Biology- Molecular Genetics Flashcards
(133 cards)
1
Q
nucleotides
A
consist of 3 parts: phosphate group, sugar, and a nitrogen base
2
Q
DNA replication
A
involves separating (unzipping) the DNA molecule into 2 strands.
Each strand then serves as a template to make a new, complementary strand
3
Q
semiconservative replication
A
consists of a single strand of old DNA (template strand) and a new, replicated DNA (the complementary)
4
Q
helicase
A
unwinds the DNA, forming a Y-shaped replication fork
5
Q
single-stranded binding proteins
A
attach to each strand of the uncoiled DNA to keep them separate and prevent them from recombining
6
Q
topoisomerases
A
break and rejoin the double helix, allowing the twists to unravel and preventing formation of knots and twists that form as a result of the unwinding done by helicase
(if you unwind a twist, the ends will get extra tight and knot up)
7
Q
DNA polymerase
A
enzyme that assembles the new DNA strand, which moves in the 3’-5’ direction along each template strand. A new complement strand grows in the antiparallel direction 5’-3’.
8
Q
In which direction does replication occur continuously?
A
3’ => 5’; the DNA polymerase follows the replication fork and assembles a 5’ => 3’ complementary strand
9
Q
leading strand
A
complementary strand made in 5’ => 3’ direction (continuous replication)
10
Q
okasaki segments
A
short segments of complementary DNA; For the 5’=>3’ template strand, DNA polymerase moves away from the replication fork
*Every okasaki segment has an RNA primer
11
Q
DNA ligase
A
enzyme that connects okasaki segments; in all cases of repair, ligase must come in to seal the backbone afterward
12
Q
lagging strand
A
for the 5 => 3 template strand the DNA polymerase has to go back to the replication fork and work away from it. complementary strand that requires more assembly time than the leading one, because it is assembled in short okazaki fragments
13
Q
primase
A
enzyme that creates a short stretch of RNA to use as a primer during DNA replication; it initiates DNA replication at special nucleotide sequences called origins of replication w/ RNA primers
The small strip of rna primer allows DNA polymerase can work since it can only add to an existing strand
14
Q
RNA primer
A
short stretch of RNA nucleotides, later replaced w/ DNA nucleotides by DNA polymerase
15
Q
elongation
A
adding of DNA nucleotides to the complement strand; happens when DNA polymerase attaches to RNA primers
16
Q
Where does the energy for elongation come from?
A
there are two additional phosphates that are attached to each nucleotide. When the bonds are broken, it provides chemical energy (same w/ transcription). Human rate 50 n/s
17
Q
Replication of Telomeres (ends of eukaryotic chromosomes)
A
Two problems can occur:
- When not enough template strand remains to which primase can attach.
- FIX: telomerase comes in - When the last primase is removed, if there is no next okazaki segment to which DNA polymerase can attach, the empty space left by the removal of the primer is left unfilled. RNA is ultimately destroyed by enzymes that degrade RNA left on the DNA, section of the telomere subsequently lost w/ each replication cycle
Prokaryotic DNA is circular so no telomeres or issue.
18
Q
telomerase
A
attaches to the end of the template strand and extends the template strand by adding a short sequence of DNA nucleotides over and over again. This allows elongation of the lagging strand to continue. However, at the end it will still be not enough for primase to attach but this loss of unimportant segment will not cause any problem.
Telomerase carries an RNA template: binds to flaking 3’ end of telomeere that compliments part of its RNA template, synthesizes to fill in over the rest of its template
Eventually, telomerase stops the elongation, and ultimately DNA polymerase will be unable to replicate new portions due to the reasons in replication of telomeres. However, the DNA in the extended region of the template is just repeating short segments of nucleotides and merely acts to prevent the loss of important coding DNA that precedes it
19
Q
one-gene-one-enzyme hypothesis
A
the gene was defined as the segment of DNA that codes for a particular enzyme
20
Q
one-gene-one-polypeptide hypothesis
A
since many genes code for polypeptides that are not enzymes (structural proteins or individual components of enzymes), the gene was redefined as a segment of DNA that codes for a particular polypeptide
21
Q
protein synthesis
A
the process that describes how enzymes and other proteins are made from DNA
22
Q
What are the 3 steps of protein synthesis?
