Exam 2 Study Guide
Why do we say the genetic code is nearly universal?
Each codon specifies the same amino acid in all organisms. Nearly universal because a few exceptions have been found - Most are termination codons - One sense codon substitutes for another
Scientists studied the effect of mutations on lac operon using partial diploids (bacteria with a complete chromosome plus an extra piece of chromosomal DNA on a plasmid). The F plasmid (F-factor), a conjugative plasmid, is preferred because...
it exists as a single copy.
List the basic components of an operon and explain their function.
- Promoter: RNA polymerase attaches here; signals the start of the operon and the location where transcription begins - Operator: regulatory protein binds here; controls transcription of structural genes - Structural genes: codes for any RNA or protein other than a regulatory protein
What is the function of the lac repressor (lacI)? The diagram shows the activity of the lac operon depending on the availability of the lac repressor.
- inhibits transcription of the lac operon by binding to the operator - When bound, it gets in the way of RNA polymerase, and prevents it from transcribing the operon - Basically acts as a lactose sensor; it normally blocks transcription of the operon, but stops acting as a repressor when lactose is present
LacY(-) mutants cannot synthesize β-galactosidase in the presence of lactose even if all the other lac genes, including lacI, are functional. Why?
- lacY controls permease and a lacY- makes a nonfunctional unit because the lactose cannot enter the cell.
A eukaryote transcription unit contains four exons. a. Draw the structure of this transcription unit using boxes and lines and label the various components. b. Draw the pre-mRNA transcribed. Label its components including the 5' UTR and the 3' UTR. c. Draw the mature mRNA produced after pre-mRNA processing. Label all its parts.
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Note that, most organisms have 30 to 50 tRNAs (about 50 in humans) that carry the 21 amino acids during translation.
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How many start codons and stop codons exist in the standard genetic code?
3 start codon-usually AUG 3 stop codons - UAG, UAA, and UGA
What are the components of the core RNA polymerase and the RNA polymerase holoenzyme in bacteria?
5 subunits: ɑ, ɑ, β', β, ω two alpha (α) subunits of 36 kDa, a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. A sigma (σ) factor binds to the core, forming the holoenzyme.
In which direction do ribosomes read mRNA during translation?
5' to 3'
What is the genetic code and how many bases constitute a codon?
64 possible combinations of nucleotide sequences - the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) 3 bases
Explain the function of the three tRNA-binding sites (A, P, E sites) in the ribosome.
A - where tRNA enters ribosome - Charged tRNA binds to A site (elongation factor Tu joins with GTP) P - initiator RNA immediately occupies - releases amino acid from tRNA - Formation of peptide bond between amino acids attached to tRNAs - Occurs in large subunit E - ribosome shifts (5'-3') and codons do not move because of anticodon pairing - tRNA that occupied P site now occupies E site and is released into the cytoplasm to be recharged with an amino acid
Explain the mechanisms of RNA editing.
A process that results in a change in the sequence of a RNA transcript such that it differs from the sequence of the DNA template - insertion/deletion: RNA base added or deleted - substitution: RNA base replaced by another sequence is altered and protein will have a completely different function
Bacterial operons can be broadly divided into inducible and repressible operons. What is the difference between the two operons?
A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription. An example is the trp operon. A(n) inducible operon is one that is usually off; a molecules called an inducer inactivates the repressor and turns on transcription.An example is the lac operon. The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose.By itself, the lac repressor is active and switches the lac operon off.
Explain the different types of pre-mRNA processing in eukaryotes.
Addition of a 5' cap - Happens rapidly after initiation of transcription - Functions in the initiation of translation - Increases stability of RNA - Influences removal of introns - Facilitates binding of ribosome to 5' end of mRNA Addition of poly(A) tail - Not encoded in DNA -- added after transcription - Increases stability of mRNA - Increases time during which the mRNA remains intact and available for translation, before being degraded by cellular enzymes - Facilitates attachment of ribosome to mRNA RNA splicing - The removal of introns - Takes place in the nucleus before RNA moves to cytoplasm - Requires presence of three sequences in the intron
There is huge anticipation that CRISPR could enable us fix many genetic disorders. Briefly describe how we could correct genetic abnormalities in humans using this technology.
