Transcription Flashcards
Single-stranded DNA binding protein
Bind to the single-stranded DNA that has been separated and keep it stable
Helicase
Opens up the double stranded DNA (like you break apart the teeth on your zipper)
DNA polymerase
ase=enzyme
Helps put together the small parts (nucleotides) of the DNA molecule. Busses in all the correct nucleotides
Uses help of RNA primase
Also corrects mistakes
RNA primer
Makes a primer for synthesis to start. Follows in helicase and lays down primer. Primer is made of RNA
RNA primase: makes RNA primer
*Doesn’t use Thymine (b/c it’s RNA). Uses uricil instead
DNA pol α lays down 25 DNA nucleotides
DNA synthesis direction
Synthesized 5’–>3’
Goes towards the 5’ far end
DNA does not control biological properties of the cell
True
What determine cell functions?
Proteins
DNA uses RNA as intermediary in protein synthesis
True
Piece of DNA
Gene
Copying a gene into RNA
Transcription
RNA is used as template to make protein. Process called________
Translation
RNA and DNA similarities
Both are linear polymers
Made of nucleotides and connected by phosphodiester bonds
RNA and DNA differences
RNA is single stranded
RNA has ribonucleotides instead of deoxyribonucleotides
RNA can fold into complex 3D structures allowing to have catalystic function
Telomerase
There is no free 3’ OH to prime DNA synthesis at the end of the lagging strand
How many major types of RNA are there?
3
rRNA
Function: structural and functional (catalytic) components of ribosomes. Form the core of the ribosome and catalyze protein synthesis
Features: stable, long-lived, GC rich, folded w/ extensive internal base pairing
80%
What are the types of rRNA?
28s (longest)
18s
5.8s
5s (shortest)
eukaryotic ribosome has 83 different proteins
tRNA
Function: carry AA’s to ribosomes to make polypeptide chains
Features: stable, small, has modified bases
15%
Cloverleaf: has CCA at 3’ end (carries AA), anticodon (base-pairs w/ codon in mRNA)
How many different tRNA’s are there?
56 different tRNA’s
mRNA
Function: carrier of genetic info from genes to ribosomes for protein synthesis. Direct protein synthesis. Non-coding RNA serve as enzymatic and structural components for many biological processes
Features: short-lived (like mission impossible..”self destruct”)
1-5%
snRNA
These are packaged with proteins to form small nuclear ribonucleoproteins (snRNP’s or “snurps”) that are part of “spliceosomes.” They are involved in the splicing of precursor mRNA and export of mature mRNA
i.e. U1 snRNA
siRNA
Small interfering RNA: regulate eukaryotic gene expression by degrading select mRNA
These are short (21-24 nucleotides) antisense transcript derived from transposons and complementary to certain mRNAs. siRNAs inhibit the translation of target mRNAs and enhance their degradation in RNA-induced silencing complexes (RISCs)
miRNA
Micro RNA: regulate gene expression by blocking translation of selective mRNA
Transcription begins with….
Begins with binding of RNA polymerase to promoter on DNA
Nucleotides are covalently linked by _______
Phosphodiester bonds on the backbone
3’OH—-5’ phosphate
Transcription: Reaction catalyzed by ________
RNA polymerase
RNA transcribed in which direction?
5’–>3’
Released as a single strand
New RNA sequence is same as (except it has U for T)
RNA sequence is same as coding/non-template/sense strand (5’–>3’)
General transcription factors for polymerase II:
TFIIA, TFIIB, TFIIC, TFIID etc
Assemble at the promoter before transcription
What is function of TFII’s? (transcription factors for polymerase II)
- Help position RNA polymerase correctly at promoter
- Help pull apart the two strands of DNA to allow for transcription
- Release RNA polymerase from promoter into elongation mode once transcription has begun
Eukaryotic Transcription-Initation
- TFIID binds to TATA box (causes distortion in DNA)
- TFIIB recruited, followed by TFIIF, RNA Pol II, TFIIE and TFIIH
- All these factors join to make transcription initiation complex
- TFIIH unwinds the DNA double helix and exposes template strand
- RNA Pol II makes short lengths of RNA
- Phosphorylation of CTD(carboxy terminal domain) by TFIIH (causes polymerase to leave promoter and begin elongation/transcription
General steps of Transcription
Initiation, Elongation and Termination
Key features of Initiation
- Histone acetylation/deacetylation reaction (acetylation/deacetylation of lysines on histone tails by Histone Acetyl Transferase (HAT) and histone deacytelases (HDAC)
- Formation of an RNA dinucleotide
- Formation of 7-methylguanosine cap at 5’ end
Promoters
Where polymerase binds. Helps polymerase find start site for transcription.
