What are the two main causes of mutation in cells?

Spontaneous or introduced by a mutagen that is a physical agent or chemical agent.

How serious are the consequences of each of these types of mutations to the affected protein? To the cell/ organism?

Substitution mutations: no effect to some effect in protein confirmation to protein truncation or prevention of protein synthesis altogether. Silent mutation: no change Missense: change in nucleotide added to to sequence Nonsense: change leads to premature stop codon and truncation Insertion and deletion mutations: severe effect on reading frame (if the shift is less than or more than a multiple of three), function in the cell and organism. Frameshift mutation: Only if the insertion or deletion is less than or more than a multiple of three. Nonfunctional polypeptide.

Translation: Role of hydrogen bonding

Temporarily keep the tRNA's anticodon bound to the mRNA's codon sequence. This gives time for the ribosome to form a peptide bond between the amino acids in the P and A sites.

You have a drug that blocks the activity of helicase. What would be the effect of this?

The DNA could not be replicated because the h-bonds between the two strands would not open enough for replication to occur.

The "leading strand" terminology refers to the fact that this strand is the first daughter DNA strand to be completed from a given replication fork. Explain why the leading strand is completed before the lagging strand.

The DNA polymerase leading moves toward the fork in the 3' to 5' direction, so the lagging strand must also move 3' to 5'. The lagging parent strand is antiparallel to the leading strand so the synthesis is completed in sections called Okazaki fragments and then "glued" together by ligase. DNA polymerase can already complete synthesis and covalent bonding for the leading strand faster.

You have a mutant DNA polymerase that is partially defective. In vitro experiments using the mutant DNA polymerase gives an error rate of 10-3, as compared to the expected error rate of 10-6 . What activity/function is the mutant polymerase likely to be missing, as compared to the normal DNA polymerase?

The DNA polymerase may be missing the proofreading function.

Why does replication of the two strands go in opposite directions?

The DNA polymerase must read the strand 3' to 5' and lay nucleotides 5' to 3' and the molecule is anti-parallel.

Why is DNA replication said to be semi-conservative? What is the value of this to the cell?

The finished molecule has one parent strand and one is the daughter strand. This is beneficial for error repair.

Be able to describe the Central Dogma of Biology and its relevance in understanding human disease and disorders.

The flow of genetic information from DNA to RNA. Genetic mutation can result in cancer. If there is an issue with DNA there may or may not be an issue with the protein because the other steps are flexible (wobble nucleotides in codons). We can use drugs to inactivate bacterial components (ex. ribosomes) so the process will halt. This helps you to fight infection. If genetic information is passed from DNA to RNA then you can always regulate the process.

Once the cell has produced a new RNA molecule, what does it do with it? What is the importance of this step?

The new RNA molecule goes through post-transcription modifications. A ponytail is added to the 3' side and a 5' cap to the other side. Introns are spliced out of the RNA molecule. This step ensures that the protein is prepared for translation. 5' cap acts as a beacon for the ribosome and guides the strand out of the nucleus. The 5' cap and 3' cap protect the RNA from proteins in the cytoplasm that will degrade the sequence.

What would happen if the terminator sequence was mutated?

The process would be stuck in elongation and the RNA strand would continue to grow until finding another terminator sequence in the DNA. The protein would not work correctly.

Why are the changes in the 3rd position less serious than changes in the 1st or 2nd positions?

The reading frame is not changed for the codons.

Why does the DNA double helix have a uniform diameter?

The rules of complementary base pairing require the purines to pair with pyrimidines. Pyrimidines have 1 section while purines have 2 so every nucleotide h-bond contains 3 sections.

What is complementary base pairing? What are the "rules" of complementary base pairing? What is complementary base pairing an important feature in the cell?

The rules that govern the pairing of the nucleotide bases. Adenine always goes with Thymine. Guanine and Cytosine always go together. Complementary base pairing is important because it ensures that the cell makes two identical copies of DNA during replication. It also ensures that RNA molecules carry accurate instructions for making proteins; the DNA strands are bonded by hydrogen bonds, while the backbone is covalently bonded.

What would happen if the 5' cap was not added in regards to the function of the protein?

The strand could not navigate out of the nucleus and no protein would be made.

How many different kinds of monomers are there in DNA? How do they differ from one another? How are they alike?

There are four types of nucleotides: adenine, cytosine, thymine, and guanine. The difference is the type of nitrogenous base, between RNA and DNA.

