Chapter 7: RNA and the Genetic Code Flashcards

Question

MCAT concept check the genetic code 7.1 page 256 question 5

Answer 1

The creation of mRNA from DNA is known as transcription. DNA cannot leave the nucleus as it will be quickly degraded. So mRNA is used.

Answer 2

Transcription produces a copy of only one of the two strands of DNA. Helicase and topoisomerase unwind and keep the DNA from supercoiling, allowing the machinery to access the gene of interest in the DNA. Transcription results in a single strand of mRNA, synthesized from the template or antisense strand. The mRNA strand is both complimentary and antiparallel to the DNA template strand.

Answer 3

RNA is synthesized by DNA dependent RNA polymerase. In eukaryotes, RNA polymerase II is the main one. It contains a TATA box, known for its high concentration of adenine and thymosine, which binds to promoter regions. (RNA polymerase I: rRNA; RNA polymerase III: tRNA and rRNA) RNA polymerase locates regions of interest through transcription factors and promoter regions.

Answer 4

No. Unlike DNA polymerase, which requires a primer region, RNA polymerase does not require a primer.

Answer 5

RNA polymerase revels along the strand in the 3’-5’ direction, which allows for the construction of transcribed mRNA in the 5’-3’ direction.

Answer 6

Unlike DNA polymerase, RNA polymerase, does not proofread its work, so the synthesis transcript will not be edited.

Answer 7

The coding strand of DNA is not used as a template during transcription. Because the coding strand is also complementary to the template strand, it is identical to the mRNA transcript save for uracil replacing thymine in RNA.

Answer 8

The first base transcribed from DNA to RNA is defined as the +1 base. Bases to the left of the starting point (upstream toward the 5’ end) are given negative numbers. Basis to the right of the starting point (downstream toward the 3’ end). The TATA box, where the RNA polymerase binds is around -25. No nucleotide in the gene is numbered zero.

Answer 9

When RNA polymerase reaches a termination sequence or stop signal, transcription will discontinue. The product of transcription is termed heterogenous nuclear RNA (hnRNA). hnRNA will be posttranscriptionally modified to mRNA.

Answer 10

hnRNA is heterogenous nuclear RNA and is the precursor for mRNA. hnRNA (heterogenous nuclear RNA) gets posttranscriptionally modified to mRNA.

Answer 11

hnRNA must undergo three specific processes before it can leave the nucleus and interact with the ribosome. Modifications are required to survive the conditions of the cytoplasm. The three things that happen are: Intron/Exon splicing 5’ cap 3’ poly tail heterogenous nuclear RNA (hnRNA) is posttranscriptionally modified to mRNA.

Answer 12

The three things that happen are: Intron/Exon splicing 5’ cap 3’ poly tail

Answer 13

hnRNA must have introns (noncoding) excised and exons (coding) spliced. Spliceosomes splice together exons in hnRNa. In the spliceosome, small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (snRNP or snurps) splice sites of the introns. The non coding regions are excised in the form of a lariat and then degraded.

Answer 14

The small nuclear RNA and small nuclear ribonucleoprotein complex (snRNA/snRNP) complex regained the 3’ and 5’ splice sites of the introns and excise the introns for degradation.

Answer 15

At the 5’ end of the hnRNA molecule, a 7-methylguanylate triphosphate cap is added. This is recognized by the ribosome as the binding site. It also protects the mRNA from degradation.

Answer 16

The 3’ tail is a polyadenosyl tail (poly-A) and protects the 3’ end from degradation. It is composed of adenine bases. The 3’ poly tail: Assist with the export of the mature mRNA to the cytoplasm. Works as a fuse. The longer the poly a tail, the longer it will last before degradation in the cytoplasm.

Answer 17

The primary transcript of heterogenous nuclear RNA (hnRNA) may be spliced together in different ways to produce multiple variants of proteins and coded by the same original gene. This is referred to as alternative splicing.

Answer 18

RNA polymerase II binds to the TATA box, which is located in the promoter region of a relevant gene at about -25.

