review questions Flashcards
What are the 3 types of horizontal gene transfer
transduction- viral integration
transformation- integration of dead DNA
conjugation- bacteria to bacteria
what is a serological variant or serovar?
a serovar is a group of closely related microbes that share a common set of antigens
what are regulatory proteins
special proteins that bind to specific regulatory sequences of DNA and act to switch genes on and off and thereby regulate the transcription of genes.
how to determine whether DNA is right handed or left handed
if DNA has both strands moving clockwise then it is right handed both strands moving counter clockwise then it is left handed
what is the common name for DNA b
DNA helicase
DnaC what is the common name?
helicase loader protein that guides helicase into place
what are the three plasmid genes used in segregation
pare, parM, and parR. The pare DNA sequence
is analogous to the centromere of eukaryotic chromosomes. The DNA-binding protein ParR binds to the paresequence and forms a ParR-pare plasmid complex. ParM protein is an actin-like molecule that forms long filaments as it hydrolyzes ATP. The ParM filaments are dynamically unstable, constantly elongating and shortening. However, each end of a ParM actin-like filament can bind to a ParRpare plasmid. When both ends of a ParM filament contact ParR-pare plasmid complexes, the filament stabilizes and elongates until the two plasm ids hit the opposite poles of the cell. The plasmid is thus dislodged from the filament, and the filament quickly dissociates.
What are restriction endonucleases? Know the 2 types of ends that can be produced
The cut may produce blunt ends or staggered
ends; in staggered ends, the top strand is cut at one
end of the site and the bottom strand cut at the other (Fig.
7.27A). Staggered ends are also called “cohesive ends”
because the protruding strand of one of those ends can
base-pair with complementary protruding strands from
any DNA fragment cut with the same restriction endonuclease, regardless of the source organism.
What is PCR? What do you need for PCR? What are the 3 steps?
In this technique, specific oligonucleotide primers
(usually between 20 and 30 bp) are annealed to known
DNA sequences flanking the target gene. A thermostable
DNA polymerase uses these primers to replicate the target DNA.
What is Sanger DNA Sequencing?
the Sanger dideoxy strategy. Ingenious in its simplicity,
the dideoxy method relies on the fact that the 3’ hydroxyl
group on 2’-deoxyribonucleotides (shown in Fig. 7.4A)
is absolutely required for a DNA chain to grow. Thus,
incorporation of a 2’,3’-dideoxynuc1eotide (Fig. 7.30) into
a growing chain prevents further elongation because without the 3’ OH, extension of the phosphodiester backboneis impossible. ultimately this cleaving results in different lengths of DNA fragments whcih can be tagged and then run through a gel to produce peaks
what is illumina DNA sequencing
This sequencing method is based on reversible dye-terminators that enable the identification of single bases as they are introduced into DNA strands. It is often employed to sequence difficult regions, such as homopolymers and repetitive sequences. It can also be used for whole-genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation profiling, and genome-wide protein-nucleic acid interaction analysis
jacard similarity matrix
Jaccard similarity coefficient (originally coined coefficient de communauté by Paul Jaccard), is a statistic used for comparing the similarity and diversity of sample sets. The Jaccard coefficient measures similarity between finite sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets
RNA polymerase is made up of
core polymerase which contains the essential protein constituents and a sigma factor which is just needed for initiation of RNA synthesis but not elongation
what is the RNA polymerase core function and what are the subunits of the core
the function of the core is to elongate the chain of RNA the subunits contained in the core include two alpha (n) subunits, one beta (P) subunit, and one beta-prime (13’) subunit for every core enzyme
sigma factors do what?
A sigma factor binds RNA polymerase through the alpha subunit and then helps the core enzyme detect a specific DNA sequence, called a promoter, which signals the beginning of a gene.
The
specific sigma factor used to initiate transcription of
a given gene will vary, depending on the gene
what is a holoenzyme
a biochemically active compound formed by the combination of an enzyme with a coenzyme
what is a consensus sequence
a sequence of DNA having similar structure and function in different organisms.
or the most likely base or series of bases at a position as predicted by a promoter
Which strand codes for mRNA
anti sense DNA codes fro sense mRNA
describe initiation of transcription
RNA polymerase bonds to a promoter region of the DNA the sigma complex then helps to unwind the DNA and the RNA polymerase begins transcription moving along the length of the gene to lay down each new base a nucleoside triphosphate group is cleaved and this energy is used to form a new bond
the first rNTP is usually what type of nucleotide
a purine
What is the function of the antibiotic, Rifamycin
it bonds to bacterial RNA polymerase beta subunit and blocks the exit site for the RNA chain
What are the 2 ways to terminate transcription?
One termination mechanism, called Rho-dependent,
relies on a protein called Rho and an ill-defined sequence
at the 3’ end of the gene rho binds down stream of this sequence and when the RNA reaches the stop codon rho pulls itself to the RNA polymerase when they touch rho causes the unwinding of the RNA-DNA heteroduplex which releases the RNA
the second method is Rho independent in this method a GC rich sequence causes weakening of the bonds between RNA polymerase and the DNA leading to termination of transcription
What is the Shine-Delgarno sequence
a ribosomal binding site in prokaryotic mRNA, generally located around 8 bases upstream of the start codon AUG.[1] The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon.
what are the parts of tRNA
the anti-codon loop harbors a complimentary three base strand to code for the appropriate codon. the three prime end is called the acceptor end because this is where amino acids bond to the molecule
dihydrouridine and TPC loops contain only modified bases that increase structural integrity
what is the name of the molecule that charges tRNA
aminoacyl-tRNA synth etases
what is fMET
is a derivative of the amino acid methionine in which a formyl group has been added to the amino group. It is specifically used for initiation of protein synthesis from bacterial and organellar genes, and may be removed post-translationally. fMet plays a crucial part in the protein synthesis of bacteria, mitochondria and chloroplasts.
what are the ribosomal subunits
the 30s subunit made up of ribosomal proteins and the 50s made up of proteins the molecule that actually attaches new amino acids peptidyltransferase is a ribosyme
can transcription and translation occur at the same time
yes but only in bacterial cells
Where is fMET found?
on the N terminis of proteins
fMET can be found in what type of proteins? How do white-blood cells utilize fMET?
fMET is only found in bacterial cells therefore it is an easy target for white blood cells to attack
what are the two types of proteins that aid in protein folding
chaperonins in the form of heat shocked proteins and groEL and groES chaperonins
Describe the protein folding vs. Degradation Triage Pathway. Know the steps.
chaperonins hunt for misfolded proteins and attempt to refold them. if the protein is not fixed it can either be reengaged by the chaperone or killed by a protease
What is tmRNA
tmRNA acts as both mRNA and tRNA and allows ribosomes stuck on damaged mRNA to be freed first the tRNA protion bond to the ribosome’s active cite then a death sequence is added to the protein via the mRNA portion and a disloge sequence codes ofr release
What are the 2 types of protein degradation machines? Bacteria contain which one?
Proteasomes are protein -degrading
organelles of eukaryotes. The protein-degrading enzymes
are classified as serine, cysteine, or th reonine proteases,
depending on the key residue in their active sites.
There is a striking resemblance between prokaryotic
and eukaryotic ATP-dependent proteases
why is the n terminis important
Many normal proteins contain degradation signals
called degrons that dictate the stability of a protein. The
N-te rminal rule describes one type of degron. The rule
states that the N-terminal amino acid of a protein directly
correlates with its stability.
