Module 5 - Notes Flashcards
What was Mendel’s contribution to the discovery of DNA?
Inheritance
Chromosomal theory of inheritance
Who was responsible for the “one gene - one polypeptide” thinking?
Beadle and Tatum
When was DNA discovered?
Late 1800s
When did scientists make the connection between DNA and inheritance?
1950’s
What was the significance of Griffith’s transformation experiments?
He showed that hereditary information could be transferred between bacteria using bacteria and mice
What was the advancement of the Avery, MacLeod and McCarty experiment?
They developed a way to test (prove) DNA was responsible for inheritance.
How did Alfred Hershey and Martha Chase contribute to identifying DNA was responsible for inheritance?
They confirmed that DNA was responsible for inheritance with experiments with bacteriophages.
32P-labelled DNA and 35S-labelled protein coat marked bacteriophages to test if viral protein or viral DNA entered the host cell.
What were the results of the experiment by Alfred Hershey and Martha Chase?
After centrifugation
The 35S-labelled protein coat remained in the pellet and the 32P-labelled DNA was found in the supernatant (bacteria)
What does it mean to have C & G rich bacteria?
They have more Cytosine and Guanine in the genome.
What makes up DNA?
Deoxyribose sugar
Phosphate
Nitrogenous base
What is meant by 5’ to 3’ and vice versa?
refers to directionality
Nucleoside triphosphates combine with each other by covalent bonds known as 5ʹ-3ʹ phosphodiester bonds to form the sugar-phosphate backbone of DNA
Do DNA strands run parallel or antiparallel to each other?
antiparallel
The nitrogenous bases are complementary
A - T and C- G
The sugar-phosphate backbone runs from 5’ to 3’ on one side and 3’ to 5’ on the other side.
What happens when DNA is denatured?
The bonds break between the nitrogenous bases.
What causes DNA to denature?
heat
95-100 degrees celsius will break the bonds.
What is the function of DNA?
Contains genetic information
There is no structural function.
How is DNA organized in cells?
Organized into a chromosome
What do Eukaryotic chromosomes look like?
Linear (uses the protein histone)
Haploid or diploid
multiple copies
Histone is present
What do prokaryotic chromosomes look like?
single copy
circular (supercoiled by topoisomerase)
haploid
lack histone
What do Archaea chromosomes look like?
Have both circular and linear
supercoil & histone
Mix of both.
What are extrachromosomal DNA?
genes that are non-essential
plasmids - found in archaea & bacteria
Mitochondrion & Chloroplast in Eukaryia
If a DNA strand contains the sequence 5’-ATTCCGGATCGA-3’ which of the following is the sequence of the complementary strand of DNA?
A. 5’-ATTCCGGATCGA-3’
B. 5’-TCGATCCGGAAT-3’
C. 5’-TAAGGCCTAGCT-3’
D. 3’-TAACCGGTACGT-5’
B. 5’-TCGATCCGGAAT-3’
Reverse complementary
What is the central dogma?
The flow of information
DNA -> RNA -> Protein
What is the process from DNA to RNA?
Transcription
What is the process from RNA to Protein?
Translation
(a new language)
What types of RNA can be transcribed from the DNA?
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
How does the transcription process in a eukaryotic cell compare to that of a prokaryotic or archaic cell?
Eukaryote
1 gene = 1 protein
Prokaryote & Archaea
more than 1 gene for an RNA molecule
What is the conservative DNA replication process?
What is the semi-conservative DNA replication process?
What is the dispersive DNA replication process?
How many origins of DNA replication does a bacteria have?
1 origin of replication
How many origins of DNA replication does a eukaryote have?
Many origins of replication
What removes the twist of a DNA strand in bacterial DNA replication?
topoisomerase / gyrase
How many origins of replication does an archaea have?
1 or multiple
What starts the replication process in bacterial DNA replication?
RNA primer
Bacterial DNA replication is bidirectional. It creates a bubble in the DNA molecule splitting the DNA into 2 strands. What are the 2 strands called?
Leading Strand
Lagging Strand
Which strand has continuous synthesis during DNA replication in bacteria?
The Leading Strand
The synthesis is moving in the direction that moves into the fork of the bubble
Which strand has discontinuous synthesis resulting in Okazaki fragments during DNA replication in bacteria?
The lagging strand
The synthesis is moving in the direction away from the fork of the bubble.
What is the consequence of having bidirectional replication?
