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Microbiology 340 > Ch8 > Flashcards

Ch8 Flashcards

1
Q

The Griffith Experiment

A

identification of DNA as the genetic material through this experiment

(1928) Frederick Griffith took 2 strains of bacterium Streptococcus pneumonia (S(smooth) and R(rough))

S cells killed the mice, but R cells did not;
heat-killed S cells did not kill the mice
BUT A MIXTURE OF heat killed S cells and live R cells KILLED THE MICE

the transformation principle was the name!!!

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2
Q

Deinococcus (D.) radiodurans

A

gram-positive bacterium that possesses gram-negative like an outer membrane; can withstand 1,000 times the radiation that would kill a person (100 times it would take for e.coli)

first isolated in 1956

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3
Q

how does radiation kill organisms?

A

primarily by causing damage to DNA (cell cannot repair damage and dies)

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4
Q

transformation

A

a type of horizontal gene transfer; free DNA is taken by a cell; change causes it to become like cancer

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5
Q

Avery, MacLeod, and McCarthy Experiment

A

proved that DNA was the cellular factor that could be transferred to another cell and change it.

(they purified the transforming factor, and found it was mostly composed of DNA; DNAase RNAase)

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6
Q

Hershey-Chase experiment

A

third experiment construucted to prove that DNA is the hereditary molecule

(used bacteriophage T2 (since a virus is made up of a protein and DNA); utilized sulfur attached it to protein and phosphorous attached to DNA)

blah it invaded E.coli and it was found that phosphorous was present… BOOM DNA is the hereditary molecule

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7
Q

Streptococcus pneumoniae? HABITAT
DESCRIPTION
KEY FEATURES

A

Commonly found in nasopharynx of humans
Gram-positive coccus, often appears in short chains
(helped define DNA as genetic material)
causes sinus and ear infections

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8
Q

DNA structure
Nucleotide structure
NucleoSide structure

A

consists of two chains (each chain is a polymer of nucleotides)

Nucleotide = 1.)a five carbon sugar (2-deoxyribose)
2.) a phosphate group (covalently links 3’ carbon of one 2-deoxyribose to the 5’ carbon of next sugar)
3.) a nitrogenous base (attached to 1’ carbon of sugar)

only a nitrogenous base attached to a sugar

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9
Q

Name the nitrogenous bases. What are the purines? What are the pyrimidines? What is the difference?

A

adenine guanine thymine cytosine

purines are adenine and guanine (have double ring structure)
pyrimidines are cytosine and thymine (have single ring structure)

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10
Q

How do the two chains of DNA align? What nucleotides always pair with each other? What does this tell you about the strands? What holds the strands together? How many per each pair?

A

they align in an antiparallel way (all linear DNA has a 5’ and 3’ end; the 5’ end of one chain is aligned with 3’ end of the other)

a always pairs with t
c always pairs with g (THEY ARE COMPLEMENTARY)

Hydrogen bonds hold the strands together (two bonds hold a & t ; three hold c and g)

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11
Q

Who is responsible for the discovery of the double-stranded structure of DNA

A

Watson, Crick, Wilkins did and recieved Nobel Prize; (Rosalind carried them but unfortunately died of cancer and was not recognized)

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12
Q

Briefly describe the organization of DNA in bacteria, archaea and eukarya. Plasmids? Histones?

A

DNA molecule is circular in bacteria in archaea and bacteria, linear in eukarya

plasmids are common in bacteria in archaea but rare in eukarya

histones in eukarya and archaea but not bacteria

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13
Q

true or false: all bacteria have circular DNA/ chromosomes

A

False; some have linear chromosomes like (Borrelia burgdorferi)

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14
Q

semiconservative replication

A

one strand of DNA is conserved in each of the newly formed double-stranded molecules and serves as a template (DNA sequence is preserved)

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15
Q

“Matthew Meselson and Franklin Stahl, researchers at the California Institute of Technology”

A

Provided good experimental evidence when it comes to DNA replication (semiconservative replication)

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16
Q

oriC

A

The origin of replication (Where DNA replication begins).
FOR BACTERIA!!!!! NOT EUKARYA!!!!!

