Biology 1105 Virginia Tech, Exam 3

Imagine that during replication an extra base is added in the coding region of a gene and that this is not recognized by the repair mechanisms. Which of the following would result from this mutation?

A. The chromosome that holds the DNA sequence will show an inversion

B. The encoded protein would have a different sequence of amino acids starting at the site of the new base and moving on.

C. The encoded protein would be produced normally

D. The encoded protein would have one altered amino acid, but everything else would be normal

B. The encoded protein would have a different sequence of amino acids starting at the site of the new base and moving on.

This is because an addition of a base would shift the reading frame, and therefore change how each codon is read. Example:

AAT GCA CTG CAT... would be read as those codons but with the addition of a base this sequence is read differently.

AGA TGC ACT GCA... this changes the amino acids.

What role does a promoter play in the process of transcription in prokaryotes?

A. It is a special factor that facilitates termination of transcription and dissociation of RNA polymerase

B. It is a carrier protein that carries mRNA out of the nucleus

C. It is a region of DNA that binds and correctly orients RNA polymerase to initiate transcription

D. It is a component of the RNA polymerase holoenzyme that unwinds the DNA template

C. It is a region of DNA that binds and correctly orients RNA polymerase to initiate transcription.

Once the entire ribosome has assembled on the mRNA, what reaction does it catalyze?

A. The formation of peptide bonds between incoming amino acids and the growing peptide

B. The formation of phosphodiester bonds between nucleotides in the mRNA

C. The formation of hydrogen bonds between 2 strands of DNA

D. The formation of phosphodiester bonds between rRNA components of the ribosome

A. The formation of peptide bonds between incoming amino acids and the growing peptide.

Crick originally proposed that there had to be an adaptor molecule that linked amino acids to short sequences of the genetic code. This linker molecule was later identified as?

A. mRNA

B. tRNA

C. rRNA

D. snRNA

B. tRNA

Which of the following is not true about the genetic code?

A. It is almost universal - with few exceptions, all organisms use the same code

B. It is a triplet code - groups of 3 nucleotides each encode one amino acid

C. It is spaced - each codon has a single nucleotide space separating it from the next one

D. It is degenerate - some amino acids are coded by more than one codon

C. It is spaced- each codon has a single nucleotide space separating it from the next one

This was discovered when Crick and Brenner did frame shift mutations to test whether the genetic code was spaced.

Crick and Brenner reasoned that the genetic code most likely consisted of a series of blocks of information called ___________, each correspoding to an amino acid in the encoded protein.

Codons

each codon consists of ___________ nucleotides, a triplet code, and reading occurs continously without punctuation between the 3-nt units.

Three

the experiments that crick and brenner did emphasized the importance of the ____a_________ for the genetic message. Because there is no punctuation, the _____a_____ established how each following codon will be read.

Reading Frame

mutations that alter the reading frame of a genetic message are called ____________________.

Frame Shift mutations

With only 20 amino acids and 64 codons, there is an abundance of codons. this mean that the code is ________, which means that ______________________________________.

Degenerate. Which means that some amino acids are specified by more than one codon.

Prokaryotes have a single RNA polymerase that has two parts: the ____________ and the __________________.

Core polymerase and the Holoenzyme.

The holoenzyme's ability to _______ _________ _________ in dna allows rna polymerase to ______ the beginning of genes, which is critical to its funtion.

Recognize specific signals.

Locate

Accurate initiation of prokaryotic transcription requires two sites in dna: one called a ___________ that forms a recognition and binding site for rna polymerase, and the actual ________________.

Promoter, Start Site

The reigon containing the rna polymerase, the dna template, and the growing rna transcript is called the ___________ because it contains locally unwound dna.

transcription bubble

What is an operon?

An operon is a single transcription unit that encodes mutiple enzymes necessary for a biochemical pathway. By clustering genes by function, they can be regulated together.

What is one major difference in Prokaryotic and Eukaryotic DNA transcription?