Homeodomain proteins (regulation of transcription)
Contain a conserved 60 residue DNA binding motif or homeodomain
Zinc finger proteins (regulation of transcription)
Have short regions containing Cys and His residues that interact w/ Zn ions that produce multiple loops or Zn fingers that insert into major grooves of DNA
Leucine zipper proteins (regulation of transcription)
Contain DNA binding sequence where every 7th residue is leucine which promotes dimerization and coiling of these sequences
Basic Helix Loop Helix proteins (regulation of transcription)
Similar to bZIP except α helical regions separated by non-helical loop sequence
Transcription Factors and cancer
Inappropriate inactivation/activation of genes that control cell growth by deregulation of transcription factors may lead to cancer.
Mutated genes for TF’s represent a significant fraction of oncogenes
Mis-regulation may occur by aberrant increase in expression or by mutations in the coding sequence that alters activity of the TF
Fragile X Mental Retardation (FMR1)
FMR1 gene encodes for a protein with neurological function
DNA sequence has 30 repeats of CGG in most people
In patients w/ FMR1 the CGG repeat expanded to >200 copies
Expansion makes it susceptible to methylation of cytosine
The FMR1 gene becomes silent even though the triplet expansion is upstream of proton coding sequence
As methylation repeat region extends into the promoter region, transcription is turned off
B form of DNA
Right handed, has 10 base pairs per turn, each base pair separated by 3.4A
A form is more compact
Z form=left handed
X-shaped chromosomes
Metaphase chromosomes are the most compact form of chromatin
4 histones
H2A, H2B, H3, H4 (w/ DNA makes nucleosomes–>chromatin)
Chromatin condenses during M phase of cell cycle into chromosomes
Transcription-General Features
Begins w/ binding of RNA polymerase to promoter on DNA
Unwind DNA double helix to get template for making RNA
Reaction catalyzed by RNA polymerase
New RNA strand is released from DNA as a single strand
Histones have a high content of what?
Argenine and lysine
RNA molecules have extensive base pairing
True
Can produce secondary and tertiary structures that are important for RNA function
Coding strand, sense strand etc
5’——3’
coding/sense/non-template
3’——5’
non-coding/antisense/template
mRNA 5’—-3’
Read in 5’–>3’ direction
NH2 terminus–>COOH terminus
Ribozymes
Usually precursors of rRNA, remove internal segments of themselves, splicing the ends together
Histone acetylation and deacetylation
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.
Histone acetylation and deacetylation are essential parts of gene regulation. These reactions are typically catalysed by enzymes with “histone acetyltransferase” (HAT) or “histone deacetylase” (HDAC) activity. Acetylation is the process where an acetyl functional group is transferred from one molecule (in this case, Acetyl-Coenzyme A) to another. Deacetylation is simply the reverse reaction where an acetyl group is removed from a molecule.
Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.
Chromatin remodeling and bromodomains
An ATP-driven chromatin remodeling complex will bind to the regions of DNA that contain acetylated histones. Bromodomains on proteins within the complex recognize the acetylated histones. Once bound, using ATP as an energy source, the complex will move and displace histones to free up an area of DNA for transcription.
mRNA’s can be degraded
mRNA can be degraded by nucleases after their synthesis in the nucleus and before their translation in the cytoplasm.
Interferon stimulates the synthesis of 2’,5’-oligo(A) which activates a nuclease that degrades mRNA
