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DAT > Biology- Molecular Genetics > Flashcards

Biology- Molecular Genetics Flashcards

1
Q

nucleotides

A

consist of 3 parts: phosphate group, sugar, and a nitrogen base

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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

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3
Q

semiconservative replication

A

consists of a single strand of old DNA (template strand) and a new, replicated DNA (the complementary)

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4
Q

helicase

A

unwinds the DNA, forming a Y-shaped replication fork

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5
Q

single-stranded binding proteins

A

attach to each strand of the uncoiled DNA to keep them separate and prevent them from recombining

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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)

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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’.

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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

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9
Q

leading strand

A

complementary strand made in 5’ => 3’ direction (continuous replication)

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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

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11
Q

DNA ligase

A

enzyme that connects okasaki segments; in all cases of repair, ligase must come in to seal the backbone afterward

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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

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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

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14
Q

RNA primer

A

short stretch of RNA nucleotides, later replaced w/ DNA nucleotides by DNA polymerase

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15
Q

elongation

A

adding of DNA nucleotides to the complement strand; happens when DNA polymerase attaches to RNA primers

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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

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17
Q

Replication of Telomeres (ends of eukaryotic chromosomes)

A

Two problems can occur:

  1. When not enough template strand remains to which primase can attach.
    - FIX: telomerase comes in
  2. 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.

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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

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19
Q

one-gene-one-enzyme hypothesis

A

the gene was defined as the segment of DNA that codes for a particular enzyme

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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

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21
Q

protein synthesis

A

the process that describes how enzymes and other proteins are made from DNA

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22
Q

What are the 3 steps of protein synthesis?

A

Transcription, RNA processing, and translation

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23
Q

transcription

A

RNA molecules are created by using the DNA molecule as a template; prokaryotes polycistronic, eukaryotes monocistronic

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24
Q

RNA-processing

A

modifies the RNA molecule that’s created by deleting or adding

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25
Q

translation

A

the processed RNA molecules are used to assemble amino acids into a polypeptide

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26
Q

What 3 kinds of RNA molecules are produced during transcription?

A

messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

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27
Q

messenger RNA (mRNA)

A

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

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28
Q

codon

A

a triplet group of 3 adj. nucleotides on mRNA, which codes for one specific amino acid

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29
Q

genetic code

A

provides the decoding for each codon.

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30
Q

How many codons actually code for amino acids?

A

61 codons, since some signal an end to translation

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31
Q

transfer RNA (tRNA)

A

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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32
Q

anticodon

A

triplet combination of nucleotides found on a portion of tRNA

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33
Q

What happens to the 3’ end of a tRNA molecule?

A

the 3’ (C-C-A) attaches to an amino acid

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34
Q

What happens to the anticodon during translation?

A

the anticodon base pairs with the codon of mRNA

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35
Q

wobble hypothesis

A

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

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36
Q

Ribosomal RNA (rRNA)

A

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

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37
Q

How many binding sites do ribosomes have?

A

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)

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38
Q

What are the 3 steps of transcription?

A

initiation, elongation, and termination

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39
Q

(transcription) initiation

A

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

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40
Q

(transcription) elongation

A

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

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41
Q

(transcription) termination

A

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’

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42
Q

mRNA processing

A
  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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43
Q

exons

A

sequences that express a code for a polypeptide

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44
Q

introns

A

intervening sequences that are noncoding

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45
Q

snRNP’s (small nuclear ribonucleoproteins)

A

delete the introns and splice the exons

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46
Q

aminoacyl-tRNA

A

amino acids attach to the 3’ end of the tRNA’s

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47
Q

What provides the energy for translation?

A

energy is provided by several GTP molecules

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48
Q

Translation (Initiation)

A

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

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49
Q

mutation

A

any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied

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50
Q

A point mutation includes what?

A

substitution, deletion, insertion, frameshift

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51
Q

point mutation

A

single nucleotide error

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52
Q

sustitution

A

occurs when the DNA sequence contains an incorrect nucleotide in place of the correct nucleotide

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53
Q

deletion

A

occurs when a nucleotide is omitted form the nucleotide sequence

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54
Q

insertion

A

occurs when a nucleotide is added to the nucleotide sequence

55
Q

frameshift mutation

A

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
Q

What results from a point mutation?

A

silent mutation, missense mutation, nonsense mutation

57
Q

silent mutation

A

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
Q

missense mutation

A

new codon codes for a new amino acid; => minor or fatal results as in sickle cell (val(new) for glu (old))

59
Q

nonsense mutation

A

occurs when the new codon codes for a stop codon

60
Q

mutagens

A

radiation or chemicals that cause mutations

61
Q

carcinogens

A

mutagens that activate uncontrolled cell growth (cancer)

62
Q

What are the various mechanisms to repair replication errors?

A

proofreading, mismatch repair, and excision repair

63
Q

proofreading

A

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.

