Gene Expression Flashcards
Where is DNA transcribed into RNA?
The nucleus
Where is RNA processed?
The nucleus
Where does mRNA exit through?
nucleopores
Where are ribosomes assembled on mRNA?
The cytosplasm
Where does translation take place?
The cytosplasm
What does the SRP do?
Directs polypeptides/ribosomes to the ER
In which organelle is the signal sequence cleaved?
The ER
The new protein is synthesized into the lumen of which organelle?
The ER
From the Golgi Apparatus the newly synthesized protein is moved to a ____, ____, or the ____.
vacuole, peroxisome, or plasma membrane
Once fused with the plasma membrane, a protein can be released into the ____.
cell wall
Number of copies of complete genome
Ploidy
All plant species have at least 1 whole genome duplication event in their evolutionary history. T or F ?
True
Contains multiple copies of complete genome from a single species
Autoploidy
Contains multiple copies of complete genome from 2 or more species
Allopolylpoidy
Loss of DNA segment from chromosome
Direct repeats
Inversion of DNA segment in chromosome
Indirect repeats
aka “jumping genes” DNA segment with ability to insert into a new location within genome
Transposons
The study of changes in organisms caused by modification of gene expression rather than alteration of genetic code itself
Epigenetics
How many ways can genome duplication occur?
Three
Chromosomes fail to segregate properly leading to abnormally diploid gametes that fuse to form an allotetraploid plant
Meiosis effect
Recombination resulting in a gene being separated from its promoter (inactivation) or a gene being placed next to a new promoter (alters gene expression patter)
Intramolecular recombination
2 classes of transposons
Retrotransposons, and DNA transposons
The enzyme which synthesizes a DNA copy of a transposon from RNA
Reverse transcriptase
The enzyme that excises and inserts transposon from DNA into a new place in the genome
Transposase
What happens when a transposon is inserted into the coding region of a gene?
Gene inactivation, protein aborted or functions poorly
What happens when a transposon is inserted near the coding region of a gene?
Gene inactivation by disrupting promoter-gene relationship, altered gene expression due to promoters on transposon
Which type of chromatin makes up 10% of genomic DNA, is in a closed state, with methylated and tightly packed histones, and is transcriptionally inactive?
Heterochromatin
Which type of chromatin makes up 90% of genomic DNA?
Euchromatin
Which type of euchromatin is transcriptionally inactive?
Euchromatin in intermediate state
Which type of euchromatin is transciptionally active?
Euchromatin in open state
Histone modification associated with gene activation
Acetylation
Histone modification associated with gene inactivation
Methylation
Enzymes that remove acetate from H3 and H4 lysines
Histone deacetylase
Enzymes that transfer acetate from acetyl-CoA to H3 and H4 lysines
Histone acetyltransferases (HATs)
Enzyme that adds CH3 group to H3 lysines
Histone methyltransferases (HMTs)
Enzyme that removes CH3 groups from H3 lysines
Histone demethylases
Enzyme that removes methylated cytosine
Glycosylase
Enzyme that adds methyl group to cytosine bases at C5 position
DNA methyltransferase
What is it called when the phenotype of 1 parent is always expressed in progeny of successive generations regardless of genetic contribution of the other parent?
Parental imprinting
What does the ddm1 mutant refer to?
Mutant with a decrease in dna methylation
At which end is the initiation site located?
5’ end
RNA polymerase acts ___ to ___ on template strand.
3’, 5’
Nascent RNA chain elongates ___ to ___.
5’, 3’
The region of DNA that is not transcribed into RNA and controls transcription of transcribed region by regulating assembly of transcription initiation complex (TIC) at TATA box
Promoter regions
A primer is not required to initiate the synthesis of RNA. T or F ?
True
Where do nuclear RNAPs bind to initiate the synthesis of RNA?
To the promoter on the TATA box
What is the transcription initiation complex composed of ?
RNAPII and 7 TFs
What are the 5 TFs common to all 3 RNAPs ?
TFIIB, TFIIE, TFIIF, TFIIG, and TFIIH
Where is the TATA box located in comparison to the transcription start site (how many bps away, upstream or downstream) ?
About 25 bp upstream
What is the TFIID complex composed of?
1 TBP (TATA-box binding protein) and 8 TAFs (TATA-box additional protein factors)
What does TFIIA do?
Binds to TFIID complex and releases inhibitor from complex
What does TFIIF do?
Binds to RNAPII
What do TFIIE, TFIIH, and TFIIJ do?
Position RNAPII at start site
What does TFIIH do?
Phosphorylates RNAPII
Regulatory elements that control transcription of a gene
cis elements
Proteins (often dimers) that bind to cis elements
Trans-acting factors (aka transcription factors)
pgs 53
-56 for methods to study cis-trans interactions
Key structural features of helix-turn-helix TF motif
2 alpha helices separated by a turn, function as dimers
Key structural features of helix-loop-helix TF motif
Short helix connected to longer helix by loop, function as dimers
Key structural features of zinc finger TF motif
Various structures coordinated by Zn, function as monomer or dimers
Key structural features of leucine zipper TF motif
Alpha helix of 35 AA; every 7th AA= Leu, dimerizes along hydrophobic surface
Key structural features of basic zipper TF motif (most common among plants)
Variation of Leu Zipper with other hydrophobic AAs in place of Leu, dimerizes along hydrophobic surface
How many RNAPs do plastids contain ?
2; E.coli RNAP and Bacteriophage-like RNAP
What subunits is the E.coli type RNAP made of ?
