AP Biology Unit 6 Review Questions

The DNA from a certain plant species is analyzed. The DNA contains 22% thymine. Determine the percent of the other bases.

22% adenine 28% cytosine 28% guanine

A section of the template strand of DNA reads: 5'-CAACACTAA- 3'. Determine the mRNA sequence and translate it. (Assume you are downstream of the start codon.)

3' - GUUGUGAUU - 5'; Val, Val, Ile

Create your own DNA sequence of 9 nucleotides (make sure to provide its directionality). Determine the corresponding mRNA sequence and the three amino acids it codes for. Using the example you created, now insert one nucleotide near the beginning of the DNA sequence and show what happens to the resulting mRNA sequence and the amino acids it codes for. (i.e. template strand 3' ATAACAGCC 5' --> try-cys-arg; remember mRNA strand codes for amino acids)

3' CATAACAGCC 5' 5' GUAUUGUCGG 3' val-leu-ser

What is the backbone of DNA composed of?

5 carbon sugar-phosphate groups

Referring to question 10: imagine if the coding strand were transcribed and translated instead. Determine the mRNA sequence and translate it. How would this error affect the polypeptide produced?

5' - CAACACUAA -3'; Gin, His, Stop If this error occured, not only would the sequence almost match the DNA template strand, but it would produce a stop codon too early, resulting in a nonsense mutation. This mutation would change the shape and function of the protein, producing an improperly made protein. Likely this mutation would be non beneficial and inflict serious implications.

If the tRNA anticodon reads 3'- CUU -5' then what does the mRNA codon read that it can bind to? Knowing this, what amino acid will the tRNA be carrying? (Remember: the amino acid the tRNA carries is based on the mRNA codon.)

5' - GAA - 3'; glutamic acid

3' - ACTAG - 5' find the complementary strand

5' - TGATC - 3'

Describe the process of conjugation.

A conjugation is where a plasmid from one bacteria cell can be shared directly with another bacteria that lacks the gene of interest or advantageous gene.

What does it mean if a gene/trait is "evolutionarily conserved"?

A generationally reserved trait is one that hasc remained unchanged ("reserved") over multiple generations.

Describe the mutation that causes cystic fibrosis.

A nonsense mutation produces a stop codon prematurely, causing the protein to end its synthesis earlier than it should, causing a change in shape, thus a change in function as well.

Describe the process of transduction.

A transduction is when a virus can accidently transfer genes from a bacterial cell to another.

Referring to question 3, what is the codon that the tRNA binds to? (methionine)

AUG

Trace the path of a newly produced polypeptide that will leave the cell? (Hint: think back to Unit 2.)

After a new polypeptide is formed, it will travel in a vesicle to the Golgi complex. The Golgi will accept the vesicle at its cisface, then undergo modifications to the protein, releasing it in the transface. After, the protein will leave the cell via exocytosis.

After fertilization a zygote forms. The cells then go through mitosis. Explain how this bundle of cells eventually forms a human with specialized cells (i.e. liver cells, blood cells, neurons, etc.)

After fertilization, cells divide and differentiate which allow for cells to become specialized structure and in function. The process morphogenesis allows for cell signals to be sent, causing changes in expression. You also have cytoplasmic determinants that involve substances from a mother's egg that add to the development. Both of these help cause pattern formation and homeotic genes will map out the body's structure. Finally, apoptosis will help the organs, such as feet and fingers, to take their shape.

Why do introns exist if they are just spliced out of the mRNA during pre-mRNA modifications?

Although introns are not expressed, they are necessary in coding for amino acids, which form/code for proteins and helping to form different variations of proteins.

When some people hear of apoptosis, they think that this is a bad thing that cells go through. Provide one example that illustrates the importance of apoptosis (in reference to embryonic development).

Apoptosis is crucial for embryonic development as it causes cells to die, allowing structures like our hands and feet to be separated as opposed to webbed.

An mRNA sequence reads: 5'- CGAUGCAGA- 3'. Translate this sequence (Assume you are downstream of the start codon. )

Arginine, cysteine, and Arginine

Fill in the blank: the mRNA nucleotide triplets are called _________. These code for ________ _________.

Codons; proteins

Mutations can be detrimental, beneficial, or neutral. Give an example of a mutation that is detrimental and an example where it is beneficial. (Your response can be general or specific. If you want to provide specific examples you may use online resources.)

