Lecture 8 - DNA processes Flashcards
T/F: every cell has DNA as its blueprint
true
what type of macromolecule is DNA?
nucleic acid
what are the monomers of DNA?
nucleotides
What are the 3 components of a nucleotide? Out of these 3, which component is different between the 4 nucleotides that make up DNA?
The 3 components of a nucleotide are sugar, phosphate, and a nitrogenous base. Out of these 3, the component that is different between the 4 nucleotides that make up DNA is the nitrogenous base. In DNA they are A, G, C, and T. In RNA they are A, G, C, and U.
What type of bond holds 1 DNA strand together? Which of the 3 components of the nucleotide are involved in this bond?
A phosphodiester (or covalent) bond holds 1 DNA strand together. The phosphate group and the sugar in this bond.
What type of bond holds 2 DNA strands to each other? Which of the 3 components of the nucleotide are involved in this bond?
The type of bond that holds 2 DNA strands together is a hydrogen bond. Of the 3 components of the nucleotide, the nitrogenous base pairs are involved in this bond.
Which nucleotides are complementary to each other (bind to each other) in DNA?
A=T
G=C
How is DNA different from RNA?
- DNA’s sugar is deoxyribose, while RNA’s sugar is ribose.
- DNA’s nitrogenous bases are A, T, G, and C, while - RNA’s nitrogenous bases are A, U, G, and C.
- DNA is double-stranded, while RNA is single-stranded.
- RNA is shorter than DNA.
- RNA is transient, and DNA is permanent
Both e.coli and humans have DNA, with their monomers as nucleotides. What are different, however?
The sequence of the letters (the bases/nucleotides) are different.
how many bases does e.coli have?
5 million
how many bases do humans have?
3.2 billion
DNA has what two strands?
two polynucleotide strands
what does DNA replication start and end with?
DNA replication starts with DNA and ends with DNA; it is just replicated
what does gene expression contain?
transcription and translation
what is the central dogma of life?
gene expression; DNA (gene) to RNA (codons) to protein (amino acids)
what is a gene?
a segment of DNA that encodes a particular product, which is usually a protein
what are bases?
nucleotides
what is dna replication?
it duplicates the DNA molecule so its encoded information can be passed on to the next generation
what are DNA’s nucleotide subunits?
-Sugar (deoxyribose) and
-Phosphate (negatively charged) backbone
-Nitrogenous bases (A,T,G,C)
is DNA a double-stranded or single-stranded helix?
double stranded
what are the complementary strands/base pair rules of DNA?
A=T
G=C
are DNA strands parallel or antiparallel? why is this important?
antiparallel; this is important because the Phosphate is connected to carbon 5 (5 ‘ prime end) and the base is connected to Carbon 3’.
One strand is synthesized in the direction in which DNA unwinds and it can be synthesized continuously. The other strand is synthesized in the opposite direction so has to be synthesized discontinuously. As more and more DNA unwinds, new primers have to be laid down to start synthesis.
is DNA supercoiled?
yes
what are RNA’s nucleotide subunits?
-Sugar (ribose) and
-Phosphate backbone
-Nitrogenous bases (A,U,G,C)
is RNA double or single-stranded?
single-stranded
is RNA shorter or longer than DNA?
RNA is always shorter than DNA
what are the three subtypes of RNA?
tRNA - transfer RNA
mRNA - messenger RNA
rRNA - ribosomal RNA
when does DNA replication occur in regard to binary fission?
it happens before binary fission
what is the starting signal for DNA replication?
Origin of replication (OriR)
In what direction does DNA replication happen?
bidirectional
DNA replication is semiconservative - what does that mean?
it uses the old DNA strand as the template for the new DNA strand; every new DNA molecule has 1 old and 1 new strand
what are the steps of DNA replication including the enzymes?
- DNA gyrase uncoils/relaxes the supercoiled DNA.
- DNA helicase separates the 2 DNA strands.
- DNA polymerase builds and adds nucleotides at the 3’ end. It also proofreads.