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17
Q

DnaA
DnaB (what is the other name for this?)
DnaC
DnaG (what is the other name for this?)

A

DNA binding protein essential for DNA replication to begin (required for replication in bacteria)

also known as helicase helps in unwinding DNA
(DnaC helps with this) (FOR BACTERIA)

also known as primase; makes short segments of RNA needed to prepare for DNA replication
(FOR BACTERIA)

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18
Q

Single-stranded DNA binding proteins (SSB)

A

attach to newly formed single-stranded DNA to keep strands from (reannealing) connecting again after being unwound

(single stranded repication bubble forms after)

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19
Q

Compare the origins of replication relative to the chromosomes of bacteria and eukarya.

A

eukarya have multiple origins of replication, while bacteria has one (already said this bud)

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20
Q

ARS
ORC
minichromosomal maintenance (MCM complex)

A

(autonomously replicating sequence)identified eukaryal replicator

(origin recognition complex) initiator composed of six different proteins (Orc1-6)

a group of 6 proteins that function (along with Cdc6 and Cdt1) as helicase when ORC binds to ARS

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21
Q

DNA polymerase

A

enzyme that speeds up production of new DNA strand from EXISTING DNA/RNA strand (by adding nucleotides using other strand as the template)

22
Q

primer

A

a short piece of single-stranded RNA complementary to the single-stranded DNA present in replication bubble

(made by primase; and RNA polymerase)

23
Q

leading/lagging strands What is the direction of elongation for the DNA strands

A

the single stranded DNA at each replication site that is extended continuously (Due to DNA polymerase only being able to elongate in 5’ to 3’ direction )

the opposite strand has discontinuous elongation, due to the fact that primers are added as helicase unwinds more DNA