Allow genetic material to be added, removed, or altered at specific locations of the genome. Bacteria capture snippets of DNA from invading viruses and use them to create DNA segments
What is the function of the CRISPR/Cas system in bacteria and archaea?
Defense mechanism against viral infection
Explain why catabolite repression of the lac operon is a positive-inducible gene regulation.
In catabolite repression, the presence of glucose inhibits or represses the transcription of genes involved in the metabolism of other sugars. Because the gene expression necessary for utilizing other sugars is turned off, only enzymes involved in the metabolism of glucose will be synthesized. Operons that exhibit catabolite repression are under the positive control of catabolic activator protein (CAP). For CAP to be active, it must form a complex with cAMP. Glucose affects the level of cAMP. The levels of glucose and cAMP are inversely proportional—as glucose levels increase, the level of cAMP decreases. Thus, CAP is not activated.
How does mRNA editing produce different types of proteins from the same gene?
It changes the sequences by either inserting/deleting a base or substituting a base with another which alters the protein and causes it to have a completely different function
Based on the type of regulatory proteins that interact with the operon, regulation of the bacterial operon is classified as positive and negative control. Explain the difference between the two types of gene expression regulations.
Negative control occurs when a regulatory protein binds to DNA and shut downs transcription Positive control occurs when a regulatory protein binds to DNA and triggers transcription Lactose is the inducer binds directly to the lac repressor; causes it to release from the operator; ends negative control of the operon E coli is negative inhibition. meaning that it involves an operon being switch off by active form of repressor protein. Positive regulation is when the regulatory protein interacts directly with the genome.
Briefly explain how expression of the lac operon is regulated in presence/absence of lactose.
Negative control occurs when the repressor binds to the operator in the absence of lactose. The operon is not transcribed. Positive control occurs in the presence of lactose when CAP-cAMP help RNA polymerase to bind to the promoter and activate transcription.
Why do we say that the lac operon is a negative-inducible system?
Negative repressible operons is when an inducer is need to bind to the operon to prevent transcription. ... The lac operon is an example of negative inducible operons. In the presence of lactose, the repressor binds to the protein altering its shape so that it doesn't bind to the lac operator, and transcription occurs.
Do all RNAs in a cell code for proteins?
No; only mRNAs are translated into proteins
How are the amino acids in a polypeptide linked together?
Peptide bonds
What is a polycistronic RNA?
Polycistronic mRNA is where one gene produces one mRNA sequence, but one mRNA can produce multiple different proteins. This is possible because there are distinct regions on an mRNA that produce different proteins. These proteins often serve functions in a same pathway. Prokaryotes have polycistronic mRNA. - a group of genes is often transcribed into a single RNA molecule - a single terminator is present at the end of a group of several genes that are transcribed together, instead of each gene having its own terminator.
What is translation?
Process by which a protein is assembled from information contained in messenger RNA Amino acids assembled into proteins the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis. The genetic code describes the relationship between the sequence of base pairs in a gene and the corresponding amino acid sequence that it encodes
Compare RNA polymerases in prokaryotes and eukaryotes.
Prokaryotes utilize one RNA polymerase for all transcription of types of RNA. In contrast, eukaryotes utilize three slightly different RNA polymerases: - RNA polymerase I: synthesize precursors of rRNA - RNA polymerase II: synthesize precursors of mRNA - RNA polymerase III: produces sRNA including tRNA 5S rRNA and some sRNA
How is transcription in eukaryotes different from transcription in prokaryotes?
Prokaryotes: - Coupled transcription and translation. - Occurs in cytoplasm. - A single RNA polymerase synthesizes all 3 types of RNA - RNAs are released and processed in the cytoplasm. - Transcriptional unit has 1 or more genes. - Little process of mRNA. Eukaryotes: - Transcription and translation are separated. - Occurs in the nucleus. - The RNA polymers I, II, III synthesizes different types of RNA. - RNA's are released and processed in the nucleus. - Transcriptional unit has only 1 gene. - Processing of RNA includes: addition of 5'cap, 3'poly A tail, and splicing.
