Term
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Definition
| Most biologists do not think of them as living organisms, |
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Term
| What dont viruses do on their own? |
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Definition
| They can’t do anything by themselves. They don’t eat, reproduce, do any metabolism on their own. |
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Term
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Definition
| Viruses are genes packaged in a protein coat. |
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Term
| How many genes can viruses have? |
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Definition
|
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Term
| What do viruses behave like? |
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Definition
|
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Term
| What do viruses use to reproduce? |
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Definition
|
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Term
| What are some Illnesses caused by viruses? |
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Definition
| colds, flu, HIV, SARS, polio, hepatitis. |
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Term
| What does viral DNA do inside a cell? |
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Definition
| expresses its genes, these encode proteins to take over cell |
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Term
| What do viral enzymes do? |
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Definition
| Enzymes for DNA replication, coat and leg proteins, regulators of the cells proteins. |
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Term
| Viruses are usually specific because...? |
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Definition
| the viral proteins need to work with specific host proteins. |
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Term
| After Many copies of the viral DNA are made and packaged into viral proteins what happens? |
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Definition
| Often cell then breaks apart to release new viruses. |
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Term
| What kind of drug doesn't work on viruses?Second step in DNA replication? |
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Definition
| Antibiotic drugs don’t work on viruses.Use of RNA primers |
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Term
| What kind of genomes do many viruses have? |
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Definition
| Many viruses have RNA genomes. |
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Term
What did Messelson & Stahl do?
using what? |
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Definition
| semi-conservative replication experiment using "heavy" and "light" N isotopes |
|
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Term
| first step in DNA replication? |
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Definition
| Strand separation, enzymes that avoid excess coiling |
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Term
| Third step in DNA replication? |
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Definition
| DNA polymerase incorporates nucleotides |
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Term
| On to what end are nucleotides incorperated during the replication of DNA? |
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Definition
| always adds to the 3' end |
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Term
| Fourth step in DNA replication? |
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Definition
| Proofreading by DNA polymerase, has exonuclease activity |
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Term
| What does a nuclease enzyme do? |
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Definition
| Cuts the damaged DNA strand at two points allowing the damaged section to be removed |
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Term
|
Definition
| Leading strand synthesized continuously, keeps adding to the 3' end proceeds in direction of replication fork |
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Term
|
Definition
| Lagging strand, Made in pieces (Okasaki fragments) |
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Term
| On the lagging strand what end does _____ ____________ add to? |
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Definition
|
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Term
| What happend to the RNA primers used to start the lagging strand replication? What is this done by? |
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Definition
RNA sequences cut out and replaced by DNA
Done by a different DNA polymerase |
|
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Term
| How are the gaps between Okazaki fragments connected? |
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Definition
| Gap connected by DNA ligase. |
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Term
| What kind of mutations affect the chromosomes? |
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Definition
| Chromosome abnormalities, breaks, rearrangements |
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Term
| As for Errors during replication most are... |
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Definition
| "point mutations" one incorrect base |
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Term
| _____ _________ fixes ___ but not all |
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Definition
|
|
Term
| Most are errors are neutral.....how? |
|
Definition
| either in non-coding regions, or "silent" |
|
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Term
| What is a silent mutation? |
|
Definition
In the ORF but causing no change in function..
such as ccc(pro) to CCA(also pro) |
|
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Term
| Additions and deletions of bases, can cause __________ |
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Definition
|
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Term
| Some things that damage DNA |
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Definition
| UV, gamma rays, reactive oxygen carcinogens, especially in tobacco smoke |
|
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Term
| What does UV cause in dna? |
|
Definition
| Dimers..covalently bonded T |
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Term
| When there is an error how do you tell which strand is in error.. what nucleotide do you beleive? |
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Definition
| The older strand (correct) has most likely become methylated and can be identified. |
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Term
| How are thymine dimers fixed. |
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Definition
| They bulge.. an enzyme recognizes, cuts them out and replaces normal T |
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Term
| In humans many diseases are due to defects in ________ enzymes. |
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Definition
|
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Term
|
Definition
| Extreme sensitivity to UV .. develop skin lesions |
|
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Term
| what is defective in xenoderma pigmentosa? |
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Definition
| Recent studies show that different people have defects in different genes (at least 7 genes), probably defective repair enzymes |
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Term
|
Definition
| polymerase chain reaction |
|
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Term
| Two things PCR allows us to do... |
|
Definition
1. Allows us to generate a large amount of DNA from almost undetectable amounts of DNA.
2. Allows us to find one particular region, e.g. one gene, in a mix of a million unrelated DNA fragments. |
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Term
| Central Dogma of Molecular biology |
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Definition
|
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Term
| DNA is the _________ ________ of the ___________ |
|
Definition
| permanent storage, information |
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Term
RNA, particularly mRNA is a copy of the parts of that information that is
....... |
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Definition
| Needed at any particular time |
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Term
| It primarily directs the synthesis of proteins |
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Definition
|
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Term
| what is the actual functional machinery of the cell.. some examples? |
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Definition
| Protein, enzymes and structural proteins |
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Term
Transcription is copying DNA into _____, both in the language of nucleotides.