A
Transcription, RNA processing, and translation
23
Q
transcription
A
RNA molecules are created by using the DNA molecule as a template; prokaryotes polycistronic, eukaryotes monocistronic
24
Q
RNA-processing
A
modifies the RNA molecule that’s created by deleting or adding
25
translation
the processed RNA molecules are used to assemble amino acids into a polypeptide
26
What 3 kinds of RNA molecules are produced during transcription?
messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
27
messenger RNA (mRNA)
single strand of RNA that provides the template used for sequencing amino acids into a polypeptide.
64 possible ways (4x4x4) ways that four nucleotides can be arranged in triplet combinations, there are 64 possible codons. 3 of them are stop codons. There are only 61 codes for amino acids
28
codon
a triplet group of 3 adj. nucleotides on mRNA, which codes for one specific amino acid
29
genetic code
provides the decoding for each codon.
30
How many codons actually code for amino acids?
61 codons, since some signal an end to translation
31
transfer RNA (tRNA)
a short RNA molecule (consisting of about 80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template strand
C-C-A-3' end of tRNA attaches to amino acid, and the other portion is the anticodon which bp with the codon in mRNA. Wobbles: exact bp of the 3rd nucleotide in the anticodon and the 3rd nucleotide in the codon is often not required allowing 45 different tRNA's base-pair with 61 codons that code for amino acid. Transports AA to its mRNA codon
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anticodon
triplet combination of nucleotides found on a portion of tRNA
33
What happens to the 3' end of a tRNA molecule?
the 3' (C-C-A) attaches to an amino acid
34
What happens to the anticodon during translation?
the anticodon base pairs with the codon of mRNA
35
wobble hypothesis
exact base-pairing between the 3rd nucleotide of tRNA anticodon and the 3rd nucleotide of the mRNA codon is often not required. This wobble allows the anticodon of some tRNA's to base-pair w/ more than one kind of codon. As a result, about 45 different tRNA's base-pair w/ the 61 codons that code for amino acids
36
Ribosomal RNA (rRNA)
molecules that are the building blocks of ribosomes.
Within the nucleolus, various proteins imported from the cytoplasm are assembled w/ rRNA to form large and small ribosome subunits. Together, the 2 subunits form a ribosome that coordinates the activities of the mRNA and tRNA during translation
nucleolus is an assemblage of DNA actively being transcribed into rRNA. As ribosome, it has 3 binding sites: one for mRNA, one for tRNA that carries a growing polypeptide chain (P site); one for 2nd tRNA that delivers the next aa (A site). Termination sequences include UAA, UGA, UAG. Together with proteins, rRNA forms ribosomes. Ribosome is assembled in nucleolus but large and small subunites exported separately to cytoplasm
37
How many binding sites do ribosomes have?
3 binding sites: one for the mRNA, one for a tRNA that carries a growing polypeptide chain (P site), and one for a second tRNA that delivers the next amino acid that will be inserted into the growing polypeptide chain (A site)
38
What are the 3 steps of transcription?
initiation, elongation, and termination
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(transcription) initiation
RNA pol attaches to a promoter region on the DNA and begins to unzip the DNA into two strands. A promoter region for mRNA transcriptions often contains the sequence T-A-T-A (called the TATA box)
most common sequence of nucleotides at promoter mRNA is called the consensus sequence; variations from it cause less tight RNA pol binding =>lower transcription rate
40
(transcription) elongation
RNA pol unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template; only one strand is transcribed. As in DNA replication, elongation of the RNA molecule occurs in the 5' => 3' direction. In contrast to DNA replication, new nucleotides are RNA nucleotides (rather than DNA nucleotides), and only one DNA strand is transcribed
41
(transcription) termination
when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes, the termination region often contains the DNA sequence AAAAAAA.
transcription is occurring in the 3' to 5' direction of the DNA template strand (but synthesis of the RNA strand is , as always, 5' to 3'
42
mRNA processing
1. A 5' cap (-P-P-P-G-5') is added to the 5' end of the mRNA; Guanine with 2 phosphate groups => GTP; providing stability for mRNA and point of attachment for ribosomes
2. A poly-A tail (-A-A-A....A-A-3') is attached to the 3' end of the mRNA; Tail consists of 200 A; provide stability and control movement of mRNA across the nuclear envelope (in prokaryotes, poly A tail facilitates degradation
3. RNA splicing removes nucleotide segments from mRNA; before mRNA moves into cytoplasm, small nuclear ribonucleoproteins (snRNP's) and the spliceosome delete the introns and splice the exons. (prokaryotes have no introns!)
