Term
| What are the implications of inheritance of somatic or germ line mutations? |
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Definition
o Germ line or gametic mutation are passed on to ½ of offspring; all cells of offspring will carry mutation; occur in cells that give rise to gametes
Somatic mutations- cannot be transmitted to next gen but can be used through vegetative propagation; only seen in diving cells; occur in nonrepro cells |
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Term
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Definition
Spontaneous mutations- caused by unknown agent
Induced mutations- caused by exposure to mutagen |
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Term
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Definition
| Base substitution- nucleotides pair in DNA is replaced with a different type of nucleotide base pair |
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Term
| Transitions vs. Transversions |
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Definition
Types of base substitutions
Transitions- purine to purine (A to G, G to A), pyrimidine to pyrimidine (T to C), most common
Transversions- purine to pyrimidine or vice versa (A to C, T to A, etc.) |
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Term
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Definition
AFFECTS ALL DOWNSTREAM CODING SEQUENCES
Alterations of proteins, truncated due to a stop codon, restoring reading frame
Large deletions- loss of genes
Many small deletions occur in introns (silent) |
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Term
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Definition
Effects are more severe than substitutions, fra
frame shiift in reading |
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Term
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Definition
| involves the DNA polymerases and their exonuclease activity ( to go backwards, to cut out bad stuff and reinsert the correct one) |
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Term
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Definition
| Removal of distorted segment and re-synthesis; base excision repair, methylation, how to enzyme recognize which strand is correct- methylation |
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Term
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Definition
| repair of the dimers caused by UV light in prokaryotic cells, photolyase enzyme? |
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Term
| Nucleotide excision repair |
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Definition
NER- mechanism to repair lesions that distorts the double helix (dimers, damaged DNA, such lesions impede DNA replication and transcription)
Found in all organisms
Damage to DNA distorts configuration → enzyme complex recognizes distortion → DNA separated, single stranded binding proteins stabilize single strand → enzyme cleaves the strand on both sides of damage → part of damaged strand removed → gap is filled in by DNA pol and sealed by ligase |
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Term
| What is a transposable element? |
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Definition
Mobile genetic elements
Insert or excise from gene, result in altered gene expression |
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Term
| What are the characteristics of a transposon? |
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Definition
Typically 50-10,000 bp in length
Can be found in individual genome from one to hundreds of thousands of copies |
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Term
| Understand the Ac/Ds elements in maize. |
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Definition
Most maize transposons exist in two forms: autonomous elements and nonautonomous
Autonomous- capable of transpositions by themselves- known as activator (Ac)
Nonautonomous- only transposed if autonomous element is also present- known as dissociation elements (Ds) |
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Term
| How do Ac/Ds elements in maize affect kernel color? |
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Definition
o When Ds moves into pigment gene you will no longer have pigment produced (yellow)
o When Ds moves out into pigment gene you have purple corn |
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Term
| Operon structural arrangement |
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Definition
| Operons are bacterial genes with related functions clustered together. The operon contains a set of structural genes (transcribed into a single mRNA → translated into individual enzymes), a promoter, and a regulator gene. |
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Term
| What role does the regulator gene play in gene expression? |
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Definition
| It binds to operator and influences transcription. |
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Term
| Know the roles of promoter and operators |
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Definition
Promoter- control expression of structural genes
Operators- DNA sequence between promoter and structural genes |
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Term
| Determine negative or positive control |
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Definition
Negative control- regulator protein is a REPRESSOR; binds to DNA inhibiting transcription; NEGATIVE inducible and NEGATIVE repressible; NEGATIVE CONTROL- REGULATOR PROTEIN REPRESS TRANSCRIPTION
