Molecular Bio Exam 1 Review
1. Know the structure and function of each cellular organelle
★ mitochondria, lysosome, etc
2. Know the similarities
and differences between prokaryotic and eukaryotic cells
3. Define replication, transcription, translation
★ Replication: copying DNA
★ Transcription: making RNA from DNA
★ Translation: proteins from RNA
4. Define haploid, diploid, triploid
★ 1x,2x,3x genetic info
5. Define dominant, recessive, codominant, homozygous, heterozygous
6. Know the difference between somatic cells and gametes in terms of genetic information ★ sperm/egg (gamete cells) – 24 chromosomes/cell → Haploid
★ regular cells (somatic cells) -- 46 chromosomes/cell → Diploid 7. Know how to perform a genetic crosses
★ punnett squares
8. Know where sex linked genes are located
★ x, y
9. Know how many chromosomes are in human somatic cells, and in human gamete cells ★ same as 6
Don't forget about the age old question of Why does psychosis happen?
10. Define chromatin and histones
★ know dna is packed
11. Know which bases pair with each other and the number of hydrogen bounds in each base pairing
★ A,T, C,G
12. Know the monomer building blocks of DNA,RNA, and Proteins
★ nucleotides, ribonucleotides, AA
13. Know the physical characteristics of DNA and RNA
14. What chemical groups are found on the 5’ and 3’ end of a DNA molecule ★ 5’: phosphate
★ 3’: hydroxyl
15. What is the central dogma of the flow of genetic information
★ DNA → RNA → Proteins
16. Define DNA melting temperature
★ temp at which half the dna separates
17. What are the properties of homologous chromosomes Don't forget about the age old question of What is the movement of energy by waves called?
★ they have the same allele but not the same sequences (homozygous dom/rec) ★ ex: white & red flower (same position different sequence)
18. What is the function of topoisomerases
★ untangles DNA
19. Know the relationship between base composition of a DNA and its melting temperature ★ AT melts at lower temp than CG bc of hydrogen bonds
20. Know the levels of DNA packing from least compact to most compact
21. Define nucleosomes
★ proteins that DNA wraps around & histones
22. What wavelength of light is absorbed by DNA, RNA, proteins
★ DNA/RNA: 260
★ Proteins: 280
23. What method can be used to see individual DNA molecules
★ Electron Microscopy & Metal Shadowing
24. How does agarose gel electrophoresis separate DNA molecules
★ Size and charge (MOSTLY SIZE)
25. Define Southern, Northern, and Western blotting
★ S: DNA DNA
★ N: looking at RNA using DNA probe
★ W: looking at proteins using antibodies If you want to learn more check out Can google docs open office files?
Don't forget about the age old question of Know the distinction between people-oriented and task-oriented leadership behavior and when each should be used.
26. What methods are available to label a probe for use in a hybridization reaction ★ Fluorescents (FISH); autoradiograph (run a gel, layer film on top, radioactivity exposes film) 27. How is double stranded DNA synthesis detected in a Real Time PCR reaction ★ ?
28. What are the components required for a PCR reaction and what are their functions ★ primer, template, polymerase, DNTPs
29. Define RTPCR
★ reverse transcription step: RNA → PCR allows to see whats expressed at any given time If you want to learn more check out Do you understand the criteria to pass?
30. Why does PCR require a special type of polymerase
★ 95 to melt
★ 55 to aneel*
★ 70 to polymerize
31. What are the steps of a PCR reaction and what is the purpose of each step ★ 90: melting
★ 55: aneeling
★ 72: elongating
32. What is the function of Reverse Transcriptase
★ RNA copy to DNA
33. What are Restriction Enzymes are what are their functions We also discuss several other topics like What does centralization mean?