Answer 19

Poly a tail 5’ end Intron/exon splicing

Answer 20

Alternative splicing is the ability of some genes to use various combinations of exons to create multiple proteins from one hnRNA transcript. This increases protein diversity and allows the species to maximize the number of proteins it can create from a limited number of genes. Alternative splicing makes different isoforms of exons and proteins.

Answer 21

Translation is the converting of the mRNA transcription into a functional protein. Translation happens in the cytoplasm. Once the mRNA transcript is created and processed, it exits through the nucleus through nuclear pores.

Answer 22

The ribosome is composed of proteins and rRNA. The ribosome are the enzymes that catalyze translation. The three binding sites of the ribosome are: A (aminoacyl) P (peptidyl) E (exit) There are large and small subunits that only bind together during protein synthesis.

Answer 23

The genes that transcribe ribosomal RNA are located in the nucleolus. This is what differentiates the nucleolus from the nucleus. Although they contain the same DNA, the nucleolus is the site of transcription of rRNA. RNA polymerase I transcribes most of the rRNA, RNA polymerase III does some rRNA but mostly tRNA.

Answer 24

The difference between eukaryotic and prokaryotic ribosomes allows us to target antibiotics such as: Macrolides like azithromycin and erythromycin Tetracycline (doxycycline) Vancomycin

Answer 25

Eukaryotic ribosomes are larger and contain different combinations of rRNA subunits.

Answer 26

Initiation (using initiation factors, IF) Elongation (using elongation factors, EF) Termination (using release factors, RF) GTP is required for each step of translation. GTP stands for guanosine triphosphate, a crucial molecule involved in cellular processes, especially in RNA synthesis and energy transfer, similar to ATP, but with a different sugar base (ribose) and nitrogenous base (guanine).

Answer 27

This is when the small and large ribosomal sub unit bind to the mRNA. Shine Delgarno sequences, in the 5’ untranslated region of the mRNA, are where the small subunit attaches on prokaryotes. 5’ cap is where the small subunit attaches in eukaryotes. The charged initiator tRNA binds to the AUG start codon through base pairing with its anticodon within the P site of the ribosome. Initiation factors assist in the binding together of the small and large subunit. IF are not permanently associated with the ribosome.

Answer 28

The charged initiator tRNA binds to the AUG start codon through base pairing with its anticodon within the P site of the ribosome. The large subunit, then binds to the small sub unit, forming the completed initiation complex.

Answer 29

The initial AA in prokaryotes is N-formylmethionine The initial AA in eukaryotes is methionine (MET, M)

Answer 30

Elongation is a three step cycle that is repeated for each amino acid added to the protein after the initiator methionine. A site: holds incoming aminoacyl-tRNA complex. This is the next AA to be added. P site: (Peptide bond site) where methionine first binds, and where all subsequent AA are joined together with PEPTIDE bonds. Requires peptidyl tranferase, an enzymatic part of the large subunit. E site: inactivated (uncharged) tRNA chills here and then leaves. GTP is used for energy in this step.

Answer 31

Elongation factors assist by locating and recruiting aminoacyl-tRNA and GTP, also helps remove GDP once energy has been used.

Answer 32

When any of the three stop codes move into the A site, a protein called release factor (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain. The water molecule allows termination factors to hydrolyze the completed polypeptide chain from the final tRNA. The two ribosome subunits dissociate after the polypeptide chain is released from the tRNA and the P site.

Answer 33

Phosphorylation: addition of a phosphate group by protein kinases to activate or deactivate proteins. Phosphorylation in eukaryotes is most commonly seen with serine (Ser, S), threonine (Thr, T), and tyrosine (Tyr, Y). Carboxylation: addition of carboxylic acid groups, usually to serve as calcium binding sites. Glycosylation: addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination. Prenylation: addition of a lipid group to certain membrane bound enzymes.

