Gen Bio Exam 4
What are the 2 key sequences of the bacteria promoter? What factor do they bind to and what does the factor do? How does the factor react when there are slightly different bases in the sequence?
-10 region and -35 region Sigma factor (σ Factor) It will still do transcription, just would decrease, or go slower
What does the intron change in Transcription Factor bHLH gene lead to
8 new bases, 8 new amino acids, and a stop codon being added
How many nucleotide bases long is tRNA? How many different tRNAs are there? What does it have and what does it bring in? What is it important for?
80 45 different tRNAs Has anticodon and brings in specific amino acid Important for translation from nucleic acid to amino acids
A high concentration of Bicoid proteins will produce Legs instead of antennae Wings and legs in Drosophila A Drosophila tail A Drosophila head
A Drosophila head
Who is David Acer
A Florida dentist that intentionally infected 5 patients with HIV/AIDS
What is Ras and what happens when it is defective?
A G prtein that turns on when a tyrosine kinase receptor is activated It always stays on
What kind of protein is HER2? How does the drug Herceptin help cancer patients?
A Receptor Tyrosine Kinase (RTK) Herceptin fills the receptor instead of the growth factor and prevents dimerization of the RTK
What are the 2 breast cancer tumor suppressores
BRCA1 and BRCA2
What do bacteriophage infect? How?
Bacteria; by squeezing their genome into the bacteria cell and reproducing
How does the acetylation and de-acetylation of histone tails affect the structure of chromatin?
By dictating how compact a chromosome can be unacetylated histones are tighter than acetylated histones; acetylation removes the positive charge on lysine, making DNA less likely to bind to histone tightly. Unacetylation allows an ionic connection to form so the DNA gets more compact
How do operons help bacteria?
By helping them respond quickly to changes in the environment and cellular/metabolic needs
What are control elements? what are they associated with?
Controle elements are segments of noncoding DNA that serve as binding sites for transcription factors that help with egulating transcription They are associated with most eukaryotic genes
What are 2 types of prion diseases? What do prions do to the brain?
Creutzfeldt-Jakob disease and Mad cow disease Causes neurodegenerative diseases by causing cells to die in brain
What does corona in coronavirus mean? What type of virus is coronavirus
Crown, because all the proteins on the outside of the virus make it look like a crown COVID is a single stranded RNA virus
How does alternative RNA processing relate to gene expression?
If a gene is transcribed in 2 different tissues, but are spliced differently, it causes them to act completely differently
How does the compaction of chromatin have an effect on transcription?
If the DNA and chromatin get too compact, the RNA polymerase cannot get in to begin translation It can get in if it is a little loose
Where are riboswitches present? What do they use to alter transcription and translation/
In amino acid synthesis, vitamins, and the production of purines Use RNA and metabolism-based structures
How many possibilities are there with just 5 modifications to the Histone amino acids? What are 4 possible modifications?
Infinite Acetylation, phosphorylation (negative charge), methylation, ubiquitination
What is a frameshift mutation?
Insertions or deletions not divisible by 3
Give an example involving cancer of intercellular (between cell) and intracellular (within cell) signaling.
Intercellular: Ras as a proto-oncogene and Intracellular: P53 in response to UV damage
When P53 is normal, what kind of signals cause it to bind to DNA?
Intracellular signals from protein kinases
A frameshift mutation... Is the insertion or deletion of bases that are not a multiple of 3 includes the insertion or deletion of any bases only includes inserted bases only includes deleted bases
Is the insertion or deletion of bases that are not a multiple of 3
What does trpR do when tryptophan is present?
It binds to and activates the repressor, blocking the transcription of the operon. It only becomes repressed when bound to tryptophan - the corepressor It binds to the operator sequence to stop translation Prevents the transcription and translation of the 5 genes in tryptophan biosynthesis
Name three kinds of proteins involved in cell communication in the cell cycle stimulating pathway that involves Ras (there are more than 3).
Receptor Tyrosine Kinase, G protein (Ras), Kinases, Transcription factors
What are the different types of point mutation? What do they cause?
Missense: amino acid change Nonsense: stop codon or alt. start codon Silent: no amino acid change
Many eukaryotic proteins are... What does this mean?
Modular each exon codes for a specific module or section. They code for entirely new responses because they are new proteins and create a platform for rapid evolution
For full-blown cancer to occur, ______ defects are almost always necessary
Multiple, more than 5
What do transcription factors controls?
Transcription factors
Why was complete dominance observed in the purple and white flower gene
Transcription factors
What do control elements bind to? What is this binding critical for?
Transcription factors The precise regulation of gene expression in different cell types
Where does transcription, translation, and viral assembly occur?
Transcription in nucleus Translation and viral assembly in cytoplasm
What is considered an exception to the Central Dogma of Molecular Biology? RNA splicing transcription regulation reverse transcriptase alternative splicing
reverse transcriptase
What complex uses both RNA and protein to remove introns? exonucleases nucleosome topoisomerases spliceosome
spliceosome
.In addition to turning on a transcription factor that turns on muscle specific proteins like myosin, MyoD also eventually turns on proteins that...
stop the cell cycle
Ernest Everett Just
stressed importance of factors on the cell membrane and in the cytoplasm as key to understanding development Argued nucleus is not important Studied fertilization and development in Marine organisms
What are epigenetic modifications? the addition of reversible changes to histone proteins and DNA the removal of nucleosomes from the DNA the addition of more nucleosomes to the DNA mutation of the DNA sequence
the addition of reversible changes to histone proteins and DNA
what does miRNAs and associated proteins cause? What does miRNA do when it binds to mRNA
the degradation of the target mRNA and blocking of translation it tags it and prevents it from being translated.
