Unit 3 (Week 9 Gene Expression at a Molecular Level) Flashcards
Fun Fact: The degree of obesity is often similar between genetically identical twins who have been raised apart. Possible hypothesis for the answer as to why people gain weight based on genetic factors?
Some people have inherited “thrifty genes” as hand-me-downs from their ancestors, who periodically faced famines and food scarcity. Such thrifty genes would be advantageous in allowing people to store body fat more easily and to use food resources more efficiently when times are lean. The negative side is that when food is abundant, unwanted weight gain, and associated diseases such as diabetes and heart disease, can constitute a serious health problem.
What can we broadly define a gene as?
A unit of heredity.
What do geneticists view at different biological levels?
Gene function
What is gene function either at the level of traits or at the molecular level?
Gene expression
What is a gene that serves as a template to make an mRNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence?
Protein-encoding gene. Most genes are protein-encoding genes.
What was used as a successful approach in answering “How do genes affect the composition and/or function of molecules found within living cells?”
The study of mutations which is a heritable change in the genetic material of an organism.
What is a common amino acid found in human diets where mutations along the metabolic pathway can cause phenylketonuria, tyrosinosis, and alkaptonuria?
Phenylalanine.
What disease would result if a person inherited two defective copies of the gene that encodes phenylalanine hydroxylase?
A person with two defective copies of phenylalanine hydroxylase would have phenylketonuria.
Who was the one responsible for focusing on the inherited disease alkaptonuria, in which the patient’s body accumulates abnormal levels of homogentisic acid (also called alkapton)?
Archibald Garrod
This compound, which is bluish black, results in discoloration of the skin and cartilage and causes the urine to appear black.
What does it mean when a disease follows a recessive pattern of inheritance?
If the disease is recessive, an individual with the disease has inherited the mutant (defective) gene that causes it from both parents.
If only one is inherited, that gene will be masked and the dominant gene will prevail.
What did Garrod (1908) describe as a genetic defect that produces an inability to metabolize a certain compound?
Inborn error of metabolism
An inborn error refers to a mutation in a gene that is inherited from one or both parents. At the turn of the last century, this was a particularly insightful idea because the structure and function of the genetic material were completely unknown.
What did American geneticists George Beadle and Edward Tatum, after being interested in Garrod’s work on gene and enzyme relationships, focus their studies on?
Neurospora crassa, a common bread mold
What did Beadle and Tatum hypothesize about genes carrying the information to make a specific enzyme?
They reasoned that a mutation, that is, a change in a gene, might cause a defect in an enzyme required for the synthesis of an essential molecule, such as an amino acid.
What are strains that are without a mutation?
Wild-type strains
What enzyme function was missing in group 2 mutants in this experiment? (See Beadle and Tatum’s photo experiment in folder)
The ability to convert ornithine into citrulline is missing.
What was the hypothesis that Beadle and Tatum made that was later changed but their work on the role of genes and metabolism earned them the Nobel prize?
One-gene/one-enzyme hypothesis
How was the one-gene/one-enzyme hypothesis modified later? (4)
- The information to make all proteins is contained within genes, and many proteins do not function as enzymes.
- Some proteins are composed of two or more different polypeptides. The term polypeptide refers to a linear sequence of amino acids; it denotes structure. Most genes carry the information to make a particular polypeptide. By comparison, the term protein denotes function. Some proteins are composed of one polypeptide. In such cases, a single gene does contain the information to make a single protein. In other cases, however, a functional protein is composed of two or more different polypeptides. An example is hemoglobin—the protein that carries oxygen in red blood cells—which is composed of two α-globin and two β-globin polypeptides. In the case of hemoglobin, the expression of two genes (that is, the α-globin and β-globin genes) is needed to produce a functional protein.
- Some mRNAs (messenger RNAs) are spliced in alternative ways so they produce two or more polypeptides. This allows a single gene to encode more than one polypeptide.
- A fourth modification to the one-gene/one-enzyme hypothesis is that some genes produce non-coding RNAs that do not specify the amino acid sequence of a polypeptide.