Cystic fibrosis is a detrimental disease that is the result of a nonsense mutation. A stop codon is produced prematurally as a substitution change coded for a stop codon instead of an amino acid. This then prevents cilia from working properly in the nostrils and mucus then builds up. Beneficial mutations include a mutated HBS, which makes red blood cells take on a sickle like, curved shape. One copy allows for malaria resistance, but two copies lead to an another unfortunate outcome as sickle-cell anemia.

What role do cytoplasmic determinants play in early embryonic development?

Cytoplasmic determinants help with the pattern formation along with the help of induction (cell to cell signals cause a change in gene expression)

Why does DNA move during gel electrophoresis?

DNA fragments are negatively charged and the positive voltage in the gel electrophoresis attracts the DNA.

Is DNA positively or negatively charged? How could you tell just by looking at a strand of DNA?

DNA is negatively charged due to the phosphorus and oxygen bonds, which can be seen in a picture of structural DNA.

How does gel electrophoresis separate DNA fragments?

DNA is separated by gel electrophoresis due to the shorter fragments of DNA being able to move towards the positive charge faster than the larger fragments. This is because macromolecules will travel through the pores at a speed inversely related to their size.

What does it mean that DNA strands are antiparallel and complementary? Draw a strand of DNA with 6 nucleotides to support your answer.

DNA strands run antiparallel, meaning one runs in the 3' to 5' direction, and the other in the 5' to 3' direction. Despite this, each strand still correctly matches the nucleotides together. 3' A T G C A G 5' 5' T A C G T C 3'

In which direction does DNA move during gel electrophoresis?

DNA will move down, towards the positive charge. The 5' ends will be more attracted to the positive charge so it is likely that DNA will move in the 3' to 5' direction??

List 3 differences between DNA and RNA.

DNA: -double stranded -has thymine that binds to adenine -deoxyribose acid RNA: -single stranded -has uracil that binds to adenine -ribonucleic acid

Describe how it is possible for only one identical twin to express an inherited disease.

Due to differences in chromatin modifications such as more or less acetyl groups on the histones or methyl on DNA can impact whether a gene in one twin is expressed verse another. Genes in heterochromatin regions are not often expressed. These regions can form from extra DNA methylation.

True or false: the genetic code is read in groups of two nucleotides at a time called the doublet code.

False, is read in groups of three at a time, called the triplet code

Differentiate between histone acetylation and DNA methylation.

Histone acetylation adds acetyl groups to histones, loosening the chromatin. DNA methylation adds methyl groups to DNA that induce the tighter wrapping of DNA around histones.

If a bacterial cell uses up its tryptophan storage, what would happen to the trp operon?

If a cell uses up all of its tryptophan storage, the operon will not be repressed and produce/synthesize tryptophan.

Describe the consequences of a chemical that prevents the 5' cap and poly-A tail from forming on eukaryotic mRNA?

If the 5' cap could not form, than the pre-mRNA would not receive the modified guanine and if the poly-A tail could not form, 50-250 adenine nucleotides would not be added to the 3' end of the mRNA. Both of these in turn would generate a loss of protection, maturity, and cause a degradation of the mRNA.

What would be the immediate effect to transcription if a cell was exposed to a drug that mutated the promoter region?

If the promoter region was mutated, RNA polymerase could not bind to the promoter, preventing transcription from occurring.

If a bacterial cell has a mutation to the trp repressor that changes the shape of the active site, how would this affect the production of tryptophan?

If there is a change in shape to the trp repressor, then the repressor will no longer bind to the operon, therefore the production of tryptophan would continue uncontrollably.

In reference to question 8, what would happen if you then add lactose to the medium?

If you added lactose, the operon would the free of the repressor and induced into synthesizing lactose.

How does transcription and translation differ between prokaryotes and eukaryotes?

In prokaryotes, translation occurs around the same time as transcription and in eukaryotes this occurs after. Also, the ribosomal subunits in prokaryotic cells is 30s for the smaller one and 40s for the larger one. In the eukaryotes is 40s for the small subunit and 60s for the large subunit. Eukaryotes can also have transcription and translation occur in the mitochondria and chloroplast.

Circle the correct item: The lac operon is repressible/inducible.