What is the Histone Code?
the different combinations of modified histone amino acids that can alter chromatin compaction, transcription, etc. All the different potential changes and location for the histones and therefore the DNA
Why is the combination of activators and enhancers key in terms of combinatorial control?
to generate the diversity of different transcriptional queues and increase the level of complexity
Which subunit of the E. coli polymerase confers specificity to transcription? α β β' σ
σ
Which of the following are involved in post-transcriptional control? control of RNA splicing control of RNA shuttling control of RNA stability all of the above
all of the above
Which of the following are true of epigenetic changes? allow DNA to be transcribed move histones to open or close a chromosomal region are temporary all of the above
all of the above
Prokaryotic cells lack a nucleus. Therefore, the genes in prokaryotic cells are: all expressed, all of the time transcribed and translated almost simultaneously transcriptionally controlled because translation begins before transcription ends b and c are both true
b and c are both true
Where does a splicosome typically cut? Where does it cut in the mutation in the bHLH gene?
between the 2 Gs in GGTA. it cuts 8 bases later
How does coordinated control affect the fight-or-flight signal transduction pathway?
by activating the genes for the response so the phosphorylating transcription factors can enter the nucleus
What property of acetyl groups is most important for regulating chromatin structure? size hydrophobicity shape charge
charge
What will result from the binding of a transcription factor to an enhancer region? decreased transcription of an adjacent gene increased transcription of a distant gene alteration of the translation of an adjacent gene initiation of the recruitment of RNA polymerase
increased transcription of a distant gene
The ara operon is an inducible operon that controls the production of the sugar arabinose. When arabinose is present in a bacterium it binds to the protein AraC, and the complex binds to the initiator site to promote transcription. In this scenario, AraC is a(n) ________. activator inducer repressor operator
inducer
What is not part of a processed mRNA? introns 3' poly A tail 5' cap 3' UTR untranslated region
introns
What are miRNA? What do they regulate?
miRNA is microRNA, which are little molecules that have short spand of RNA (single stranded RNA molecules) to help bind to regions of untranslated mRNA regions to regulate translation Bind to complementary sequences in mRNA It regulated the life of RNA
Metastatic
moves from original organ to other organs
What is on nearly all proteins? c-terminal methionine 5' cap 3' poly A tail n-terminal methionine
n-terminal methionine
The RNA components of ribosomes are synthesized in the ________. cytoplasm nucleus nucleolus endoplasmic reticulum
nucleolus
If glucose is absent, but so is lactose, the lac operon will be ________. activated repressed activated, but only partially mutated
repressed
How much energy is required during translation? In which steps?
- "charging" a tRNA with an amino acid requires 1 ATP - Ribosome assembly requires 1 GTP - Each amino acid addition requires 2 GTP - Termination requires 1 GTP
What are the 4 steps to an amino acid attaching to a t-RNA
1. Amino acid and ATP enters active site of Aminoacyl-tRNA synthetase 2. AMP joins to the amino acid, pyrophosphate is broken down and released 3. AMP is displaced by tRNA, creating a-tRNA 4. A-tRNA releases from enzyme
Describe the qualities of RNA transcription elongation (6)
1. As RNA polymerase moves along the DNA, it untwists the double helix 10 to 20 bases at a time 2. In eukaryotes, transcription progresses at a rate of 40 nucleotides per second 3. Nucleotides are added to 3' end of growing RNA molecule 4. Gene can be transcribed simultaneously by many RNA polymerases. As soon as promotor is available, another strand can be created 5. The direction of transcription is downstream -> 5' end to 3' end 6. RNA sequence is going to be complementary to template strand, but almost identical to non-template strand.
When Ras is a proto-oncogene, what are the series of steps required to activate Ras?
1. Bind growth factor, 2. Tyrosine Kinase forms dimer, 3. Dimer is phosphorylated at Tyrosine amino acids
What are the 3 ways tRNA are typically pictured? What are the benefits to each and how are they used?
1. Clover-leaf structure. Allows it to be seen in 2D and shows RNA bases/where there are modified bases. The anti codon is pictured at very bottom and the amino acid attaches to the 3' end 2. L-shape. Has a more 3D shape where the structure base pairs with itself. has information in the form of nucleic acids/bases and 3D structure/catalytic activity because it can hold onto the amino acid 3. A glob with attachment site at top and anticodon region at the bottom. Easiest to draw
Draw the series of steps, starting with a mutation that leads to the lack of purple color in a white pea flower.
1. G to A mutation in the intron of the DNA 2. This mutation results in a splicing error 8 base pairs away from the original splice site because the RNA in the spliceosome recognizes the original sequence 8 bases away. 3. The mRNA now has a frameshift mutation (because of the 8 base insert). 4. The resulting protein now has a stop codon that results in a smaller, nonfunctional transcription factor. 5. Because only a small amount of transcription factor is needed, only one functional copy in heterozygotes is enough to produce purple flowers. 6. Only when there are two defective versions of the gene do the flowers fail to produce any purple pigment.
Describe the steps of Transcription termination (3)
1. In bacteria, polymerase stops transcription at the end of terminator and falls off 2. In eukaryotes, RNA polymerase II transcribes past terminator sequence and eventually falls off
What are the 3 parts of the operon structure? What do they do?
1. Promoter sequence: Where RNA polymerase binds to. Binds to the sigma factor 2. Operator sequence: where a repressor binds to prevent transcription. It is a regulator that increases or decreases transcription 3. Enhancer or silencer regions: upstream/downstream DNA sequences that increase or decrease trascription
What are the 3 levels of protection agains cancer?
1. Proteins that stimulate the cell cycle and keep them from constantly dividing (protons-ocogenes) 2. Transcription factors that induce transcription of mRNA followed by translation of proteins that inhibit cell cycle EX: p53 3. Programmed cell death or apoptosis
What are the three levels of protection against cancer?