[Review] T/F All information to make proteins are contained within genes, and they function as enzymes.
False. Yes, all of the information to make a protein is contained in genes however, all proteins do not function as enzymes.
[Review] T/F All proteins contain more than one polypeptide.
False. Proteins can be one polypeptide or more than one polypeptide.
[Review] What does polypeptide denote? What does protein denote?
Polypeptide denotes structure while protein denotes function.
[Review] T/F A single gene can sometimes contain the information to make a protein.
True.
[Review] Since proteins can involve two or more polypeptides, what MAY be needed in order for the protein to be synthesized?
Two or more genes would needed to expression different polypeptides.
For example, hemoglobin, the protein that carries oxygen in red blood cells, is composed of two a-globin and two B-globin polypeptides. In the case of hemoglobin, the expression of two genes, that is a-globin and B-globin genes, are needed to produce a functional protein, hemoglobin.
[Review] How are single genes able to encode more than one polypeptide?
The mRNAs are spliced in alternative ways so they produce two or more different polypeptides.
[Review] The fourth modification to the one-gene/one-enzyme hypothesis indicates what about genes and RNA?
Some genes produce non-coding RNAs that do not specify the amino acid sequence of a polypeptide.
What do you call the process that produces an RNA copy of a gene, which is also called an RNA transcript?
Transcription - The process that produces an RNA copy of a gene.
Transcription literally means the act of making a copy.
What is an RNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence?
messenger RNA (mRNA)
Where does the functional mRNA carry the information it obtained from DNA?
To ribosomes.
What is the process of synthesizing a specific polypeptide on a ribosome?
Translation. The second step after transcription.
Where does transcription and translation happen in bacteria?
Cytoplasm
Where does transcription and translation happen within eukaryotic cells?
Transcription happens in the nucleus while translation happens in the cytosol. Ribosomes are located in the cytosol.
Why do we use the term “translation” in gene expression?
This is used because a base sequence in an mRNA is “translated” into an amino acid sequence of a polypeptide.
Who coined the term of central dogma which refers to the steps of gene expression at the molecular level: DNA is transcribed into mRNA, and mRNA is translated into a polypeptide?
Ya boy Francis Crick in 1958. This applies to archaea, bacteria, and eukaryotes.
What step happens between transcription and translation in eukaryotes?
RNA modification, which is the the biochemical modification of an RNA, which deals with the RNA transcript also known as pre-mRNA in the cell’s nucleus.
What is the direction of flow of genetic information?
The usual direction of flow of genetic information is from DNA to RNA to protein, though exceptions occur.
When does the direction flow from DNA to RNA to protein include exceptions?
Certain viruses use RNA as a template to synthesize DNA.
What provides a blueprint for the characteristics of every organism?
Genes that constitute the genetic material. They contain the information necessary to produce an organism and allow it to interact appropriately with its environment.
[Start Transcription] What must happen for genes to be expressed?
The information in them must be accessed at the molecular level.
Instead of accessing DNA directly, what is done to get the information?
A working copy of the DNA, composed of RNA, is made.
This occurs by the process of transcription, in which a DNA sequence is copied into an RNA sequence.
What is defined as at the molecular level, a _____ is defined as an organized unit of base sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product?
A gene
Since most genes are protein-encoding genes, what may be the functional product itself which is transcribed but never translated?
The functional product will be RNA and one such molecule is called a non-coding RNA.
What are some examples of non-coding RNA?
Transfer RNA (tRNA) - An RNA that carries amino acids and is used to translate mRNA into polypeptides.
Ribosomal RNA - An RNA that forms part of ribosomes, which provide the site where translation occurs.
What is the sequence of DNA that controls when and where transcription will begin?
The promoter sequence.
What specifies the end of transcription?
The terminator.
What regulates transcription for the binding of regulatory proteins and affects the rate of transcription? It can either be enhanced or inhibited.
Regulatory sequences
What are the three stages of transcription where various proteins interact with DNA sequences?