DNA is __________ |
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Definition
| RNA,nucleotides, transcribed |
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Term
| Translation is .....?RNA is ...... |
|
Definition
converting the nucleotide sequence of RNA into the amino acid sequence of protein.
translated. |
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Term
RNA polymerase is like DNA polymerase
It....... |
|
Definition
| uses NTPs, pairs them up with the complementary base pairs on a single strand of DNA , makes a sugar-phosphate backbone |
|
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Term
| Initiation of transcription, Sequences in the DNA are binding sites for |
|
Definition
| proteins that guide the RNA polymerase to the start of genes. |
|
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Term
| TATAAT is usually found... |
|
Definition
| often found 10 bases away from start. |
|
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Term
| In bacteria another sequence, TTGACA is found....? |
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Definition
|
|
Term
| Proteins called _________ ________ bind to the DNA Then _____ ___________ binds and separates the DNA strands |
|
Definition
| transcription factors, RNA Polymerase |
|
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Term
| “Upstream and downstream”, terms used to describe relative position.The polymerase moves ___________ |
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Definition
|
|
Term
thus the TATAAT box is 10 bases _________ of the transcription
start site. |
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Definition
|
|
Term
The codon for the first amino acid is usually _________ bases
_________of the transcription start site. |
|
Definition
|
|
Term
| Once the polymerase starts making RNA, the ___________ are not needed and usually _____ _______ |
|
Definition
| transcription factors, fall off |
|
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Term
| elongation continues with one ____ used for every base added,releases a ____ with each step. |
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Definition
|
|
Term
| Termination occurs when..... |
|
Definition
| a sequence on the DNA appears.The polymerase falls off and the RNA is released. |
|
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Term
What is the “gene”?
The promoter is |
|
Definition
the region where RNA polymerase binds
Also has specific sequences for transcription factors |
|
|
Term
What is the “gene”?
5' UTR |
|
Definition
| The transcribed (copied) region upstream of the start codon |
|
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Term
What is the “gene”?
in between 5' and 3' UTR |
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Definition
|
|
Term
| The transcribed region downstream of the stop codon? |
|
Definition
|
|
Term
Thus the RNA has all of the ________ _______ ________ plus additional sequences
upstream and downstream |
|
Definition
|
|
Term
|
Definition
| The protein-coding region is often interrupted with nucleotides that do not code for amino acids. |
|
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Term
| within the protein coding region The non-coding parts are called |
|
Definition
| introns = intervening sequences |
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Term
| Within the protein coding region The coding parts are ..? |
|
Definition
| exons = expressed sequences |
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Term
Splicing
Introns are recognized by |
|
Definition
| specific DNA sequence at the boundaries |
|
|
Term
Introns...specific DNA sequence at the boundaries
e.g. a typical sequence is______ at one end and _____ at the other. |
|
Definition
|
|
Term
| The ____________ is a complex of _________ ______ _____ that recognizes these sequences and cuts out the intron. |
|
Definition
| spliceosome, proteins and RNAs |
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Term
| Introns can vary enormously in _____ and ________ per gene. |
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Definition
|
|
Term
| Final step in making mRNA is to add a __ ______ and a _________ _______ |
|
Definition
|
|
Term
| 5’ cap and a poly-A tail seem to ......, If missing the mRNA is quickly _______ |
|
Definition
| mark the mRNA as intact and functional, degraded. |
|
|
Term
End of Transcription..