4. Alternative splicing allows different mRNA's to be generated from the same RNA transcript; by selectively removing differences of an RNA transcript into different combinations => each coding for a different protein product
note: prokaryotes generally have ready to go mRNA upon transcription. It is only eukaryotesthat you need the above processing. Because prokaryotes don't need to process their mRNA first, translation can begin immediately / simultaneously. In both prokaryotes and eukaryotes, multiple RNA polymerases can transcribe the same template simultaneously.
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exons
sequences that express a code for a polypeptide
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introns
intervening sequences that are noncoding
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snRNP's (small nuclear ribonucleoproteins)
delete the introns and splice the exons
46
aminoacyl-tRNA
amino acids attach to the 3' end of the tRNA's
47
What provides the energy for translation?
energy is provided by several GTP molecules
48
Translation (Initiation)
small ribosome unit attaches to 5' end of mRNA; tRNA methionine attaches to start sequence of mRNA AUG, and large ribosome unit attaches to form a complete complex
49
mutation
any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied
50
A point mutation includes what?
substitution, deletion, insertion, frameshift
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point mutation
single nucleotide error
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sustitution
occurs when the DNA sequence contains an incorrect nucleotide in place of the correct nucleotide
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deletion
occurs when a nucleotide is omitted form the nucleotide sequence
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insertion
occurs when a nucleotide is added to the nucleotide sequence
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frameshift mutation
occurs as a result of deletion or insertion. If a frameshift mutation occurs in a DNA segment whose transcription produces an mRNA, all codons following the transcribed mutation will change
56
What results from a point mutation?
silent mutation, missense mutation, nonsense mutation
57
silent mutation
new codon still codes for the same amino acid.
This occurs most often when the nucleotide substitution results in a change of the last of the 3 nucleotides in a codon
58
missense mutation
new codon codes for a new amino acid; => minor or fatal results as in sickle cell (val(new) for glu (old))
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nonsense mutation
occurs when the new codon codes for a stop codon
60
mutagens
radiation or chemicals that cause mutations
61
carcinogens
mutagens that activate uncontrolled cell growth (cancer)
62
What are the various mechanisms to repair replication errors?
proofreading, mismatch repair, and excision repair
63
proofreading
DNA polymerase checks to make sure that each newly added nucleotide correctly base pairs w/ the template strand. If it does not, the nucleotide is removed and replaced w/ the correct nucleotide.
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mismatch repair
enzymes repair errors that DNA polymerase misses
65
excision repair
enzymes remove nucleotides damaged by mutagens.
The enzymes identify which of the two DNA strands contain a damaged nucleotide and then used the complementary strand as a template to repair the error
66
DNA organization
DNA is packaged w/ proteins to form a matrix called chromatin. The DNA is coiled around bundles of 8 or 9 histone proteins to form DNA-histone complexes called nucleosomes. During cell division, DNA is compactly organized into chromosomes. When the cell is not dividing, the DNA is arranged as either of two types of chromatin: euchromatin or heterochromatin
67
euchromatin
describes regions where the DNA is loosely bound to nucleosomes; the DNA in these regions is actively being transcribed
68
heterochromatin
areas where the nucleosomes are more tightly compacted and where DNA is inactive; stains darker than euchromatin. Contains a lot of satellite DNA (large tandem repeats of noncoding DNA)
69
transposons (jumping genes)
can move to a new location on the same gene or to a different chromosome; transposons have the effect of a mutation, they can change the expression of a gene, turn on or turn off its expression, or have no effect at all
2 types:
insertion sequences consist of only one gene that codes for enzyme that just transports it (transposase); complex transposons code for extra: replication, antibiotic resistance, etc. Insertion of transposons into another region could cause mutation (little to no effect)
70
bacteriophages (phages)
viruses that attack only bacteria
71
What do viruses consist of?
