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1. During what part of the cell cycle is DNA replicated? Why does this happen?
The part is the S- phase portion of the interphase. This happens to promote cell division of the nucleus.
2. What are the three parts of a nucleotide? Draw/depict them and label each.
The three parts include: nucleobase, five carbon sugar phosphate groups.
3. What type of bond connects nucleotides in the sugar backbone of DNA together?
They are covalent bonds.
What type of bonding holds the two DNA strands together?
Hydrogen bonding
4. What does it mean that the two strands of a DNA molecule are anti-parallel?
It means that if they are not parallel, means that both strands can be same way using the same isomers, and using the same enzymes.
5. Explain the semi-conservative model of DNA replication. Draw/depict it.
The semi-conservative model is used to describe the mechanism in which DNA is replicated in all cells.
6. How is the DNA double helix unwound for replication? What enzymes are involved in this step and what are their functions?
DNA helicase is an enzyme that helps unwound DNA double helix making it ready for replication. Its function is to break hydrogen bonds between the complementary bases.
7. What is an RNA primer and why is it necessary to start DNA replication?
A RNA primer is several complementary strands of RNA added to the lagging strand of DNA by RNA polymerase. It is necessary ti start DNA replication because it instates the synthesis of lagging.
8. In what direction are nucleotides added to the new strand by DNA polymerase?
The direction of 5’ ti 3’ since DNA polymerase acts on the 3’-OH of the existing strand for adding free nucleotides.
9. What is the difference between the leading strand and the lagging strand?
Since the DNA process is discontinuous, in the leading strand, synthesis is continuous in the 5’ -3’ direction towards the fork while in the lagging strand, as the fork opens, multiple sites of initiation are exposed and synthesis continuous in short segments in the 5’ -3’ direction.
10. What are Okazaki fragments? What enzyme joins them together to form a new continuous DNA strand?
They are fragments of DNA that are produced during the process of DNA replication. The enzyme joining them is polymerase.
11. How does proof-reading keep the accuracy of DNA replication so high?
This is made possible in that during replication, nucleotides which compose DNA are copied, consequently, ab E coli making a copy of its DNA and making the mistakes reduce to one in every billion new nucleotides.
12. What is a telomere? Do prokaryotes have telomeres?
A telomere is a region of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from deterioration and due to lack of a linear arrangement, prokaryotes don’t have telomere.
CHAPTER 17: FROM GENE TO PROTEIN
1. What is the central dogma of biology? This is part which provided the general framework for how genetic information flows from DNA sequence to a protein product inside cells.
DNA a RNA b
_____________ ____________ _________PROTEIN___________
The arrows indicate what processes? a) TRANSCRIPTION
b) TRANSLATION
2. Most genes code for the production of what type of organic molecule?
Carbohydrate molecule
3. Where in the cell does transcription occur for prokaryotes? For eukaryotes?
In prokaryotes, transcription occurs in the cytoplasm while in eukaryotes, it occurs in the nucleus.
4. What is a codon? How do they code for amino acids?
A codon is a sequence of three nucleotides that together form a genetic code in a DNA or RNA molecule. Coding of amino acids starts from groups of three bases from a fixed point. The genetic code consists of 64 triplets of nucleotides, and each codon encodes for one the 20 amino acids.
5. What does it mean that the genetic code is universal?
It means the four basic building blocks are the same in every animal and the codons for the same amino acids in every animal on earth.
6. How is RNA different from DNA?
RNA is different from DNA in that RNA contains uracil, exists as a single molecule and uses sugar while DNA contains thymine, exists as a double standard molecule and is made of sugar deoxyribose
7. What does RNA polymerase do during transcription?
It attaches itself to the DNA strand to assemble a new chain of nucleotides to produce complementary RNA strand.
8. How does RNA polymerase know where to start?
There exist is the initiator and there is a specific sequence that tells it to start there.
In what direction are nucleotides added?
They are added in the 5’ -3’ direction.
9. Explain what occurs in the three stages of transcription: (see pages 341-342)
Initiation – here, the RNA polymerase complex binds to a promoter sequence which establishes initiation. Polymerase begins to synthesize a strand of RNA complementary to one side of the DNA strand moving into the coding sequence portion of the gene being transcribed.
Elongation – here the lengthening RNA molecule is produced by DNA polymerase as it reads the DNA triplet code on the template strand. The template will continue reading the template until it reaches a sequence that provides a signal indicating the transcribed region is at the end.