1. Proteins that stimulate the cell cycle: Proto-Oncogenes -Genes that regulate proto- oncogenes keep cells from constantly dividing. Example: Ras Tumor suppressors 2. Transcription factors that induce transcription of mRNA followed by translation of proteins that inhibit the cell cycle. Example: p53 is a transcription factor that helps make cell cycle inhibitor proteins. Repair is often the goal when the cell cycle is stopped, but not destroyed. 3. Programmed Cell Death Genes: (Apoptosis)- Genes responsible for cell suicide if major chromosomal defects occur.
Describe the steps of Transcription initiation (4)
1. RNA polymerase pulls DNA strands apart and catalyzes joining of RNA nucleotides using template strand. Does not need a primer or helicase 2. The mRNA made is complementary to the DNA template strand (only uses one strand) 3. RNA synthesis follows same base-pairing rules as DNA except uracil substitutes for thymine 4. 5' end of DNA connects to 3' end of RNA
What are the 3 steps of Translation initiation? What do the first 2 steps form?
1. Small subunit binds and scans to mRNA looking for the AUG start site 2. Binds to the initiator tRNA which holds Met so it can start at the p-site when large subunit binds 3. The large subunit attaches and the growing polypeptide will be lengthened at the p-site. The first 2 steps form the initiation complex
What does the initiation of transcription at a eukaryotic promotor have? (2)
1. TATA box 2. The box binds to many proteins/general transcription factors that are bound to DNA
What are the 2 steps of translation termination? What is a release factor? What does it bind to and what does it require?
1. The release factor binds to the a-site and displaces tRNA 2. The polypeptide is released from the tRNA and folds/bonds to form protein The release factor is a protein that 3D fits into tRNA and interphases with mRNA. It binds to the stop codon and requires energy through GTP
What are the 5 steps of the elongation of translation?
1. The second amino acid arrives at the a-site 2. Energy is used to move the complex and ribosome to the side to form new poly-peptide bonds 3. Previous amino acid joins the new one. New tRNA molecule is in p-site. Old tRNA is in e-site. 4. The old tRNA leaves once amino acid is gone. 5. Next amino acid joins a-site
How is CRISPR used? (2)
1. genome editing technology 2. to bind to viruses in the cell and destroy them - destroying viral genomes in bacteria
What percentage of the common cold are coronaviruses?
10 - 15%
Coronaviruses are one of the viruses that cause common colds. What percentage of colds are caused by Coronaviruses each year? 10-15% 90% 1% 50%
10-15%
An unprocessed pre-mRNA has the following structure. Exon(50bp)-------Intron(110bp)-----Exon(70bp)---Intron(20bp)---Exon(130bp)----Intron(75bp)----Exon(30bp) Which of the following is not a possible size (in bp) of the mature mRNA? 205bp 180bp 150bp 100bp
100bp
How much of breast cancer is caused by genetics? How much of cancer mutations are due to environmental factors
13% 1/3
In a population with 60% red alleles and 40% white alleles, what percentage of pink flowers do you expect (using the HW equation)? )
2(.4)(.6)= 48%
In any given species, there are at least how many types of aminoacyl tRNA synthetases? 20 40 100 200
20
How many amino acids are there? How many RNA bases per amino acid? What is it called?
20 3 Codon
How many aminoacyl-tRNA synthetases are there? Why that number? What do they do?
20 Because there are 20 amino acids They attach specific amino acids to tRNA molecules
Who is Dr. Funmi Olopade
2017 Mendel Medal recipient Studied breast cancer among African and African American women
A scientist identifies a pre-mRNA with the following structure. ------Exon-------intron---Exon---------Intron--------------Exon------------ What is the predicted size of the corresponding mature mRNA in base pairs (bp), excluding the 5' cap and 3' poly-A tail? 220bp 295bp 140bp 435bp
295bp
How many genes are enough for metastatic cancers?
3
Why does inserting 8 bases into the mRNA create a frameshift, but inserting 3 bases does not?
3 bases will insert an amino acid, but 8 bases changes the codon positions by 2
How many nucleotides are in 12 mRNA codons? 12 24 36 48
36
How many sets of Hox genes do humans have?
4
What are spliceosomes made of? What do they do?
4 small RNAs and a bunch of protein Recognize, complimentary base pair to, excise, and relegate mRNA to remove intron and leave exons
In the example of Colon Cancer, how many different mutations (minimally) were required for the cancer to become malignant?
5
What is the expected frequency of heterozygotes in the case of all pink flowers (using the Hardy-Weinberg equation)? - Snapdragon
50%
How many possible codons are there? How do you read the codon table?
64 possibilities Read left side first (1st mRNA base on 5' end of codon) Top is 2nd mRNA base Right side is 3rd mRNA base on 3' end of codon
What is herceptin
A cancer drug that prevents the HER2 receptor from turning on RTK receptor
What is a ligand?
A molecule that binds to something to cause a structural change
What do viruses and bacteria having in common?
A nucleic acid genome
What type of charge does lysine have? What about the backbone of DNA? Why does DNA have that charge?
A positive charge A negative charge Because of the phosphate groups
In breast cancer, the HER2 receptor is... A receptor tyrosine kinase (RTK) A tumor suppressor A trancription factor A GPCR
A receptor tyrosine kinase (RTK)
What is a A riboswitch?
A riboswitch sequence that causes termination before the transcription is complete the mRNA forms a 3D structure that binds to a ligand, forming a distinctive shape that blocks transcriptions - negative feedback
What causes the flower to be white in Mendel's experiments?
A single base pairs change in intron 6 from G to A between axons 6 and 7 in transcription factor bHLH gene This change does not change amino acid sequence, but ruins the protein, making it white by creating an mRNA with extra bases in it
Except for the first aminoacyl tRNA, where do all the other tRNAs bind first? A site exit channel E-site P site
A site
What are the 3 sites of the large subunit? What do they do?
A site: aminoacyl-tRNA binding site. This is where the amino acids start P site: Peptidyl-tRNA binding site. This is where the peptide bonds are being made and the protein is emerging from E site: Exit site. Where the molecule eventually gets kicked off from.