elongation is bi-directional

24
Q

Okazaki fragments

A

newly made DNA and RNA primers that match/correspond

25
DNA polymerase I DNA polymerase III DNA ligase
adds deoxynucleotide phosphate to free 3'-OH on existing nucleotide removes RNA primer and fills the short gap links the final 5'-phosphate and 3'OH ends before DNA strand is complete (for bacteria)
26
When it comes to DNA REPLICATION of bacteria, eukarya, and archaea, state the origin recognition primase helicase replication enzyme removal of primers litigation
Table 8.2
27
Briefly describe what happens at the end of DNA replication in bacteria
ter sites (termination sites) are theusally opposite side of the oriC when Tus protein binds to one of the ter sites and stops one of the replication forks, and when the other fork is stopped we get two identical double stranded DNA molecules that are stuck together Topoisomerase II separates these.
28
telomerase
RNA dependent DNA polymerase relative to linear chromosomes creates telomeres (DNA repeats at 3 ends of chromosomes, reversing DNA loss from each replication
29
transcription
where strands of single-stranded RNA are made from DNA segments (RNA may be used to make proteins)
30
gene
any segment of DNA that gets transcribed (copied) in to a piece of single-stranded RNA
31
Briefly compare and contrast DNA and RNA (easy don't overthink)
both are polynucleotide the sugar in RNA is ribose not 2-deoxyribose RNA has nitogenous base uracil instead of thymine
32
When it comes to transcription, how much of the genome of bacteria and eukarya are transcribed
in bacteria, most of the genome is transcribed in eukarya a lot is not
33
mRNA tRNA rRNA miRNA Which are translated and which aren't?
messenger RNA - coding molecules that are translated into proteins transfer RNA - has to do with translation (charged with amino acids) ribosomal RNA - behind the structural components of ribosomes micro RNA - helps with regulation mRNA is translated, the rest IS NOT
34
RNA polymerase
the enzyme that transcribes DNA in all organisms (DNA dependent RNA polymerase)
35
promoters
regions of DNA where the transcription process starts (RNA polymerase binds to this to begin)
36
coding strand
the template strand of DNA relative to the complementary single-stranded RNA that is made by RNA polymerase (though U instead of T)
37
What is the difference between DNA polymerase and RNA polymerase
RNA pol. does not need a primer, it can just add ribonucleotides directly
38
What does the bacterial RNA polymerase consist of? What is the core enzyme and and sigma (σ) factor do? WHAT is +1? specifically, what is it in bacteria?
"five different polypeptides: α, β, β′, ω, and σ" the core enzyme (made of"β, β′, ω and two copies of σ") and sigma factor combine and form the RNA polymerase sigma recognizes promoter and RNA pol. is bound (not exactly on it BUT AROUND IT) +1 is the first transcribed base (in bacteria it is usually A or G)
39
upstream/downstream sequences
bases transcribed before the promoter (start site) ard upstream (indicated as -1 & -2) (5' of transcription site) downstream is the opposite (3' of transcription site)
40
is the sigma factor there the whole time
nah, when the elongation process starts, the "σ" factor separates itself and the core enzyme continues on as the RNA stretches, it separates itself from the coding strand and the DNA will reanneal
41
Where are the defined regions at which RNA polymerase binds (usually) relative to the promoter? What can be used to see this?
approximately -10 and -35 gel shift assay
42
TATA box
coding strand of the most commonly expressed genes is TATAAT at -10 element
43
RNA polymerase I, II, and III
(ONLY apply to eukarya, as bacteria only use one) I - transcribes all ribosomal DNA (except 5S rRNA) II - transcribes all protein-coding genes III - tRNA genes, 5S rRNA, and genes that encode other small non-coding RNA molecules
44
In eukarya, does RNA polymerase II bind directly to the promoter? WHAT is TBP and TFIIB? Where is the TATA box usually located?
Nope, transcription factors (DNA binding proteins) have to bind to promoter first (this is the TATA-binding protein binding to the TATA box for most eukaryal organisms TFIIB also binds, making a transcription initiation complex 25 bp upstream
45
When it comes to transcription, discuss the enzyme that transcribes.
Like bacteria, archaea only has one RNA polymerase, but it looks like the RNA pol. II of eukarya, and does not bind directly to DNA like eukarya Has TPB and transcription factor B (TFB) that resembles (TPB and TFIIB of eukarya) the promoter itself is a lot like eukaryal promoters
46
What inhibits the RNA polymerase of archaea but not bacteria?
the antibiotic rifampicin
47
How does transcription end in bacteria?
either rho-independent or rho-dependent termination rho-independent (intrinsic) termination - where genes end with a short segment of inverted GC rich repeats followed by adenines hairpin is formed through this, and RNA polymerase falls tf off. rho-dependent termination - a protein (the rho factor) binds to RNA molecule (polymerase) and it slows down when termination site is reached the rho factor displaces the RNA polymerase (the end)
48
Describe transcriptional termination in eukarya (RNA pol. I, II, III)!
termination of transcription of RNA pol. I resembles rho-dependent termination RNA pol. III transcription termination resembles rho-independent termination RNA pol. II, ........... (post translational modification) RNA pol II transcripts/products pre-mRNA molecules before leaving nucleus RNA is given a 5' cap (special modified nucleotide 7-methylguanosine) (usually happens as soon after transcription begins) poly(A) adds adenosine monophosphate (AMPs) to 3' end of molecule (becomes a 3' poly(A) tail) the cap and tail prevent RNA degradation!!! 5' cap is signal for translation introns are removed, resulting in exons coming together
49
what is post-translational modification? exons introns
RNA pol II transcripts/ pre-mRNA molecules undergo processing before leaving nucleus introns - non-coding regions exons - coding regions/ sequences
50
translation? Briefly describe what happens.
the process of protein making (mRNA sequence is a template to create amino acid sequence) ribosomes read the mRNA sequence 3 nucleotides at a time (codon; groups of 3 nucleotides) tRNA have an anticodon (3 nucleotides complementary to a codon) as well as a specific amino acid attached to it so as ribosome reads the mRNA sequence, a tRNA is recruited for each codon, bringing specific amino acids together

Microbiology 340 (16 decks)

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