Exam 3 Flashcards
Acetylation
-Covalent modification
Acetylation of lysine weakens DNA-histone interaction
Easier for transcription factors to access cytosine
Transcription factor for RNA polymerase
Uses histone acetyl transferases (HATs)
Euchromatin
loosely packed
Transcriptionally active
Gene sequence available to RNA polymerases
DNA Methylation
DNA methylation restricts differentiation potential of a cell.
Increase DNA methylation = decrease cell potential
Also, the presence of “CG” patterns increases the chance of methylation
DNA methylation changes throughout development
Base Pairings
C-G and T-A unless it is transcription then T is replaced with U
Bidirectional
Bidirectional with multiple origins
Starts at several points (origins)
Replication “bubble” is formed
Read from 5’-3’
Translation uses mRNA which is read 5’-3’
Parental strand reads from 3’-5’
Synthesized 5’-3’
RNA primers are used in which process?
DNA replication
Ligase
DNA ligase joins nucleotides in fragments by forming phosphodiester bonds
REQUIRES ATP
Connect Okazaki fragments
Replication Fork
Homologous recombination = uses info from unaffected chromosome to fix; usually if error at replication fork
Replication fork
Unwound by helicase which needs ATP.
What functions ahead of the replication fork?
Answer: Topoisomerases (Chap. 7 slide 16)
During DNA replication, nucleotides are added to the ________ end
3’
“__________ transcription factors regulate the number of RNA polymerases transcribing simultaneously”
Specific
Transcription complex assemble on the DNA strand
TATA
Initiating Transcription
TFIIH phosphorylates RNA polymerase II causing a conformational change which initiates transcription
… is added to mRNA to prevent…
5’ cap
The 5’ end of RNA is capped with a methyl guanosine (AKA 5’-Cap)
These prevent degradation by exonucleases
___________ is a complex of proteins found in the nucleus used in mRNA production.
Spliceosome
3rd position in Wobble Hypothesis
The 3rd base on the codon binds with the 1st base of the anti-codon and determines the amino acid
Look at Genetic Code Chart (nonsense, missense, silent mutation)
TATA
During transcription the promotor region is often a TATA sequence called a TATA box
TATA box directs RNA polymerase II
TATA binding protein binds to TATA box
Is read in the ______ direction
3’ to the 5’ end
mRNA is read in the 5’-3’ direction during translation
Results in a codon that codes for ___________ instead of _________
A stop codon An amino acid
An example of when this happens is sickle cell anemia (nonsense mutation)
Anticodon
Recognizes a codon for a specific amino acid
Flipped 3’-5’ to pair, but always written 5’-3’
First base in anticodon can pair with multiple options
“Which amino acid is most likely to be found at the N-Terminal of all newly synthesized proteins?”
Methionine
Movement of ribosomes
5’-3’ on mRNA
Directed by signal sequence on protein to the ER or to be free (lacking signal)
Composed of rRNA
“Which of the following would cause the termination of translation”
UGA at the A site
Termination of translation would result from the stop codon UAG, UGA, or UAA at the A site.
Post-translational
Changes controlled by miRNA
Generally active
Trimming- Slicing of a protein using endoprotease to make it active
Covalent modification-
phosphorylation, glycosylation, hydroxylation, carboxylation or acetylation
Can begin while still being synthesized by ribosome
Medial Golgi complex adds tags for lysosome
Bud off vesicles
Vesicles with secretory proteins bud off from golgi complex (constitutive secretion)
Vesicles with regulatory proteins bud off from golgi complex (regulated secretion)
Lysosomal trafficking: Protein buds off from golgi complex
From the same gene
Alternative splicing = taking out different introns
Make multiple proteins from a single gene
The shorter the half-life.
Proteosomal protein degradation
Degrades proteins with shorter half life
Enzymes of the proteosome use which part of a protein to identify its half-life?
N-terminal amino acid
Proline, Glucine, Serine, Threonine degrade fastest
Proteins Targeted
Proteins targeted to the ER have a special sequence located where? N-Terminal
Possible Extra Credit: (Chap. 11 Slide 22) Zellweger Syndrome
Where modification occurs
Called cotranslational modification (occurs while translation is still happening) Trimming Covalent (just need to know what they add) Phosphorylation (phosphate) Glycosylation (glucose/sugar) Produces glycoproteins = specificity O-linked N-linked- occurs in the Golgi complex / RER Hydroxylation (hydroxyl group, -OH) Proline and lysine in collagen Vit C Carboxylation (Carboxyl group, -COOH) Vit K needed Clotting, bone formation Acetylation (acetyl group, -OCH3) Lysine on histones
before it will be active
A protein must undergo post translational modification before it will be active
Trimming
Mitochondria
Which protein is required for transport of translated protein into the mitochondria? (translocase)
y (gamma) DNA polymerase is located in the mitochondria and has both 5’-3’ polymerase function and 3-5 exonuclease function
Free ribosomes synthesize proteins for mitochondria
What is the minimum number of ubiquitins necessary to be recognized by the regulatory protein of the proteasome?
4
Determine half-life by the N-terminal of the Amino Acid
Which of the following is not typically degraded by lysosomes?
Improperly folded proteins
INTO THE NUCLEUS
proteins made in the nucleus usually go to the cytosol but can go in the nucleus- Nuclear proteins, nucleus requires enzymes for DNA replicatoin and transcription must contain nuclear localisation signal transcription which allows protein to pass through nuclear pore with help from importin which is released after the protein is inside the nuclear envelope.
rRNA
Each ribosome contains 4 rRNA
3 located in larger subunit
1 located in smaller subunit
Too many repeats
Trinucleotide repeat expansion: too many repeats are added, so final protein has extra copies of AA
“The default pathway for proteins that are made by free/cytosolic ribosomes is to send them to the _______.”
The default pathway of protein trafficking is from the ribosome to the cytosol.
DNA repeats, present at the ends of chromosomes, that act to protect it from degradation are called:
Telomeres
Enzymes of the proteosome use which part of a protein to identify its half-life?
N-Terminal Amino Acid
In regulated secretion, proteins made at the RER are
Stored in granules in the cytosol for later release