Which of the following is Not one of the ways that a proto-oncogene can become an oncogene? A stop codon is inserted into the protein, ruining it's function Multiple copies of the gene are made, amplifying it The gene has a point mutation making it hyperactive or resistant to being destroyed The gene moves to a more effective promoter
A stop codon is inserted into the protein, ruining it's function
The protein that either causes pea flowers to be purple or white in Mendel's peas is... A transcription factor An enzyme A purple pigment protein A white protein
A transcription factor
For Mendel's white flower trait, what kind of protein is defective when you see a white flower?
A transcription factor (and/or and activator)
What is p53 in terms of cancer and what happens when it is defective?
A tumor supressor It causes continuous growth in cell cycle
What are the names of the two clades (Genera) of coronaviruses that cause human colds?
Alphacoronaviruses and Betacoronaviruses
All of the Human common cold coronaviruses (choose all that apply): A) Were transferred from other animals to humans. B) Started infecting humans in the last 1000 years. C) Have been infecting humans for millions of years D) Are members of Alphacoronavirus E) Are members of Betacoronavirus F) Are both Alphacoronaviruses and Betacoronaviruses
A) Were transferred from other animals to humans. B) Started infecting humans in the last 1000 years. F) Are both Alphacoronaviruses and Betacoronaviruses
What is required to attach the amino acid covalently to the tRNA?
ATP - energy input
What percentage of proteins are made in the lumen of the ER? Where are the rest made?
About 30% Cytoplasm
What does MoD do as a transcription factor?
Activate muscle specific proteins and turn off the cell cycle indirectly
What bind to enhancer DNA sequences? What does this provide?
Activators and specific transcription factors They provide a new level of specificity
What is added during RNA processing? What is taken away?
Added: 5' cap; Poly-A-Tail; 5' UTR; 3'UTR Taken: Introns
What is it called when introns can be removed in different ways?What are introns a great place for and why?
Alternative splicing Great place for crossing over because it allows you to mix up alleles and parts of a single gene
Where is albumin made? What about chrystalin?
Albumin is made in the liver Christallin is made in the lends of the eyes
Which organisms use the codon table?
All living organisms on earth
Alternative splicing has been estimated to occur in more than 95% of multi-exon genes. Which of the following is not an evolutionary advantage of alternative splicing? Alternative splicing increases diversity without increasing genome size. Different gene isoforms can be expressed in different tissues. Alternative splicing creates shorter mRNA transcripts. Different gene isoforms can be expressed during different stages of development.
Alternative splicing creates shorter mRNA transcripts.
What type of transcription factor is the pea bHLH gene?
An activator
How are muscle cells reproduced if damaged
An indifferentiated cell nearby is injected with MoD and other transcription factors and proteins to become a muscle cells
A cancer causing gene that stimulates the cell cycle is called... An oncogene A transcription factor A tumor suppressor A receptor tyrosine kinase (RTK)
An oncogene
In Drosophila, gradients of transcription factors are responsible for determining which two axes in the adult fly?
Anterior-Posterior and Dorsal-Ventral
How much of gene expression is estimated to be regulated by miRNAs? How long are miRNAs and how many of them are in the human genome?
At least 1/2 of the human genes Approximated 22 nt long About 2000 miRNAs are in the human genome
What are the 4 types of vaccines? How are they each used?
Attenuated virus: using a less harmful version of the virus that is treated with a chemical, radiation, or heat Inactivated or dead virus: using a virus that has been heat or chemically killed, so only the shell/proteins are left Protein/subunit: using a viral surface protein to generate immunity. These are most common mRNA: using an mRNA to encode for a viral protein to stimulate immunity
As bacteria become resistant to antibiotics, what are being considered for therapeutic uses? Why is it useful?
Bacteriophage because it is a natural attacker of bacteria
Why does glycine biosynthesis decrease?
Because it acts as a negative feedback loop
You find out that the pink coloring in the energy bars you eat causes your intestinal cells to divide at twice the normal rate. Why might this be a bad thing?
Because most cancer mutations occur due to errors during cell division, anything that increases numbers of cell division will increase the frequency of those random errors, and therefore the risk of cancer.
Why are the histone tails where a lot of eukaryotic regulation of transcription occur? What residues do the histone tails have a lot of?
Because there are specific residues thatt can be modified with covalent bonds Lysine residues that can be chemically modified to have an acetyl group added
Why do snapdragons show incomplete dominance?
Because they are controlled by enzymes in the pathway... having 2 red ales produces 2x as much enzyme so cutting the red pigment in half produces pink
.What are the Bicoid and Dorsal proteins in Drosophila, and what do mutants look like for these genes?
Bicoid - determines the Anterior-Posterior axis. Mutants have two tails and no head. Dorsal determines the Dorsal-Ventral axis. Mutants have 2 backs and no belly.
What is meant by "triple negative" breast cancer?
Breast cancer that does not involve the three previous receptors as oncogenes - more difficult to treat in many cases
How does cAMP begin transcription of lactose?
By binding to an inactive Cap, activating it and making it act as a promotor to promote RNA polymerase to bind and begin transcription
How many control elements can an enhancer have? How many activator proteins can each control element bind to?
Up to 10 1 or 2
What is CRP and what does it promote?When is cAMP high?
CRP is a promoting factor and an activator Promotes the binding of RNA polymerase to the lac promoter only when cAMP is abundant. cAMP levels are high when glucose levels are slow
What does the Large subunit of the ribosome do? Proofreading to ensure correct amino acid-tRNA coupling. mRNA scanning. Catalysis of peptide bonds. Positioning the methionine tRNA at the AUG start codon.
Catalysis of peptide bonds.
What kinds of proteins are produced when P53 is activated?