Describe the major differences between prokaryote and eukaryote protein synthesis.
Prokaryotic protein synthesis uses 70 S ribosomes and eukaryotic protein synthesis uses 80 S ribosomes. In eukaryotes protein synthesis occurs in cytoplasm. In prokaryotes protein synthesis occurs before transcription of mRNA molecule is completed. In eukaryotes, most of genes have introns but in prokaryotes there are no introns. In prokaryotes splicing does not occur but in eukaryotes splicing occurs. Only two initiating factors are involved in prokaryotic protein synthesis but nine initiating factors are involved in prokaryotes. No poly A tail is added to bacterial mRNA in prokaryotes but it is added in eukaryotes. No 5'G cap is formed in prokaryotes but it is formed in eukaryotes.
Give an example of mRNA editing in humans
RNA editing by C to U deamination - common in mammals - this is catalyzed by a complex known as the editosome, which induces a deaminase example: C -> U : UAA = stop codon - translation will stop
What is the role of the spliceosome?
Removes introns from a transcribed pre-mRNA
Describe the two major consensus sequences in bacterial promoters. What is their function?
Represent the most commonly encountered nucleotides at each position -10 consensus sequence- 5' TATAAT 3' -35 consensus sequence- 5' TTGACA 3'
What happens to the DNA template after transcription?
Rewinds back together It uses DNA as a template to make an RNA molecule. RNA then leaves the nucleus and goes to a ribosome in the cytoplasm, where translation occurs. ... It is the transfer of genetic instructions in DNA to messenger RNA (mRNA). During transcription, a strand of mRNA is made that is complementary to a strand of DNA.
There are two major mechanisms of transcription termination in prokaryotes: rho-dependent and rho-independent terminations. What is the difference between the two?
Rho-dependent: are able to cause the termination of transcription only in the presence of an ancillary protein called the rho (ρ ) factor Rho-independent: are able to cause the end of transcription in the absence of rho. - Multiple steps - AAAAAA on template of DNA strand
What is alternative splicing and how does it affect the mRNA and the protein produced?
Single pre-mRNA can be spliced in more than one way to yield multiple types of mRNA that are translated into different amino acid sequences, and thus, different proteins Alternative splicing is a process where a single pre-RNA is spliced in different ways so that segments of a transcript are treated as introns or as part of exons. For example, this produces mRNAs with different coding regions from a single gene, which ultimately leads to the synthesis of more than one polypeptide.
What are the differences between prokaryote and eukaryote ribosomes?
Small unit of prokaryote binds to the shine-dalgarno sequence of mRNA prokaryote ribosomes - 30S and 50S = 70S ribosome eukaryote ribosomes - 40 S and 60S = 80 S ribosome - synthesized in the nucleolus (suborganelle located within the nucleus of an eukaryotic cell)
What is the consensus sequence of the TATA box in eukaryote promoters?
The TATA box is a component of the eukaryotic core promoter and generally contains the consensus sequence 5'-TATA(A/T)A(A/T)-3'
Explain the wobble rule.
The Wobble Hypothesis explains why multiple codons can code for a single amino acid. One tRNA molecule (with one amino acid attached) can recognize and bind to more than one codon, due to the less-precise base pairs that can arise between the 3rd base of the codon and the base at the 1st position on the anticodon.
tRNAs carry amino acids on their 3′ end (amino acid acceptor end). Because all tRNAs have the same acceptor end (CCA), they cannot distinguish between two amino acids. Still, a tRNA carries only a specific type of amino acid. For example, a tRNA that carries leucine does not bind serine. Explain how a tRNA binds to a specific amino acid.
