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Micro Exam 2 (Chpt. 6: Molecular Information Flow and Protein Processing)

Terms in this set (54)

central dogma flow?
DNA -> RNA -> Protein
exception to central dogma?
retroviruses
RNA -> DNA -> RNA -> protein
What role does Gyrase play in bacterial DNA replication
Removes supercoiling ahead of replication fork
What role does Helicase play in bacterial DNA replication
Unwinds the double helix at replication fork

Uses ATP
What role does Single-strand binding proteins play in bacterial DNA replication
Helps prevent strands from pairing with each other

Binds to single strands of DNA
What role does Primase play in bacterial DNA replication
Adds RNA primers to new strands of DNA

Primers serve as a starting point for DNA synthesis
What role does DNA polymerase III play in bacterial DNA replication
Involved in DNA replication

Can only adds nucleotides in the 3' OH

Adds in 3' → 5' direction (lagging strand)

Needs RNA primers
-Primer added to 3' OH group
What role does Tau play in bacterial DNA replication
Holds DNA polymerase I & III & helicase together

Bidirectional replication (Bacteria & Archaea), Replisome
What role does Ligase play in bacterial DNA replication
Joins Okazaki Fragments together
How is replication initiated?
DNA must be unwound to expose template strands at the replication fork by helicase

DNA synthesis begins at a single site on the chromosome called the origin of replication

Primase and DNA polymerase are loaded onto DNA

Initiation of DNA replication can occur
Occurs at the leading strand
--Leading strand adds in the direction of the replication fork
--Requires ONE RNA primer

There is ALWAYS a free 3' OH at the replication fork
--New nucleotides can be added continuously
Continuous replication
Occurs at the lagging strand
--Lagging strand builds AWAY from the replication fork
--Requires SEVERAL RNA primers

No 3'OH available to which nucleotides can attach to
--Primase must synthesize multiple RNA primers to provide 3'OH groups for DNA Pol III
Several short DNA fragments are produced (discontinuous)
Okazaki Fragments
DNA Ligase
--DNA Pol I removes the primers and replaces it w/ DNA
Moves in the 5' → 3' direction
Discontinuous replication
what replication occurs at the leading strand?
continuous replication
In continuous replication, what strand adds in the direction of the replication fork
leading strand
How many RNA primers are required for continuous replication
one RNA primer
What is always at the replication fork in continuous replication?
ALWAYS a free 3' OH, where new nucleotides can be added continuously
what replication occurs at the lagging strand?
Discontinuous replication
what type of strand builds away from the replication fork?
lagging strand
how many RNA primers are required for discontinuous replication
SEVERAL RNA primers
What is not available to which nucleotides can attach to in discontinuous replication
No 3'OH
In what replication must there be the synthesis of multiple RNA primers to provide 3'OH groups for DNA Pol III, and what does the synthesizing?
Discontinuous replication; Primase
what is produced in discontinuous replication
Several short DNA fragments --Okazaki Fragments
In discontinuous replication, what removes the primers and replaces it w/ DNA, and in what direction does it move?
DNA Pol I and moves in the 5' → 3' direction
RNA polymerase must recognize
--promoters (initiation sites)
Promoters are recognized by sigma
--Sigma factors are key in recognizing promoter sequences to initiate transcription
--Pribnow Box (TATA box, -10 region) & -35 region are sequences within the promoter that are recognized by sigma

RNA polymerase binds to a promoter = transcription is initiated
Transcription initiation in bacteria
G-C rich sequence containing an inverted repeat

Transcribed & then RNA forms a stem-loop structure to finish transcription

Rho Dependent termination
--Rho protein will bind mRNA transcript can cause the mRNA molecule to be released from the DNA template
--Rho protein will cause the RNA polymerase to be released from DNA as well, ending transcription
Transcription termination in bacteria
What major enzyme catalyzes transcription?
RNA polymerase - single stranded
How are plasmids similar to and different from the bacterial chromosome?
The plasmid is a circular double-stranded extra-chromosomal DNA structure of bacteria while the chromosome is a well-organized thread-like structure that contains genomic DNA tightly coiled with proteins.

Plasmid: Relatively short circular or linear, extrachromosomal, Double-stranded DNA

Bacterial Chromosome: Extremely long, usually circular, Double-stranded DNA
what is smaller than bacterial chromosome?
plasmids
what in bacteria does not encode functions essential to host?
plasmids
what in bacteria contains few genes and confer selective growth advantage and usually antibiotic resistance?
plasmids
what is similarity between bacterial plasmids and chromosomes?
both contain their own genes and Double stranded (dd) DNA
three ways that eukaryotic mRNAs are processed after transcription?
RNA Splicing

5' Capping (Unique to eukaryotes)

