SFN – Chemistry Flashcard

DEFINE TRANSITION MUTATION
A MUTATION IN PURINE–> PURINE BASE OR A PYRAMIDINE TO PYRAMIDE
DEFINE TRANSVERSION MUTATION
A MUTATION OF A PURINE TO A PYRAMIDINE OR VICE VERSA
DEFINE NONSENSE MUTATION
A MUTATION THAT CHANGES THE SEQUENCE TO A STOP CODON
DFINE MISSENSE MUTATION
A MUTATION THAT CHANGES THE AMINO ACID SEQUENCE
DEFINE SILENT MUTATION
A MUTATION THAT DOES NOT CHANGE THE AMINO ACID SEQUENCE
NAME 3 STRUCTURAL FEATURES UNIQUE TO TRNA.
ANTICODON, 3′ CCA ACCEPTOR FOR AMINOACYLATION, NUCLEOSIDES ARE HIGHLY REGULATED, MANY NON-WATSON CRICK BAS PAIRS, 5′ PHOSPHATE
DEFINE THE TERM REPRESSOR
A PROTIEN THAT BINDS TO THE OPERATOR REGION OF DNA TO INHIBIT TRANSCRIPTION
DEFINE THE TERM OPERATOR
DNA SEQUENCE TO WHICH THE REPRESSOR BINDS
DEFINE THE TERM PROMOTOR
DNA SEQUENCE TO WHICH RNA POLYMERASE BINDS
DESCRIBE THE DIFFERENCES IN DNA TRANSLATION IN PROKS AND EUKS
PROKS:
-SHINE DALGARNO SEQUENCE UP FROM THE START CODON
-SITE RECOGNIZED BY 3′ END OF RRNA