Inducible

What if you were performing gel electrophoresis and the molecule you were examining moved towards the negative electrode? What does this mean about the charge of the molecule you are analyzing?

It means the charge of the molecule is positive.?

Think back to Unit 1. Identify the major classes of macromolecules and then identify their monomers and polymers.

Lipids: fatty acids/glycerol; no polymer Proteins: amino acids; polypeptides Carbohydrates: monosaccharides; polysaccharides Nucleic Acids: nucleotides; DNA/RNA

If an error occurs in DNA replication, how is it fixed?

Mismatch repair will take place and enzymes will remove/replace incorrect nucleotides. When segments are damaged, nuclease removes and DNA nucleotides replace it.

How can mutations lead to natural selection?

Mutations can alter phenotypes and cause genetic variation. They can be on a large (chromosomal) or small (substitutions, insertions, or deletions) scale which could be favorable or unfavorable for the organism. In some cases, mutations can help an organism to increase its survival rate.

What does it mean that DNA strands are antiparallel?

One strand runs in the 3 prime to 5 prime direction and the other runs in the 5 prime to 3 prime direction, with complementary base pairs still matching up.

Describe step-by-step how DNA is replicated.

Origins of replication bind to the DNA, and various proteins will attach. This allows for the replication fork to form and helicase will unwind DNA strands at each replication fork. Single stranded binding proteins will bind to DNA, stabilizing it and keep it open. Topoisomerase relaxes and prevents supercoiling and preventing damage. Primase adds short segments of RNA primers to the parental strand. DNA polymerase III comes in and attaches to each primer, moving along in the 3' to 5' strand (synthesizing in the 5' to 3'). The leading strand requires one primer, while the lagging strand requires multiple primers. Leading strand is synthesized in one continuous segment while the lagging strand is done in okazaki fragments. DNAP I replaces RNA nucleotides with DNA nucleotides.

How can PCR be used to produce copies of a gene?

PCRs can be used to take short segments of DNA and produce large amounts of DNA. First, a sample is heated until it denatures and the DNA strands separate. Hydrogen bonds holding the DNA strands together will be broken. After, the sample is cooled, annealing, the lowering of temperature, allows the DNA primers to bind to DNA. Third, extending raises the temperature and the enzyme "Taq Polymerase" synthesizes the new strands of DNA. DNA nucleotides get added to the PCR reaction for Taq Polymerase to use in synthesis.

What are the three parts of an operon?

Promoter- RNA polymerase attaches Operator- switches genes on and off Genes- code for related enzymes

Differentiate between purines and pyrimidines.

Purines, adenine and guanine, have two ring structures whereas pyrimidines, cytosine, uracil, and thymine, have only one ring structure.

List and describe the steps of transcription.

RNA polymerase molecules bind to the promoter region. Eukaryotes need transcription factors to allow for this process to occur. The second stage, elongation, involves RNA polymerase opening the DNA and reading its triplet code of the template strand (moves in 5' to 3' direction). In the last stage of transcription, called termination, a termination sequence in prokaryotes and polyadenylation sequence in eukaryotes is released. Prokaryotic cells release mRNA without any extra modifications need, whereas eukaryotes require modifications (5'Cap, Poly-A tail, RNA splicing).

Why is redundancy in the genetic code important?

Redundancy is crucial since it allows or slight errors in codons to not have a large overall affect on the phenotype or genotype of the protein.

Differentiate between a repressible and inducible operon.

Repressible operons are normally on but can be turned off and an inducible operon is normally off but can be turned on.

What are restriction enzymes? Where do they come from?

Restriction enzymes cut up DNA where the viral DNA has injected itself into. These enzymes are found in bacteria and are produced by bacteria.

In which stage of the cell cycle does DNA replicate?

S phase of interphase

Errors in DNA replication can lead to natural selection. Why? Would natural selection still occur if all errors were corrected? Why or why not?

Since errors in replication can alter phenotypes, increasing genetic variation, this forces organisms to adapt to their environment in a new way. This would not happen naturally if the corrections to the mutations were made since the organism would already be adjusted to their phenotypes

Describe the Meselson and Stahl experiment that supported the semi-conservative model of DNA replication.