mRNA then exits the nucleus, through the ________, ready for ____________. |
|
Definition
|
|
Term
| tRNAs are ...... with..... |
|
Definition
| small RNA , ~80 nucleotides |
|
|
Term
tRNAs double helical regions, can be represented as _______ __________
actual 3D structure is ___ ________ |
|
Definition
| cloverleaf structure, “l” shaped |
|
|
Term
tRNA One end contains the __________
The other end of tRNA has an ________ _______attached __________ |
|
Definition
| anticodon, amino acid, covalently |
|
|
Term
| How many tRNAs are there? |
|
Definition
|
|
Term
| aminoacyl tRNA synthetases |
|
Definition
| Binds an amino acid and a tRNA and pairs them up |
|
|
Term
| Binds an amino acid and a tRNA and pairs them up |
|
Definition
| aminoacyl tRNA synthetases |
|
|
Term
| How many aminoacyl tRNA synthetases ? |
|
Definition
| 20 different ones, for each amino acid |
|
|
Term
| aminoacyl tRNA synthetases: two step reaction, binds___________ first, high-energy bond (acyl bond) uses _____, then binds ___________, transfers amino acid to end of tRNA |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| called rRNA, 4 different strands of RNA |
|
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Term
|
Definition
|
|
Term
The RNA forms the ______ of the ribosome and appears to do much of the
____________ of the reactions. |
|
Definition
|
|
Term
| Two pieces of a ribosome? |
|
Definition
small ribosomal subunit (30S in E. coli)
large ribosomal subunit (50S in E. coli) |
|
|
Term
| What do you need to make a protein? |
|
Definition
| mRNA, ribosomes, aminoacyl tRNAs, Translation factors (helper proteins), GTP |
|
|
Term
Know the steps involved in
Initiation: |
|
Definition
| mRNA binds small ribosomal subunit, first tRNA binds, Large ribosomal subunit binds |
|
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Term
|
Definition
| 2nd tRNA binds, ribosome binds together aas w/ peptid bond.. 1st tRNA falls off (exit slot) |
|
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Term
|
Definition
| Ribosome moves down RNA, GTP is used to move ribosome |
|
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Term
|
Definition
| Stop codon in acceptor site, termination factor cleaves bond between previous tRNA and AA. |
|
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Term
| Protein maturation - How does the protein get folded up into the correct shape? |
|
Definition
| For most proteins this occurs spontaneously, driven by the amino acid sequence |
|
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Term
| Protein maturation - How does the protein get folded up into the correct shape? |
|
Definition
| a few use helper proteins..Chaperones |
|
|
Term
| Prions ... some diseases..? |
|
Definition
| mad-cow disease, kuru, Creutzfeldt-Jakob disease |
|
|
Term
Prions
Some rare proteins can ________ in alternative stable forms |
|
Definition
|
|
Term
Prions
________ __________ make them fold stably in an alternate form |
|
Definition
|
|
Term
Prions,
If you mix a correctly folded protein with an incorrectly folded one |
|
Definition
| the incorrect one can catalyze incorrect folding. |
|
|
Term
| Some evidence suggests that prion protein can act as an... |
|
Definition
|
|
Term
Prions
Transmitted by ...? |
|
Definition
|
|
Term
| In humans prions cause... |
|
Definition
| brain degeneration, proteins aggregate |
|
|
Term
Control of genes and proteins can be:
transcriptional |
|
Definition
| - Is the gene copied into RNA? |
|
|
Term
Control of genes and proteins can be:
translational |
|
Definition
| - Is the mRNA made into protein? |
|
|
Term
Control of genes and proteins can be:
post-translational |
|
Definition
|
|
Term
| lactose metabolism in E. coli - great model of ___________ _________ |
|
Definition
|
|
Term
|
Definition
| a disaccharide, glucose+galactose |
|
|
Term
|
Definition
| by the enzyme ?-galactosidase |
|
|
Term
| If you feed E, coli glucose and lactose it will |
|
Definition
|
|
Term
The Lac Operon
Investigated by .... |
|
Definition
|
|
Term
| Isolation of mutants by ________ ______ |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| have ?-galactosidase, can’t take lactose into cell lack the transport protein |
|
|
Term
|
Definition
| have ?-galactosidase all the time, expression "constitutive " |
|
|
Term
| genes in a special type of cluster, called an ________ |
|
Definition
|
|
Term
Operons
common in _________, no operons in _________ |
|
Definition
|
|
Term
| Why isnt b-galac made all the time? |
|
Definition
| Lac I codes for a repressor protein |
|
|
Term
| What does the lac I repressor protein do? |
|
Definition
| Binds at 5' end of LacZ and Y, prevents polymerase from reading the dna |
|
|
Term
| Why does b-gal appear when lactose is present? |
|
Definition
| lactose binds to the repressor protein causing it to fall |
|
|
Term
| If lactose and glucose are present why does e. coli eat glucose first? |
|
Definition
| Cell can monitor level of glucose. Low glucose levels trigger cyclic AMP production which binds to CAP and goes to the Lac Operons and attracts RNA polymerase |
|
|
Term
| role of cAMP and the CAP protein |
|
Definition
| In absence of glucose cAMP is made, it binds to CAP protein and facilitates RNA polymerase reading Lac Operons |
|
|
Term
| Portion of DNA where inhibitor protein binds? |
|
Definition
|
|
Term
| Where does cAMP+CAP bind? |
|
Definition
|
|
Term
| Repressor is ______ control |
|
Definition
|
|
Term
| CAP+cAMP are ______ control |
|
Definition
|
|
Term
| role of helix-turn-helix motif |
|
Definition
| exact fit to 6-20 nucleotides, often 2-4 sites where it can bind |
|
|
Term
| effect of the inducer on repressor protein |
|
Definition
| lactose changes shape of the protein and causes it to fall off the DNA |
|
|
Term
Know the relative sizes of different genomes (approximate).
