Molecular Flashcards
How many times does DNA loop around histone octamer to form nucleosome?
Twice
Histones are rich in what two amino acids?
Lysine and arginine
Which histone is responsible for stabilizing the chromatin fiber
H1
DNA and histone synthesis occur in what cell cycle phase?
S-phase
Barr bodies have what type of chromatin structure?
Heterochromatin
Which chromatin is transcriptionally active?
Euchromatin
What inactivates transcription and increases condensation of chromatin?
Increased methylation and decreased acetylation
What is methylated on DNA to suppress transcription
CpG islands
What is the purpose of cytosine and adenine methylation during DNA replication
Allows DNA repair enzymes in prokaryotes to distinguish old from new strand in DNA replication
What relaxes DNA coiling allowing transcription
Histone acetylation
What usually reversibly represses DNA transcription
Histone methylation
Phosphodiester bonds in nucleotides are linked in what direction
3’ to 5’ direction
What end of the nucleotide has the triphosphate group?
5’ end
What is the target of the nucleotide 3’ hydroxyl group?
Nucleotide triphosphate bond
Purines are composed of how many rings
One
What are the purines
Adenine and Guanine
Which nucleotide has a methyl group?
Thymine
Deamination of what nucleotide makes uracil
Cytosine
Deamination of what nucleotide makes guanine
Adenine
Methylation of what makes thymine?
Uracil
What increases the melting temperature of DNA
Increased G-C bonding
How many bonds are formed between C-G
3 bonds
Amino acids necessary for purine synthesis
Glycine, Aspartate, Glutamine (GAG)
Ribose-5-phosphate for purine synthesis is derived from what pathway
PPP
The first step of the pyrimidine/purine pathway involves what?
Ribose-5-P converted to PRPP by PRPP synthetase
PRPP can go into which two pathways?
Pyrimidine or purine pathway
In the purine pathway, what inhibits PRPP conversion to IMP?
6-mercaptopurine (6-MP) and its prodrug azathioprine
IMP in the purine pathway gets converted to what?
AMP or GMP
What enzyme converts AMP and GMP into uric acid
Xanthine oxidase
What drug inhibits dihydroorotate dehydrogenase
Leflunomide
What drug inhibits ribonucleotide synthetase
Hydroxyurea
What drug inhibits thymidylate synthase
5-fluorouracil
5-fluorouracil forms what intermediate to inhibit thymidylate synthase
5-F-dUMP
Inhibition of thymidylate synthase will cause a decrease in what product?
dTMP
Carbamoyl phosphate is made from glutamine and CO2 using what enzyme
Carbamoyl phosphate synthetase II
Orotic acid synthesis is inhibited by what drug
Leflunomide
What is impaired in orotic aciduria
Conversion of orotic acid to UMP
What inhibits the conversion of IMP to GMP
Mycophenolate or ribavirin
What enzyme is inhibited by mycophenolate
IMP dehydrogenase
Mycophenolate will cause a decrease in what product
GMP
Inhibition of dihydrofolate reductase by methotrexate prevents what
Conversion of DHF to THF
What drugs inhibit dihydrofolate reductase
Methotrexate, trimethoprim, and pyrimethamine
What is the function of ribonucleotide reductase
Convert ribose sugars into deoxyribose sugars for DNA synthesis
In rapidly diving cancer cells what drug is used to prevent the conversion of thymine, preventing DNA synthesis
5-Fluorouracil (5-FU)
In a bacterial infection, what drug is used to prevent the conversion of DHF to THF
Trimethoprim
What enzyme is required for the degradation of adenosine and deoxyadenosine?
Adenosine deaminase
What is a complication of adenosine deaminase deficiency
Increased dATP leading to toxicity in lymphocytes
What disease is associated with adenosine deaminase deficiency
SCID
What is the genetic inheritance of SCID
Autosomal recessive
Lesch-Nyhan syndrome is a defect in what pathway
Purine salvage pathway
What is the defect in Lesch-Nyhan syndrome
Absent HGPRT
What is the function of HGPRT in the purine salvage pathway
Convert hypoxanthine to IMP and guanine to GMP
What is the result of Lesch-Nyhan syndrome
Excess uric acid production and de novo purine synthesis
Intellectual disability, gout, dystonia, self-mutilation with aggression and hyperuricemia describe what syndrome
Lesch-Nyhan syndrome
What is the first-line treatment for Lesch-Nyhan syndrome
Allopurinol
What is the second-line treatment for Lesch-Nyhan syndrome
Febuxostat
What medication will inhibit uric acid excretion
Aspirin
What medication will increase uric acid excretion
Probenecid
What medication will prevent the synthesis of uric acid
Allopurinol
What medication will inhibit xanthine oxidase
Allopurinol or febuxostat
What nucleotides are used in the Purine salvage pathway
Guanine and Adenine
DNA synthesis occurs in what direction
5’ to 3’ direction
Unwinds DNA template at replication fork
Helicase
What prevents strands from reannealing
Single-stranded binding proteins
What create single or double stranded breaks in DNA helix to remove supercoils
DNA topoisomerases
What makes an RNA primer on which DNA polymerase III can initiate replication
Primase
DNA pol III proofreads in what direction
3’ to 5’ direction
What is the function of primase
To make an RNA primer for DNA pol III
DNA pol III synthesizes DNA in what direction
5’ to 3’ direction
DNA pol I and pol III are used by what type of organisms
Prokaryotes only
Catalyzes the formation of Phosphodiester bonds within a strand of dsDNA
DNA ligase
Joins Okazaki fragments
DNA ligase
RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of chromosomal material with every duplication
Telomerase
Eukaryotes have how many origins of replication
Multiple
Elongates lagging strand until it reaches primer of preceeding fragment
DNA pol III
Which type of Nucleotide substitution causes the most severe damage