What main factors allow DNA replication to occur so quickly?

There are many origins of replication and both strands are replicated simultaneously.

You have a drug that blocks the activity of ligase. Describe what effect this drug would have on replication of the lagging strand.

There will be no "glue" to join the Okazaki fragments. DNA will still be unwound by Topoisomerase.

What enzymes are involved? What is the role/contribute of each?

Topoisomerase unwinds the strands, helices breaks the hydrogen bonds, DNA polymerase adds free nucleotides to the original strand and bonds them together covalently, Ligase bonds the Okazaki fragments of the lagging strand covalently.

What would happen to transcription if DNA polymerase was not present?

Transcription would occur like normal.

True or False: DNA polymerase forms a covalent bond between a phosphate group and a hydroxyl group.

True

True or False: DNA polymerase moves along the template strand in the 3' to 5' direction.

True

True or False: Shortly after DNA replication has begun, you find two replication forks moving in opposite directions away from the Origin of Replication.

True

True or False: Synthesis of DNA for both the lagging and the leading strands is in the 5' to 3' direction.

True

How is DNA replicated in a cell?

Two strand of parental DNA separate and each strand becomes a template for the assembly of a complementary strand.

stop codons are

U Are Annoying (UAA), U Are Gross (UAG), U Go Away (UGA)

DNA Replication: Role of hydrogen bonding

Weak hydrogen bonds allow for the DNA strands to separate, also keep parent and daughter strand together.

DNA Replication: When it happens

When an organism/ body needs more cells

Translation: When it happens:

When mRNA is exported into the cytoplasm, signals on mRNA tell nearby ribosomes to translate mRNA into protein

What are the effects of Tay Sachs disease?

Insertion in HEXA gene results in a premature stop codon and a subsequent truncation of the polypeptide chain. The protein formed is nonfunctional and the lysosomes of the cells cannot remove waste from the cell. Lipids accumulate in the brain and fat builds, swelling the brain and strangling critical brain cells. Degeneration of neurons in the brain and spinal cord.

What are some advantages to DNA replication?

It ensures all the cells in a multicellular organism carry the same genetic information and have the genetic instructions for gamete development.

What major types of RNA are produced in cells? How do they differ in processing, final location, function, and whether or not they are a final or intermediary gene product?

mRNA is intermediary gene product, formed in the nucleus, transcribed from DNA to carry the genetic information to the cytoplasm for translation. tRNA is a final gene product, formed in the nucleus upon post-transcription modifications, reads mRNA and converts the info to amino acids. rRNA is a final gene product, formed in the nucleolus after combining with ribosomal proteins.

What is the repeating subunit (monomer) of DNA? What is the structure of this subunit?

nucleotide: phosphate group, deoxyribose sugar, nitrogenous base.

DNA Replication: Where it happens

nucleus

Where in a eukaryotic cell do you expect to find the enzyme RNA polymerase?

nucleus

How does the enzyme know where to start and stop transcription?

promoter region and terminator region.

What are the different types of RNA? What are their functions?

ribosomal RNA makes up the ribosome, transfer RNA adds free amino acids to the polypeptide chain based on the mRNA codon, messenger RNA is used to determine amino acid sequences.

What is the main purpose of DNA replication? What are 2 reasons why DNA would replicate?

Main purpose: make more cells so each cell has its own DNA. Organismal growth, wound repair.

Translation: Why it happens

Necessary to make proteins to carry out many different functions in the cell and body

DNA Replication: Why it happens

New cells are made for organismal growth/ development and wound repair

Are all mutations heritable? Explain.

Only mutations in the gametes are heritable. Somatic cells are not inherited by offspring so any mutations in them only impact the individual organism.

What portions of the DNA does a cell use for transcription to make an RNA molecule?

Only one DNA strand with the particular gene that is supposed to be read. The part of the strand that is downstream of the promoter and before the terminator.

What is RNA? List the features of RNA.

RNA is ribonucleic acid. It contains uracil rather than thymine, it is single stranded and it contains a hydrogen in its sugar that makes it ribose (rather than DNA's deoxyribose).

Why does A% not equal U% and G% not equal C%?

RNA is single stranded.

What are the similarities and differences between RNA and DNA?

