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Flashcards in Lecture 4 Deck (51):
1

Genome

entire genetic complement of an organism; includes its genes and nucleotide sequences

2

Bacterial chromosome

usually ds, closed circular DNA

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Plasmids

usually much smaller ds, closed circular DNA molecules; the genes carried on the plasmid are not essential for growth under all conditions

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prophage

the genetic material of a bacteriophage which has incorporated into the genome of a bacterium and can form more phages if activated

5

DNA replication uses

a DNA-dependent DNA polymerase

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What does semiconservative DNA replication mean?

new DNA molecules compose of one original strand and one daughter strand

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Proteins required for DNA replication complex

helicase, ssDNA-binding protein (DBP), primase, DNA polymerase (a DNA-dependent polymerase)

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topoisomerase

removes helical stress that accumulates from unwinding of the two DNA strands during replication

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bacterial gyrase

target for quinoline antibiotics

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All chain growth in DNA replication occurs in ___ direction

5' to 3'

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Semidiscontinuous DNA synthesis

Leading strand synthesized continuously and lagging strand synthesized discontinuously 

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Why do two parental DNA strands need to be synthesized differently?

Because they are antiparallel

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DNA polymerase III

DNA polymerase that E. coli use. One is needed for each parental strand

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RNA primase

special type of RNA polymerase. Makes RNA primer chains to help initiate synthesis of both leading and lagging strand

*RNA primers are only temporary 

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RNA primers

chains of Okazaki fragments covelently attached to a RNA primase

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Okazaki fragment

DNA chains 100-1000 bases long that are covelently attached to a RNA primase. Beginning bases are RNA nucleotides

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DNA polymerase I

a repair enzyme; replaces RNA nucleotides of Okazaki fragments with DNA nucleotides ("nick translation")

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DNA ligase

links together nucleotides to make a higher molecular weight DNA (seals sugar-posphate backbone)

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primase

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Rate of error for:

DNA polymerase:

after proof-reading:

after addictional error correcting mechanisms:

1 in 10000 nucleotides

1 in 10,000,000

1 in 109-1011

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22

Bacterial DNA is methylated on which bases by what?

adenine bases (rarely on cytosines) by restriction modification systems 

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restriction modification system

a methylase and restriction endonuclease that recognize and modify the same nucleotide sequence

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Restriction modification systems are important for

1. protection against viral infection and incoporation of foreign DNA into host chromosome

2. Knowing which strand is the parental strand during mismatch repair 

25

Bidirectional beginning from _____ creates theta structures in bacterial DNA

replication origins

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OriC

origin for replication in E. coli

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Can replication of a second DNA molecule begin before the first is completed?

ya

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sigma factor

helps RNA prolymerase find the promoter region for transcripiton initiation

Used to switch on or off large groups of genes by modifying RNA polymerase to detect different promoters

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coding strand is ___ to the template strand 

complementary

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what has the same sequence as the RNA transcript? (Coding strand or template strand)

the coding strand (besides T in DNA and U in RNA)

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Are promotor sequences transcribed?

No

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A strong promoter will result in 

many RNA molecules

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Differences between RNA polymerase and DNA polymerase (5)

1. RNA pol does not require 3' OH primer to begin transcription

-although it does require one for elongation

2. RNA pol does not require helicase

3. RNA pol is slower than DNA pol

4. RNA pol lacks proofreading function

34

Why is a proofreading fuction not neccessary in RNA polymerase?

RNA is temporary in a cell

35

What % genes are expressed in bacteria? What are the other ones doing?

75% are expressed at all times. Others are dormant until cell needs them. This saves energy

36

Operons

clusters of coregulted genes that allow bacteria to respond to changes in thier environment. Code multiple proteins in the same mRNA (polycistronic)

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regulatory gene

has its own promotor and terminator. Results in an mRNA that encodes a single protein (monocistronic)

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promotor binds to ____.

terminator ends ___. 

RNA polymerase

transcription of the operon

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Inducible operons 

example?

Must be activated by inducer. 

e.g. Lactose operon: allows E. coli to use lactose when no glucose is available

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Repressible operons

Example?

transcribed continually until deactivated by repressors

e.g. Tyrpotophan operon (repressed in the presence of Trp)

41

Prokaryotic ribosome subunits?

50S and 30S for a total of 70S (no that's not a typo)

30S subunit has important 16S rRNA

42

How many codons specify amino acids?

61

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initiation codon? what does this code after chain has already been started?

AUG is the initiation codon. It also codes for Met within a polypeptide chain

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the 3 STOP codons? what are these recognized by?

UAA, UAG, UGA

recognized by release proteins to terminate translation

45

Size of tRNA?

~75 nt or 4S

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amino acyl-tRNA synthetase

consumes ATP to covalently attach an amino acid to the 3' end of a specific tRNA

-recognizes the amino acid and anticodon of the tRNA and pairs them up

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Bacterial polycistronic mRNAs

transcribed from operons

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Shine-Dalgarno sequences 

located in mRNAs a few nts 5' to AUG codon. Function as ribosome binding sites. Complementary to a portion of the 16S rRNA of the 30S subunit

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UTR

untranslated region

50

Eukaryotic mRNA is:

monocistronic (encodes a single polypeptide chain), spliced to remove introns from pre-mRNA (occurs in nucleus), and has modifed 5' and 3' ends b4 it leaves nucleus 

51

What is the first amino acid that all bacterial proteins begin with?

all bacterial proteins begin with a formylated-Met at their amino terminus