The enzyme aminoacyl-tRNA synthetase (aaRS) covalently links tRNAs to the correct amino acid during tRNA charging. There are 20 different aaRS enzymes, one for each amino acid. Each aaRS recognizes a specific amino acid by its shape and the matching tRNA(s) by their anticodons. During tRNA charging, the carboxyl group of the amino acid (-COOH) is attached to the OH group of the 2 or 3 carbon of A (the last nucleotide) in tRNA
Explain important properties of the genetic code.
Triplet code Non-overlapping - codons do not overlap No internal punctuation - Once you start reading, you don't stop until you reach the end. You read every nucleotide. Degenerate - There are multiple codons for each amino acid.Out of 64 codons , 61 coding and 3 noncoding codonssome amino acids are only coded for by one codon; whilst for others there are six different codons that can get you that particular amino acid Non-ambiguous - The nuclear genetic code does not change Co-linear - The beginning of the gene corresponds to the beginning of the protein; the same applies for the middle and end. (If applicable, introns are spliced out.) Universal - The codon charts are for the nuclear code in most organisms but chloroplasts and mitochondria do it slightly different, as they have their own chromosomes Ordered - Codons for an amino acid are group and codons for amino acids with similar properties are also grouped (ex. basic amino acids grouped together)
E. coli cells are growing in a medium that contains lactose but not glucose. Explain whether the following conditions increase, decrease, or do not change the expression of the lac operon. a. Addition of large amounts of glucose. b. A mutation that inactivates β-galactosidase. c. A mutation that prevents dissociation of the lac repressor from the operator. d. A mutation that inactivates permease. e. A mutation that prevents binding of cAMP-CAP to a site near the promoter.
a. Addition of large amounts of glucose. - As glucose increases, cAMP decreases. With low cAMP the CRP protein won't bind to help the RNA polymerease bind to the promoter site, so expression of lac operon decreases. b. A mutation that inactivates β-galactosidase. - If B-galactosidase is inactive, then allolactose can't be formed, and the lac operon cannot be turned on, so expression of lac operon decreases. c. A mutation that prevents dissociation of the lac repressor from the operator. - This would make the lac repressor permanently bound to the DNA and permanently turn off the lac operon so expression of lac operon decreases d. A mutation that inactivates permease. - If galactose can get in the cell then allolactose can't be formed, and the lac operon cannon be turned on, so expression of lac operon decreases. e. A mutation that prevents binding of cAMP-CAP to a site near the promoter. - The CRP protein won't bind to help the RNA polymerase bind to the promoter site, so expression of lac operon decreases.
Gene expression is controlled at multiple points during the flow of information from DNA to protein synthesis. Explain the major events in each of the following control points: a. Epigenetic control b. Transcriptional control c. RNA processing d. RNA stability e. RNAi f. Translation control and polypeptide processing g. Protein localization h. Protein turnover
a. Epigenetic control - control of gene expression by altering the chromatin structure (relaxed or compact) - compact DNA is inaccessible for transcription - compaction of the chromatin is influenced by modifications to histones and the DNA - the overall pattern of chromatin modification in a cell or an organism is called epigenome - ex: paramutation; effect of maternal diet on baby's development; genetic imprinting b. Transcriptional control - transcriptional activators bind to enhancers and increase transcription by stimulating / stabilizing the assembly of the basal transcription apparatus - insulators block the action of enhancers c. RNA processing - capping, splicing, poly(A) addition, alternative splicing, RNA editing d. RNA stability - degradation of the 5'cap, poly(A) tail, the 5' UTR, the RNA-coding region, and the 3' UTR affect stability of mRNA e. RNAi - uses short double-stranded RNAs known as miRNA and siRNA as a guide to suppress gene expression - only eukaryotes - RNA cleavage; blocking translation; chromatin condensation f. Translation control and polypeptide processing - translatoin initiation proteins bind to the 5' UTR and facilitate the binding of ribosomes - the translation of some RNAs is affected by the binding of proteins to sequences in the 3' UTR - some mRNAs regulate translation by forming secondary structures g. Protein localization - protein marked by Ubiquitin - proteasome recognize, choose protein, and recycle amino acids h. Protein turnover
What are the three steps of transcription? Describe the major events in each step.
a. Initiation - the transcription apparatus (transcription factors and RNA polymerase) assembles at the promoter to begin transcription. b. Elongation - RNA polymerase unzips the DNA double strand and adds new nucleotides to the growing RNA in a 5′ to 3′ direction. c. Termination - RNA synthesis stops.