Initiation, elongation, and termination.
What are similarities and differences between the function of DNA polymerase and that of RNA polymerase?
Both DNA and RNA polymerase use a DNA strand as a template and connect nucleotides to each other in a 5′ to 3′ direction based on the complementarity of base pairing. One difference is that DNA polymerase needs a pre-existing strand, such as a RNA primer, to begin DNA replication, whereas RNA polymerase can begin the synthesis of RNA on a bare template strand. Another key difference is that DNA polymerase connects deoxyribonucleotides, whereas RNA polymerase connects ribonucleotides.
What are the steps of initiation in transcription?
- Sigma factor binds to RNA polymerase.
- Sigma factor then recognizes the base sequence of a promoter and binds there.
- Sigma factor, therewithin, allows RNA polymerase to bind to the promoter as well.
- Initiation phase is complete when the DNA strands are separated near the promoter to form an open complex that is approx 10-15 bp long.
[Review] What is a protein that recognizes the promoter in a bacterial gene and binds RNA polymerase to the promoter as well?
Sigma factor
[Review] What is the enzyme that synthesizes strands of RNA during gene transcription?
RNA polymerase
[Review] When is the initiation phase completed?
When the DNA strands separate near the promotor.
[Review] What is formed when the DNA separates and the initiation phase is complete? How many bp long is it?
The open complex and it is approximately 10-15 base pairs long.
What is the second stage of transcription or translation, where RNA strands or polypeptides are made, respectively?
Elongation
What is synthesized during elongation after sigma factor is released and RNA polymerase begins to slide along the DNA that maintains an open complex as it goes?
RNA transcript
What is the DNA strand that is used as a template for RNA synthesis or DNA replication?
Template strand
What is the other strand called for protein-coding genes which is opposite of the DNA strand?
Coding strand - This has the same base sequences as the resulting mRNA, except that uracil replaces thymine inside the nucleotides.
Why is the coding strand named the way it is?
If you think about it, when DNA strands are separated, the resulting mRNA strand is complementary to the DNA. This means that, the opposite strand, which is also complementary to the template strand, has the information to code a polypeptide.
How would the DNA template with the sequence of
3’-TACAATGTAGCC-5’ be transcribed into an RNA sequence?
5’-AUGUUACAUCGG-3’
What does the DNA do behind the open complex?
It rewinds back into a double helix.
What is the direction RNA polymerase slides and what is the direction that RNA transcript is synthesized?
RNA polymerase slides along the template strand in the 3’ to 5’ direction, while it synthesizes RNA transcript in the opposite, 5’ to 3’ direction.
What causes RNA polymerase and the RNA transcript to dissociate from the DNA?
The terminator. The final stage of transcription, in which the RNA dissociates from the DNA, or of translation, in which the polypeptide is released from the ribosome.
When multiple genes are transcribed within a chromosome, say three genes, two of the genes are transcribed using the bottom strand but what about the third?
Instead of being transcribed from left to right, the third gene is transcribed from right to left using the TOP strand. Transcribed genes, however the orientation, always go from 5’ to 3’. The template strand is always read in the 3’ to 5’ direction
Since transcription is universal in all living things, what differs in eukaryotic cells?
Tends to involve a greater complexity of protein components than does the transcription of bacterial genes.
In eukaryotic cells, what polymerase is responsible for transcribing mRNA from eukaryotic protein-encoding genes? What about non-encoding genes, like tRNA and rRNA?
RNA polymerase II is responsible for transcribing mRNA while RNA polymerase I and II is responsible for transcribing tRNAs and rRNAs.
Bacteria has a single type of RNA polymerase that transcribes all genes. They do however have different sigma factors that can recognize different promoters.
E. Coli just needs sigma factor to recognize the promoter, but by comparison, RNA polymerase II of eukaryotic cells need what to initiate transcription?
5 transcription factors.
These are proteins that influences the ability of RNA polymerase to transcribe genes.
This binding of polymerase to the promoter and the five transcription factors form a preinitiation complex.