Cell cycle inhibitors ( or DNA repair proteins, or apoptosis proteins)
How does the regulation of gene expression support continued evolution of more complex organisms? Cells can become specialized within a multicellular organism. Organisms can conserve energy and resources. Cells grow larger to accommodate protein production. Both A and B.
Cells can become specialized within a multicellular organism.
What is the flow of genetic information from DNA-> RNA-> Protein called? What about DNA-> RNA? What about RNA-> Protein? What about DNA -> Protein
Central Dogma of molecular biology Transcription Translation Genotype vs phenotype
What is the difference between a cladogram and a phylogram?
Cladogram shows order of branching only Phylogenetic tree gives us information of indication of time or DNA difference on the y-axis
Where does transcription and translation occur in bacteria?
Cytoplasm
What part of the spliceosome allows for the recognition of specific bases in the DNA to splice? A. The protein B. The DNA that codes for the spliceosome C. The mRNA of the spliceosome D. The RNA involved in the protein/RNA complex that makes up the spliceosome. e. All of the above.
D
Which of the following does not apply to Mendel's Purple/White flower gene? (Choose all that apply) A. Transcription factor B. Splice site mutation C. Intron mutation D. Exon mutation E. DNA insertion F. mRNA insertion G. Activator H. Frameshift mutation I. Premature Stop Codon J. Defective recessive allele
D and E
What is DNA methylation and what does it lead to? What nucleotide is this typically done to and where? What does this lead to?
DNA methylation = reduce transcription. It leads tot he long-term inactivation of genes in cellular differentiation Cytosine, typically when the C is followed by a G Leads to areas with reduced or less accessible transcription
What is the difference between Determination and Differentiation in a developing muscle cell?
Determination is when MyoD has been transcribed, but before the cell has changed appearance because of muscle-specific proteins. Differentiation is the process of becoming a muscle cell through the expression of muscle-specific proteins.
What are transcription factors responsible for in terms of the body?
Determining the identity of body segments
Annie Parker
Discovered BRCA1 and BRCA2, which increase risk of breast and cervical cancer
A scientist compares the promoter regions of two genes. Gene A's core promoter plus proximal promoter elements encompasses 70bp. Gene B's core promoter plus proximal promoter elements encompasses 250bp. Which of the scientist's hypotheses is most likely to be correct? More transcripts will be made from Gene B. Transcription of Gene A involves fewer transcription factors. Enhancers control Gene B's transcription. Transcription of Gene A is more controlled than transcription of Gene B.
Enhancers control Gene B's transcription.
How do enhancers and promoters differ? Enhancers bind transcription factors to silence gene expression, while promoters activate transcription. Enhancers increase the efficiency of gene expression, but are not essential for transcription. Promoter recognition is essential to transcription initiation. Promoters bind transcription factors to increase the efficiency of transcription. Enhancers bind RNA polymerases to initiate transcription. There is no difference. Both are transcription factor-binding sequences in DNA.
Enhancers increase the efficiency of gene expression, but are not essential for transcription. Promoter recognition is essential to transcription initiation.
How does influenza enter the cell? What facilitates viral entry and what are they called? What is important with these proteins for protection from the flu?
Enters via receptors Surface proteins like HA and NA facilitate viral entry by specifying which cells to invade These proteins are primary targets for the vaccine
What are the 3 breast cancer oncogenes
Estrogen receptor, Progesterone receptor, HER2 receptor (receptor tyrosine kinase)
What are the three receptors found in breast cancer?
Estrogen, Progesterone, and HER2
How can the avian flu or swine flu become a human flu?
Evolution of viral proteins that allow for human cell entry and fusion of animal virus with established human virus
The trp operon is an example of regulating a catabolic process. True or false
False
Some cancer researchers say that cancer is mostly "bad luck". What do they mean by that statement?
For 2/3 of the genes mutated in cancer, those mutations are replicative errors - errors occurring during mitosis. The mutations occur in cells that divide very often regardless of the environment.
What is meant by "three strikes and you're out?"
For many cancers, only three mutations are needed to create metastatic (bad) cancer - usually one oncogene and 2 broken tumor suppressors
Why are the 5' UTR and 3' UTR added? Where? How do they differ?
For regulatory purposes 5' UTR added between 5' cap and start codon 3' UTR added between poly-a-tail and stop codon 5' UTR: ribosomes attach here 3' UTR: polyadenylation signal (many As and some Us)
What are two kinds of proteins usually involved in the reception of cell signals?
GPCRs and Receptor Tyrosine Kinases (note that RAS is not a GPCR)
What 2 molecules serve as direct sources of energy in the Ras signaling pathway?
GTP and ATP
What do oncogenes lead to?
Gene amplification
How does gene therapy use viruses? How can it improve our immune system? What is a complication to using the viruses?
Gene therapy: to deliver genetic information to cells, like a replacement gene for a defective one Immune system: by boosting immune system or targeting specific proteins Viruses can launch an immune response or can be injected in a bad place of the genome, causing cancer
Which viruses have membranes? Which ones do not?
HIV, Influenza and Ebola have membranes Bacteriophage, adenovirus and tobacco mosaic viruses do not. they have proteins on outside
Which common cold viruses are most similar to the current SARS CoV2 viruses?
HKU1 and OC43 (the two Betacoronavirues - SARS CoV2 is also a Betacoronavirus
What vaccine is the first to prevent cancer? Who was it marketed for at first and why?
HPV vaccine. For girls because it prevents cervical cancer
Coronaviruses that cause the common cold... Have been in humans for milllions of years Are transferred from humans to other species every year Have been in humans since 1200 AD Originated in humans in the last 20 years
Have been in humans since 1200 AD
Bicoid
Having 2 tails and no head
Antennaphia
Having legs grow instead of antenna in drosophila
What can the 3D shape of RNA do? What are the different types of structural or enzymatic RNAs?