The lac operon enables E. coli to metabolize the disaccharide lactose (Lac). Describe the function of the following components of the lac operon. a. Lac promoter (Plac) b. Lac operator (lacO) c. LacZ d. LacY e. LacA
a. Lac promoter (Plac) - sigma factor binds for polymerase b. Lac operator (lacO) - binding site for regulator protein Repressor(only binds when there is NO lactose) c. LacZ - breaks down lactose d. LacY - A membrane protein transporting lactose into cell e. LacA - unknown function
Describe the function of the following components of the CRISPR/Cas9 system in the bacterium Streptococcus pyogenes: a. The CRISPR repeat-spacer array (CRISPR array) b. The trans-activating crRNA (tracrRNA) region c. The CRISPR-associated protein (Cas) operon
a. The CRISPR repeat-spacer array (CRISPR array) - Cas9 uses the spacer to identify matching sequences in the viral DNA known as protospacers b. The trans-activating crRNA (tracrRNA) region - transcribed into tracrRNA, which is complementary to the palindromic repeats in the pre-crRNA - the tracrRNA also binds to the Cas9 enzyme to form the effector complex c. The CRISPR-associated protein (Cas) operon - cleavages the target gene
Know the function of the following genes and the regulatory sequences in the lac operon: a. lacI (lac repressor) b. lacP (lac promoter) c. lacO (lac operator) d. lacZ (β-galactosidase) e. lacY (lac permease) f. lacA (transacetylase)
a. lacI (lac repressor) - a protein that represses (inhibits) transcription of the lac operon by binding to the operator b. lacP (lac promoter) - the binding site for RNA polymerase, the enzyme that performs transcription c. lacO (lac operator) - a negative regulatory site bound by the lac repressor protein. The operator overlaps with the promoter, and when the lac repressor is bound, RNA polymerase cannot bind to the promoter and start transcription. d. lacZ (β-galactosidase) - encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. e. lacY (lac permease) - encodes a membrane-embedded transporter that helps bring lactose into the cell f. lacA (transacetylase) - function is unknown
Gene regulation (or control of gene expression) refers to...
cellular processes that control the rate and manner of gene expression
What is the function of the sigma factor?
controls the binding of RNA polymerase to the promoter
We discussed in class how enhancers, activator proteins, coactivators, mediators, and general (basal) transcription factors influence initiation of transcription in eukaryotes. Explain the role of each of these components and how they interact with each other to increase transcription.
enhancers - an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. activator proteins - determine which genes are expressed (could be cell specific); special transcription factors that interact with distal.proximal elements and promote (activators) or block (repressors) the recruitment of RNA pol to the promoter in response to certain cues coactivators - proteins required for the function of activators. Unlike activators, coactivators don't have DNA-binding domains. E.g., histone demethylases and histone acetyltransferases mediators - link activators to the basal transcription apparatus general (basal) transcription factors - needed for minimal transcription
Draw the structures of a eukaryote gene containing three exons. Include the control elements. What is the structure of the corresponding precursor RNA (pre-RNA) and the mature mRNA? What is the difference between pre-mRNA and mRNA?
example on SG - pre-mRNA is the immediate product of transcription which is comprised of both exons (coding sequences) and introns (non-coding sequences)
Mutations are usually designated using a "+" and a "-" sign. "+" is the normal or wild type and "-" is the mutant version. Describe effect of mutations on the right on expression of the lac operon.
lacI(-): operator-binding site is nonfunctional lacZ(-): functional permease - lac can enter, but can't be metabolized lacY(-): nonfunctional permease - can't use lactose because it can't enter the cell.