The assembled structure consisting of RNA polymerase II and transcription factors (GTFs) at the TATA box prior to transcription of eukaryotic protein-encoding genes.
Gene function either at the molecular level or at the level of traits is referred to as gene _______.
Expression
A unit of heredity can be broadly defined as a(n) _______
gene
Beadle and Tatum hypothesized that genes carry the information to make specific enzymes. They reasoned that a mutation might cause a defect in an enzyme required for the synthesis of an amino acid or another essential molecule such as a(n) ______.
Vitamin
What term refers to gene function at the level of traits or at the molecular level?
Multiple choice question.
Gene duplication
Gene expression
Genetic variation
Gene expression
An RNA copy of a gene is produced via the process of ______.
transcription
What is the function of mRNA?
Multiple choice question.
It contains the genetic information that is passed on from one generation to the next.
It carries information from DNA to ribosomes.
It catalyzes biochemical reactions required for cellular activities.
It corrects mutations that occur in cells.
It carries information from DNA to ribosomes.
In bacteria, transcription and translation occur in the ______.
Multiple choice question.
cytoplasm
nucleus
mitochondria
cytoplasm
Beadle and Tatum hypothesized that a mutation in a gene could cause ______.
an inborn error of metabolism
a change in ribosome structure
a defect in an enzyme
a defect in an enzyme
The ______ that constitute the genetic material provide a blueprint for the characteristics of every organism.
cells
genes
membranes
organelles
genes
At the molecular level, a gene is defined as an organized unit of DNA sequences that enables a segment of DNA to be transcribed into ___________, resulting in the formation of a functional product.
mRNA
For some genes, the functional product is the RNA itself. The RNA from a(n) ______ gene is never translated.
Non-coding
What type of RNA translates the language of mRNA into that of amino acids?
Multiple choice question.
Messenger RNA
Transfer RNA
Ribosomal RNA
Transfer RNA
The characteristics of an organism are rooted in the activities of cellular _____ encoded by genes.
Proteins
What must eukaryotic mRNA transcripts undergo?
Modifications to produce functional mRNA; typically longer RNA called pre-mRNA.
pre-mRNA undergoes modifications before being released from the nucleus.
What in eukaryotes, transcription produces a longer RNA, called pre-mRNA, which undergoes certain modifications before it exits the nucleus to form what as the final functional product?
mature mRNA or simply, mRNA
Of the three common modifications to pre-mRNA, what two involve the ends of the strand?
Capping and tailing.
Addition of a 5’ cap and a polyA tail.
What is the third modification that pre-mRNA undergoes?
Splicing; this involves removing internal segments called introns
What are the segments that are retained when pre-mRNA is spliced called?
Exons
What modified form in mature mRNAs of eukaryotes is covalently attached at the 5’ end, an event known as capping?
Modified form of guanine.
Capping - The process in which 7-methylguanosine is covalently attached at the 5´ end of pre-mRNAs of eukaryotes.
When does capping typically happen?
When pre-mRNA is being synthesized by RNA polymerase, usually when the transcript is 20-25 nucleotides long.
What is so important about this 5’ cap on mRNA?
It is recognized by cap-binding proteins to exit the nucleus.
It helps prevent degradation in the cytosol.
Additionally, it is recognized by cap-binding proteins to enable the mRNA to bind to ribosomes for translation.
What is the string of adenine nucleotides at the 3’ end of most mature mRNAs in eukaryotes?
Poly A tail.
Typically how long is the poly A tail what are the benefits (2)?
100-200 nucleotides in length and added enzymatically after the pre-mRNA has been completely transcribed.
- Long poly A tail aids in the export of the mRNA from the nucleus.
- Stabilizes the mRNA so it can exist for a longer period of time in the cytosol.
What effect, surprisingly, does a poly A tail have on mRNA within bacteria?
It makes it degrade more rapidly.
What were scientists astonished by in natural gene splicing?
That coding sequences within many eukaryotic protein-encoding genes are separated by sequences that are transcribed but not translated into protein.