4 subunits: 2 alpha, beta prime and beta;
1 regulatory unit: sigma
Where are the core subunits encoded?
in the plastid genome
Where is the regulatory subunit encoded?
in the nucleus genome
Where is bacteriophage-like RNAP encoded?
in the nucleus
Clusters of 2 or more genes transcribed by RNAP from single promoter
Polycistronic transcription units (PTUs)
Plastids adjust number of active promoters depending on stimuli. T or F?
True
What is the function of the 5’-cap (m7Gppp)?
Required for exit from the nucleus, increases efficiency of translation initiation (ribosome loading), and protects against degradation prior to translation
Addition of 5’-cap is done by….
Addition of guanosine to nascent mRNA, then methylation of guanosine at position N7
What is the function of polyadenylation ?
Protects against exo-RNase degradation prior to translation, role in initiation of translation
Addition of poly-A tail is done by…
a signal sequence in 3’-UTR (AAUAAA), downstream sequence cleaved by endonuclease, 20-250 adenosines added to 3–end by poly-A polymerase),
What is the function of RNA splicing ?
Removal of introns from pre-mRNAs and pre-tRNAs , the release of rRNAs from pre-rRNAs
Where are introns located ?
In nuclear genes, chloroplast genes, and mitochondria genes
How are introns classified?
By structural features and splicing mechanism
What are the splice sites for pre-mRNA introns?
5’ splice site (donor site): 5’-GU
3’ splice site (acceptor site): 3’-AG
Where does the branch site structural element bind?
To the 5’-end of intron during excision (about 40 nt from 3’ splice site)
spliceosome assembly
slide 82
initiation of splicing
slide 83
completion of splicing
slide 84
How do self-splicing introns that form ribozymes work?
Guanosine cofactor attacks 5’ splice site, cleavage of 3’ splice site, ligation of exons
initiation of self-splicing
slide 87-88
What functional enzyme do mobile introns contain ?
DNA endonuclease
What function do DNA nucleases serve in mobile introns?
Recognize intron-less allele, generate double-strand break near insertion or “homing” site, initiate replicative integration of intron
Which group of self-splicing introns have features in common with nuclear pre-mRNA splicing?
Group II
What is the difference between Group II self-splicing introns and pre-mRNA splicing?
Group II intron does not form spliceosome
Where are Group III self-splicng introns found?
in Euglenoid plastids
Are most mitochondrial mRNAs transcribed as monocistronic units or polycistronic units?
Monicistronic
5’-end of nuclear mRNA?
5’-cap (m7Gppp)
5’-end of chloroplast mRNA?
5’-monophosphate
5’-end of mitochondria mRNA?
5’-triphosphate
3’-end of nuclear mRNA?
Poly-A tail (-AAAA)
3’-end of chloroplast mRNA?
Stem-loop structure
3’-end of mitochondria mRNA?
Stem-loop structure
What are the precursor sections for nuclear rRNA processing ?
17S, 5.8S, and 25S
Which precursor sections H-bond after spacer sequence is removed?
5.8S and 25S
Which section of nuclear rRNA is unusual compared to other rRNAs and why?
5S, its transcription is independent of other rRNA genes, requires no processing
What is present in most tRNA genes?
introns
What are tRNAs encoded by ?
gene clusters
How many tRNAs are present in plastids?
30
How many tRNAs are present in mitochondria?
16
Which organelles have/don’t have sufficient tRNA for protein synthesis?
Plastids do, Mitochondria don’t
What is the minimum requirement for protein synthesis with wobble codons?
23 tRNAs
What are the 2 RNA editing mechanisms?
Insertion/deletion and Conversion (modifications, substitution)
Purpose for amino acid conversions?
Often to restore highly conserved protein
Purpose for ORF conversions?
Can shorten open reading frames, may form new start or stop codons
Requirements for mRNA translocation ?
5’-cap
poly-A tail
introns removed
Requirements for rRNA translocation ?
PTU cleavage
introns removed
Requirements for tRNA translocation ?
PTU cleavage
introns removed
What are the requirements for gene silencing?
dsRNA, Dicer, RISC (RNA induced silencing complex)
What does the dicer do?
cleaves dsRNA into short or small interfering RNAs (siRNAs)
Biological roles for post-transcriptional gene silencing
Protection, development , Experimental utility
Multiple ribosomes simultaneously translating 1 mRNA
Polyribosomes
Requirements for protein synthesis
mRNA, ribosomes, protein cofactors, enzymes, inorganic ions, GTP, tRNAs, and amino acids
A site:
aminoacyl-tRNA
P site:
peptidyl-tRNA
E site:
uncharged tRNA exiting ribosome
What enzyme catalyzes the charging of tRNAs ?
tRNA synthetase
Components required for initiation?
mRNA, charged tRNA(fmet), small ribosomal subunit, large ribosomal subunit, initiation factors (proteins), GTP
A ribosomal binding site in mRNA, generally located around 8 bases upstream of start codon AUG. Initiates protein synthesis by aligning the ribosome with the start codon.
Shine-Dalgarno sequence
What does IF3 do?
Binds 30S ribosomal subunit
What does IF2 do?
Binds GTP, then binds to 30S ribosomal subunit at the P-site
What does IF1 do?
Binds charged tRNA and deliver tRNA to IF2 bound to 30S subunit
What is the enzyme that catalyzes polypeptide elongation?
Peptidyltransferase
How is the peptide bond formed ?
Dehydration, condensation reaction
What activity do intervening protein sequences have?
endonuclease activity