What are the major molecules required for protein synthesis?
mRNA rRNA tRNA
Define a polyribosome (polysome).
mRNA with several ribosomes attached in both prokaryotes and eukaryotes
What are the major gene regulation mechanisms in bacteria?
negative control - the regulatory protein is a repressor (decreases transcription) positive control - the regulatory protein is an activator which interacts with RNA pol and increases transcription CRISPR/Cas systems - sequence-specific defense systems in bacteria/archaea against viruses and plasmids
In bacteria, the holoenzyme recognizes and binds directly to the promoter. In eukaryotes, binding to the promoter and initiation of transcription requires the action of many accessory proteins. List three proteins needed in the transcription of eukaryote genes and explain their roles.
regulatory proteins that bind the enhancer and help RNA pol bind the promoter enhancers - an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. activator proteins - determine which genes are expressed (could be cell specific); special transcription factors that interact with distal.proximal elements and promote (activators) or block (repressors) the recruitment of RNA pol to the promoter in response to certain cues coactivators - proteins required for the function of activators. Unlike activators, coactivators don't have DNA-binding domains. E.g., histone demethylases and histone acetyltransferases mediators - link activators to the basal transcription apparatus general (basal) transcription factors - needed for minimal transcription
List the four steps of translation. Briefly explain what happens at each step.
tRNA charging - Entails the binding of amino acids to RNAs Initiation - The components necessary for translation assemble at the ribosome Elongation - The amino acids are joined, one at a time, to the growing polypeptide chain Termination - Protein synthesis stops at the termination codon, and the translation components are released from the ribosome
Why do we say protein synthesis is an energy demanding process?
tRNA charging requires ATP, while the other steps in translation require GTP. It takes quite a bit of energy to accomplish all the steps of protein synthesis
What are the components of ribosomes?
the small ribosomal subunits, which read the mRNA the large subunits, which join amino acids to form a polypeptide chain. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins
How does a ribosome identify mRNA for translation from the rest of the RNA species in the cell?
the small subunit moves along mRNA and finds the initiation codon
How many different types of amino acids are there?
20
How is translation terminated?
- When a ribosome comes across a termination codon - Release factors bind to ribosome
Note that, we do not use 5' and 3' notations to describe the beginning and the end of a polypeptide. We use the N-terminal and the C-terminal instead. N and C indicate the free amino end (-NH2) and the free carboxyl end (-COOH), respectively.
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Please watch the animations: lac operon, effect of lac mutations, and catabolite repression on the course website.
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Remember that mRNA is translated in a 5′ 3′ direction (that is, left to right).
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The cartoon on the right depicts the structure of a typical eukaryote gene with four exons, three introns, and its control elements.
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What is an operon?
An operon is a group of genes that share a common promoter and are transcribed as a unit, producing a single mRNA molecule that encodes several proteins. Prokaryotes generally contain the operon
Explain what happens to the nucleosomes during transcription in eukaryotes.
Because eukaryotic DNA is tightly wrapped around nucleosomes and the positive charges of the histones tightly bind the negative charges of the DNA, nucleosomes essentially act as a physical barrier to transcription factors that need to bind to certain regions of DNA
What are the major modifications in polypeptides?
Cleavage Chemical modifications: methylation, phosphorylation, acetylation, glycosylation Proper folding Targeting to cellular organelles Assembly of subunit polypeptides
What is a reading frame? Explain what will happen to the polypeptide produced if there is a deletion or insertion of a base in the mRNA.
Each different way to read a sequence; any sequence of nucleotides has three potential reading frames It will change the sequence of the reading frame and change what protein is to be synthesized
Expression of the human globin genes is developmentally regulated. For example, fetal hemoglobin is mainly composed of two α and two γ globin polypeptides and adult hemoglobin contains two α and two β globin polypeptides. Fetal hemoglobin is efficient at binding oxygen than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream. How is expression of the fetus and adult hemoglobin regulated?
Enhancers control the developmental regulation of these genes. - During the fetal stage, LCR activates expression of the y genes; the B globin genes are turned off. - In adult human, LCR enhances expression the B gene; the y globin gene is silenced.
List some of the functions of proteins.