1. A nucleic acid, either RNA or DNA (but not both), contains the hereditary info of the virus. The DNA or RNA may be double-stranded (dsDNA or dsRNA) or single-stranded (ssDNA or ssRNA).
2. A capsid, or protein coat, encloses the nucleic acid. Identical protein subunits, called capsomeres, assemble to form the capsid
3. An envelope surrounds the capsid of some viruses. Envelopes incorporate phospholipids and proteins obtained from the cell membrane of the host
72
lytic cycle
a virus penetrates the cell membrane of the host and uses the enzymes of the host to produce viral nucleic acids and viral proteins
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lysogenic cycle
viral DNA is temporarily incorporated into the DNA of the host cell. It remains dormant (dormant state: provirus/prophage if bacteria) until an external environmental stimulus (such as radiation or certain chemicals), causes the virus to begin the lytic cycle
74
provirus (or, if a bacteriophage, a prophage)
a virus in dormant state in which the viral DNA is temporarily incorporated into the DNA of the host cell
75
retroviruses (variation in lytic cycle)
ssRNA viruses that use reverse transcriptase to make a DNA complement of their RNA => transcribed immediately to manufacture mRNA, or it can begin the lysogenic cycle by becoming incorporated into the DNA of the host. Human immunodeficiency virus (HIV, the cause of AIDS) is a retrovirus
76
DNA virus (variation in lytic cycle)
the DNA is replicated to form new viral DNA and the DNA is transcribed to produce viral proteins (DNA + viral proteins assemble to form new viruses
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RNA virus (variation in lytic cycle)
the RNA serves as mRNA or as a template to make mRNA => translated into protein (protein +RNA => new virus)
78
Are bacteria prokaryotes or eukaryotes?
prokaryotes; they do not contain a nucleus, nor do they posses any of the specialized organelles of eukaryotes. The primary genetic material of a bacterium is a chromosome consisting of a single, circular DNA molecule (tightly condensed and called a nucleoid). They have no histones or other assoc. proteins. Replicated DNA in both directions single point of origin ("theta replc.")
79
How does a bacterial cell reproduce?
binary fission; the chromosome replicates and the cell divides into 2 cells, each cell bearing one chromosome. lacks nucleus, spindle apparatus, microtubules, and centrioles found in eukaryotic cell divisions
80
Bacteria also contain PLASMIDS
short, circular DNA molecules outside the chromosome; plasmids replicate independently of the chromosome. replicate independently;
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episomes
plasmids that can become incorporated into the bacterial chromosome
82
How is genetic variation introduced into the genome of bacteria?
conjugation, transduction, transformation
83
conjugation
DNA exchange between bacteria. A donor bacterium produces a tube, pilus, that connects to a recipient bacterium. Through the pilus, the donor bacterium sends chromosomal or plasmid DNA to the recipient and recombinant can occur; pili are also used for cell adhesion
84
F plasmid
contains genes that enable a bacterium to produce pili
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R plasmid
a group of plasmids that provide bacteria w/ resistance against antibiotics
86
transduction
DNA is introduced into the genome of a bacterium by a virus. When a virus is assembled during a lytic cycle, some bacterial DNA is incorporated in place of viral DNA. When this virus infects another cell, the bacterial DNA that it delivers can recombine w/ the resident DNA
87
transformation
bacteria absorb DNA from their surroundings and incorporate it into their genome. Specialized proteins on the cell membranes of some bacteria facilitate this kind of DNA uptake
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operon
unit of DNA that controls gene transcription. It contains the following: promoter, operator, structural genes, and a regulatory gene
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promoter region
sequence of DNA to which the RNA polymerase attaches to begin transcription
90
operator region
can block the action of the RNA polymerase if this region is occupied by a repressor protein
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structural genes
contain DNA sequences that code for several related enzymes that direct the production of some particular end product
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regulatory gene
lies outside the operon region and produces repressor proteins and activator proteins
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repressor proteins
made by a regulatory gene, these are substances that occupy the operator region and block the action of RNA polymerase
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activator proteins
assist the attachment of RNA polymerase to the promoter region.