Answer 34

Nascent polypeptide chains are subject to post translational modification before it will become a functioning protein. A few things can happen: Proper folding by chaperones is essential. Modified by cleavage events, like insulin. (Insulin needs to be cleaved from a larger and active peptide to achieve its active form, makes sense) Joining of subunits to come together to form quaternary structures (hemoglobin as an example) Attachment of bio molecules to the peptide, such as phosphorylation, carboxylation, glycosylation, and prenylation.

Answer 35

Initiation Elongation Termination

Answer 36

A site: binds incoming aminoayl tRNA using codon anticodon pairing. P site: holds growing polypeptide until peptide transferase forms a peptide bond and polypeptide is handed to E site. E site: transiently holds uncharged tRNA as it exits the ribosome.

Answer 37

Proper folding of proteins by chaperones Formation of quaternary structure Cleavage of proteins or signal sequences Addition of biomolecules, including phosphorylation, carboxylation, glycosylation, and prenylation.

Answer 38

An operon is a group or cluster of genes, transcribed as a single mRNA. Operons are a hallmark of prokaryotic genomes, rare in eukaryotes. The simplest example of an on off switch that regulates gene expression levels in prokaryotes was discovered in E. coli. The trp operon regulates the expression of many genes according to food sources available to the E. coli in the environment. Five genes arranged in a cluster on the chromosome in the E. coli encode for enzymes that manufacture tryptophan.. This cluster of gene shares a single common promoter region on the DNA sequence, and these genes are transcribed as a group known as the trp operon (for TRYPTOPHAN operon)

Answer 39

In the Jacob Monod model, operons contain structural genes, an operator site, a promoter site, and regulator gene. Operons are a hallmark of prokaryotic gene organization, much less common in eukaryotes. The structural gene codes for the protein of interest. The operator site is upstream of the structural gene and is a non-transcribing region of DNA that is capable of binding a repressor protein. The promoter site is further upstream from the operator site, it is similar in function to promoters in eukaryotes: it provides a place for RNA polymerase bind. Furthest upstream is the regulator gene which codes for a protein known as the repressor.

Answer 40

Inducible and repressible systems offer a simple on off switch for gene control in prokaryotes.

Answer 41

In inducible systems, the repressor act as a roadblock as it is bonded tightly to the operator system. The repressor blocks RNA polymerase from the promoter to the structural gene. (The repressor is in the way) Inducible systems may be either positive or negative control mechanisms. Systems in which the binding of a protein reduces transcription is negative control system. Systems in which the binding of a molecule increases transcription is positive control mechanism.

Answer 42

Inducible systems are analogous to competitive inhibition of an enzyme because as the concentration of the inducer increases, it will pull more copies of the repressor off of the operator region, freeing up those genes for transcription. This is a useful system because it allows gene products to be produced only when they are needed.

Answer 43

The lac operon it’s a classic example of an inducible system with a positive control mechanism. The lac operon contains the gene for lactase. Bacteria can digest lactose, but it is more energetically expensive than digesting glucose. Therefore, bacteria only want to use this option if lactose concentration is high and glucose concentration is low. The lac operon is induced by the presence of lactose, thus these genes are only transcribed when it is useful to the cell. Again, the lac operon is an inducible system with a positive control mechanism. The lac operon is assisted by binding of the catabolite activator protein (CAP). Falling levels of glucose cause an increase in the signaling molecule cyclic AMP (cAMP), which binds to catabolite activator protein (CAP). This induces a confirmational change in CAP that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene.

Answer 44

Negative control: the binding of a protein to DNA stops transcription. Positive control: the binding of a protein to DNA increases transcription. Inducible system: the system is normally off, but can be made to turn on given a particular signal. Repressible system: the system is normally on, but can be made to turn off given a particular signal. Any combination of control and system are possible: The lac operon is a induced negative control mechanism because, in the absence of lactose, a repressor protein binds to the operator region, preventing RNA polymerase from binding to the promoter and initiating transcription of the operon's genes. The trp operon is a negative control repressor system because, in the presence of sufficient tryptophan, the trp repressor protein binds to the operator, preventing RNA polymerase from transcribing the genes involved in tryptophan synthesis.