- RNA primers add spots to add bases. Primers are made by Primase.
- DNA helicase continues to unzip the strands, while DNA polymerase continues to add nucleotides.
- DNA ligase binds fragments together in the lagging strand.
- This process stops at the terminating site.
how many RNA primers do the leading strand use?
only uses one RNA primer
is the leading strand continuous or discontinuous replication?
continuous
how many RNA primers do the lagging strand use?
many RNA primers
is the lagging strand continuous or discontinuous replication?
discontinuous
how do DNA polymerase and DNA ligase play a part in the lagging strand?
DNA polymerase adds nucleotides and replaces all RNA primers with DNA nucleotides. DNA ligase binds fragments together.
what is transcription?
DNA - RNA
the synthesis of mRNA from DNA
what direction does transcription go?
unidirectional
which DNA strand is used for the template for RNA?
either one of the DNA strands can be used as the template for RNA
is RNA permanent or transient?
transient
what are the base pair rules for RNA?
A=U
G=C
how does transcription start?
it begins when the RNA polymerase binds to the promoter, on either on of the strands of the DNA
what are the steps of transcription?
- Starts with the RNA polymerase binding onto the promoter, on either of the strands of the DNA.
- Transcription can now begin.
- RNA polymerase moves across the template strand of the DNA, synthesizing the complementary single-stranded messenger RNA molecule.
- Synthesis goes from the 5’ end to the 3’ end.
- When RNA polymerase reaches the transcription terminator sequence, the mRNA and the RNA polymerase stop and dissociates from the DNA.
what is translation?
RNA - protein
mRNA has 3-letter codons that code for what 3 things?
-Amino acids
-Start codons
-Stop codons
how many codons are there for 20 amino acids?
61 codons for 20 amino acids
what is the start codon RNA and amino acid?
Codon: AUG
Amino acid: Methionine (f-Met)
what are the 3 stop codons?
UAA
UAG
UGA
what 3 things does translation need to occur?
-mRNA (the substrate)
-Ribosome (both units to make proteins)
-tRNA with amino acids (the interpreter)
what exactly is the tRNA?
it is connected to the anticodons on one side, and amino acids on the other side
what is the purpose of the anticodon on tRNA?
it recognizes the codon on the mRNA
what are the 3 steps of translation?
-Initiation
-Elongation
-Termination
what happens during initiation in translation?
-The ribosome subunits join the mRNA.
-The tRNA with f-Met enters the P-site (peptidyl site) and binds to the start codon (AUG).
-The second tRNA with its amino acid enters the A-site (acceptor site).
what happens during elongation in translation?
-The ribosome moves to the next codon (which is the next 3 amino acids) along the mRNA.
-A new tRNA with its amino acid enters the A-site.
-The empty tRNA exits via the E-site (exit site).
-The polypeptide chain grows in length.
what happens during termination in translation?
-The stop codon terminates the process.
-Enzymes will free the new polypeptide.
-The ribosomes and mRNA break apart and can be reused.
-The protein product can be modified (ex: folded into a functional protein).
is there a tRNA molecule that recognizes a stop codon in termination?
NO
how are the amino acids linked in translation
the amino acids are linked by peptide bonds
summary:
what are the substrates, end products, start signal, stop signal, and enzymes/molecules needed in replication, transcription, and translation?
-Replication:
1 DNA, 2 DNA, OriR, terminating site, DNA gyrase, DNA helicase, DNA primase, DNA polymerase, and DNA ligase.
-Transcription:
DNA, RNA (or mRNA), DNA promoter sequence, DNA terminator sequence, RNA polymerase.
-Translation:
mRNA, protein, start codon, stop codon, amino acids, ribosomal subunits, mRNA, tRNA.
difference between prokaryotes and eukaryotes here in gene expression **
**
in prokaryotes, is mRNA poly or monocistronic? what does that mean?
polycistronic; means one long mRNA, and this mRNA has info for more than 2 genes. It needs only 1 promoter and 1 stop signal.
what are the ribosomes in prokaryotes?