The Meselson and Stahl experiment cultured bacteria with a heavy isotope N^15, which was then transferred into a medium with N^14, a light isotope. DNA was spinned and analysed. As each generation was added to the light isotope, two of the strands contained 1/2 the parental and 1/2 recombinant.

What is a promoter region? Are promoter regions upstream or downstream of the gene?

The promoter region is the sequence where RNA polymerase binds to, which is upstream of the interested gene.

Summarize the purpose of translation in 1-2 sentences.

The purpose of translation is to translate an mRNA strand from the nucleus, into a chain of polypeptides with the ultimate goal of forming a protein.

During gel electrophoresis, which size of DNA (long vs short fragment) will move the furthest? Why?

The shortest fragment since it is smaller and the speed at which macromolecules will travel through the pores is inversely related to the size of the fragment.

What are the two reproductive cycles of bacteriophages? Describe each.

The two cycles of reproduction for bacteria includes the lytic cycle and lysogenic cycle. In the lytic cycle, DNA is replicated and the phage proteins are produced, making new bacteriophages. Once maturing, the cell will lyse and release those bacteriophages. In the lysogenic cycle, the bacteriophages/virus use the bacteria cell as a host cell by inserting and incorporating itself into the DNA.

Fill in the blanks: The process of ________ converts DNA to RNA. The process of ______ turns RNA into proteins.

Transcription; translation

If one bacterial cell has a gene that is promoting its survival, explain how other bacterial cells can benefit from it.

Transformations allows for the other bacteria cells surrounding the cell with the advantageous gene to uptake the DNA from that cell (via a plasmid) or exchange/transfer the DNA through a conjugation.

Describe transformation. Are all bacteria competent?

Transformations are where bacteria uptake DNA from a nearby cell, likely with an advantageous gene via a plasmid. Not all bacterial cells are competent of this process.

When does translation stop?

Translation stops when a stop codon binds to the A site of a ribosome.

If a bacterial cell does not need tryptophan and it builds up inside of the cell, what would happen to the trp operon?

Trp operon would bind to a repressor, thus shutting off the production of tryptophan

True or false: plasmids replicate separately from chromosomal DNA.

True

Using a codon chart determine what UAU codes for?

UAU --> Tyrosine

Can a transformed organism pass on its new traits to its offspring?

Yes since organisms who have transformations when they divide and produce offspring, that offspring will likely receive that transformation after division. Also, they are considered a form of epigenetic inheritance.

If a bacterial cell is grown in a nutrient rich, lactose free medium, what would you expect to see at the lac operon?

You would still expect to see the lac repressor binds to it since no allolactose is able to bind to the repressor, thus the synthesis of lactose through operon will not occur.

Fill in the blanks: tRNA has an ________ region which is complementary and antiparallel to _______.

anticodon, mRNA

What functional group defines the 3' end of DNA?

free hydroxyl group

Referring to question 3, which amino acid does this tRNA carry? (first tRNA)

methionine

What is the center of DNA composed of?

nucleotides paired together via hydrogen bonds

Fill in the blank: A change in an organism's genotype can cause a change in the organism's_________.

phenotype

What functional group defines the 5' end of DNA?

phosphate group

Compare eukaryotic and prokaryotic DNA.

prokaryotic: -circular DNA in the nucleoid region eukaryotic: -linear DNA in the nucleus

Circle the correct item: The trp operon is repressible/inducible.

repressible

Where does translation occur?

ribosomes in the cytoplasm

Differentiate between silent, missense, and nonsense mutations. Predict which would be most detrimental and why?

silent: a substitution causing a change that still codes for the same amino acid missense: a change in nucleotides (via substitution) that results in an different amino acid nonsense: a change in nucleotides that result in a stop codon being produced prematurely A nonsense mutation would be the most detrimental since it would stop protein synthesis early, thus creating a nonfunctional, prematurely made protein.

The very first tRNA will enter at which site on the ribosome (A, P, or E)?

site p

Circle the correct option: substitutions are small/large scale mutations.

small

In eukaryotic cells where does transcription occur?

the nucleus

Fill in the blanks: protein synthesis occurs in two stages _______ and _________.

transcription, translation

Circle the correct option: microRNAs and siRNAs block transcription/translation.

translation; by interacting with mismatch pairs

True or false: morphogenesis is the process that gives an organism its shape.

true

True or false: only the template strand of DNA is transcribed during transcription.

true