Positive control- regulator protein is an ACTIVATOR; binds to DNA stimulating transcription’ POSITIVE inducible and POSITIVE repressible |
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Term
| Inducible vs. Repressible (decipher how a given operon is regulated) |
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Definition
INDUCIBLE- transcription normally off
-Negative: normal: regulator protein bound to operator, no transcription → inducer binds to reg protein → reg protein changes shape → reg protein can no longer bind to operator → transcription
-Positive: normal: transcription off → inducer attaches and activates reg protein for binding to DNA
REPRESSIBLE- transcription normally on
-Negative: normal: transcription occurring → reg protein is a repressor (normally inactive) → repressor activated by co-repressor binding to operator → transcription stops
-Positive: normal: transcription occurring, reg protein bound → substance binds to reg protein → transcription stops |
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Term
| Understand the arrangement and regulation of the lac Operon. |
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Definition
3 structural genes:
-LacZ- encodes beta-galactosidase- converts lactose → glucose and galactose for use in glycolysis; also converts lactose → allolactose
-LacY- encodes permease- enzyme that allows lactose to enter cell
-LacA- encodes transacetylase- removal of toxins due to lactose digestion
All 3 expressed at same time |
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Term
| Negative inducible of lac operon |
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Definition
No lactose (allolactose) present: repressor gene product bings to lacO (lac operator)
Blocks RNA polymerase → no transcription |
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Term
| How does lactose induce expression |
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Definition
Lactose (allolactose) binds to repressor gene product preventing it from binding to operator
RNA polymerase binds → transcription |
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Term
| cAMP-CAP regulation related to glucose presence |
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Definition
CAP- catabolite activating protein
CAP must bind to promoter region for RNA pol to bind and transcribe → no glucose → CAP binds to cyclic adenosine monophosphate → low glucose = high cAMP → cAMP alters structure of CAP → CAP-cAMP complex binds to promoter |
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Term
| Understand the arrangement and regulation of the trp Operon |
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Definition
trp operon- 5 structural genes; produces enzymes that synthesizes tryptophan
regulator gene (trpR): product = regulator protein- repressor
Low tryptophan levels → repressor binds to DNA operator → RNA pol binds and transcription occurs → tryptophan results
If there is tryptophan in system, RNA pol can’t bind → no transcription |
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Term
| Why is it negative? In reference to trp operon |
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Definition
| The presence of tryptophan causes a conformational change in the repressor protein that blocks transcription |
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Term
| Why is it repressible? In reference to trp operon |
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Definition
| When tryptophan is LOW, repressor is blocked and transcription occurs |
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Term
| How does chromatin structure serves as the on/off switch |
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Definition
| Prior to transcription, chromatin remodeling takes place. Dnase I hypersensitivity, histone acetylation, and/or methylation of cytosine bases; chromatin relaxes/opens allowing transcription to occur; once opened, the promoters are exposed (enhancers and transcription factors can then regulate transcriptions). |
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Term
| Understand the role of transcriptional activators? |
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Definition
2 distinct functions: (1) bind to consensus sequence; regulatory promoter or enhancer, requires one of more of the binding motifs, binding brings the enhancer or regulatory promoter into contact with the transcription appartus. (2) Interact with other transcriptional components
Regulatory proteins that bind to DNA sequences and affect expression |
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Term
| What is an enhancer? How do they influence transcription? |
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Definition
| Enhancers are time and tissue-specific gene expressions that are required for full level transcription. Transcription activator proteins bind to the enhancers and alter chromatin structure, causing DNA to bend or loop |
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Term
| Elongation and termination |
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Definition
elongation
the increase of polypeptide chain by 1 A seq of next codon dictates type of tRNA that will bind next to met
termination
when A binding site reaches stop codon chain is released from P site. |
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Term
| What is the function and assembly of a Ribosome? |
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Definition
P(peptidyl) site = first site and found to f-met
A(aminoacyl) site= binding is the second site and receives second AA
releases tRNA |
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Term
| How is translation initiated? |