Help with translation, or block ribosomes to prevent its own translation tRNA, rRNA, and mRNAs
Hox genes
Homeotic genes/transcription factors that are the same across all animals
What is an operon?
a group of genes that are regulated together ti maximize efficiency and establish a common regulatory mechanism
What is a co-activator and what does it do?
It is a protein object that brings everyone together, including RNA polymerase
When a virus is take into the cell whole and explodes in the cytoplasm, what is this due to? What happens to this virus? What is viral shedding?
It is due to low pH. It goes through transcription to create new genome and particles to shed Viral shedding is the shedding of the virus out the host cell
What is early development and what does the mother lay down for the embryo after fertilization?
It is marked by gradients of transcription factors and signaling molecules The mother lays down a gradient of proteins that are transcription factors and signaling molecules
If someone gets cancer, how likely is it that they will pass those genetic mutations on to their children? Explain.
It is not very likely. Inherited defective alleles that increase the chance of cancer like BRCA1 exist and it is a good idea to screen for inherited defects, but they are less likely overall compared to mitotic errors.
Who won the Nobel prize for CRISPR for genome editing
Jennifer Doudna
What are the 2 subunits of ribosomes? What do they consist of? How many proteins are in each subunit for prokaryotic and eukaryotic ribosomes?
Large and small RNA molecules and protein complexes Prokaryotic: 34 for large and 21 for small Eukaryotic: 49 for large and 33 for small
Describe the 2 cycles bacteriophage can go through?
Lytic cycle: cell bursts open (lysis) and releases the virus particles to infect new bacteria Lysogenic cycle: the cell divides before lysis to make new cells full of the phage. The goes through lytic cycle
What are some betacoronaviruses
MERS, SARS, and COVID-19
What do you want to happen if lactose and glucose are abundant at the same time?
Make sure the glucose is all used up before using lactose
What are the 4 mutations of colon caner?
Mutation of APC Activation of Ras oncogenes to develop polyps Loss of SMAD4, a tumor supressor Loss of p53, a tumor supressor
What is bacteria translation based on?
Necessity
What control do prokaryotes have? Eukaryotes?
Negative Positive
In snapdragons, the alleles for flower color show incomplete dominance. There is a red allele and white allele. If a population with only pink flowers is discovered, is the population in Hardy-Weinberg equilibrium?
No
Are promoters specific between 2 different genes? What about the enhancers? What happens when an activator binds to an enhancer sequence?
No Yes It activates the genes
Do bacteria have processing of mRNA? Why
No because there are no introns
When Ras is an oncogene, what are steps required to activate Ras?
None
What are the 3 main components of a virus? Which acts as the genome for the virus and what are the 4 different types?
Nucleic acid, proteins, and sometime membranes Nucleic acid Single strand DNA, double strand DNA, single strand RNA, double strand RNA
What are the 2 factors at play for the lac operon?
Presence of glucose and lactose
What is apoptosis, and why is it a good thing to have?
Programmed cell death, a result of cell signaling - destruction of defective cells (to prevent cancer) or unwanted cells (like the webbing between fingers and toes) are necessary
What do transcription factors bind to? What do activators bind to? How do activator proteins and general transcription proteins communicate?
Promoter sequence Enhancer sequences Through co-activators
What are the promoter, RNA polymerase, start point, and transcription unit?
Promoter: the DNA sequence where RNA polymerase binds to RNA poly: the enzyme that initiates and drives RNA synthesis Start point:where transcription begins, depicted by a crooked arrow Transcription unit: the DNA sequence coding for RNA molecule and termination sequence; the DNA that RNA uses as a guide
What binds to the promoter?
RNA polymerase and transcription factors
What is non-coding RNA (ncRNA)?
RNA processing and transport that can be places for regulation
What are riboswitches?
RNA structures that are pieces of RNA that can turn translation on and off
Which viruses are made from RNA? Which from DNA?
RNA: HIV, influenza, tobacco mosaic, ebola DNA: Bacteriophage, adenovirus
How do Ras and P53 differ when they are cancer-causing?
Ras stimulates the cell cycle and is an oncogene when defective - P53 is a tumor suppressor, stopping the cell cycle when normal
What are the three stages of cell signaling?
Reception,Transduction and Response
What is trpR? What does it use to determine if synthesis of tryptophan must occur?
Repressor of the trp operon ; a gene for the repressor protein Uses tryptophan
What do many antibiotics target?
Ribosomes and translation machinery Protein synthesis
Which event contradicts the central dogma of molecular biology? Poly-A polymerase enzymes process mRNA in the nucleus. Endonuclease enzymes splice out and repair damaged DNA. Scientists use reverse transcriptase enzymes to make DNA from RNA. Codons specifying amino acids are degenerate and universal.
Scientists use reverse transcriptase enzymes to make DNA from RNA.
What is SRP and what does it do?
Signal Recognition Particle It binds to a sequence of amino acids to pause translation and move the whole unit to the ER so it can finish translation in the lumen of the ER
What are prions? What do they do to large proteins?
Small misfolded proteins that can induce misfiling in other proteins. They cause large protein to aggravate by changing the 3D shape and forming huge networks of misfolded proteins
What is the small subunit responsible for? What about the large one?
Small: decoding the mRNA sequence and recognizing it. It binds to the start site and begins the process of translation initiation Large: Catalysis of the protein into a peptide bond. Beginning protein synthesis
If all cancer is genetic, how is it that smoking causes cancer?
Smoking damages DNA and this damage makes genetic mutations and mitotic errors in the lung more likely (and other places as well)
What are the different pandemics (6)? Which one affect younger people and healthier people?
Spanish (1918) Influenza (H1N1) HIV: 36+ million fatalities Ebola: 11,000+ fatalities Swine flu - dangerous form of seasonal flu that can affect younger people and healthier people SARS CoV1 & MERS SARS CoV2 or COVID 19: 5-19 million deaths
What can an actomer do?
Start or stop translation
What does sigma factor do when transcription occurs?