95
What are two kinds of operons found in the bacterium E.coli?
lac operon and trp operon
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lac operon
(in E. coli) controls the breakdown of lactose. A regulatory gene produces an active repressor that binds to the operator region. When the operator region is occupied by the repressor, RNA polymerase is unable to transcribe several structural genes that code for the enzymes that control the uptake and subsequent breakdown of lactose.
When lactose is available, however, some of the lactose (in a converted form) combines w/ the repressor to make it inactive. RNA pol is then able to transcribe the genes that code for the enzymes that break down lactose. Since a substance (lactose, in this case) is required to induce the operon, the enzymes that the operon produces are said to be inducible enzymes
Note: consists of 3 lac genes (Z,Y, A) which code for B-galactosidase, lactose permease, and thiogalactoside transacetylase. Also know that low glucose means high cAMP levels => cAMP binds to CAP binding site of promoter => RNA polymerase more efficiently transcribes => high lactose levels
97
trp operon
(E. coli) produces enzymes for the tryptophan synthesis. A regulatory gene produces an inactive repressor that does not bind to the operator. As a result, the RNA polymerase proceeds to transcribe the structural genes necessary to produce enzymes that synthesize tryptophan.
When tryptophan is available to E.coli from the surrounding environment, the bacterium no longer needs to manufacture its own typtophan.
In this case, rising levels of tryptophan induce some tryptophan to react with the inactive repressor and make it active. Here tryptophan is acting as a corepressor. '
The active repressor now binds to the operator region, which, in turn, prevents the transcription of the structural genes. Since these structural genes stop producing enzymes only in the presence of an active repressor, they are called repressible enzymes
98
regulatory proteins (eukaryotic cells)
repressors and activators, operate similarly to those in prokaryotes, influencing how readily RNA polymerase will attach to a promotor region. In many cases, numerous activators are acting in concert to influence transcription.
99
nucleosome packing
influences whether a section of DNA will be transcribed. DNA segments are tightly packed by methylation (addition of methyl groups) of histones, making transcription more difficult.
In contrast, acetylation (addition of acetyl groups) of histones allows uncoiling the transcription of specific DNA regions
methylation also used in X-inactivation and on DNA bases to repress gene activity
100
RNA interference
short interfering RNAs (siRNAs) block mRNA transcription or translation or degrade existing mRNA. Under certain conditions, an RNA molecule will fold back and base-pair w/ itself, forming dsRNA. An enzyme then cuts the dsRNA into short pieces (siRNAs), which then base-pair to complementary DNA regions-those regions that made the original RNA molecule-preventing further transcription of that gene.
The siRNAs also inactivate mRNA already produced by base-pairing w/ it. In other cases, siRNAs combine w/ enzymes to degrade existing mRNAs w/ complementary sequences. dsRNA gets chopped up, then made single stranded. The relevant strand will bind to DNA (prevent transcription) or mRNA (signals destruction)
101
recombinant DNA
contains DNA segments or genes from different sources. DNA transferred from 1 part of a DNA molecule to another, from one chromosome to another chromosome, or from one organism to another all constitute recombinant DNA.
the transfer of DNA can occur through viral tranduction, bacterial conjugation, or transposons or artifically through technology. Crossing over during prophase of meiosis produces recombinant chromosomes.
Recombinant DNA uses restriction enzymes to cut up DNA. Restriction enyzmes are very specific, cutting DNA at specific recognition sequences of nucleotides.
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restriction enzymes
used in recombinant DNA technology to cut up DNA; they are obtained from bacteria that manufacture these enzymes to combat invading viruses
(e.g. EcoRI; BamHI) normally used by bacteria to protect against viral DNA (protect their own DNA via methylation)
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sticky end
the cut across a double-stranded DNA is usually staggered, producing fragments that have one strand of the DNA extending beyond the complementary strand. The unpaired extension is called the sticky end
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vector
to insert a foreign DNA fragment into another cell, the fragment is first introduced into another DNA molecule; plasmids are commonly used as vector because they can be introduced into bacteria by transformation
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How to introduce foreign DNA into a plasmid
1. the plasmid is treated w/ the same restriction enzyme used to create the foreign DNA fragment, producing the same sticky ends in both foreign DNA and plasmid segments
2. Mixing foreign DNA w/ the cut plasmid allows base-pairing at the sticky ends. Application of DNA ligase stabilizes the attachments.