Similarities: monomers = nucleotides (phosphate, sugar, nitrogenous), location in prokaryotes = cytoplasm. Differences: sugar type = deoxyribose vs ribose, 2 strands vs 1 strand, Location in eukaryotes = nucleus vs nucleus & cytoplasm.

A biochemist isolated and purified molecules needed for DNA replication. When some DNA was added replication occurred, but the DNA molecules formed were defective. Each consisted of a normal DNA strand paired with segments of DNA a few hundred nucleotides long. Which of the following had been left out of the mixture? A. DNA ligase B. Helicase C. Nucleotides D. DNA polymerase

A. DNA ligase

Transcription: Role of hydrogen bonding

Allow the DNA strands to separate for RNA polymerase, weak bonds temporarily keep the RNA nucleotide in place while RNA polymerase forms a covalent bond with the adjacent RNA nucleotides of the growing pre-mRNA strand.

What is the meaning of the word 'anticodon'? What type of molecule contains anticodons? How do codons and anticodons interact during translation?

An anticodon is a special triplet of bases that is complementary to the codon triplet of the mRNA. There are 61 codons that translate into an amino acid so 61 anticodons carried by tRNA.

What is a gene mutation?

Any change in the nucleotide sequence of a cell's DNA; can involve large regions or a single nucleotide.

When (at what points) can eukaryotic cells regulate gene expression?

At transcription, RNA splicing, adding of 5' cap and polyAtail, translation. Methylated before transcription so its too tight to unwind and read, inhibition of promoter site in transcription, regulate splicing, additions AND flow out into the cytoplasm, mRNA can be broken down in cytoplasm, the 5' cap can be inhibited so the small ribosomal subunit cannot bind, proteins can inhibit the translation, post-translation modifications can be inhibited or changed.

What is the function of the 5' cap on an mRNA? What about the 3' poly A tail?

5' navigates out of the nucleus, acts as a landing site for ribosome and protects RNA from degradation in cytoplasm. 3' protects from degradation in cytoplasm.

Suppose you are provided with an actively dividing culture of E. coli bacteria to which radioactive thymine has been added. What would happen if a cell replicates once in the presence of this radioactive base? 1. One of the daughter cells, but not the other, would have radioactive DNA. 2. Neither of the two daughter cells would be radioactive. 3. All four bases of the DNA would be radioactive. 4. Radioactive thymine would pair with nonradioactive guanine. 5. DNA in both daughter cells would be radioactive.

5. DNA in both daughter cells would be radioactive.

What is the meaning of the word 'codon'? How many different codons are there? What type of molecule contains codons?

A codon is a special triplet of bases that is complementary to the anticodon triplet of the tRNA. There are 64 codons carried by mRNA.

how can a eukaryotic cell selectively express, or not express, a gene?

A gene can be turned on at transcription, but can be turned off at any other step in the process after.

What insights did Watson and Crick contribute to their "model" or description of DNA structure?

Base pairing rules: A with T, G with C; DNA is double stranded.

Distinguish between base substitution mutations and insertion/deletion mutations.

Base substitution mutations occur when DNA polymerase places a nucleotide that does not follow the complementary base pairing rule. Insertion and deletions are frameshift mutations that edit the reading frame of the subsequent tRNA. These result in added or subtracted nucleotides in any place on the sequence.

DNA Replication: What/How it happens

Briefly (you need to know specifics) 1. Two strands of parental DNA separate 2. DNA polymerase attaches free DNA nucleotides to the parental strand following base-pair rules; DNA polymerase forms covalent bond; builds DNA in the 5' to 3' direction 3. DNA ligase forms covalent bond between okazaki fragments in order to make a continuous/solid strand 4. End result: 2 identical daughter molecules

Describe the role of complementary base pairing in protein synthesis.

Complementary base pairing dictates that there is only one possible anticodon for every codon. When the complementary anticodon is lined up with the mRNA codon, the particular amino acid is added to the polypeptide.

DNA Replication: Who/What is involved

DNA (double stranded) template strand, DNA Nucleotides (A, T, G, C), Topoisomerase, Helicase, DNA polymerase, Ligase

How is RNA related to DNA?

DNA is the transcribed into RNA. RNA is used as a template to make proteins through the process of translation.

What is meant by the description "antiparallel" regarding the strands that make up DNA?

DNA molecule is made up of 2 strands. The two strands are h-bonded together so the 5' (phosphate) end of one strand and the 3' (deoxyribose) end of the other strand are adjacent.