CH8 Transcription, Translation, and Bioinformatics Flashcards
what is an example of transcription factors
sigma factors
purpose of sigma factors in transcription
help RNA polymerase find the promoter on the DNA
the region that RNA polymerase binds to is called what?
a promoter
what are the three types of RNA in eukaryotes and what are their functions
- RNA polymerase I transcribes rRNA genes
- RNA polymerase II transcribes mRNA
- RNA polymerase III transcribes tRNA and 5S rRNA genes
what sequences do sigma genes bind to
the -30 and -10 shine dalgarno sequences
what is the house keeping sigma gene
sigma 70
what are the consensus sequences for sigma 70 promoters
-35: TTGACAT
-10: TATAAT
the three phases of transcription
- initiation
- elongation
- termination
characteristics of streptomyces bacteria
- versatile in metabolism: suggests that they have high control over transcription making the slow growing
what happens to the sigma factor when RNA polymerase attaches to the promoter?
the sigma factor leaves
Two aspects to termination
- rho which is a hexomer that causes termination when it connects with RNA polymerase
- Hairpin loop: contact between hairpin, NusA protein and rna polymerase causes termination
what antibiotic inhibits RNA polymerase thus transcription
Rifampin
what is the purpose of actinomycin D as an antibiotic
-blocks transcription
-inhibits dna replication by inhibiting primer formation
purpose of small RNAs or regulatory rnas
Controls transcription, translation, or RNA stability
purpose of tmRNA
Frees ribosomes stuck on damaged mRNA
purpose of catalytic RNA
(ribosimes)
carries out enzymatic reactions
Least stable RNA (shortest half-life)
mRNA
Ecoli has a complex of four proteins that break down RNA. what are they called?
degradosomes
what is the start codon
AUG
how many stop codons?
three
1. UAA
2. UAG
3. UGA
Transfer RNA structure
First transfer RNA to be vizualized
Alonien tRNA
using chromatography columns to purify the RNAse
what is charging tRNA
- it is used in translation as a form of energy to make proteins
- the tRNA is charged when the amino acid attaches to hydrolized AMP (cleaved 2 phosphate groups off ATP)
where are plasmids and DNA in nucleoid located in a cell?
plasmid at the poles and nucleoid in the middle
indicating that the two forms of DNA
are bacteria polycistronic or monocistronic?
polycistronic: If a stretch of replicating DNA contains more than one cistron, it is called polycistronic
are eucaryotic cells polycistronic or monocistronic?
monocistronic: If a stretch of replicating DNA contains a single cistron (or gene), it is called monocistronic
what are the three initiation factors involved in translation
- initiation factor 1: 30s subunit binds to IF1 and mRNA
- IF2: interacts with initiator tRNA
- IF3: all initation factors fall off and GTP becomes hydrolized causing translation to occur
From DNA to protein video
https://www.youtube.com/watch?v=gG7uCskUOrA
What is the purpose of tmRNA?
has the properties of a tRNA and an mRNA. tmRNA uses these two functions to release ribosomes stalled during translation and target the nascent polypeptides for degradation.
what assistant protein is used to help proteins take their shape and what else happens to proteins to help them take the right shape
- GroEL chaperone (protein) after heat shock
- phosphorylation
- acetylation
what happens to proteins after heat shock?
their shape changes and chaperones are used to put them back together
what is the purpose of a proteasome
to degrade proteins
what are proteases
proteases are enzymes that break down protein
Ex: ClpQ
what are ATPases
ATPases are a class of enzymes that catalyze the decomposition of ATP into ADP
ex: ClpY
where is a protein degraded
on the active site of proteosomes
what does the stability of a protein depend on?
the N-terminal rule
(half-life)
what are the three possible locations you can send a protein
- membrane
- periplasm if its gram negative
- outside the cell
what guides a protein to its destination
SRP (signal recognition particle)
the periplasmic proteins are secreted via what kind of system?
the Sec system
protein transport video: https://www.youtube.com/watch?v=2aguTUg1sJk
where does SRP bind during protein secretion and what happens after it sends off the signal sequence?
FtsY receives then passes the signal sequence to the secYEG
when is translation completed?
when the ribosome reaches FtsY
what organism is responsible for strep throat?
Streptococcus pyogenes
- HtrA is a cluster of secretory systems
what does the TAT system do
transfer a folded protein instead of an unfolded one
ABC transport system directs proteins from point A to point B
what is point A and what is point B?
A: cytoplasm
B: outside the cell
what are the two types of ABC transporters and what do they do?
- influx: bring in macronutrients
- efflux: pump out antibiotics.
ABC transport video:
https://www.youtube.com/watch?v=LwSKgrdomPM
what encodes proteins in eukaryotes
Exons
what is sequence homology
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history
(common ancestor)
what is a paralog gene?
note: Homologous sequences are paralogous if they were separated by a gene duplication event
note: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous
answer: -same genome different function
what is an ortholog gene
genes have the same function but are in different species
note: Orthologs are defined as genes in different species that have evolved through speciation events only. Paralogs, on the other hand arise by duplication events
what is the CAZyme gene
in Japanese ppl so they can get the ability to degrade red algae.
how are genes transfer
horizontally
- non-sexual movement of genetic information between genomes