Answer 45

Repressible systems allow constant production of a protein product. In contrast to inducible systems, the repressor made by the regulator gene is inactive until it binds to a corepressor. This is a negative feedback.

Answer 46

The trp operon operates like this: When tryptophan is high in the local environment, it acts as a co-repressor. The binding of the two molecules of tryptophan to the repressor causes the repressor to bind to the operator site. The cell turns off its machinery to synthesize its own tryptophan, which is an energetically expensive process because of its easy availability in the environmental. The trp operon (tryptophan trp w) operon is a repressive system with a negative control mechanism.

Answer 47

Transcription factors are transcription activating proteins that search the DNA looking for specific DNA binding sites. Transcription factors tend to have two recognizable domains: DNA binding domain: binds to a specific nucleotide sequence in the promoter region or to a DNA response element (a sequence of DNA that binds only two specific transcription factors) to help recruit transcriptional machinery. Activation domain: allows for the binding of several transcription factors and other important regulatory proteins (such as RNA polymerase, and histone acetylases) which function in the remodeling of the chromatin structure.

Answer 48

Cis regulators: promoters, enhancers, and response elements (DNA regulatory base sequences) are known as cis regulators because they are in the same vicinity as the gene they control. Trans regulators: transcription factors, as they need to be produced in translocated back to the nucleus; trans regulators because they travel through the cell to their point of action.

Answer 49

Gene amplification is accomplished by eugenic cells through enhancers and gene duplication. Sometimes expression must be increased beyond basal transcription (moderate but adequate levels of protein and encoded by a gene in the cell)

Answer 50

Enhancers are a form of gene amplification. Response to elements outside the normal promoter regions can be recognized by specific transcription factors to enhance transcription levels. Several response elements may be grouped together to form an enhancer, which allows for the control of one gene expression by multiple signals. Examples of signal molecule and receptor are: cAMP (cyclic AMP response element binding protein CREB) Cortisol (glucocorticoid (cortisol) receptor Estrogen (estrogen receptor) By utilizing enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.

Answer 51

By utilizing enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.

Answer 52

Cells can increase the expression of a gene product by duplicating the relevant gene. Genes can be duplicated in series on the same chromosome yielding many copies in a row of the same genetic information. Genes can also be duplicated in parallel by opening the gene with helicases and permitting DNA replication only of that gene. Cells can continue replicating the gene into hundreds of copies of the gene exist in parallel on the same chromosome.

Answer 53

Recall that heterochromatin is tightly coiled DNA that appears dark under the microscope, is tightly coiled and inaccessible to transcription machinery. Recall that chromatin is loose and appears light under the microscope in transcription machine machinery can access the genes of interest. Remodeling of the chromatin structures regulates gene expression levels in the cell. Histone acetylation is an example.

Answer 54

Histone acetylation is a form of regulation of chromatin structure, where acetylation histone proteins allow for easy access to transcriptional machine machinery to DNA. Histone acetylase: acetylates lysine residues found in histone proteins, decreasing the positive charge on histone, weakening the histone interaction with DNA, effectively allowing for easier access of the transcriptional machinery to DNA. Histone deacetylase: removes acetylation of histones. Effectively silencing genetic expression in those regions.

Answer 55

DNA methylation is a mechanism of control over gene expression in eukaryotes. DNA methylation is involved in chromatic remodeling and regulation of gene expression levels in the cell. DNA methylase adds methyl groups to cytosine and adenine nucleotides; methylation of genes often linked with the silencing of gene expression.

Answer 56

Signal molecules include steroid hormones and second messengers which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA binding domain to attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can then promote increased expression of the relevant gene.

Answer 57

Histone deacetylation and DNA methylation will both down regulate the transcription of a gene. (DNA acetylation and demethylation up regulate transcription) These processes allow the relevant DNA to be lumped more tightly, increasing the proportion of heterochromatin.