70s (50s + 30s)
how many ribosomes on mRNA can prokaryotes have?
one or more
when does/can translation occur in prokaryotes?
translation can start while mRNA is still being made
in eukaryotes, is mRNA poly or monocistronic? what does that mean?
monocistronic; meaning eukaryotes have only mRNA for every gene. They need a promoter and terminator for each gene.
is mRNA processed in eukaryotes? what does that mean?
yes, it means it has:
1. Caps at the start and tails at the ends of mRNA for stability.
2. Introns and cut out and removed, and exons are kept in the mRNA and connected together.
when can translation occur in eukaryotes?
mRNA needs to leave the nucleus into the cytoplasm before translation can begin
what are the ribosomes in eukaryotes?
80s (40s+60s)
which of the following pairs of terms do NOT belong together?
1. Replication: RNA primers.
2. Transcription: DNA polymerase.
3. Eukaryotic translation: tRNA with amino acid.
4. Prokaryotic translation: polycistronic mRNA.
- Transcription: DNA polymerase.
This is wrong because it should be RNA polymerase instead.
what is gene regulation?
it turns on certain genes when they are needed
E. coli has 5,000 genes, but they aren’t all used to make proteins, so E. coli can turn on and turn off certain genes. Why does it have this gene regulation?
E. coli has gene regulation because it doesn’t always need the 5,000 base pairs at every instance. This way energy and ATP are saved.
why is gene regulation important?
to preserve energy and ATP
do all genes for cell functioning need to be turned on at all times?
No
what is constitutive expression? + what is an example of the types of genes?
When the genes are always on; for example: housekeeping genes, like glycolysis because it is an essential metabolic pathway. Other examples are RNA and DNA polymerase.
what is inducible expression? +an example of the types of genes?
When in default, all genes are OFF. Examples: usually function in CATABOLIC pathways. Synthesis induced by chemical signal (ex: lactose).
what is repressible expression? +examples of those types of genes?
When in default, all genes are ON. Examples: usually function in ANABOLIC pathways. Repressed by high levels of the end product (ex: tryptophan).
what are two ways to regulate gene expression? AKA how do we switch genes on and off?
- Pre-transcriptional: no mRNA; this is the most energy efficient.
- Post-transcriptional:
- When translation is blocked; no enzyme.
- When the protein is blocked; the enzyme activity is regulated using inhibitors.
(Post-transcriptional can also be Post-translational)
does a gene always make a protein?
no, it can make tRNA or rRNA as well. (mRNA codes for a protein)
you can either stop what three things when you want to regulated gene expression?
-Transcription
-Translation
-Final chemical reaction
during pre-transcriptional gene regulation, what stops DNA replication/transcription *?
A repressor protein or DNA tag/methylation stops DNA replication and is like a roadblock.
during post-transcriptional gene regulation, how is transcription stopped?
by small interfering RNA
during post-translational gene regulation, how is translation stopped?
by enzyme inhibitors blocking the protein
what is an operon?
a series of related genes controlled by a region called an operator
in which organisms are operons located?
in prokaryotes only
what is an operator?
it controls whether genes are on or off.
what is the structure of the operon? what does it contain?
it contains:
1. The promoter - where RNA polymerase binds.
2. The operator: the regulatory region
is the operator a pre-transcriptional or post-transcriptional control?
pre-transcriptional
what is the lac operon?
an “inducible” operon that makes enzymes that break lactose down when lactose is present in the environment
what is the default of the lac operon?
Default - the switch is off. The repressor bound to the operator prevents the transcription.
Lactose is an inducer that does what?
Lactose is an inducer that binds to the repressor causing it to fall of the operator.
complete the following:
when an inducer is available, what operator does what?
when an inducer is available, the operator turns on.
when lactose is NOT available:
1. is the repressor bound?
2. does transcription happen?
3. is the operon on or off?
- Yes, the repressor protein binds to the operator to prevent it from continuing.