A. The creation of a leading and lagging strand
B. The creation of Okazaki fragments
C. The creation of a discontinuous fragment
D. The need for 2 DNA Polymerases to be attached to the replisome.
E. All of the above
E. All of the above.
What is primase?
The enzyme that synthesizes RNA primers that are needed to start replication.
What is DNA Polymerase III?
The main enzyme that adds nucleotides in the 5’ to 3’ direction.
What is helicase?
The enzyme that opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases.
What is Ligase?
The enzyme that seals the gaps between the Okazaki fragments on the lagging strand to create one continuous DNA strand.
What is the role of the sliding clamp?
Helps hold DNA pol III in place when nucleotides are being added.
What is Topoisomerase II (DNA Gyrase)
The enzyme that relaxes supercoiled chromosomes to make DNA more accessible for the initiation of replication.
Which component(s) is/are associated for DNA replication?
Primase - RNA polymerase doesn’t start without primase
DNA ligase - If you have breaks it will lead to mutations
Helicase - Needed to open up the strand.
What is the central dogma?
DNA to RNA to Protein
What is the function of mRNA?
serves as an intermediary between DNA and protein. Used by ribosome to direct synthesis of protein it encodes.
What is the function of rRNA?
Ensures the proper alignment of mRNA, tRNA and ribosome during protein synthesis. Catalyzes peptide bond formation between amino acids.
What is the function of tRNA?
Carries the correct amino acid to the site of protein synthesis in the ribosome.
Describe to process of Transcription to create an mRNA.
RNA Polymerase
-5’ - 3’ direction, no primer is needed
DNA is the template
-One strand is transcribed
Resulting RNA
-antiparallel and complementary
Transcriptional Unit
-single mRNA molecule
What are the promoter regions in transcription?
Specific DNA sequence
Sigma Factor (recruits the RNA Polymerase)
ex. Pribnow box (-10) TATAAT
ex. -35 region - TTGACA
The stronger the match, the stronger the binding will happen
Alternative sigma factors - response to different stresses/signals/environments
Why do bacteria have more than 1 sigma factor?
It provides genetic regulation of transcription and helps bacteria respond to their environment
What is polycistronic mRNA?
Multiple genes are under the control of one promoter.
How does transcription know when to stop?
Termination Sequence
-specific sequence
Stem Loop
- GC rich sequence
-inverted loop
-causes the polymerase to fall off
Rho-Dependent (Protein)
-Rho causes RNA to release
Which of the following components is involved in the initiation of transcription?
A. Primer
B. Origin
C. Promoter
D. Start Codon
C - Promoter
just need a promoter to recruit your enzymes to initiate the process.
Which of the following types of RNA codes for a protein?
A. tRNA
B. mRNA
C. rRNA
D. RNase
B. mRNA
What is the purpose of Translation?
Changes the language going from nucleic acid to proteins.
How are proteins synthesized in translation?
Protein synthesis requires amino acids. Each Amino acid sequence has its own code
What is codon bias?
bacteria prefer certain codons.
Ex. GC rich bacteria
They don’t use all the codons equally
ex.CUU, CUC, CUA & CUG code for Leu. But GC rich bacteria may only code for Leu when they read either CUC or CUG
In translation, what is the a-site, p-site and e-site?
A-site - acceptor
P-site - growing peptide chain
E-site - tRNA (exit)
What are the Svedberg units for prokaryotic RNA?
30S rRNA (small sub-unit)
made of 16S + Proteins
50S rRNA (large sub-unit)
Made of 23S + Proteins
70S rRNA (complete
made of 30S + 50S
When thinking about the gene (ie. DNA sequence) the sequence of the tRNA anticodon is?
The exact same of the DNA template (but with uracil)
Which of the following components is involved in the initiation of translation?
A. Ribosome Binding Site
B. Start Codon
C. Promoter
D. Primer
B.Start Codon
Which components are involved in translation?
What happens in Initiation?
transitional complex forms, and tRNA brings first amino acid in polypeptide chain to bind to start codon on mRNA
What happens in elongation?
tRNAs bring amino acids one by one to add to the polypeptide chain
What happens in termination?
Release factor recognizes stop codon. translational complex dissociates, and a completed polypeptide is released.
You are developing a drug that will target a newly identified archaeal pathogen. Your drug targets transcription but exhibits high toxicity towards eukaryotic cells. What is the best explanation?
The drug targets the RNA polymerase and prevents its activity
How can we control the flow of genetic information and regulation?