3' polyadenylation (poly A tail)
Way in which eukaryotic mRNAs are processed after transcription;
--Spliceosome excise introns and link exons
Forms a continuous mRNA
--Occurs in the nucleus
RNA Splicing
Way in which eukaryotic mRNAs are processed after transcription;
--Addition of a methylated guanine nucleotide on the 5' phosphate end of mRNA
--Protects transcript from being broken down
--Needed to initiate translation
5' Capping (Unique to eukaryotes)
Way in which eukaryotic mRNAs are processed after transcription;
--Addition of 100-200 adenine residues
--The poly(A) tail stabilizes mRNA against nuclease attack
--Prevents enzymatic degradation of mRNA
--Must be removed after translation
3' polyadenylation (poly A tail)
3 main classes of RNA involved in protein synthesis
tRNA
mRNA
rRNA
tRNA
Transfer RNAs function to carry amino acids to the translation machinery

Contains anticodons
--Group of 3 nucleotides that recognize a codon on mRNA

Specific amino acid binds to a tRNA molecule
--The correct amino acid (called the cognate amino acid) is linked to a specific tRNA by an enzyme called an aminoacyl-tRNA synthetase
mRNA
Contains the complementary genetic code in the form of codons
--Carry the coding sequence of proteins

Each codon specifies a particular amino acid
--3 bases per codon
rRNA
Ribosomal proteins combine with rRNA to form a ribosome
--Ribosomes are the site of protein synthesis

Facilitates initiation by base pairing w/the ribosome binding site on mRNA

Catalyzes formation of peptide bonds
Short, single stranded, secondary structure

Contain some purine and pyrimidine bases that are modified from the bases found in other classes of RNA, and these modifications occur after transcription

Anticodon loop

Acceptor stem

T C Loop

D Loop

Acceptor end (3' end)
-3 unpaired nucleotides
-Cytosine-cytosine-adenine (CCA)
Essential for function
general structure of tRNA?
Multiple codons will code for the same amino acid, but never for more than one.
Degenerative Genetic Code
Base pairing is more flexible for the third base of the codon than for the first two
The wobble concept:
Initiation in bacteria(video)
Ribosomes: composed of proteins and rRNA

Initiation begins with a free 30S ribosomal subunit
--GTP is also required

A 50S ribosomal subunit is added to the complex to form the active 70S ribosome
--rRNA recognizes a specific AUG on the mRNA as a start codon with the aid of an upstream sequence in the mRNA called the ribosome-binding site (RBS) (also called the Shine-Dalgarno sequence)

Requires start codon
--AUG: encodes a chemically modified methionine called N-formylmethionine
Elongation in bacteria(video)
Two important sites on the 50s subunit.
--A (acceptor) site:
++where the incoming charged tRNA first attaches
++loading of a tRNA into the A site is assisted by the elongation factor EF-Tu

--P (peptide) site:
++where the growing polypeptide chain is attached to the prior tRNA
++the growing polypeptide chain moves to the tRNA at the A site as a new peptide bond is formed
++In addition to EF-Tu, elongation factor EF-Ts, as well as more GTP, is required
Translocation in bacteria(video)
tRNA holding the polypeptide is translocated from the A site to the P site, thus opening the A site for a new charged tRNA
--requires elongation factor EF-G and one molecule of GTP for each translocation event
--the ribosome advances three nucleotides

Translocation pushes the now amino acid-free tRNA to a third site, called the E (exit) site, and it is from here that the tRNA is released from the ribosome
Termination in bacteria(video)
when the ribosome reaches a stop codon (Table 6.4) because no tRNA binds to a stop codon

--proteins called release factors (RFs) recognize the stop codon and cleave the attached polypeptide from the final tRNA
--ribosomal subunits dissociate, and the 30S and 50S subunits are then free to form new initiation complexes and repeat the process.
a complex of several ribosomes translating a single mRNA molecule simultaneously

--increase both the speed and efficiency of translation
Polysome
Why are prokaryotes able to carry out coupled transcription and translation while eukaryotes cannot?
Prokaryotic translation and transcription occur in the same place within the cell (cytoplasm)

--No need to transfer the mRNA out of the nucleus to start translation (eukaryotes)
--Therefore, transcription and translation in prokaryotes happens simultaneously
role of chaperone proteins
Protein folding assistants

Fold proteins that do not fold spontaneously

Refold partially denatured protein

Assemble multiprotein complexes

Prevent improper aggregation of proteins

Untangle RNAs

Incorporate cofactors into enzymes

Chaperones can be a type of heat shock protein
--Synthesis accelerated when cell is under stress by extensive heat
--Refold denatured proteins
Sec system in bacteria
Unfolded proteins exported from the cytoplasm are recognized by SecA proteins or signal recognition particle (SRP)

Protein folds
Tat System:
Protein folding occurs BEFORE translocation
--Contain cofactors, cytochromes, etc
protein secretion system types present in gram-negative bacteria
Type I Secretion System: 1-step

Type II systems: 2-step

Type III Systems:1-step

Type IV Systems:1-step

Type V systems:2-step

Type VI Systems:1-step
the two protein secretion systems in gram negative bacteria which are 2-step translocases
type II and type V systems
Molecules secreted by these systems allow bacteria to interact with the environment and other organisms
Type I through Type VI protein secretion systems
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