Prokaryotes have a single RNA Polymerase, whereas Eukaryotes have three.

We call the rna synthesized by rna polymerase II the ________________, which is processed to produce the ______________

Primary Transcript, Mature RNA

How is the primary transcript modified?

1. Addition of the 5' cap

2. Addition of the 3' Poly-A tail

3. mRNA splicing of coding and noncoding regions.

The noncoding regions in the primary transcript are termed ____________ whereas the coding regions are termed ___________.

Introns, Exons.

How many proteins are formed from a single gene in Prokaryotes and in Eukaryotes?

In prokaryotes a single transcript codes for one protein. In eukaryotes a single transcript can code for multiple proteins due to mRNA splicing.

What are the two functions of the ribosome?

The two functions of the ribosome involve decoding the transcribed message, and forming peptide bonds. the formation requires the enzyme peptidyl transferase, which resides in the large subunit.

Which of the following does NOT have an effect on gene expression?

A. Binding of proteins to the mRNA transcript to prevent ribosome binding

B. siRNA degrades mRNA transcripts

C. Multiple ORIs to facilitate greater copying of genetic material

D. Targeted degradation of proteins

C. Multiple ORIs to facilitate greater copying of genetic material

Which of the following is NOT true with regards to changes in chromatin structure?

A. micro RNAs can act to slide nucleosomes along chromatin fibers

B. Histone proteins can be modified to alter the structure of chromatin

C. DNA can be methylated to alter the structure of chromatin

D. ATP energy can be used to remove histones and remodel chromatin structure

A. micro RNAs can act to slide nucleosomes along chromatin fibers.

In Eukaryotes _____________________________ bind to the promoter and are necessary for transcription to occur. However, they do not affect the rate of transcription. ____________________ on the other hand, act in a tissue- or time-dependent manner to activate greater rates of transcription.

A. General transcription factors; specific transcription factors

B. Tryptophans; lactoses

C. Enhancers; repressors

D. bHLH proteins; Homeodomain proteins

A. General transcription factors; specific transcription factors

Which of the following is a function of a regulatory protein in the control of gene expression?

A. Regulatory proteins modulate the ability of DNA Helicase to unwind the DNA

B. Regulatory proteins affect the lifetime of tRNA molecules

C. Regulatory proteins modulate the ability of RNA polymerase to bind to the promoter of a gene

D. Regulatory proteins alter the sequence of DNA

C. Regulatory proteins modulate the ability of RNA polymerase to bind to the promoter of a gene.

Under what conditions will expression of the lac operon be the greatest in a Prokaryote?

A. When lactose is high and glucose is high: repressor not bound, CAP not bound

B. When lactose is high and glucose is low: repressor not bound, CAP bound

C. When lactose is low and glucose is low: repressor bound, CAP bound

D. When lactose is low and glucose is high: repressor bound, CAP not bound

B. When lactose is high and glucose is low: repressor not bound, CAP bound.

Which type of organism regulates gene expression more quickly: Prokaryotes or Eukaryotes?

Prokaryotes. Prokaryotes regulate gene expression based on changes in the environment, whereas Eukaryotes regulate gene expression based on development and homeostasis.

Transcriptional regulation utilizes _______ that bind to DNA to either ______ or ____________.

Proteins that bind to DNA to either block or advance its effects.

What is the most common type of gene regulation?

Transcriptional regulation, in both eukaryotes and prokaryotes. Although, it is particularly common in Prokaryotes.

A __________ consists of a regulatory DNA sequence upstream from the transcription start site.

Promoter Region

Regulatory proteins regulate gene expression by-

influencing the ability of RNA polymerase to bind to the core promoter.

RNA polymerase binds to the __________________ to initiate transcription.

Core Promoter

In the case of __________________, the genes are expressed only when an active regulator protein, e.g. an activator, is present.

Positive control

Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Like in the case of CAP, the gene is ONLY expressed if CAP is bound.

