The Central Dogma Flashcards
_____ is the main key enzyme for
transcription
RNA polymerase
RNA polymerase moves along the DNA, unwinding the DNA helix
just ahead of the active site for polymerization. Catalyzes a new ________ on the newly-forming strand of RNA
phosphodiester bond
RNA polymerase works in a ___ to ____ direction
5’ to 3’ direction
Which of the following bonds contribute to the stability of the DNA helix?
B) H-bonds
what do the following compose?
- 147 base pairs wrapped around a histone core
- Octamer of H2A, H2B, H3 and H4
- H1 linker protein
Nucleosomes
Chromatin: complex of DNA + tightly bound protein. heterochromatin is ____ while Euchromatin is ____
packed, dispersed
coding sequence of a gene
exon
noncoding sequences of a gene § Removed via splicing after transcription
intron
____ of the human genome does not encode protein
98.5%
What is the name of the non-coding sequence removed during splicing?
Intron
___ always occurs in a double-stranded helix. While ___ is single-stranded. RNA can therefore fold up into various shapes
DNA, RNA
Some sequences of DNA are transcribed into RNA then do not get translated into proteins. What are these called?
non-coding RNA
_____ serves as enzymatic, structural, and regulatory components of a wide variety of processes in the cell
Non-coding RNA
Small nuclear RNA (snRNA) functions in the ______
spliceosome
_____ are needed for the basic structure of the ribosome complex. Involved in catalysis of the peptide bond between amino acids
ribosomal RNA
_______ are needed in translation to carry the correct amino acid to the growing polypeptide chain. tRNA folds into a unique cloverleaf shape.
Transfer RNA (tRNA)
____ Regulate gene expression via post-transcriptional silencing
Block/prevent translation of specific mRNAs & promote their degradation
miRNA (micro RNA):
_____ Reduce gene expression
Direct degradation of specific mRNA
siRNA (Small interfering RNA)
____ Regulate gene expression
Can increase or decrease transcription
lncRNA (long non-coding RNA):
Which of the following RNA molecules are involved in gene regulation
siRNA, miRNA, lncRNA
_______ moves along the DNA, unwinding the DNA helix just ahead of the active site for polymerization. Catalyzes a new phosphodiester bond on the newly-forming strand of RNA
RNA polymerase
RNA polymerase makes mistakes at a rate of 1 for every 10^4 nucleotides. DNA polymerase makes mistakes at a rate of 1 in every 10^7 nucleotides. What is the significance of this?
DNA in a cell is constant - if there is a change in the DNA, then it affects the proteins that are being synthesized. While a change in the mRNA only affects that synthesis ONCE
Transcription can be divided into 4 stages:
Initiation, elongation, processing and termination
Transcription initiation factors help RNA polymerase recognize where to start.
Transcription initiation factors
what is a general transcription factor?
TFII
TFII recognizes and binds a consensus sequence in the promoter region. What is an example?
The TATA box
TATA box is located ____ nucleotides
upstream from the transcription start site.
~25
_____ is the specific TFII
that binds the TATA box. Other transcription factors join. Then _____ joins.
TFIID. RNA Polymerase II
Transcriptional activator proteins bind upstream sequences of DNA called ____. They ____ the rate of transcription by attracting the RNA polymerase II enzyme.
enhancers, increase
What might happen if there was a mutation in an enhancer sequence of DNA?
We may not be able to enhance our protein synthesis rate - which may affect the activation our of mRNA formation
Once RNA Polymerase
begins transcribing DNA, most of the general transcription factors (TFII) are _____
released
Various _______ are needed to help reduce the likelihood that RNA polymerase dissociates from DNA before it reaches the end of a gene.
elongation factor
________ help the RNA polymerase navigate the chromatin structure
Chromatin remodeling complexes
_______ partially disassemble &
reassemble nucleosomes as an RNA Polymerase passes through
Histone chaperones
In Eukaryotes DNA ______ removes this super-helical tension by breaking ______ bonds.
topoisomerase, phosphodiester
pre-mRNA has to go through ______ in order to be called mRNA
processing
A modified _______ nucleotide is added to the 5’ end of the transcribed premRNA. This occurs early, once ~25 nucleotides of RNA have been transcribed
guanine
This 5’ cap facilitates _____ of the mRNA into the nucleus and is involved in translation
export
Splicing is performed by ______
spliceosomes
Splicing allows the same gene to produce a variety of different ______
proteins
Once cleaved, _____ A nucleotides are added to the mRNA
~200
Poly A tails protects the mRNA from ______ and facilitates export from
the nucleus
degradation
How is Prokaryotic transcription different?
- no process is required (no 5’ cap, splicing, or poly-A tail
- no export from the nucleus (thus, translation can happen right away)
- mRNA transcript is polycistronic (codes for more than one protein on a single mRNA)
There are ___ possible combinations of of 3
nucleotides but only __ amino acids
64, 20
The Shine-Dalgarno
enables initiation of protein synthesis by aligning the ribosome with the start codon in prokaryotes
special punctuation in eurokaytoes
AUG
aminoacyl-tRNA synthetase
catalyzes the attachment of correct amino acid to tRNA
Protein synthesis is performed in the
ribosome
The ribosome complex is composed of
various ribosomal proteins and ribosomal
RNA (rRNA). and what two subunits?
small subunit and large subunit
- tRNA caries the amino acid meth
- met-tRNA is loaded into the small ribosomal subunit at the P site with initiation factors
- small ribosome binds to 5’ end of mRNA (5’ cap helps with recognition)
- small ribosome moves along and scans for AUG (ATP hydrolysis is required)
- Initiation factors dissociate & the large ribosome subunit assembles to complete the ribosome complex
initiation of translation
Newly charged tRNA binds to the A site of the ribosome complex
tRNA binding of elongation
- The carboxyl end of the polypeptide chain is released from the tRNA at the P site & joins the amino acid linked to the tRNA at the A site
- This new peptide bond is catalyzed by peptidyl transferase enzyme contained within the large ribosomal subunit
peptide bond formation of elongation
Large ribosomal subunit moves relative to the mRNA held by the small subunit
- Two tRNAs are shifted to the
E and P sites
Translocation of large subunit of elongation
- Small subunit shifts by 3 nucleotides
- tRNA in the E site is ejected
Translocation of small subunit of elongation
Elongation proceeds efficiently and
accurately with the help of ______
elongation factors (EFs)
These elongation factors enter and leave the
ribosome during each cycle & are coupled with GTP hydrolysis
A ___ codon marks the end of the translation. These include ___, ___, and ___. Not recognized by a tRNA & does not specify an amino acid
STOP. UAA, UAG, UGA
Release factors bind to ribosomes with a stop codon in the A site
Peptidyl transferase catalyzes the addition of a _____ molecular rather than ____. This frees the carboxyl end and releases the polypeptide
water, amino acid
In prokaryotes: The synthesis of proteins occurs
on _____.
polysomes
Multiple initiations take place on each mRNA molecule being translation
Once fully translated, what happens next?
Protein is folded into a specific 3-D shape
Proper folding is important since the structure of a protein dictates its _____
function!
blocks binding of aminoacyl-tRNA to the A side of the ribsome
tetracycline
prevents the transition from translation initiation to chain elongation and also causes miscoding
streptomycin
blocks the peptidyl transferase reaction on ribosomes
chloramphenicol
binds in the exit channel of the ribosome and thereby inhibits elongation of the peptide chain
erythromycin
blocks initiation of the RNA chains by binding to RNA polymerase (prevents RNA synthesis)
rifamycin