- No, transcription doesn’t occur.
- The operon is off.
when lactose is available:
1. is the repressor bound?
2. does transcription happen?
3. is the operon on or off?
- No, the lactose repressor PREVENTS the repressor protein from binding to the operator. This allows the process to happen, and transcription follows.
- Yes.
- The operon is on.
During lac operon, after transcription and translation happen, how many proteins do we get from this specific pathway?
3
in the biphasic growth curve chart, which shows glucose and lactose metabolism, which sugar is preferred and why?
glucose is preferred because it is metabolized first. when glucose is exhausted, lactose is then metabolized.
in the biphasic growth curve chart, how many lag phases are there?
There are two because e. coli likes glucose more and if it is available, the operator for lactose is off. The second lag phase is the time it takes for the lactose operator to turn on.
in the biphasic growth curve chart, how many stationary phases are there and why?
only 1 because it has completely run out of all food.
is the tryptophan operon inducible or repressible?
repressible
what does the tryptophan operon do?
it makes the amino acid tryptophan
T/F: some operons are inducible and some are repressible
true
what is the structure of the tryptophan operon?
it has a promoter, an operator, and 5 genes
when too much tryptophan is made, what happens?
the tryptophan binds to the repressor to stop the operon
is the repressor active when there’s low tryptophan?
no, it is inactive since we don’t need to block the making of tryptophan
what does the word epigenetics mean?
“above” genetics
what is epigenetics the study of?
-The study of how DNA (or RNA) interacts with a multitude of small molecules (epigenetic factors) found within cells to activate or repress genes.
-Basically, they are molecules that can turn on or off genes.
what is the source of epigenetic factors?
our environment (diet, medications, etc.)
what are examples of epigenetics?
DNA methylation or histone modification (they sit on DNA and turn it off)
what type of genetic regulation are DNA methylation and histone modification?
pre-transcriptional control
can epigenetic factors change over your lifetime? can some factors also be inherited over several generations, like trauma?
yes
what do epigenetic factors affect?
human development, aging, cancer, heart disease, mental illness, addiction, etc.
what is RNA interference? what type of genetic regulation are they?
RNA interference is the silencing of gene expression by either degradation of the target mRNA or blocking the translation of the target mRNA.
They are post-transcriptional control.
what is RNA interference mediated by?
by short interfering RNA (siRNA)
what 3 things are RNA interference important for?
-For controlling the expression of cellular or viral genes.
-To research the function of genes by knocking their expression.
-In therapy to turn off the expression of harmful genes.
which of the following represents post-transcriptional gene regulation:
1. Short interfering RNA
2. DNA methylation
3. Lac operon
4. Histone modification
- Short interfering RNA
Ciprofloxacin and erythromycin are antibiotics used to treat bacterial infections. Ciprofloxacin inhibits DNA gyrase, and erythromycin binds the A site on the 70S ribosome (50S subunit). Using your knowledge of nucleic acids and the DNA processes, explain in detail how these drugs work at the molecular level.
Answer: Ciprofloxacin binds and inactivates DNA gyrase. DNA gyrase is an enzyme that relaxes the supercoiling in a DNA molecule to allow for DNA replication and transcription. When these processes are blocked, bacteria cannot replicate their DNA or make proteins. As they cannot perform routine cellular functions or reproduce, bacteria die.
Erythromycin binds and blocks the A site (acceptor site) on the 70S ribosome. This is the site where new tRNA molecules with their amino acids dock to the mRNA (using complementary codon-anticodon binding). When tRNA docking is blocked, no new peptide bonds can form, and protein synthesis is halted. Since proteins are needed for bacterial functioning, the bacteria die.
DNA is characterized by what of the following:
1. A single strand of nucleotides with internal hydrogen bonding
2. Presence of the sugar, ribose
3. Nucleotides bonded A:C and G:T
4. Two strands of nucleotides running antiparallel
5. Use of the U base instead of the T base
- Two strands of nucleotides running antiparallel
If the DNA base sequence [3’ AATGCACCCG 5’] was transcribed into mRNA, what would the product be (in order)?