In the case of ________________, the genes in the operon are expressed unless they are switched off by a repressor protein.

Negative Control

Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated.

What are the DNA components of Operon regulation?

A core promoter region, an operator (repressor proteins), and an activator binding site.

Operons _______ have a promoter, but have __________ activator binding sites and operators, depending on the gene regulation mechanisms.

always; any number or combination of

The lac operon is both positively and negatively controlled meaning that-

it is regulated by both an activator and a repressor protein.

When does the lac repressor bind, and what is its effect on transcription?

The lac repressor protein inhibits transcription by binding when lactose is NOT present in the environment. This conserves materials and energy.

When does the CAP activator bind and what is its effect on transcription?

The CAP activator protein binds to the CAP binding site when glucose is ABSENT, and it promotes transcription. This is because transcription allows the cells to break down lactose, and if glucose is present then the cell prefers to use it rather than lactose so transcription would be a waste of materials.

What effect do the environmental scenarios have on lac transcription?

A. Lactose is absent, glucose is absent

B. Lactose is present, glucose is present

C. Lactose is present, glucose is absent

A. Repressor and Activator bind, no transcription

B. Neither bind, no transcription

C. Activator binds, transcription

What effect do the environmental scenarios have on Tryp transcription?

A. Tryptophan is present

B. Tryptophan is absent

A. Tryptophan binds to the repressor to change conformation, so that the repressor may bind. No transcription.

B. No tryptophan to bind to repressor, repressor does not bind. Transcription

Molecules may bind to regulatory proteins and therefore ________ or ___________ transcription.

Stimulate/induce ; Inhibit/repress

Example of Repression?

Repression occurs when tryptophan in the environment inhibits transcription from the trp operon.

Example of Induction?

Induction occurs when transcription from the lac operon is stimulated by the presence of lactose in the environment, because it represses the repressor.

What is induction?

When a molecule in the environment stimulates transcription.

What is repression?

When a molecule in the environment inhibits transcription.

What is Positive Control?

A TYPE OF PROTEIN, when transcription is regulated by an activator protein.

What is Negative Control?

A TYPE OF PROTEIN, when transcription is regulated by a repressor protein.

What are general transcription factors?

Only present in eukaryotes, general transcription factors assemble at the core promoter and recruit RNA Polymerase II to enable basal (minimum) transcription. NEEDED FOR ANY TRANSCRIPTION TO OCCUR.

What is the initiation complex?

TFIID binds the TATA box of the promoter and recruits other transcription factors and RNA Polymerase II. This assembly is called the initiation complex.

Where are specific transcription factors found and where do they bind?

In BOTH prokaryotes and eukaryotes. They MAY NOT ALWAYS bind at the core promoter, particularly in eukaryotes. Some bind to DNA enhancers, which causes the DNA to bend.

What is methylation?

Methylation is the modification that winds the DNA more tightly around the histone, and therefore makes the DNA unable to be transcribed.

What is Acetylation?

Acetylation is the process by which an acetyl group is added to the histone tail, loosing the histone winding, and making the DNA more accessible for transcription.

In what organisms does Post transcriptional regulation occur?

Eukaryotes, because it involves the processing of RNA in the nucleus before export. In Prokaryotes, the processes of transcription and translation are coupled.

What are the four different types of post transcriptional regulation?

1. mRNA alternative splicing, or editing

2. Inhibition of transcript export from the nucleus

3. Inhibition of translation

4. mRNA regulation by small RNAs

What is alternative splicing?

In eukaryotic organisms, the primary mRNA transcript is "spliced" to remove exrons from the sequence. Some primary transcripts can be spliced several ways to produce transcripts for more than one protein. (depending on the needs of the cell).

What is an example of alternative splicing?

The Thyroid gland and the Hypothalamus. Both come from the same DNA sequence, but alternative splicing ultimately produces two very different proteins through different organization of exons.

What is mRNA editing?