★ the cut at specific DNA
★ viral defense mechanism for bacteria
34. What is a shuttle vector and why does it have two origins of replication
★ vector: carrier/plasmid
★ shuttle plasmid: grow in bacteria and yeast
★ copying DNA in a bacteria is diff than yeast (linear vs circular chromosome) 35. What are the components of a Yeast Artificial Chromosome
★ components of any chromosome: end has telomeres, middle is centromeres ★ yeast components
36. Define gene library
★ cut up lots of DNA put it in a vector, grow them, bacteria has lots of diff pieces of DNA for you to study
37. What is the function of DNA ligase
★ Links the ends of 2 DNA molecules
38. What kind of gene is typically used as a selection marker in plasmids
★ grow it on a plate with antibiotics with antibiotic markers on the plasmid
Molecular Bio Exam 2 Review
1. How are DNA chips probed?
DNA chip technology relies on the hybridization of DNA to DNA
2. During DNA sequencing, what causes DNA polymerase to terminate chain elongation? Insertion of dideoxy nucleotide causes terminated chain elongation
3. How do nanopore detectors work?
They contain pores that only allow single stranded DNA to pass through.
4. How does exon trapping work?
method for determining eukaryotic coding sequences relies on flanking splice recognition sites, which are used during RNA processing.
5. What is metagenomics?
Study of genetic material relies on the fact that all organisms have nucleic acids.
6. Describe all the stages of the cell cycle.
3 parts: Interphase, mitosis and cytokinesis
G1 newly formed daughter cell matures
S DNA is replicated to prepare for cell division
G2 the cell grows more and prepares to divide.
Prophase where the chromosomes become visible and the nuclear membrane dissolves. Centrioles form and move to opposite sides.
Metaphase Chromosomes line up in the middle
Anaphase cell begins to divide, spindles pull the chromatids apart
Telophase spindles disappear, nucleoli and envelope reappear, chromosome lengthen and unwind to form chromatin
3)Cytokinesis divides the cytoplasm to make two daughter cell ( each contains one of the new nuclei).
7. What is semiconservative replication?
All DNA replication results in two copies of doublestranded DNA, each copy having a parent strand and a newly synthesized strand.
8. How many origins of replication are there in prokaryotes, eukaryotes?
9. How do origins of replication operate?
The origin of replication is AT rich, two regions of repeatsà 13bp and 9bp. DnaA first binds to four base pair repeats of 9bps and 3 base pair repeats of 13bps. As more DnaA binds the 13bps are unwound. DnaB (2) and DnaC bind to the 3 base pair repeats region of 13bps, displacing DnaA, and causing the DNA strand to open at the AT rich region.The two DnaB regions now form the two replication forks.
10. What is the function of helicase?
Separate double helix DNA during replication.
11. Where does RNA polymerase bind to initiate transcription?
Promoter Site of DNA (TATA BOX 10 bp)
12. What is transcription?
The first step of gene expression, when DNA is copied into RNA by DNA polymerase.
13. Where on the DNA does the sigma subunit bind?
35 bp to 10 bp
14. What does RNA polymerase I transcribe?
Transcribes rRNA found in ribosomes
15. What does RNA polymerase II transcribe?
Transcribes the proteincoding genes
16. What does RNA polymerase II transcribe? ( i think he meant III)
Transcribes tRNA genes
17. What are constitutive genes?
Genes that are expressed continuously.
18. What are the steps involved in RNA processing?
The first step is the addition of the Cap.
The next step is the addition of the polyA tail.
The final step is splicing of introns and the joining of exons by the spliceosome. The snRNA can recognize the end of the intron and work with snRNP.
19. What is the function of poly A polymerase?
It adds the polyAtail to eukaryotic mRNA during processing. It binds to the tail signal (AAUAA), the CA dinucleotide, and the GU rich tract. Once the mRNA is cleaved at the CA dinucleotide, the polyApolymerase adds the PolyA tail, to the free end.
20. What are ribozymes?
A ribozyme is an RNA molecule that shows enzymatic activity, such as tRNA and selfsplicing introns.