1. CGGGUGCAUU
2. TTACGTGGGC
3. UUACGUGGGC
4. CGGGTGCATT
5. None of the above
- UUACGUGGGC
Which of the following is true about DNA replication?
1. It is semiconservative
2. It requires many RNA primers on the leading strand
3. It proceeds continuously on both strands
4. It adds new nucleotides in the 3’ to 5’ direction
5. It is unidirectional
- It is semiconservative
Which molecule carries an anticodon, and what is its purpose?
1. DNA; replication
2. mRNA; transcription
3. tRNA; translation
4. rRNA; transcription
5. Amino acid; translation
- tRNA; translation
In an inducible operon, such as the lac operon, a(n) ___________ binds to the operator to prevent transcription of a gene or genes.
1. Activator
2. Repressor
3. Terminator
4. Producer
5. Inducer
- Repressor
A gene is a piece of DNA that has information to produce…?
tRNA, rRNA, mRNA, proteins
Pick out the wrong pair:
1. DNA polymerase - build new DNA strand
2. Promoter - start signal of DNA replication
3. DNA ligase - glues DNA fragments of the lagging strand
4. DNA helicase - unwinds double-stranded DNA
5. DNA gyrase - relaxes DNA supercoiling
- Promoter - start signal of DNA replication
Transcription proceeds in which direction:
5’ to 3’
Translation can proceed without:
1. ribosomes
2. DNA
3. amino acids
4. tRNA
5. mRNA
- DNA
Which of the following is (are) a type of pre-transcriptional gene regulation?
1. inducible operon
2. miRNA
3. enzyme inhibitors
4. siRNA
5. DNA methylation
- Inducible operon and
- DNA methylation
What are the three main components in the covid-19 mRNA vaccine?
- mRNA molecules that encode the spike protein of the virus.
- Lipid bubble or nanoparticle that encloses these mRNA molecules.
- Sugar and salt molecules that surround the nanoparticle to keep it intact.
What happens to the mRNA once it enters our cells? Does the mRNA alter our genetic material?
- The lipid membrane of the nanoparticle fuses with the lipid plasma membrane of our cells, releasing the mRNA in the cytoplasm. Here, mRNA is translated by ribosomes to make viral spike proteins, which are then transported to the plasma membrane. Our immune cells recognize the “foreign” viral spike proteins and mount an immune response to produce antibodies and “memory” cells.
- Viral mRNA in our cells is like a snapchat message - short-lived and is quickly destroyed. It never enters the cell nucleus, where DNA is stored. So, the vaccine does NOT alter our genetic material.
How does the vaccine protect us during a real infection?
In case of a real infection by the virus, antibodies and “memory” cells produced during vaccination help to immediately and effectively clear out the virus from our body.
What are the advantages of an mRNA vaccine over more traditional vaccines?
- It is faster to make as you just need to alter the mRNA portion of the vaccine for each new pathogen.
- It is safer as it does not contain inactivated or weakened pathogen, but just an mRNA of one of the pathogen proteins.
What are the three types of RNA and what are their roles?
The three types of RNA are:
mRNA: messenger RNA is made in transcription, and has 3-letter codons that code for amino acids, start codon, and stop codon.
tRNA: transfer RNA, which helps in translation, with one side being connected to a codon, and the other side being connected to an amino acid.
rRNA: ribosomal RNA, which helps to make proteins.
Why do organisms need to replicate their DNA?
Organisms need to replicate their DNA in order to divide, and the daughter cells get all the genetic material.
Where does DNA replication start and stop?
DNA replication starts at the origin of replication and ends at the terminating site.
Why is one strand of DNA replicated as the leading strand and another as the lagging strand?
Because the 2 strands are anti-parallel. One strand is synthesized in the direction in which DNA unwinds and it can be synthesized continuously. The other strand is synthesized in the opposite direction so has to be synthesized discontinuously. As more and more DNA unwinds, new primers have to be laid down to start synthesis.