The chemical modification of bases so that the original nucleotide resembles another, which changes how it is read by the ribosome during translation. For example, editing a base to create a stop codon and shortening the mRNA.

What is export inhibition?

It regulates the translation of mRNA by never allowing the transcript to leave the nucleus.

What is Translation Inhibition?

Translation Inhibition is done by altering the availability of proteins required for translation, or producing an inhibitory protein that binds only to a specific mRNA.

What are the two RNAs that prevent mRNA transcripts from being translated?

microRNAs (miRNAs) - Single strand of RNA that folds into a hairpin to produce small segment of double-stranded RNA

Small-interfering RNAs (siRNAs)- Derived from long segments of double-stranded RNA that are then cut down to produce smaller double stranded segments.

Where does each type of small RNA originate?

miRNAs are typically encoded in an organism's genes. siRNAs can be exogenously introduced.

How does post translational gene regulation work?

Through protein modification in degradation mechanisms.

In metaphase of mitosis, chromosomes align individually along the metaphase plate. In metaphase I of meiosis, homologous pairs of chromosomes align randomly along the metaphase plate. Why are these differences important to meiosis?

A. They prevent the uncontrolled division of cells and the formation of cancer

B. They allow for segregation of homologous pairs of chromosomes and independent assortment

C. They allow for the formation of chiasmata

D. They allow for the generation of new somatic cells and the m-phase promoting factor

B. They allow for the segregation of homologous pairs of chromosomes and independent assortment

The synaptonemal complex forms in prophase I of meiosis and results in the formation of bivalent chromosomes. What process is happening in these cells?

A. Mitosis

B. The formation of somatic cells

C. Crossing over or recombination

D. Cytokinesis

C. Crossing over or recombination

In a diploid, interphase cell prior to replication, chromosomes come in pairs with each one of the pair called a ___________________. After replication, each member of the pair consists of ________________________.

A. 34 nm fiber; 2 karyotypes

B. homologues; 2 sister chromatids

C. nucleosome; 2 haploids

D. cohesin; 2 microtubules

B. Homologues; 2 Sister Chromatids

Proto-onco genes are characterized by all of the following EXCEPT:

A. these genes detect problems in the cell cycle and have the ability to stop the cycle

B. can become oncogenes when mutated

C. when it becomes an oncogene, it is overexpressed or stuck in the "on" state

D. only one copy needs a mutation for the gene to fail

A. these genes detect problems in the cell cycle and have the ability to stop the cycle

______ enymes control passage through checkpoints during cell divison. These checkpoints can delay cell division, but not stop it completely (T, F). There are 3 checkpoints known as _________.

A. MPF, F, G1/S + spindle checkpoint + late metaphase checkpoint + G2/M

B. MPF, T, G1/S + late metaphase checkpoint + spindle checkpoint

C. Cdk, T, G1/S + spindle checkpoint + G2/M

D. Cdk, F, G1/S and the late metaphase checkpoint

C

How do prokaryotic cells reproduce?

Through binary fission, in which a single cell splits into two. The two chromosomes separate to opposite ends and a structure termed the septum separates them.

How do Eukaryotic Cells reproduce?

Through Meiosis (division of genome) and Cytokenesis (division of the cytoplasm)

What is the result of the gain or the loss of a chromosome?

Death of the cell or the organism, since one chromosome can contain thousands of genes.

What is a karyotype?

The particular array of chromosomes in an individual organism

What is a haploid?

One set of chromosomes, represented by 1n. In humans that is 23 chromosomes.

What is a diploid?

Two sets of chromosomes. Humans are diploid, meaning we have two complete sets of chromosomes (46).

What is a Centromere? A Kinetochore?

A centromere is a point of constriction, and a kinetochore is a complex of proteins that allows the chromosome to attach to the microtubules on the mitotic spindle.