Stays at the promoter while the RNA polymerase subunits begin stranscription
While containing information about protein synthesis, mRNA also acts as a .... How do you know?
Structure molecule Because it can base pare with itself to forma a 3D shape
What does an oncolytic virus do?
Target to infect and kill cancerous cells.
Which bases in codon determine the amino acid in most cases? How are the amino acids clumped together on the codon table? Which amino acids only have 1 codon?
The 1st 2 Clumped together based on the 1st 2 bases AUG (Met) and UGG (tryp)
What do the parts of the operon structure impact?
The 5' UTR, 3' UTR, and the protein coding region/open reading frame
What do the 8 dots represent for the H1N1 avian virus? What happened in 1992?
The 8 pieces of single-stranded RNA in an influenza virus. In 1992, human, pig and avian viruses all ended up in one individual producing a recombined virus that lead to the 2009 pandemic.
The three most common breast cancer oncogenes are... BRCA1, BRCA2 and Ras BRCA1 and any other 2 genes The Estrogen receptor, the Progesterone Receptor, and the HER2 receptor BRCA1, p53, and Ras
The Estrogen receptor, the Progesterone Receptor, and the HER2 receptor
What is special about how the HIV virus makes new virus within the cell. What is this process called? What is it dependent on?
The RNA genome is reverse transcribed into DNA by reverse transcriptase, then made to RNA, the proteins to make a new virus This is called reverse transcription and it is RNA dependent
What do MyoD and the Purple/White flower protein have in common?
The are both the same kind of transcription factors with the same 3D structure.
What occurs when there is low glucose and lactose is unavailable
The cell starves because there is no sugar to eat Repressor is binding, so transcription cannot occur cAMP is present
What is chromatin?
The combination of DNA and associated histone proteins
What did Ernest Everett Just consider to be the most important parts of an unfertilized egg? Was he correct? Explain.
The cytoplasm and the ectoplasm (the membrane). He was correct when we consider maternal effect genes and the induction of adjacent cells using membrane receptors. However, he claimed that the nucleus was not important, which is incorrect.
What happens to the cell cycle when there is cancer
The gates at each checkpoint disappear and the cells keep dividing
.Which genes are responsible for the production of Bicoid and Dorsal proteins in the early Drosophila embryo? a. The genes of the embryo b. The genes of the father of the embryo c. The genes of the mother of the embryo d. A combination of the above
The genes of the mother of the embryo
What regulates lactose metabolism? What is lactose and what is lactose metabolism? What is a better energy source for bacteria and why?
The lac operon Lactose is a sugar and energy source for bacteria Lactose metabolism is the breakdown of lactose for utilization of its energy Glucose because it does not require energy to cross the membrane
What occurs in bacteria when lactose is present?
The lactose promotes transcription by binding to the repressor protein and changing its shape so the protein cannot bind to the operator. Therefore, transcription can occur
It the large or small subunit at the top of the ribosome and why?
The large because it has the 3 binding sites for tRNA molecules
What is epigenetic inheritance?
The layer above the actual genetic code inheritance of traits not directly involving the nucleotide sequence
What is the expected frequency of heterozygotes in the case of all pink flowers (using the Hardy-Weinberg equation)? Is a population of all red flowers in HW equilibrium? Defend your answer
Yes p=1 q=0 p2=1, 2pq=0, q2 = 0
mRNA is escorted from nucleus through... What enters the nucleus using this?
The nuclear pore complex Proteins
In choosing between two different phylogenetic trees, we will choose a tree that requires only one mutation over a tree that requires more than one mutation. This criterion is... The principle of parsimony The mutation hypothesis The Hardy-Weinberg Therom Natural Selection
The principle of parsimony
What is the primary on/off switch for the trp operon?
The repressor
The white allele in both Snapdragons and in the Pea Plant Purple Pigment Pathway are defective. How does the defect affect the color of snapdragons in a heterozygote, but does not affect the color of purple heterozygotes?
The while allele in snapdragons is a defective version of an enzyme in the pigment pathway - so heterozygotes make 1⁄2 the amount of red pigment in heterozygotes 1⁄2 red = pink. (See the above for the reason defective white allele still make purple flowers when heterozygous.
What occurs when there is high glucose levels and lactose is unavailable
There is no transcription because the repressor binds to the promotor sequence
What kind of proteins do Hox genes make in both Drosophila and in Humans? In what way are Hox genes similar in all animals?
They are Master regulator transcription factors. They are in the same order on the chromosome as they are expressed in the organism and they control roughly the same regions in all animals
How are Pea bHLH and MoD similar?
They are the same kind of transcription factor and have the same 3D structure
How are activators specific?
They are tissue specific
Why is a 5' cap added? What is it made of?
To help prevent degradation and protect mRNA. Made of modified guanine nucleotide - a guanine with 3 phosphated
What does phylogenetic trees allow us to do? What is it done using?
To organize the history of life on earth from its origins DNA sequences
Why is a poly-a-tail added? Where? What is it made of?
To protect mRNA On 3' end 50-250 adenine nucleotides
Where does transcription, translation, and mRNA processing occur for eukaryotic cells?
Transcription: nucleus Translation: cytoplasm Processing: Nucleus
What is the synthesis of tryptophan dependent on? What are the parts of it? Is it polycistronic?
Trp operon Promoter, operator sequence within promotor Yes
What is it called when a new stop codon stops protein synthesis early? What is it called when a base pair insertion makes all the amino acids downstream of the insertion wrong?
Truncation mutation Frame-shift mutation
Which of the following is not a hypothesis for the purpose of splicing and alternative splicing? Increasing the number of gene products without increase the number of genes. Having less consequential regions of DNA for crossing over. Establishing 'modular' protein domains that can be mixed and matched. Using less overall energy (ATP) for gene expression.
Using less overall energy (ATP) for gene expression.
How do viruses enter eukaryotic cells?