e.coli |
|
Definition
|
|
Term
Know the relative sizes of different genomes (approximate).
Neurospora |
|
Definition
|
|
Term
Know the relative sizes of different genomes (approximate).
Arabidopsis |
|
Definition
|
|
Term
Know the relative sizes of different genomes (approximate).
Drosophila |
|
Definition
|
|
Term
Know the relative sizes of different genomes (approximate).
Human |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| core is 8 proteins named histones, highly conserved DNA is wrapped around outside 2 times – about 200 bps |
|
|
Term
| Gene structure in eukaryotes |
|
Definition
no operons, genes with related functions typically scattered throughout
the genome. |
|
|
Term
| Much DNA in higher organisms is ...? |
|
Definition
non-coding, repetitive DNA of unknown
function. |
|
|
Term
Gene structure in eukaryotes
Genes are ....? |
|
Definition
bigger
coding region not really bigger, proteins about the same size
5’ region has bigger regulatory region,
Introns can be very large, much larger than the coding region |
|
|
Term
| Enzyme which seperates dna strand during replication? |
|
Definition
|
|
Term
| Enzyme which assembles RNA primers during DNA synthesis? |
|
Definition
|
|
Term
| enzymes that avoid excess coiling in synthesis? |
|
Definition
|
|
Term
|
Definition
nucleosome structure has to be modified when genes are
transcribed |
|
|
Term
| Transcription factors ...? |
|
Definition
|
|
Term
| How many transcription factors in higher eukaryotes? |
|
Definition
|
|
Term
|
Definition
genes can have many introns, 10 or more not unusual
therefore have many exons, not all are included in all mRNAs
one gene can give rise to many variations in proteins |
|
|
Term
How do you clone a gene?
Define cloning..? |
|
Definition
| as making many genetically identical copies |
|
|
Term
| First step in cloning a gene? |
|
Definition
| Use PCR to get a small amount of the gene |
|
|
Term
| Second step in cloning a gene? |
|
Definition
. Cut end with restriction endonucleases.
Enzymes made by bacteria.
Cut DNA only at specific sequences, pallindromes
example GAATTC
CTTAAG
makes a "sticky end" |
|
|
Term
| Step three in cloning a gene? |
|
Definition
3. Cut plasmid DNA with the same endonuclease. plasmid is a DNA circle with
1. origin of replication, in bacteria with be replicated very
accurately by the bacterial enzymes.
2. gene for antibiotic resistance |
|
|
Term
|
Definition
4. Mix human gene and plasmid
sticky ends will bind
ligate with ligase |
|
|
Term
| Step 5 in cloning a gene? |
|
Definition
. Transform bacteria, grow on medium containing penicillin
Only those cells that have taken up the plasmid will grow.
Each bacterial cell will have many copies of the plasmid.
Can grow many bacteria, get many copies of the plasmid DNA.
Can always cut it out again with the restriction enzyme |
|
|
Term
| Step 1 in making a microarray |
|
Definition
| 1. Use PCR to get small amount of all genes |
|
|
Term
| Step 2 in making a microarray |
|
Definition
2. Put a spot of each DNA at a marked place on a glass slide.
Can put 1000's of spots a single glass slide.
Know the identity of each spot |
|
|
Term
| Step 3 in making a Gene chip |
|
Definition
3. Prepare mRNA from experimental cells and reference
label one with red dye, other with green dye
mix together, |
|
|
Term
| Step 4 in making a Gene chip |
|
Definition
4. soak the slide in a mix of the red/green labeled RNAs
The RNAs will bind to the gene from which they are derived |
|
|
Term
| Step 5 in making a Gene chip |
|
Definition
5. Use a machine to look at each spot, determine how much red
and green dye is bound to each gene
If same ? yellow, = no change
or high/low? |
|
|
Term
| What did gene chip analysis of malignant vs. benign breast tumors show? |
|
Definition
| found 70 genes that correlated with spreading (metastasis) of tumor |
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