After replication, each chromosome is composed of two identical DNA molecules, which are termed sister chromatids. Each sister chromatid has a centromere and a kinetochore, and they remain attaches through cohesin proteins until the late steps of mitosis.

What are the four levels of DNA packaging?

DNA, nucleosomes, solenoids, and mitotic chromosomes.

What are the phases of the cell cycle?

G1, S, G2, M Phase

What happens in G1?

The cell focuses on duplicating contents such as the plasma membrane, organelles, and macromolecules. This is the primary growth phase.

What happens in S phase?

Synthesis, or DNA replication.

What happens in G2?

Another gap or growth phase, in this phase the cell not only grows slightly larger but also begins to prepare for M phase. The cell duplicates the centromere which organizes the microtubule array in the cell. Centromeres are used as markers for centrosomes during duplication. The two structures serve as the organizing poles of the mitotic spindle.

What happens in M phase?

Also called the mitotic phase, the cell almost completely rearranges its contents to execute processes of nuclear division and cytoplasmic division.

What is interphase?

G1, S, and G2. The part of the cell cycle in which the cell grows and carries out normal function.

What are the stages of mitosis?

Prophase, Prometaphase, Metaphase, Anaphase, Telophase, and Cytokenesis.

What happens in Prophase?

The bipolar mitotic spindle and the chromosomes condense into readily visible structures.

What happens in pro metaphase?

DIRECTLY BEFORE: disassembly of the nuclear envelope, and the chromosomes are released into the cytosol. The kinetochores of the chromosomes attach to the microtubules of the mitotic spindle and are oriented so that one sister chromatid interacts with one pole and the other with the other. The chromosomes then congress, or move, to the spindle equator (metaphase plate).

What happens in metaphase?

Once the chromosomes are lined up at the spindle equator, the cell is said to be in metaphase.

What happens in Anaphase?

The sister chromatids will separate and move towards the poles as the connecting microtubules shorten. The poles then move farther away, to segregate as much as possible.

What happens in Telophase?

After the cell is segregated the chromosomes begin to decondense and the nuclear envelope begins to reform.

What happens in cytokenesis?

In animals, cleavage furrow begins to form due to actomyosin, and eventually the single cell will split into two. Plant cell cytokinesis happens through formation of a structure called the cell plate.

What are the two irreversible points in the cell cycle?

Replication of genetic material (S phase) and separation of the sister chromatids (Transition to Anaphase)

What are the three major cell checkpoints?

1. G1/S checkpoint: based on growth factors

2. G2/M checkpoint: is replication complete? any DNA damage?

3. M Phase: Are all chromosomes aligned along the mitotic plate?

What are proto-oncogenes?

Normal genes that become oncogenes when mutated, and are overexpressed. Gain of function mutation (only one copy needs to be mutated)

What are tumor suppressor genes?

Normal genes that code for proteins that detect problems and stop the cycle at checkpoints. Loss of function mutation: both copies of the gene need to be mutated.

Meiosis includes two round of ______________ but only one round of _______________.

Division, DNA replication.

What is synapsis?

association between homologous chromosome pairs in Meiosis I

What is crossing over?

the ability of homologues to exchange DNA segments (gene sequences)

The sites of crossing over are termed ______________.

Chiasmata.

When a heterozygote displays some aspect of multiple different alleles, but neither overpowers the other, this is known as _____.

A. incomplete dominance

B. half recessive

C. codominance

D. half dominant

C. Codominance

Sometimes one gene pair will interact so as to control the expression of a second gene pair in an interaction called ___.

A. dominance.

B. gene regulation.

C. pleiotropy.

D. epistasis.

D. Epistasis

In an experiment, pure red colored flowers are crossed with pure blue colored flowers. If blue is a dominant trait and red is a recessive trait, the first filial (F1) generation would contain ____ red flowers and the second filial (F2) generation would contain _____ red flowers.

A. 75%, 100%

B. 50%, 50%

C. 0%, 25%

D. 25%, 0%

C. 0%, 25%