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Definition
Small subunit first binds to the RNA
o In prokaryotes, there is a Dalgarno? Sequence that helps line the ribosome up
o Initiation factor 3 binds to the small subunit
o Charged tRNA comes in with initiation factor 1 and 2, once RNA is in place, all initiation factors leave and large subunit comes on |
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Term
| What is aminoacyl-tRNA synthetase? |
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Definition
| A group of enzymes whos specific functions are to identify particular tRNA and catalyze the attachment of the appropriate AA at the 3’ terminus |
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Term
| How do amino acids bind to tRNA? |
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Definition
0-50 different tRNA
aminoacyl-tRNA synthase binds the AA to its tRNA
20 different aminoacyl-tRNA synthases
specific to each AA |
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Term
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Definition
for nuclear derived mRNA
attaches to mRNA to cut it in a 4 step process
1) cleaves 5’ splice site
2) forms a lariat intron structure which binds 5’ end to branch point adenine
3) cleaves 3’ splice site
4) ligated exons and releases lariat intron to be degraded |
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Term
| Know how pre-mRNA is processed |
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Definition
5’ cap is added to protect from degradation
poly-A tail is added to slow degradation
about 11-30 nucleotides from start
introns are removed to obtain a functional RNA |
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Term
| What is the 5’ cap? How is it added? |
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Definition
only on transcripts generated by RNA pol II
additional guanine at 5’ end
position 7 of the base is methylated
methyl groups can also be added to the second and third nucleotides
added right after start of transcription
protects pre-mRNA from nuclease degradation
facilitates binding to ribosome during translation |
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Term
| What is the 3’ poly A tail? How is it added? |
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Definition
the 3’ end of mRNAs is modified with the addition of poly A tail
AAUAAA represents recognition site in pre-mRNA
3’ end is cleaved 11 to 30 nucleotides from AAUAAAA
multiple adenine residues are the added by the enzyme poly-adenylate polymerase
the poly A tail confers stability because it slows down degradation
histone mRNAs are exceptional in that they do not contain a poly A tail
prevents degradation by nucleases
3’ poly A tail
exon splicing
RNA editing |
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Term
| Be familiar with mRNA structure |
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Definition
pre-mRNA
5’ cap + introns + exons + 3’poly-A tail
mRNA
5’ cap + exons + 3’ poly-A tail |
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Term
| What is the product of transcription? |
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Definition
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Term
| RNA polymerase I of eukaryotes: |
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Definition
Eukaryotes
RNA pol I:
transcribes large rRNA molecules
termination factor that binds to DNA sequence downstream of termination site |
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Term
| Be familiar with the arrangement of gene components: Prokaryotes vs. Eukaryotes |
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Definition
Promoters: contain sequence that define start of gene
enable communication between environment
Prokaryotes:
TATAAT box- 10 bp upstream of start site
pribnow box
sigma subunit finds this box
TTGACA box- 35 bp upstream of start
Eukaryotes
TATAAAA boc- TATA box=30 bp from start
GGCCAATCT-CAAT box= 80 bp from start
Coding Sequences: spells out sequence of amino acids
Prokaryotes:
no introns usually
one promoter with multiple genes
genes that encode for enzymes are often linked into single unit called operon
Eukaryotes:
genes encode single protein or single RNA
each gene is expressed independently
one gene:one product
possible to get different genes depending on what exons are spliced out
terminating sequence: sequence that has a stop codon |
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Term
| Be familiar with the Central Dogma of genetics |
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Definition
DNA-------mRNA--------Protein
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trasncription translation
when info in genes is decoded to produce other molecules that determine phenotype. |
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Term
| Understand how codons stipulate amino acid sequence |
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Definition
mRNA carries specific instructions from DNA to ribosomes
w/ specific sequence for amino acids
every 3 nucleotides is a codon
mRNA then transcribes it and makes an anti-codon
anti-codon is then transferred to ribosome where amino acid is brought over by tRNA |
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Term
| Understand the role of transcription in gene expression |
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Definition
| process of generatng a mRNA or structural RNA based on gene sequence. |
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Term
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Definition
determines which strand to transcribe
transcription apparatus recognizes promoter and binds