3. The recombinant plasmid is then introduced into a bacterium by transformation. Bacterium must be "made competent" to take up the plasmid (electroporation or heat shock CaCl2)
After this process, bacteria can be grown to produce product, form clone libaray, etc. Use antibiotic resistance/screen method to filter out the ones that don't have the recombinant DNA.
By following this procedure, the human gene for insulin has been inserted into E. coli. The transformed E. coli produces insulin which is isolated and used to treat diabetes.
106
gel electrophoresis
DNA fragments of different lengths are separated as they diffuse through a gel material under an electric field. DNA is neg. charged (phosphate groups) and therefore moves from the negative cathode to the positive anode. Shorter fragments migrate further through the gel than longer, heavier fragments. Gel electrophoresis is often used to compare DNA fragments of closely related species in an effort to determine evolutionary relationships.
After electrophoresis: DNA can then be sequenced, or probed to identify location of specific sequence of DNA
DNA probe is radioactively labeled single strand of nucleic acid used to tag a specific DNA sequence
You can do gel electrophoresis of proteins too. ADD SDS (denatures+linearizes+adds neg. charge)
107
restriction fragment length polymorphisms (RFLPs)
restriction fragments between individuals are compared, fragments differ in length are observed because of polymorphism (different length in DNA sequences). Inherited in Mendelian fashion so often used in paternity suits, RFLP analysis sued at crime scenes to match suspects.
108
DNA fingerprinting
RFLPs produced from DNA left at a crime scene are compared to RFLPs from the DNA of suspects.
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short tandem repeats (STRs)
repeat of 2-5 base pairs and different between all individuals except identical twins.
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complemenatry DNA (cDNA)
reverse transcriptase (obtained from retroviruses) is used make a DNA molecule directly from mRNA; it lacks the introns that suppress transcription
111
polymerase chain reaction (PCR)
uses synthetic primers (the primer may be RNA or DNA oligonucleotides) to clone DNA (rapidly amplify). Taq polymerase (heat stable) + nucleotides + primers+ salts (buffer) necessary. that initiate replication at specific nucleotide sequences.
1. DEnaturation (>90C) 2. Primers + Anneal (55C) 3. Elongation (Taq Polymerase is about 70 C).
112
DNA Pol 1
replaces BPs from the primer and does DNA repair
has 3' => 5' exonuclease: breaks phophodiester backbone on a single strand of DNA and removes a nucleotide. Exonuclease can only remove from (in this case of 3' end) of chain
also has 5' => 3' exonuclease, to take off the primer; and can also proof with 3' to 5' when laying down a new chain
113
DNA Pol 3
pure replication [eukaryotes have different polymerases: alpha gamma etc-not important]
has 3' => 5' exonuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. Can only remove from 3' end
Pol 3 can do some proofreading; if it makes a mistake it will go back and use this to replace it
114
Summarize Pol 1 and Pol 3
Pol 3 mainly replicates the DNA 5' to 3' but can also proofread via 3' to 5' exonuclease. Pol 1 primary breaks down RNA primer via 5' to 3' exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5' to 3' polymerase while proofreading as it goes, can proofread via 3' to 5' exonuclease as well.
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reduncy/degeneracy
genetic code is universal for nearly all organisms and most AAs have more than one codon specifying them
116
translation
assembly of amino acids based on reading of new RNA; uses GTP as energy source
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translation (elongation)
next tRNA binds to A site, peptide bond formation, tRNA w/o methionine is used, the tRNA crrently in A site moves to P site (translocation) and the next tRNA comes into A site and repeat process
118
translation (termination)
encounters the stop codon UAG, UAA, UGA. Polypeptide and the two ribosomal subunites all release once release factor breaks down the bond between tRNA and final AA of the polypepetide. While polypeptide is being translated AA sequences is determining folding confomration; folding process assisted by chaperone proteins
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translation (post-translation)
translation begins on a free floating ribosome; signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the ER, in which case the polypeptide is injected into the ER lumen. If injected, polypeptide may be secreted from the cell via Golgi. In general, post-translational modifications (addition of sugars, lipids, phosphate groups to AAs) may occur. May be subsequently processed by Golgi before it is functional
a.a. are placed starting from the 5' end of the mRNA and move all the way down to the 3' end. tRNA codons for matching are 3' to 5'. Can occur simultaneously with transcription in prok., but not in euk. Multiple ribosomes may simultaneously translate 1 mRNA.