Enzymes Structural components Transport substances Regulatory, communication, or defense function
Chromatin (the complex of DNA and histones) is classified into euchromatin and heterochromatin. What is the difference between the two chromatins?
Euchromatin: undergoes the normal process of condensation and decondensation in the cell cycle - Where transcription takes place Heterochromatin: remains in a highly condensed state throughout the cell cycle, even during interphase
We discussed in lecture that removal of introns and stitching exons together is the most common type of mRNA processing. Splicing is a resource demanding process because it requires the synthesis of many proteins and snRNAs. Therefore, it makes no sense to have introns if they are removed during pre-RNA processing. Discuss any possible reasons why introns are present in eukaryotic genes.
Eukaryotes might need this diversity in proteins because they have many types of cells all with the same set of genes. Therefore, introns are a way to generate different proteins or different amounts of proteins that are unique to a cell type. Introns might also allow for faster evolution
Briefly describe the history of the discovery of the genetic code
Francis Crick confirmed in 1961 that the genetic code is a triplet code Nirenberg and Matthaei created synthetic RNAs
A tRNA carries the anticodon GUU. What is the corresponding codon and the amino acid carried by this tRNA?
GGA - Gly
Why do you think regulation of gene expression is important?
In bacteria, gene regulation maintains internal flexibility, turning genes on and off in response to environmental changes. In multicellular eukaryotic organisms, gene regulation also brings about cellular differentiation
Compare transcription termination in prokaryotes and eukaryotes.
In eukaryotes transcription is terminated by two elements: a poly(A) signal and a downstream terminator sequence Prokaryotes is done by either rho-dependent or rho-independent mechanisms
Some genes in bacteria are organized into operons. How is the structure and regulation of an operon in bacteria different from a eukaryote transcription unit?
Many prokaryotic genes are organized into operons and are transcribed into a single RNA molecule → most eukaryotic genes have their own promoters and are transcribed separately. DNA must partly unwind from the histone proteins before transcription can take place nuclear membrane in eukaryotic cells separates transcription and translation in time and space
Do prokaryote mRNAs undergo any processing
No transcription and translation happen at the same time
How is RNA editing different from alternative splicing?
RNA Editing: - alters the nucleotide sequence of RNA from the original sequence encoded by the gene - synthesize different proteins from same gene - insertion/deletion: RNA base added or deleted - substitution: RNA base replaced by another Alternative Splicing: - produces different types of mRNAs from the same pre-mRNA allowing the production of multiple proteins from the same gene - subset of splicing, joined together - during splicing introns are removed from the pre-mRNA and exons are joined
The template DNA has this sequence: GGG ATC GAT GCC CCT TAA AGA GTT. What is the amino acid sequence?
Template - 5' - GGG ATC GAT RNA 3' CCC UAG CUA 5' → translate ALWAYS 5' → 3' (reconverte it) 5'-AUC GAU CCC-3' LLE Asp Pro
Give an example of alternative splicing in humans.
The best example is the Drosophila Down syndrome cell adhesion molecule (Dscam) gene, which can generate 38,016 isoforms by the alternative splicing of 95 variable exons
What determines the amino acid sequence of a protein?
The nucleotide sequence the genetic code. The triplet of nucleotides in tRNA which are complementary to the base pairing of specific triplet nucleotides (codons) in mRNA during the translation phase of protein synthesis
Operons are common in prokaryotes. Do eukaryotes have operons?
Very few operons in eukaryotes In eukaryotes, each gene is made on individual mRNAs and each gene has its own promoter.
How do bacteria choose glucose over lactose if both sugars are present in the medium? Hint: explain using catabolite repression involving cAMP and the catabolite activator protein (CAP), also referred to as cAMP receptor protein (CRP).
when both glc and lac are present, E coli will use glc because it is energetically cheaper - a gene regulation mechanism known as catabolite repression enables bacteria to use glc over others - catabolite repression inhibits expression of genes for the metabolism of other sugars in the presence of glc - the enzyme adenylate cyclase (AC) serves as a glc sensor - AC synthesizes cAMP from ATP - AC is sensitive to high Glc concentration