Using receptors on the cell or by membrane fusion
How many transcription factors are needed to turn on the gene? What does this mean in one transcription factor is modified?
Very little The transcription factor in the other allele can keep the pink color
How big are viruses in comparison to bacteria, and what is their niche?
Very small, about 100x small than bacteria Niche: obligate intracellular parasites - they require a host and they life in a cell
What occurs when glucose levels are low and there's is lactose available?
We go to lactose. The cAMP activator protein binds to the promoter region, allowing RNA polymerase to bind and transcription rate to be high Lactose changes the shape of repressor
What occurs when there is high glucose, and lactose available?
We metabolize the glucose first before lactose The cAMP protein does not bind the repressor does not bind nothing is promoting or stopping transcription There is a low level of expression
What is feedback inhibition? What is it a type of?
When a molecule blocks or inhibits its own production. A negative feedback loop It is an example of molecular feedback
What is transgenerational gene silencing?
When a significant physiological trauma occurs that causes changes in DNA/genomic imprint that can be passed on through generations
What is positive regulation? What is it a type of?
When a substrate/product promotes its own metabolism/transport It is an example of molecular feedback
What is coordinated control?
When eukaryotes have to activate multiple genes at the same time that are found in different parts of the genome Needs the simultaneous expression of genes that are spread through the genome, but have common enhancer sequences and activators
When does bacteria synthesize tryptophan? How is the trp operon set up?
When ir is not abundant in the environment and the bacteria is lacking it It is set up to only be activated when tryptophan synthesis is necessary
When are the signaling molecules a mother lays down used? Where do signal adjacent cells begin in an embryo? What do they do
When the cell starts dividing At the bottom Induce signal transduction pathways to turn on genes
What makes viruses nearly impossible to eradicate? What are 2 examples of viruses that do this?
When they integrate their genome into the host cell's genome. 2 examples are HIV and HPV
What does alternative RNA spicing explain? How many of the human protein-coding genes undergo alternative splicing?
Why there are a low number of genes in the human genome for a lot of expressed proteins 90-95%
Who is Robert Webster
Winner of Mendel Medal Determined influenza viruses come from bird to pig to man
What is a B riboswitch?
a riboswitch that prevents prevents ribosome binding by forming a unique structure change that contains a unique ribosome structure site. The site is masked, which stops translation
Polycistronic
a single mRNA transcript with multiple start sites for multiple genes. They gave multiple start and stop sites for making different proteins
Which of the following are more likely to be cell-type specific in multicellular organisms? general transcription factors activators RNA polymerase TATA box
activators
What is lactose called? What is permease?
an inducer The lactose transporter
Which of the following is an example of positive feedback for transcription regulation at the lac operon? cAMP RNA polymerase lactose operator
cAMP
Oncogene
cancer causing gene How error in communication can cause overstimulation of cell cycle
The AUC and AUA codons in mRNA both specify isoleucine. What feature of the genetic code explains this? complementarity nonsense codons universality degeneracy
degeneracy
When gene expression changes from one point of development to another, this is an example of what? developmental morphogenesis alternate expression temporal distortion differential expression
differential expression
What describes the broad reason bacteria use operons to control gene expression? efficient use of resources maximize speed ensure all genes are transcribed maintain genome integrity
efficient use of resources
Control of gene expression in eukaryotic cells occurs at which level(s)? only the transcriptional level epigenetic and transcriptional levels epigenetic, transcriptional, and translational levels epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
Differentiation definition
formation of specialized cells from unspecialized cells (stem cells)
What is not true for pre-mRNA? only encodes for proteins found in bacteria and eukaryotes contains introns and exons is processes in the nucleus
found in bacteria and eukaryotes
What binds to the eukaryotic promoter sequence? enhancers co-activators activators general transcription factors
general transcription factors
Select the correct answer for transcription. mRNA: 3' --> 5' template: 3' --> 5' mRNA: 3' --> 5' template: 5' --> 3' mRNA: 5' --> 3' template: 3' --> 5' mRNA: 5' --> 3' template: 5' --> 3'
mRNA: 5' --> 3' template: 3' --> 5'
CRISPR - a bacterial viral defense system - is now being used for what purpose? genome editing genetic counseling antibiotics keeping lettuce fresh
genome editing
What is a riboswitch? mRNA rRNA tRNA repressor protein
mRNA
What are the 5 molecular components of Translation
mRNA, tRNA, Aminoacyl-tRNA synthetase, amino acids, and ribosomes
What is a single piece of mRNA that encodes multiple proteins? polycistronic polysomes alternate transcripts multi-transcript
polycistronic
What causes protein degredation?
proteasome
What do chromatin-modifying enzymes do?
provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery
Ireland has the highest rate of Cystic Fibrosis - caused by a mutation in a single gene. 1/1461 babies are born with cystic fibrosis in Ireland. What is the estimated percentage of the population that are carriers of cystic fibrosis?
q2=1/1461= 0.000684462696783 q= 0.02616223799263 p= 0.97383776200737 2pq= 5% (5.09 percent)
What are the 2 components of ribosomes? what do they provide and have? What are they responsible for?
rRNA and proteins Provides location and has enzymic activity Responsible for synthesizing the polypeptide
What sequences are highly conserved between related species? How do they vary and why?
rRNA sequences. Vary in the introns because they have no role in structure
Post-translational control refers to: regulation of gene expression after transcription regulation of gene expression after translation control of epigenetic activation period between transcription and translation
regulation of gene expression after translation
Parsimony
the simplest explanation is the right one You want the tree with the least amount of steps
What is combinatorial control?
the successful process of transcription only if you have the right combination of activator proteins in the right time and location
What step of gene expression is altered by micro RNAs? translation RNA processing RNA transport transcription
translation
What enzymes are needed for the synthesis of tryptophan?
trpE, trpD, trpC, trpB, and trpA