Lecture 4-6: Transcription+Translation Flashcards
RNA is synthesized in the
5’-3’ direction
New nucleotides for RNA are added onto the —- of the growing strand
3’ OH
RNA polymerase unwinds about — of DNA at a time
17bp
DNA template strand is being read —–, RNA is made —–
- 3’-5’
- 5’-3’
Exon
Included in the mature RNA, will be transcribed into protein
Intron
Noncoding, not included in the mature RNA (spliced out)
Transcription starts (2)
- end of promotor
- the +1 site
Transcription initiation begins at
promotor sequences
Introns begins with —- and end with —
- GU
- AG
Upstream is
towards the 5’ end
Downstream is towards the
3’ end
The template strand is also called the (2)
- antisense strand
- noncoding strand
Non template strand is also called the
- sense strand
- coding strand
unless told otherwise, given gene= — strand
sense strand
mRNA looks exactly like the — strand but has — instead of T
- Sense strand
- U
Amino group is the — end
N-terminal
The carboxyl group is the —- end
c-terminal
Components of an amino acid
- amino group
- R group
- Carboxyl group
mRNA codon helps buffer
transition SNPS
tRNA molecule has an anticodon loop oriented
3’-5’
Amino acid is attached to the —– end of the tRNA molecule
3’
What attaches the amino acid to tRNA?
aminoacyl-tRNA synthetase
Ribosome move along mRNA in the —— direction
5’-3’
What catalyzes the formation of the peptide bond in amino acid chain?
Peptidyl-transferase center
Shine-Dalgarno sequence
in prokaryote mRNA, is recognized by rRNA in the ribosome small subunit so it bind.
Kozak Sequence (2)
relative to start codon?
- in Eukaryotes and helps position the ribosome
- upstream of start codon
Silent mutation+ its impact on potein (2)
- encodes the sae amino acid
- Fairly small impact on protein function
Missense mutation conservative+ex
Encodes a chemically similar amino acid
- makes a different amino acid
- ex: both lys and arg are + charged amino acid-> fairly minor impact on overall protein function
Missense mutation nonconservative+ex
- encodes a chemically different amino acid
- ex: thr is not charged, lys is charged
i
Nonsense mutation
encodes a stop codon
Insertions and deletions result in
frameshift mutations
When might a silent mutation not be completely silent? (2)
- the mRNA sequence has changed: If the silent mutation is near the end of an exon, it can interfere with splicing
- alterations in mRNA structure or stability (ex:G instead of C cause mRNA to fold uo on itself and be less acessible to translation machinary)
Wetern block
- used to detect a particular protein from a mixture of protein
Steps for a western blot analysis
- extract protein from cells/tissue
- Boil the sample and add detergent to allow seperation of protein based only on number of amino acids
- perform gel electrophoresis on a polyacrylamide gel
- Use probes/antibody to bind to the protein or primary antibody
Silent mutation vs SNP
If this occured in an intron or non-coding region, we wouldn’t use silent mutation and would instead just call it a SNP
Difference between ribose and deoxyribose
Ribose has an OH group on 2’ carbon
RNA polymerase
A complex enzyme containing multiple subunits which promotes the formation of phosphodiester linkages between incomming ribonucletotides (ribonucleoside triphosphates)
Characteristics of RNA synthesis (3)
Require+ uses+ does not
- Reaction requires all four ribonucleotides : ATP, GTP, CTP, UTP
- RNA synthesis uses DNA as a template
- RNA polymerase does not require a primer to begin synthesis
How is new nucleotide attached?
- 3’OH of growing strand: nucleophillic attach on the alpha phosphate of the incoming nucleotide
Genome
The entire set of DNA found in cell
Gene
Segments of DNA that are transcribed into RNA and then into protein
mRNA
tRNA
rRNA
- mrna codes for the protein sequence
- tRNA are compoents of the machinery that translate mRNA into protein
Transcription in Prokaryotes: 3 stages
- Inititation: Transcription is initiated at promoter sequences in the DNA template
- Elongation: RNA strand complementary to template DNA is synthesized by RNA polymerase
- RNA strand synthesis stops and RNA polymerase is released
Promotor sequences
what do they do?
- directs the RNA polymerase to the proper site for transcription initation
Promotors are located — of the coding region on the —- strand
- upstream
- sense
RNA polymerase subunits (6)
what is the entire thing called?
- entire enzyme complex is called the holoenzyme
- Alpha: required for assembly of core enzyme; interacts with regulatory factors
- Beta: Takes part in all stages of catalysis
- Beta prime: Binds to DNA; takes part in catalysis
- Omega: required to restore denatured polymerase to its native form
- Sigma 70: Takes part in promotor recognition
Talk about the sigma subunit (5)
- helps the polymerase to find the correct start site for transcription
- Decrease affinity of RNA polymerase for general binding to DNA
- Enables RNA polymerase to recognize promoter sites
- sigma subunit is released after transcription is initated
- Other sigma subunits recognize other promoter sequences (for genes that are expressed in certain environmental conditions)
Distinct feature on the 5’ end of the newly synthesized prokaryotic RNA:
The 5′ end of newly synthesized RNAs bears a triphosphate derived from the first transcribed nucleotide
In transcription, DNA strand is being —- newly synthesized RNA is being made ——
- 3’-5’
- 5’-3’
Transcription bubble contains (3):
- The RNA polymerase
- The unwounds DNA
- Newly formed RNA
Rho independent Termination (3)
only in+used
- only in prokaryotes
- Terminator sequence in mRNA base pairs, coded from DNA strand pairs with itself to form a G-C hairpin as the mRNA base pairs are inverted (CCCCG-…….-GGGGC) followed by a string of U’s. This hairpin causes RNA polymerase to stall and dissociate
- No ATP is used
Rho Dependant Termination (3)
only in+steps (4)
- only in prokaryotes
- Rho binds to RNA on the recognition sequence
- Move along the RNA via ATP
- RNA polymerase pauses at terminator and Rho catch up
- Terminator sequence in mRNA is recognized and bound by the Rho helicase which unwinds the RNA from the template DNA and RNA polymerase by breaking H bonds.