Termination – during termination, transcription is triggered with the RNA polymerase encounters a particular DNA sequence, causing the polymerase to lose affinity for the DNA template. Here the polymerase disengages from the DNA and the RNA is molecule is released for translation.
10. Does RNA processing occur in prokaryotes?
No
11. Where does RNA processing occur in the cell?
In the nucleus of a cell
12. What are the three ways that pre-mRNA is processed?
1) Capping why are the altered ends important?
2) Splicing
3) cleavage/polyadenylation
The altered ends are important to remove introns before being transported to the cytoplasm where they are translated into ribosomes.
13. Which will be kept and translated, an exon or intron?
Introns.
14. Are introns just a waste of space? How might they be helpful?
No because introns enable alternative splicing.
15. What are the monomers that make up a protein polymer? Amino acids
How many different types of these monomers exist? 20 monomers
16. A protein polymer is called amino acids
The covalent bond that joins protein monomers is called a peptide bond
17. Does translation occur in the nucleus? NO
What cellular structure performs translation? Ribosome
Do all living organisms have this structure (even prokaryotes)? Yes
18. The DNA strand provided below is the template strand. Fill in the complementary RNA nucleotides, then use the genetic code (Fig17.5) to fill in the amino acids (use 3-letter abbreviations) that the RNA codons specify.
DNA: TAC – TGG – ACA – GCG – TCA – CAT – ATT
RNA: UAC – UGG – ACA – GCG UCA CAU – AUU
AMINO ACIDS: Tyr- Trp- Thr – Ala- Ser- His- Ile
19. What is tRNA? Explain the role of tRNA in translation. How does tRNA bring the correct amino acid (explain the anti-codon)?
This is a member of nuclei acid family known as ribonucleic acid whose role is to read the message of nuclei acid and translate it into proteins or amino acids. The correct amino acid is brought through the attachment of amino acids to tRNA through the ribosome by proteins called elongation factors.
20. Draw a ribosome attached to a strand of mRNA. Label the 5` and 3` ends of the mRNA and draw an arrow to show which direction the ribosome will move along the strand.
21. For translation to start, what are all of the things that must come together?
Protein/RNA complex (ribosome), codon, tRNA, and enzyme.
22. How is translation terminated?
This occurs when the ribosome encounters a stop codon, where a release factor reads the triplet and polypeptide synthesis ends.
23. Where are free ribosomes found in the cell? Cytoplasm
Where are attached ribosomes found in the cell? So as to make proteins that will be used inside the cell and proteins made for export out of the cell.
Attached ribosomes make secreted proteins. Explain what this means.
It means the proteins secreted are used by the cell membrane or exported to other parts of the body.
24. What is a point mutation? This is a mutation that changes one nucleotide in a gene or DNA sequence by substitution, deletion or addition.
Define: Substitution – this is a mutation that exchanges one base for another.
Insertion – this is a type of mutation that results in addition of extra nucleotides in a DNA sequence or chromosome.
Deletion – this is a type of mutation in which part of chromosome or a sequence of DNA is lost during replication.
25. Why are insertions and deletions often more serious mutations than a substitution? What is a frame shift?
Because they are deemed harmful. A frame shift means all the downstream amino acids will be changed.
26. Explain: Silent – type of mutation in DNA that do not significantly alter the phenotype of the organism.
Mis-sense – a form of mutation that results from a codon that codes different amino acid.
Non-sense – this is a point in mutation in a sequence of DNA that results in a premature stop codon in the transcribed mRNA and in an incomplete nonfunctional protein.
27. What is a mutagen? What are some examples?
An agent or substance that can cause genetic mutation. For example, benzene, x-rays, gamma rays etc.
28. Do all RNA’s get translated into polypeptides? Yes.
We can amend the Central Dogma to DNA RNA functional product
What are some functional products besides proteins? Carbohydrates.
CHAPTER 18: REGULATION OF GENE EXPRESSION
1. What is an operon? How are these useful for PROKARYOTES?
An operon is a unit of genetic material that functions in a coordinated manner by means of an operator, a promoter and structural genes that are transcribed together. They are useful to prokaryotes in that they allow the organism to make their own amino acids if necessary.
2. Fill in the table:
Trp Operon Lac Operon
Repressible or Inducible Repressible Inducible
Default ON or OFF ON OFF
Is on when… Repressed Lactose is present
Is off when… Amino acid trp is present Induced
Catabolic or Anabolic Anabolic Catabolic
3. What do the enzymes coded for in the trp operon do?
Make trp.