DNA -> RNA (transcription)
control mRNA production
RNA -> Protein (Translation)
control mRNA stability or control translation
Protein (Post-transcriptional)
control protein activity
If you want to stop transcription, a regulator should bind
A. The promoter region
B. The operator region
C. The start codon
D. The origin of regulation
A & B
The Promoter Region - If you bind it you prevent the sigma factor from binding to it and prevent the whole assembly
The Operator Region - If you bind the operator you will block transcription
Why would cells have genetic regulation?
Maximize the uses of resources
- coordinate numerous reactions
Genes are constitutively expressed
- essential function
Genes are expressed when needed
- only transcribed under specific conditions
Control the amount of protein produced
- transcription and translation
- genetic regulation
What are the transcription factors in genetic regulation?
Transcription
- more mRNA = more protein
Transcription Factors
- allosteric
Activator
- turn on expression
- help recruit RNA polymerase/sigma factor
Repressor
- turn off expression
- block RNA polymerase/sigma factor binding
Effectors
- change binding affinity
What is the protein activator in genetic regulation?
CAP
Which co-factor binds with CAP to increase RNA synthesis?
cAMP
How does repression block RNA synthesis?
When tryptophan (trp) is present, it allows the repressor to bind to the operator and blocks RNA synthesis.
The operator is only important in repression
How does de-repression allow RNA synthesis to proceed?
When lactose is present, the repressor is released from the operator, and the transcription proceeds.
What would happen if you removed the ability of a repressor protein to recognize the operator region?
The genes would never be repressed.
How would you increase the production of a protein when a specific molecular signal is present?
design an activator that recognizes the molecular signal (ie. inducer)
What is an operon in genetic regulation?
refers to 1 promoter that results in many genes - (polycistronic)
What is a regulon in genetic regulation?
refers to 1 regulator with many promoters. Dispersed throughout the chromosome
Vitamin synthesis requires multiple proteins encoded by many genes. All genes must be under the control of the same regulator but can have many promoters. Which genetic organization will you use?
A. an operon
B. a regulon
C. Multiple operons
D. Multiple regulons
B. A Regulon
Not all RNAs are translated. Some are regulatory. What are some examples of regulatory RNA?
tRNA
rRNA
sRNA
ribosymes
What is sRNA?
Small RNA
Not translated
40-400 nucleotides long
from the non-template DNA strand of a gene.
known as silencing RNA - they silence the mRNA to prevent translation
How does sRNA regulate translation?
Affects mRNA stability
- binds to the mRNA coding region
Blocks RBS (ribosome binding site)
- blocks translation
Changes the secondary structure
- unfolds mRNA making RBS accessible and allows translation to proceed
How does the levels of tryptophan affect transcription?
High levels of tryptophan speed up transcription so quickly that it destroys the structure
Low levels of tryptophan allows the transcription to proceed at a rate that allows for a much more stable shape
How do riboswitches regulate transcription?
you need a small molecule
Turns off transcription - terminator stem loop.
How do riboswitches block translation?
you need a small molecule
blocks the ribosome binding site.
You want to control protein activity without affecting the amount of mRNA or protein produced. What mechanism could you use?
A. Feedback inhibition
B. Post-translation modification
C. protein sequestration
D. All of the above
E. None of the above
D. All of the above
What are the mechanisms to regulate protein activity?
Inhibit activity - feedback inhibition
- Control how much mRNA is produced
change enzymatic activity / post-translational modification
- Control whether or not the mRNA gets translated
- Control whether or not the transcription moves forward
Remove the protein
-sequestration (changes its availability)
-degradation (destroys protein)
What are the mechanisms of a two-component regulatory system?
Two part
- sensor histidine kinase
- response regulator
Stimuli induces autophosphorylation at the histidine residue
Transfer of phosphate to regulator
Feedback loop
- remove phosphate
You are trying to develop a biosensor to detect a small-molecule pollutant. What regulatory system could you use to detect the pollutant?
A. a riboswitch
B. A two-component system
C. An activator
D. A repressor
E. All of the above
D. None of the above
E. All of the above
How do bacteria communicate with each other?
quorum sensing
What are the quorum sensing molecules?
Acyl horoserine lactones (AHL)
AI-2: cyclic furan deriviative
AI = Autoinducer
Small peptides
What is the classic example of quorum sensing?
Allivibrio fischeri
produce bioluminescence at a very high density
You want to silence a gene post-transcriptionally. Which methods would work best?
A. Use a repressor with an inducer
B. Use feedback inhibition
C. Use post-translational modification
D. Use small RNA
E. None of the above
D. use small RNA
It is the only one on the list that is post-transcriptional