Hence, the removal of introns and the excretion of exons.
What are the intervening DNA sequences that are found in between the coding sequences of genes?
Introns
What is the portion of RNA that is found in the mature mRNA molecule after splicing is finished?
Exons
What is the average amount of introns in a human gene?
9 introns. This can range from a few dozen to over 100,000 nucleotides. Rare among bacteria and archaea.
What is the complex of several subunits known as snRNPs that removes introns from the eukaryotic pre-mRNA?
Spliceosomes
What is the splicing of pre-mRNA in more than one way to allow the production of two or more different polypeptides from the same gene?
Alternative splicing
What does alternative splicing accomplish?
This increases the size of the proteome while minimizing the size of the genome.
How does rRNA and tRNA remove their introns?
Through self-splicing.
The phenomenon in which an rRNA or a tRNA catalyzes the removal of its own intron(s).
A biological catalyst that is an RNA molecule - Ribozyme
What is the code that specifies the relationship between the sequence of bases in the codons found in mRNA and the sequence of amino acids in a polypeptide?
Genetic code
How is the genetic code read?
Groups of three nucleotide bases called codons.
A sequence of three nucleotide bases that specifies a particular amino acid or a stop codon; codons function during translation.
How many different codons does the genetic code consist of?
64
T/F The genetic code is nearly universal with little exceptions.
True
What is the characteristic of the genetic code that more than one codon can specify the same amino acid?
Degenerate
The third base in the codon is the degenerate, or variable, base.
What is a three-base sequence—usually AUG—that specifies the first amino acid in a polypeptide?
Start codon
What does a large portion of mRNA function as?
coding sequence - the region of a gene or a DNA molecule that encodes the information for the amino acid sequence of a polypeptide.
What are one of three three-base sequences—UAA, UAG, and UGA—that signals the end of translation?
Stop codon; also called a termination codon or codon.
If a mutation eliminated the start codon from a protein-encoding gene, how would the mutation affect transcription, and how would it affect translation?
A protein-encoding gene would still be transcribed into RNA if the start codon was missing. However, it would not be translated properly into a polypeptide.
What refers to the order in which codons are read during translation?
How are the groups of three bases otherwise called?
Reading frame.
Triplet - in the 5’ to 3’ direction
What functions as the translator or intermediary between an mRNA codon and an amino acid?
Transfer RNA
What is a three-base sequence in tRNA that is complementary to a codon in mRNA?
Anticodon - Complimentary means they can bind each other. The anticodon in a tRNA corresponds to the amino acid that it carries.
What is a mixture of components isolated from cells that is capable of synthesizing polypeptides if mRNA is added or cell-free translation system?
In vitro translation system.
What is a mixture of components isolated from cells that is capable of synthesizing polypeptides if mRNA is added or cell-free translation system?
In vitro translation system.
Who made synthetic mRNA, they then determined which amino acids were incorporated into polypeptides?
Nirenberg and Ochoa - they radiolabeled 1 of 20 amino acids, in 20 different test tubes using one type of triplet.
The genetic code specifies the relationship between the sequence of nucleotides in ______ and the sequence of amino acids in a polypeptide.
Multiple choice question.
tRNA
mRNA
rRNA
mRNA
Why does translation need more components than transcription?
The sequence of codons in an mRNA molecule must be translated into a sequence of amino acids according to the genetic code.
What is mRNA?
Contains the information for the amino acid sequence of a polypeptide according to the genetic code.
What is tRNA?
A molecule with two functional sites: one site, termed the anticodon, binds to a codon in mRNA, and a second site is where an appropriate amino acid is attached.
What is Ribosome?
Composed of many proteins and rRNA molecules, the ribosome provides a location where mRNA and tRNA molecules can properly interact with each other. The ribosome catalyzes the formation of covalent bonds between adjacent amino acids to make a polypeptide.
What is translation factors?