determines transcription start site |
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Term
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Definition
| DNA sequence that is copied into RNA |
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Term
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Definition
DNA sequence that signals for transcription to end
Termination occurs after the terminator sequence has been copied |
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Term
| Prokaryotes transcription process |
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Definition
Bacterial RNA polymerase
usually 1 type that synthesizes all RNA
large enzyme
core has 5 subunits
sigma factor- controls binding of RNA polymerase to the promoter
Initiation: sigma unit regonizes promoters
binds to DNA
DNA unwinds
haloenzyme intiates elongation
TATAAT-10bp
TTGACA-35 bp
elongation:afer sigma subunit dissociates and RNA polymerase continues elongation
Termination: RNA is released from RNA polymerase
two types:
rho-dependent terminator sequences
binds to unstructured RNA
RNA polymerase pauses
when Rho catches and unwinds DNA-RNA hybrid
transcription stops
intrinsic termination
inverted repeates
6 adenine nucleotides follow second inverted repeats
transcribed into RNA |
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Term
| Eukaryotes transcription process |
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Definition
3 different RNA polymerases
RNA pol I- transcribes large rRNA
RNA pol II- transcribes mRNA
RNA pol III- transcribes tRNA
nucleosome alteration chromatin remodeling- needed to enable access to DNA
enhancer:
sequences that increase rate of transcription
can involve DNA loops to bridge physical distance between different transcription factors and RNA polymerase
transcription factors
form basal trasncripton apparatus w/ RNA polymerase
Promoter
core promoter= TATA box 30 bp
TFIIB 35 bp
initiator element
regualtory promoter= CAAT box up to 2 kb
GC box
OC box |
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Term
| e familiar with the techniques used to study bacteria |
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Definition
reproduction is rapid
high population #
genome allows for mutations to be expressed
growing them is easy and takes little space
there are techniques to isolate and manipulate genes
can be genetically engineered to produce substances of commercial value. |
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Term
| What are plasmids? Their functions? |
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Definition
2-20 kb is size (on average)
Not essential for bacterial growth
Often provide selective advantage to the bacterium
May get lost over time when the selective pressure is removed
Rely on DNA-replication enzymes used for chromosomal replication (plasmid does not encode its own polymerase)
High copy plasmids- up to 50 copies/cell
Low copy number plasmids- 1 or 3 copies/cell
Important tools for genetic engineering of bacteria
Insert novel genes in plasmid to produce recombinant protein
Insulin for diabetes patients is now made in bacteria, as opposed to isolated from pig pancreas
Transferred through congugation
Extrachromosomal DNA
Usually separate from bacteria chromosome |
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Term
| Be familiar with the methods of gene transfer in bacteria. |
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Definition
Conjugation- involves physical contact via a pilus
The F plasmid in E. coli encodes the genes needed to make the pilus
F+ is donor, F- is recipient
Single stranded DNA is transferred
Becomes dsDNA in recipient
F plasmids are low copy number plasmids
They replicate once per cell cycle and segregate to both daughter cells during division
F plasmids (100 kb) can occasionally integrate into the bacterial chromosome
Transformation- a donor molecule (free DNA Molecule) is taken up from the surrounding medium and incorporated into the genome of a recipient cell |
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Term
| What is the F Plasmid and its role? |
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Definition
Creates the one way transfer of genetic material
F- factor (fertility factor) is transferred from donors to recipients.
donors are F+ cells and recipients are F-
F plasmid carries the genes for conjugation
only donor cells can initiate conjugation
100kb in length; w/ about 40 genes to control conjugation
F plasmids are low # plasmids |
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Term
| Be familiar with some unique features of viral genetics (types of viruses, reverse transcription, overlapping genes encoded in the same DNA) |
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Definition
reverse transcription and transcriptase allows gene to go from mRNA to cDNA
allows for reproduction of DNA |
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Term
| RNA pol II of eukaryotes: |
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Definition
mRNA
recognizes and binds to the promoter consensus sequence in eukaryotes
cleavage complex
• follows RNA pol II until consensus terminator is encountered |
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Term
| RNA pol III of eukaryotes: |
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Definition
transcribes all tRNA
transcribes a terminator sequence
• a string of uricil nucleotides in an RNA molecule |
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Term
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Definition
| one type that synthesizes all mRNA, tRNA and rRNA |
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