21. What is the structure of the mRNA cap?
Guanine nucleotide connected to mRNA thru unusual 5’ to 5’ triphosphate linkage.
22. Define intron, exon, intein, extein.
Intron: noncoding sections of an RNA transcript, or the DNA encoding it, that are spliced out before the RNA molecule is translated into a protein.
Exon: The regions of transcript that contain protein coding sequence
Intein:is a segment of a protein that is able to excise itself and join the remaining portions ( protein introns)
23. Define codon, anticodon
Codon three base sequence on mRNA
Anticodon three base sequence on tRNA
Condon and anticodon complement each other and produce protein.
24. What is translation?
The transmission of information from mRNA to protein.
25. What are tRNAs, snoRNA, snRNAs?
tRNA: The RNA type that brings amino acids to the protein synthesis machinery snoRNA:
26. What are the functions of amino acyl tRNA synthetases?
The enzyme that links the appropriate amino acid to the acceptor stem of specific tRNAs
27. Define peptide bond.
The type of covalent bond that forms between adjacent protein monomers.
28. Define competitive inhibitor, non competitive inhibitor
Competitive inhibitor= Substances that mimic the structure or behavior of the true substrate. Same Vmax and different Km.
Non competitive inhibitor= Same km different Vmax. In binds to the allosteric site, changing the structure of the enzyme, changing the ability of the true substrate to bind.
29. How do enzymes catalyze chemical reactions?
They lower the activation energy of the reaction.
30. Define allosteric?
Allosteric= relating to the binding of a protein through the binding of an effector molecule at a specific site. Enzyme that changes shape, when it binds to a small molecule.
31. What is the driving force for secondary structure formation?
32. What is the driving force for tertiary structure formation?
33. How are proteins denatured?
By changes in pH, temperature, and salt concentration.
34. Define proteome.
Is a total set of proteins encoded by the organism’s genome.
35. How does SDS PAGE work?
Denaturation of protein using detergent and high temperature.
36. How does a western blot work?
An antibody is attached to a target protein, then a secondary antibody is used to locate and visualize them (secondary antibody can be fluorescent).
37. What is phage display?
When a virus displays multiple peptide sequences.
38. Define primary, secondary antibody.
Primary: binds to the specific antigen or protein in a Western blot.
Secondary: binds to primary antibody to help with detection, sorting and targeting antigens.
Molecular Bio Exam 3 Review
What is negative regulation?
Repressor protein binds to an operator to prevent transcription.
Gene transcription is OFF when molecule is attached to repressor. Once molecule is gone, repressor releases and transcription begin.
What is positive regulation?
Transcription factor is required to bind at the promoter in order to begin transaction. Gene transcription is OFF when molecule is not attached to repressor. One molecule is present, repressor changes shape and is released from the operator.
Describe the lac operon?
Physical description: section of DNA found in some prokaryotes allowing for regulation over protein synthesis
Five Components: 1) Promoter Specific segment of DNA where RNA poly attaches to begin transcription.
2) Operator located between promoter and gene
3) Regulator sequence of DNA found in chromosome. Codes for the production of repressor protein
4) Repressor protein which can bind to operator, leading to no transcription. 5) Inducer which can activate/inactivate repressor
How is the lac operon induced?
Repressor binds to DNA in the absence of lactose and prevents transcription. One the inducer binds to to lac repressor, it dissociates from DNA and transcription begins.
What are gratuitous inducers?
A molecule which is structurally similar to another molecule that induces transcription for a specific product, and can initiate transcription for that product when official inducer is absent.
How is transcription regulated in prokaryotes?
RNA polymerase binds to the promoter gene and initiates transcription a few bases away from the promoter site. Activator proteins bind to their target DNA sites (positive regulation) and repressor proteins are inhibited from binding to their target sites (negative regulation).
What is the function of a two component regulatory system, what are the molecular components?
The system enables bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. The components are ATP and histidine kinase (HK).
What is autoregulation?
Occurs when a repressor binds to its own gene to prevent transcription.