EUKS
-ELF-4 BINDS TO 5’CAP OF MRNA
-FIRST AUG CODON WILL BE START

WHICH FACTOR IS REQUIRED FOR THE BINDING OF AMINOACYL TRNA DURING ELONGATION IN EUKS?
EF-1ALPHA
NAME 2 TRUE STATEMENTS ABOUT RELEASE FACTORS.
THEY RECOGNIZE STOP CODONS
AND
THEY ARE PROTIENS
GIVE THE ANTICODON SEQUENCE OF THE TRNA FOR:
GCU (5′–> 3′)
CGI (3′–> 5′)
IN WHAT TYPE OF RNA IS THERE DIHYDROURIDIN AND PSUEDOURIDIN?
TTRNA
GIVE 4 EXAMPLES OF POST-TRANSLATIONAL PROTIEN MODIFICATION
-ACYLATION
-GLYCOSALATION
-PHOSPHORLATION
-PROTIEN FOLDING
-PROTEOLYTIC PROCESSING
WHY CANT ATTENUATION OCCUR IN EUKS?
– ATTENUATION IS THE COUPLING OF TRANSCRIPTION AND TRANSLATION
-EUKS CANNOT COUPLE BECAUSE THEY HAVE COMPARTMENTS FOR THESE PROCESSES
WHY DO WE MAKE PRO-INUSLIN INSTEAD OF DIRECTLY MAKE INSULIN?
– ENSURES A 1:1 RATIO OF THE BETA AND ALPHA CHAINS
– THIS HELPS FORM THE DISULFIDE BONDS BETWEEN THE ALPHA AND BETA CHAINS
WHAT POST-TRANSLATIONAL MODIFICATION OF LYSINE RESIDUES IN HISTONES WILL ALTER GENE REGULATION AND WHY?
-ACETYLATION
-REDUCES THE ELECTROSTATIC BONDS AND MAKES THE DNA MORE ACCESSIBLE TO TRANSCRIPTION FACTORS AND RNA POLYMERASE
WHAT TYPE OF PATHWAY IS CONCENTRATION DEPENDANT AND DOES NOT REQUIRE ENERGY TO TRANSPORT INTO CELL?
PASSIVE DIFFUSION
WHERE IS THE SITE OF ACTION FOR OLIGONUCLEOTIDE ANTISENSE?
NUCLEUS AND CYTOCOL
CHOLESTEROL _____ TRANSPORT INTO CELLS IN CONJUGATION TO SIRNA.
INCREASES
NAME THE ORDER OF ENZYMES GOING FROM PRI-MIRNA TO PRE-MIRNA TO PRERNA IN THE CELL?
DROSHKA, EXPORTIN, DICER
NAME A FALSE STATEMENT ABOUT SIRNA.
IT IS HYDROPHOBIC
WHAT ARE HTE 2 MECHANISMS THAT OLIGONUCLEOTIDES CAN DISRUPT TRANSLATION.
– DESTRUCTION OF MRNA BY RIBONUCLEASES
– RIBOSOME MOVEMENT BLOCKED
WHY IS TRANSLOCATION OF 2 GENES THE BEST TARGET FOR ANTISENSE STRATEGIES
IT IS A UNIQUE OR QUALATATIVE TARGET VS A QUANTATIVE TARGET
WHAT WAS THE FIRST FDA APPROVED FDA DRUG AND WHAT WAS IT FOR?
VITRAVENE FOR CMV RETINITIS
DESCRIBE A DIFFERENCE BETWEEN SIRNA AND MIRNA.
– MIRNA IS NOT USUALLY A COMPLETE TARGET MATCH
– MIRNA USUALLY TARGETS MULTIPLE GENES AS ONE
– MIRNA REQUIRES MORE PROCESSING THAN SIRNA
WHY DO CPG MOTIFS STIMULATE THE IMMUNE SYSTEM?
THEY LOOK SIMILAR TO BACTERIAL DNA
WHAT IS THE MOST LIKELY PHARMACOLOGICAL TARGET OF APATMER? SIRNA? ANTIGENE? ANTISENSE?
PROTIEN
MRNA
DNA
MRNA
ON A PHOSPHATE GROUPS THERE ARE 2 HYDROXYL GROUPS. WHAT ARE THEIR PKA?
2 AND 7
IF YOU HAVE A “NH2+ UP” WHAT WILL THE PKA BE?
4
IF YOU HAVE 2 EWG AND A NH DOWN WHAT WILL BE THE PKA?
8-10
IF YOU HAVE A CARBOXYLIC ACID (COOH)WHAT WILL BE THE PKA?
3-5
WHAT HYPOTHESIS SAYS THAT ONE TRNA CAN RECOGNIZE SEVERAL DEGENERATE CODONS?
WOBBLE
WHAT MUTATION INTRODUCES A STOP CODON?
NONSENSE
WHAT ARE 2 FUNCTIONS OF THE AUG CODON?
START CODON FOR TRANSLATION AND CODES FOR MET
WHAT CONTROL ELEMENT UPSTREAM OF STRUCTURAL GENES FO YOU EXPECT TO BE PALINDROMIC?
OPERATOR
WHAT IS THE MAJOR DIFFERENCE BETWEEN THE OPERON OF THE LAC AND TRYPTOPHAN?
– IF NO IDUCER IS PRESENT THE LAC REPRESSOR BINDS TO THE OPERON TO REPRESS GENE EXPRESSION
– TRP REPRESSOR ONLY BIND TO THE OPERATOR TO REPRESS GENE EXPRESSION IF A CO-REPRESSOR IS PRESENT
WHAT IS THE FUNCTION OF ATTENUATION?
A MECHANISM TO CONTROL EXPRESSION IN PROKS
WHICH MODIFICATION TO THE HISTONE AND DNA COMMONLY AFFECTS GENE EXPRESSION IN EUKS?
-ACETLYATION
-METHYLATION
WHAT IS THE MAJOR SOURCE OF ENERGY FOR THE RIBOSOMAL PROTIEN SYNTHESIS?
– GTP
IDENTIFY 2 SEPERATE FAMILIES OF MIDIFICAITONS TO INCREASE OLIGONUCLEOTIDE STABILITY AND GIVE AN EXAMPLE.
SUGAR: 2′-F
BACKBONE: MP
LIST 2 OLIGONUCLEOTIDE MODIFICATIONS AND THE SPECIFIC UNDESIRED EFFECT FOR THAT MODIFICATION.
-MP: LOSES WATER SOLUBILITY
-2’F: LOSS OF RNASEH
DICER DEGRADES DOUBLE STRANDED ____ INTO ____ WHICH RESULTS IN THE DEGRADATION OF MRNA.
RNA; SIRNA
RIBOZYMES HAVE ____ ACTIVITY.
CATALYTIC
WHAT IS THE CENTRAL DOGMA?
DNA MAKES RNA MAKES PROTIENS
WHICH DNA MODIFICATION MAY RESULT IN INACTIVATION OF GENE EXPRESSION?
METHYLATION
WHAT IS THE MATCHING FOR 5′–> 3′ ACGT?
5′–> 3′ ACGT
WHAT ARE THE 2 MAJOR GROUPS OF NUCLEASES THAT CAN DEGRADE OLIGONUCLEOTIDES?
ENDONUCLEASES AND EXONUCLEASES
WHAT TYPE OF NUCLEASE IS THE MAJOR REASON PHOSPHODIESTER OLIGONUCLEOTIDES DEGRADE IN THE PLASMA
3′- EXONUCLEASE
NAME THE TARGET AND THE HYDROGEN BONDING OF THE ANTIGENE OLIGONUCLEOTIDE.
DNA; HOOKSTEIN
NAME THE TARGET AND HYDROGEN BONDING OF THE ANTISENSE OLIGONUCLEOTIDE.
RNA; WATSON CRICK BASE PAIRING
NAME THE TARGET AND THE HYDROGEN BONDING OF THE APTAMER.
PROTIEN; HYDROGEN BONDING
WHAT MECHANISM IS MOST LIKELY INVOLVED IN THE INTRACELLULAR TRANSPORT OF OLIGONUCLEOTIDES.
ENDOCYTOSIS
LIST A MODIFICATION TO INCREASE THE INTRACELLUAR TRANSPORT OF OLIGONUCLEOTIDES.
CHOLESTEROL ADDITION OR USE OF LYSOSOMES
BESIDES CMV ID ONE BIOLOGICAL TARGET AND GENE THAT IS TARGETED BY OLIGONUCLEOTIDES.
PSORIASIS; ICAM-1

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