When trp is present, are the genes in the trp operon transcribed?
No. they are not transcribed.
4. What is a repressor?
A repressor is a regulatory protein that binds to an operator and blocks transcription of] f genes of an operon.
5. What is an operator?
Is a segment of the DNA to which transcription factor binds to regulate gene expression?
6. What is an inducer?
An inducer is a molecule that regulates genes expression.
7. Which operon (trp or lac) is controlled by feedback inhibition?
Trp operon.
8. Are operons found in eukaryotes?
No
9. Explain differential gene expression… different cell types in a multicellular organism are due to what?
This is because cells within the same genome express a different gene.
10. Chromatin structure: this is meant to help regulate gene expression location of the genes promoter sites where the DNA attaches to the chromosome modifications to chromatin and histone proteins.
Does acetylation prevent or allow transcription? It allows transcription to occur.
Does DNA methylation prevent or allow transcription? It prevents transcription to occur.
How does chromatin density affect transcription? Chromatin density is caused by changes which cause the DNA to be densely packed to an extent it cannot be transcribed. However, those that are loosely packed can be transcribed.
11. In EUKARYOTES, regulation of transcription involves transcription factors.
What is the role of general transcription factors?
They are useful for the transcription of all protein they bind to a DNA sequence or protein.
What are specific transcription factors called?
They are called activators.
*There are DNA segments where transcription factors bind (control elements) that are upstream of the gene:
Enhancers (distal) bind which type of transcription factor?
They bind specific transcription factors.
Proximal control elements bind which type of transcription factor?
They bind close to the promoter general transcription factors bind
12. In all organisms (prokaryotes and eukaryotes), there is a promoter upstream of the gene. What important enzyme for transcription binds here?
Enzyme RNA polymerase
Is the promoter a protein or a segment of DNA?
It is a segment of DNA.
13. Thinking about differential gene expression in EUKARYOTES (of course… proks are single-celled) … explain how activators drive differential gene expression in different types of cells. See Figure 18.11 for help.
The cells can contain different groups of activator proteins which will determine which genes are expressed.
14. Alternative RNA splicing is a form of post-transcriptional regulation. Explain how alternative splicing affects gene expression.
It is possible for it to multiply the number of possible human proteins which allows one gene to code for more than a protein.
15. What 3 processes must occur for a multicellular organism to develop from a fertilized egg: (state & define each one)
1) Cell division – this is a series of mitotic divisions.
2) Cell differentiation – where cells become specialized in structure and function.
3) Morphogenesis – this is creating the physical arrangement of cells, which are organized and distributed non- randomly in an organism.
16. Besides a haploid nucleus, what else is in an egg that comes from the mother?
RNA and proteins.
17. Early development is directed by: (explain each)
Cytoplasmic determinants – this are maternal substances in an egg that influence the course of early development
Induction – this are signals from other cells that cause change in target cells.
18. What does it mean when a cell becomes determined? Using Figure 18.18 as an example, how does control of gene expression relate to cell determination?
It means that fate is set in early development and it signals the other cells to lead the activation of the aster regulatory gene.
19. Proto-oncogenes code for proteins that function in what process?
Stimulation of normal cell division process.
Explain 1 way that a proto-oncogene may become an oncogene? (See Fig 18.23)
Because genetic changes ex-gene moves to a new locus resulting into multiple copies of a gene, mutation in control element or within with a gene.
Cancer can be caused by a mutation in a proto-oncogene that causes there to be too little or too much of the proto-oncogene protein made?
Too much.
20. Tumor-suppressing genes code for proteins with what function?
Preventing uncontrolled cell division.
Cancer can be caused by a mutation in a tumor-suppressing gene that causes there to be too little or too much of the tumor-suppressing protein made?
Too little.
21. Explain how mutations that occur over time accumulate and contribute to cancer. Use colon cancer and Figure 18.26 as an example.
Mutations are either proto-oncogenes or tumor-suppressing genes which can lead to loss of the cell cycle control more than mutation is needed to produce cancer cells.
22. Individuals can have a genetic predisposition for certain types of cancer, but environment also plays a big role in development of cancer. Explain how genetics and environment (smoking, UV light, chemical exposure, radiation, etc…) can be synergistic in causing cancer.
In genetics perspective, some are born with mutations and in the environment perspective, new mutations can develop throughout one’s lifetime.
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