64
Q

mismatch repair

A

enzymes repair errors that DNA polymerase misses

65
Q

excision repair

A

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
Q

DNA organization

A

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
Q

euchromatin

A

describes regions where the DNA is loosely bound to nucleosomes; the DNA in these regions is actively being transcribed

68
Q

heterochromatin

A

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
Q

transposons (jumping genes)

A

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
Q

bacteriophages (phages)

A

viruses that attack only bacteria

71
Q

What do viruses consist of?

A
  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
Q

lytic cycle

A

a virus penetrates the cell membrane of the host and uses the enzymes of the host to produce viral nucleic acids and viral proteins

73
Q

lysogenic cycle

A

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
Q

provirus (or, if a bacteriophage, a prophage)

A

a virus in dormant state in which the viral DNA is temporarily incorporated into the DNA of the host cell

75
Q

retroviruses (variation in lytic cycle)

A

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
Q

DNA virus (variation in lytic cycle)

A

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

77
Q

RNA virus (variation in lytic cycle)

A

the RNA serves as mRNA or as a template to make mRNA => translated into protein (protein +RNA => new virus)

78
Q

Are bacteria prokaryotes or eukaryotes?

A

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
Q

How does a bacterial cell reproduce?

A

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
Q

Bacteria also contain PLASMIDS

A

short, circular DNA molecules outside the chromosome; plasmids replicate independently of the chromosome. replicate independently;

81
Q

episomes

A

plasmids that can become incorporated into the bacterial chromosome

82
Q

How is genetic variation introduced into the genome of bacteria?

A

conjugation, transduction, transformation

83
Q

conjugation

A

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
Q

F plasmid

A

contains genes that enable a bacterium to produce pili

85
Q

R plasmid

A

a group of plasmids that provide bacteria w/ resistance against antibiotics

86
Q

transduction

A

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
Q

transformation

A

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

88
Q

operon

A

unit of DNA that controls gene transcription. It contains the following: promoter, operator, structural genes, and a regulatory gene

89
Q

promoter region

A

sequence of DNA to which the RNA polymerase attaches to begin transcription

90
Q

operator region

A

can block the action of the RNA polymerase if this region is occupied by a repressor protein

91
Q

structural genes

A

contain DNA sequences that code for several related enzymes that direct the production of some particular end product

92
Q

regulatory gene

A

lies outside the operon region and produces repressor proteins and activator proteins

93
Q

repressor proteins

A

made by a regulatory gene, these are substances that occupy the operator region and block the action of RNA polymerase

94
Q

activator proteins

A

assist the attachment of RNA polymerase to the promoter region.

95
Q

What are two kinds of operons found in the bacterium E.coli?

A

lac operon and trp operon

96
Q

lac operon

A

(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
Q

trp operon

A

(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
Q

regulatory proteins (eukaryotic cells)

A

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
Q

nucleosome packing

A

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
Q

RNA interference

A

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
Q

recombinant DNA

A

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.

102
Q

restriction enzymes

A

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)

103
Q

sticky end

A

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

104
Q

vector

A

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

105
Q

How to introduce foreign DNA into a plasmid

A
  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
Q

gel electrophoresis

A

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
Q

restriction fragment length polymorphisms (RFLPs)

A

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
Q

DNA fingerprinting

A

RFLPs produced from DNA left at a crime scene are compared to RFLPs from the DNA of suspects.

109
Q

short tandem repeats (STRs)

A

repeat of 2-5 base pairs and different between all individuals except identical twins.

110
Q

complemenatry DNA (cDNA)

A

reverse transcriptase (obtained from retroviruses) is used make a DNA molecule directly from mRNA; it lacks the introns that suppress transcription

111
Q

polymerase chain reaction (PCR)

A

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
Q

DNA Pol 1

A

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
Q

DNA Pol 3

A

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
Q

Summarize Pol 1 and Pol 3

A

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.

115
Q

reduncy/degeneracy

A

genetic code is universal for nearly all organisms and most AAs have more than one codon specifying them

116
Q

translation

A

assembly of amino acids based on reading of new RNA; uses GTP as energy source

117
Q

translation (elongation)

A

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
Q

translation (termination)

A

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

119
Q

translation (post-translation)

A

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
Q

prions

A

not viruses or cells. Misfolded versions of proteins in brain that cause normal version to misfold too. Fatal

121
Q

teichoic acids

A

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

122
Q

repressible enzymes

A

when structural genes stop producing enzymes only in presence of an active repressor

123
Q

constitutive

A

(constantly expressed) either naturally or due to mutation

124
Q

human genome

A

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)

125
Q

recombinant DNA

A

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.

126
Q

reverse transcriptase

A

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.

127
Q

southern blotting

A

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.

128
Q

northern blotting

A

same as sourthern blot, but for RNA fragments

129
Q

Western blot

A

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

130
Q

gene cloning

A

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)

131
Q

hybridization

A

complementary BP’s annealing

132
Q

How to test for specific gene sequence in someone’s DNA

A

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

133
Q

Notes *

A

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

DAT (18 decks)

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