Proteins needed for the three stages of translation. Initiation factors are required for the assembly of mRNA, the first tRNA, and ribosomal subunits. Elongation factors are needed to synthesize the polypeptide. Release factors are needed to recognize the stop codon and disassemble the translation machinery. Several translation factors use GTP as an energy source to carry out their functions.
What does the two-dimensional structure of tRNA resemble?
A clover leaf proposed by Robert Holley.
The structure has three stem-loops and a fourth stem with a 3′ single-stranded region
What is the stem in a stem-loop in tRNA? What about the loop regions?
The stem in a stem-loop is a region where the RNA is double-stranded due to complementary base pairing via hydrogen bonding, whereas the loop is a region without base pairing.
Where is the anticodon located in the stem-loop region?
The middle stem-loop region.
Where is the amino acid attachment site located on the stem-loop model?
The 3’ single-stranded region.
What does the three-dimensional structure of tRNA involve?
The folding of the secondary structure.
How did Nirenberg and Leder experimentally demonstrate the relationship between mRNA triplet sequences and amino acid sequences?
They synthesized synthetic RNA molecules with specific base sequences and determined which amino acids were incorporated into polypeptides.
How is a tRNA named?
According to the amino acid it carries.
Can a cell produce more than one type of tRNA Ser?
Yes, because the genetic code contains six different serine codons.
What is an enzyme that catalyzes the attachment of amino acids to tRNA molecules?
Aminoacyl-tRNA synthetase
What are the steps for aminoactyl-tRNA synthetases to attach an amino acid to a tRNA?
First, a specific amino acid and ATP bind to the enzyme.
Next, the amino acid is activated by the covalent attachment of adenosine monophosphate (AMP), and pyrophosphate is released.
In a third step, the activated amino acid is covalently attached to the 3′ end of a tRNA molecule, and AMP is released.
Finally, the tRNA with its attached amino acid, called a charged tRNA, or an aminoacyl tRNA, is released from the enzyme.
Which of the following components are necessary for translation?
mRNA
translation factors
tRNA
ribosomes
What is a ribosome composed of?
Large complex of structures called large and small subunits.
Ribosomal subunits are called XXS which refer to the rate at which these subunits sediment when subjected to a centrifugal force. How are they described?
This rate is described as a sedimentation coefficient in Svedberg units (S) in honor of Swedish chemist Theodor Svedberg, who invented the ultracentrifuge.
Where is the synthesis of eukaryotic rRNA occur?
In the nucleolus; a droplet organelle in the nucleus specialized for this specific purpose.
Where are ribosomal proteins made?
The ribosomal proteins are made in the cytosol and imported into the nucleus.
What are the names of the three sites where tRNA molecules bind to the ribosome?
The aminoacyl site
The exit site
The peptidyl site
James Watson proposed the two-model site, while Nierhaus and Rheinberger expanded it to a three-site model to include the exit site.
What molecules must assemble during the initiation stage of translation?
Multiple select question.
the first tRNA
ribosomal subunits
mRNA molecule
the DNA molecule
the first tRNA
ribosomal subunits
mRNA molecule
What is a protein that facilitates the interactions between mRNA, the first tRNA, and the ribosomal subunits during the initiation stage of translation?
Initiation factor
What promotes the binding between the mRNA and the small ribosomal subunit?
A region near the 5′ end of the mRNA is complementary to a region of rRNA in the small subunit. These complementary regions hydrogen bond with each other to promote the binding of the mRNA to the small ribosomal subunit.
Elongation continues until a stop codon moves into the A site of a ribosome. The three stop codons, UAA, UAG, and UGA, are recognized by a protein known as a release factor. The three-dimensional structure of a release factor protein mimics the structure of tRNAs, which allows it to fit into the A site.
Most antibiotics are small organic molecules, with masses of less than 2,000 Da. In some cases, antibiotics exert their effect because they inhibit or interfere with bacterial translation. Because the components of translation differ somewhat between bacteria and eukaryotes, some antibiotics inhibit bacterial translation without affecting eukaryotic translation. Therefore, they can be used to treat bacterial infections in humans, pets, and livestock.