What is the most common point used to regulate eukaryotic transcription? initiation
What are housekeeping genes and what frequency are they transcribed? They are constitutively active genes that maintain basic cellular functions and are expressed in all genes.
What is euchromatin?
Is loosely packed chromatin
What is heterochromatin?
Tightly packed, activity of gene is modified or suppressed.
What is the function of histone acetylation?
allow nucleosomes to be less aggregated
What is Xinactivation?
Shuts down one of the two X chromosomes in females.
What is the function of the Xist gene?
a gene encoding an untranslated RNA involved in Xinactivation
What is the function of transcription factors?
Modulate gene expression in response to a specific stimulus
In eukaryotic cells how is negative and positive regulation achieved? Negative regulation occurs by interfering with activators.
What triggers RNAinterference?
What are the components of the RNA interference pathway?
What are the components of the siRNA pathway?
Dicer, Ago, RISC
What is the CRISPR system?
Is a system which destroys incoming viral DNA and RNA ( only in bacteria?)
How is translation inhibited by the miRNA pathway?
miRNA inhibits translation of mRNA by binding to the 3’UTR of the mRNA and prevent translation
What is the function of the primer extension assay?
To determine the transcriptional start site
What is a gel shift assay?
Used to study protein, DNA or protein RNA interactions
What methods quantify the number of mRNAs within a cell?
Microarrays and SAGE methods
What is the function of DNA footprinting?
Determining the location of a DNA binding sequence
What is a northern blot?
Procedure used to detect specific sequences of RNA by hybridization with cDNA
How do transferable plasmids copy themselves?
Transferable plasmids use rolling circle replication as a form of replication during transfer.
How does rolling circle amplification occur?
begins when the origin of replication is nicked and one strand is unrolled
How does bidirectional plasmid replication occur?
Occurs at the origin of vegetative replication
What causes plasmid incompatibility?
Plasmid incompatibility is caused when because plasmids in the same family have similar DNA sequences in the replication genes.
What are the components of virus?
1) a nucleic acid genome and 2) a protein capsid that covers the genome
What causes viral plaque formation?
Result of viruses lysing bacteria
What are the differences between virus that infect bacteria and viruses that infect animal cells?
What are the steps of the viral lifecycle?
What are the components required for RNA viruses to replicate themselves? Viral RNA polymerase, host cell
How do viral mRNAs compete for host cell ribosomes?
They flood the cell to increase the probability of ribosomes translating them What does R0 tell you about viral infectivity?
AKA the basic reproduction number, it measures the spread of a disease in a population. If it is less than 1, the infection will die out. If it is greater than 1, the infection will spread.
What is herd immunity and why is it important?
A form of indirect protection from infectious disease that occurs when a sufficient population of the community is immune to an infection, thereby providing a measure of protection for those who are not. This is important because not everybody has access to vaccinations or can even be administered a vaccine, either due to age (too young or too old) or other illnesses that are present.
What are defective copies of transposable elements called?
What is conservative transposition? What enzymes are required and what are their functions?
Conservative transposition generates doublestranded breaks in the DNA
What is replicative transposition? What enzymes are required and what are their functions?
Resolvase are required.
What elements are common to all transposons?
DNA sequences that code for enzymes that insert a copy of themselves into a new DNA site They cannot replicate away from the host chromosome
Generate two daughter copies of the original transposon
During transposition, what is the function of reverse transcriptase?
Makes a DNA copy of the RNA to insert in a new location
Any DNA or RNA molecule that has an origin of replication.
How do cells inhibit transposon activity?
Organisms go to great effort to expose germ line activity
TiRNA react with piwi proteins, repress transposon activation in the germ line, they recognize the transposable elements; they know its not in the germ line,
There is only one genetically pure cell in the body germ cell
MiRNA: gene product, regulates development because its production is controlled SiRNA: Virus or lab destroys foreign bodies
PiRNA: represses transposable