The Central Dogma Flashcards by Tori Whalen

_____ is the main key enzyme for
transcription

RNA polymerase

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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

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RNA polymerase works in a ___ to ____ direction

5’ to 3’ direction

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Which of the following bonds contribute to the stability of the DNA helix?

B) H-bonds

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what do the following compose?
- 147 base pairs wrapped around a histone core
- Octamer of H2A, H2B, H3 and H4
- H1 linker protein

Nucleosomes

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Chromatin: complex of DNA + tightly bound protein. heterochromatin is ____ while Euchromatin is ____

packed, dispersed

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coding sequence of a gene

exon

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noncoding sequences of a gene § Removed via splicing after transcription

intron

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____ of the human genome does not encode protein

98.5%

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What is the name of the non-coding sequence removed during splicing?

Intron

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___ always occurs in a double-stranded helix. While ___ is single-stranded. RNA can therefore fold up into various shapes

DNA, RNA

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Some sequences of DNA are transcribed into RNA then do not get translated into proteins. What are these called?

non-coding RNA

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_____ serves as enzymatic, structural, and regulatory components of a wide variety of processes in the cell

Non-coding RNA

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Small nuclear RNA (snRNA) functions in the ______

spliceosome

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_____ are needed for the basic structure of the ribosome complex. Involved in catalysis of the peptide bond between amino acids

ribosomal RNA

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_______ 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)

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____ Regulate gene expression via post-transcriptional silencing
Block/prevent translation of specific mRNAs & promote their degradation

miRNA (micro RNA):

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_____ Reduce gene expression
Direct degradation of specific mRNA

siRNA (Small interfering RNA)

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____ Regulate gene expression
Can increase or decrease transcription

lncRNA (long non-coding RNA):

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Which of the following RNA molecules are involved in gene regulation

siRNA, miRNA, lncRNA

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_______ 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

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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

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Transcription can be divided into 4 stages:

Initiation, elongation, processing and termination

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Transcription initiation factors help RNA polymerase recognize where to start.

Transcription initiation factors

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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?

1. no process is required (no 5' cap, splicing, or poly-A tail 2. no export from the nucleus (thus, translation can happen right away) 3. 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

1. tRNA caries the amino acid meth 2. met-tRNA is loaded into the small ribosomal subunit at the P site with initiation factors 3. small ribosome binds to 5' end of mRNA (5' cap helps with recognition) 4. small ribosome moves along and scans for AUG (ATP hydrolysis is required) 5. 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