Frameshift mutation
What is a transversion mutation
Purine switched for pyrimidine or vice-versa
Cause of most silent mutations
tRNA wobble in 3rd position of codon
Nucleotide substitution that codes for the same amino acid
Silent mutation
Sickle cell disease is what type of nucleotide substitution
Missense mutation
What is a conservative missense mutation
Nucleotide substitution that codes for similar amino acid
Nucleotide substitution that codes for different amino acid
Missense mutation
What amino acids are substituted in sickle cell disease
Glutamine to Valine at position 6
Nucleotide substitution resulting in a stop codon
Nonsense mutation
Type of mutation that usually results in nonfunctional protein
Nonsense mutation
UAG, UAA, UGA are what type of codons
Stop codons
Nucleotide substitution resulting in misreading of all nucleotides downstream
Frameshift mutation
Tay-Sachs disease and Duchenne muscular dystrophy are examples of what type of nucleotide substitution
Frameshift mutation
Direction of protein synthesis
N-terminus to C-terminus
Responsible for posttranscriptional regulation of gene expression by targeting 3’ untranslated region of specific mRNAs for degradation or translational repression
microRNAs
Function of alternate splicing
Combine different axons to make unique proteins
Intervening noncoding segments of transcript
Introns
Part of transcript that contains actual genetic information coding for proteins
Exon
Antibodies to spliceosomal snRNPs (anti-Smith antibodies) are highly specific for what disease
SLE
Primary transcript combines with snRNPs and other proteins to form what
Spliceosome
AAUAAA does what to RNA
Adds poly-A tail to RNA molecule
Site of RNA 5’ capping, addition of poly-A 3’ tail, and splicing of RNA molecule
Nucleus
Where does translation of mRNA occur
Cytosol
RNA pol that makes tRNA
RNA pol III
Types of polymerase in prokaryotes
1 type for all RNA molecules
Types of polymerase in eukaryotes
RNA pol I-III
RNA pol that makes mRNA
RNA pol II
Smallest RNA molecule
tRNA
RNA pol that makes rRNA
RNA pol I
Largest RNA molecule
mRNA
alpha-amanitin found in death cap mushroom inhibits what RNA pol
RNA polymerase II resulting in decreased mRNA
Site of repressor binding
Silencer
Where do activator proteins bind to
Enhancer region for alteration of transcription
Site of DNA that alters gene transcription by binding transcription factors
Enhancer
What is contained in the Promoter region
CAAT and TATA boxes
Site where RNA pol II and other transcription factors bind to DNA upstream from gene locus
Promoter
What does a promoter mutation result in?
Decrease in level of gene transcription
Codes for methionine which may be removed before translation is complete in eukaryotes
AUG
mRNA start codon
AUG
DNA repair mechanism defective in ataxia telangiectasia
Non-homologous end joining
What DNA repair mechanism is defective in Lynch syndrome
Mismatch repair
Nucleotide excision repair occurs in what cell cycle phase
G1 phase
What is responsible for repair of pyrimidine dimers formed from excessive UV light
Nucleotide excision repair
What conditions cause basal expression of Lac gene
High glucose, lactose available
What conditions cause Lac gene to not be expressed
High glucose, lactose unavailable and low glucose, lactose unavailable
What conditions cause Lac gene to be expressed
Low glucose, lactose available
Splice site mutations may result in what type of diseases
Some cancers and beta-thalassemias, dementia and epilepsy
Protein with impaired or altered function is typically a result of what type of DNA mutation
Splice site mutation
Type of mutation resulting in retained intron in mRNA
Splice site mutation
Promoter region is located upstream from what?
Gene locus
What is responsible for scrutinizing amino acid before and after it binds to tRNA
Aminoacyl-tRNA synthetase
Aminoacyl-tRNA binds to what on tRNA molecule
A site
What catalyzes peptide bond formation in a growing polypeptide
rRNA
What part of the ribosome accommodates growing peptide
P site
Ribosome advances 3 nucleotides toward what end of the mRNA
3’ end
What holds empty tRNA as it exits ribosome
E site
What transfers growing peptide to amino acid in A site
Ribozyme (rRNA)
Intracellular protein involved in facilitating and/or maintaining protein folding
Chaperon proteins
HSP60 is what type of protein
Chaperone protein
Process that removes N-terminus or C-terminus from zymogen to generate mature protein
Trimming
Covalent alterations are what type of modifications
Posttranslational modifications
What part of tRNA accepts the amino acid
CCA end located on 3’ end
Section of tRNA located opposite 3’ aminoacyl end
Anticodon
Binds tRNA molecule to the ribosome
T arm of tRNA molecule
Contains dihydrouridine residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase
D arm of tRNA molecule
Activation of tRNA molecule converts ATP into what
AMP + Pi
What is required for the initiation phase of protein synthesis
Initiation factors and GTP
What happens during the initiation phase of protein synthesis
40s ribosomal subunit is attached with the initiator tRNA and released when to mRNA and the 60s subunit assemble with the complex
Moving peptidyl tRNA from A site to P site
Translocation
Macrolides mechanism of action
Target prokaryotic 50s ribosomal subunit - prevent Elongation
Aminoglycosides mechanism of action
Target prokaryotic 30s ribosomal subunit - prevent Initiation
Chloramphenicol mechanism of action
Block prokaryotic 50s ribosomal subunit
Tetracyclines mechanism of action
Block prokaryotic 30s ribosomal subunit
Clindamycin mechanism of action
Block prokaryotic 50s ribosomal subunit
DNA has what type of charge
Negative
Histones have what type of charge
Positive