Start codon in bacteria is n-formylmethionine
120
prions
not viruses or cells. Misfolded versions of proteins in brain that cause normal version to misfold too. Fatal
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teichoic acids
on cell wall of bacterium are used as recognition + binding sites by bacterial viruses that cause infxns; also provide cell wall rigidity: only found on gram-positive bacteria
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repressible enzymes
when structural genes stop producing enzymes only in presence of an active repressor
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constitutive
(constantly expressed) either naturally or due to mutation
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human genome
97% of human DNA does not code for protein product; noncoding DNA: regulatory sequences, introns, repetitive sequences never transcribed, etc. Tandem repeats abnormally long stretches of back to back repetitve sequences within an affected gene (e.g. Huntington's)
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recombinant DNA
contains DNA segments or genes from different sources. The transfer of these DNA segments can come from viral transduction, bacterial conjugation, transposons, or through artificial recombinant DNA technology. Crossing over during prophase of meiosis produces recombinant chromosomes.
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reverse transcriptase
introns often prevent transcriptions, this enzyme makes DNA molecule directly from mRNA. DNA obtained from this manner is complementary DNA (cDNA) which lacks introns that suppress transcriptions.
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southern blotting
technique to ID target fragments on known DNA sequence in a large population of DNA. Electrophoresis fragments first, then transfer the SS DNA fragments to nitrocellulose membrane, then add probe which will hybridize and mark it.
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northern blotting
same as sourthern blot, but for RNA fragments
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Western blot
similar method for proteins: electrophoresis, blot to membrane, primary antibody specific to protein added to bind to that protein, then secondary anti-body-enzyme conjugate will bind to primary and mark it with enzyme for visualization.
Note: SNOW DROP to distinguish between blotting techniques
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gene cloning
plasmids are circular dsDNA that have restriction sites. Cut there=> linear piece of DNA. Also has a promoter region+some gene product(s) (e.g. antibiotic resistance). We want to cut, add genes, close plasmid, add to something like bacteria to replicate it. Bacteria dislike plasmids => only fraction of them get taken up by some bacteria. Use antibiotic resistance gene to determine which bacteria were "transformed" that will survive on certain medium. Plasmid also has origin of mammalian cell => need to add poly A tail for mRNA to survive.
If making eukaryotic gene product in prokaryotic cell => need to make sure no introns (use reverse transcriptase on the mRNA product to get the desired DNA fragment)
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hybridization
complementary BP's annealing
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How to test for specific gene sequence in someone's DNA
Method 1 (single test only): take blood drop, cut up DNA, use PCR method w/ specific primer for that region. If that gene is there => lots of copies. Gene not there => no copies.
Method 2 (test for many things at same time): take blood drop, PCR it to amplify. We have a solid support w/ pieces of ssDNA w/ specific sequence covalently attached => will hybridize to anything complementary (e.g. disease genes). On that same support we can put sSDNA pieces specific for other genes, can do this hundreds of times at different spots on this DNA microarray. Take desired amplified DNA, heat it to denature, add to DNA microaarray, any DNA that hybridizes is a match. The amplified DNA we added is already fluorescently tagged => hybridization was to get rid of weakly bound sequences (e.g. not a complete match) => add a dye that will show heavily if something has bound to our microarray. CAn also do this starting w/ mrNA =>reverse transcriptase => PCR amplify => etc
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Notes *
endonucleases cleave the phosphodiester backbone to chunk out NT's, whereas exonucleases cut out just the NT's.
it is ubiquitin, not ubiquinon, that marks proteins for degradation via proteasome. Totipotent/pluripotent is wrong too: totipotent (not mature cells that dedifferentiate) can give rise to any and all human cells, and even an entire funcitonal organism. Pluripotent can give rise to all tissue types, but not an entire organism. Multipotent can give rise to limited range of cells within a tissue type