In the lagging strand, what are Okazaki fragments?
They are discontinuous fragments that are made from the discontinuous replication and the addition of many RNA primers.
In the lagging strand, which enzyme replaces RNA in Okazaki fragments with DNA?
DNA polymerase
in the lagging strand, which enzyme is needed to join Okazaki fragments?
DNA ligase.
What is the composition of the new DNA molecules formed after replication (parent, new, mixed)?
The composition of the new DNA molecules formed after replication is mixed and it is semiconservative, meaning the old strand is used as a template for the new strand.
What is a gene? What are the 2 processes involved in gene expression?
A gene is a segment of DNA that codes for a protein (mRNA), rRNA, or tRNA. The two processes involved in gene expression are transcription and translation.
What enzyme is involved in transcription and what is its job?
The enzyme involved in transcription is RNA polymerase, and it binds to the promoter, moves across the gene, “melts” the DNA, and adds complementary nucleotides to make RNA.
Where does transcription start and stop?
Transcription starts at the DNA promoter sequence and ends at the DNA terminator sequence.
what is the job of tRNA with amino acids in translation?
tRNA with amino acids: the interpreter with 2 ends, one connected to the bases (anti-codon) and the other connected to the amino acids.
How many nucleotides are required to specify an amino acid? What are the groups of nucleotides called? Which RNA molecule(s) contain this information? What is the reading frame and why is it important?
3 nucleotides are required to specify an amino acid. The groups of nucleotides are called codons. The RNA molecule that contains this information is the mRNA. The reading frame is the 3 bases at a time read in mRNA
What are codons and anticodons? What does codon “degeneracy” mean?
Codons are 3 nucleotide bases in mRNA, and each codon is specific for an amino acid. Anticodons are on the tRNA and recognize the codon on the mRNA. Degeneracy is when there is more than one codon coding for the same amino acid.
Where does translation start and stop?
Translation starts at the start codon, AUG. It ends at the stop codon, and there is no tRNA for the stop codon.
Explain 3 ways in which the expression of a gene can be turned off.
Expression of a gene can be turned off by:
Pre-transcriptional gene regulation
Post-transcriptional gene regulation
Post-translational gene regulation
How is gene expression different between prokaryotes and eukaryotes?
Gene expression is different between prokaryotes and eukaryotes by:
- Prokaryotes’ mRNA can be polycistronic
- Eukaryotes mRNA are monocistronic
- In prokaryotes, translation can start while mRNA is still being made
- In eukaryotes, the mRNA that needs to leave the nucleus before translation can begin
- In prokaryotes, the mRNA is not processed.
- In eukaryotes, the mRNA is processed.
What is an operon? How are “inducible” operons different from “repressible” operons?
An operon is a series of related genes controlled by an operator, only in prokaryotes. Inducible operons have a default of the genes being off and they can be turned on with an inducer, whereas repressible operons’ default genes are on and turned off by excess product
Explain gene expression of lac operon in the absence and presence of lactose. Is this an example of pre- or post-transcriptional gene regulation?
- In the absence of lactose, the repressor protein is bound to the operator to prevent it from continuing gene expression. Transcription does not occur, and the operon is off.
- In the presence of lactose, the lactose binds to the repressor such that its shape changes and it prevents the repressor protein from binding to the operator. This allows gene expression to happen. Transcription does occur, and after transcription and translation happen, we get three proteins from this specific pathway. The operon is on in this case.
This type of gene regulation is pre-transcriptional.
Define epigenetics and RNA interference. Are they examples of pre- or post-transcriptional gene regulation?
Epigenetics: The study of how DNA or RNA interacts with a multitude of small molecules, called epigenetic factors, found within cells to activate or repress genes. Pre-transcriptional
RNA interference: The silencing of gene expression by either degrading the target mRNA or blocking the translation of the target mRNA. This is an example of post-transcriptional gene regulation.
