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121 Cards in this Set
- Front
- Back
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What is the structure of Chromatin?
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Negatively charged DNA looped TWICE around nucleosome cores - forms NUCLEOSOME BEADs
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What does a Nucleosome core consist of?
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2 each of +charged:
H2A H2B H3 H4 |
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What ties nucleosomes together in a string?
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H1
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So the only histone that is NOT in a nucleosome core is:
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H1
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What happens to Chromatin during Mitosis?
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It CONDENSES into mitotic CHROMOSOMES
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What is the condensed chromatin during periods of transcription INACTIVITY called?
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Heterochromatin
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What is EUchromatin?
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Less condensed and Transcriptionally ACTIVE
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What are the PURINES?
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Pur As Gold
-Adenine -Guanine |
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What are the PYRIMIDINES?
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CUT the PY
-Cytosine -Uracil -Thymine |
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How are the purines different from pyrimidines?
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Purines - 2 rings
Pyrimidines - 1 ring |
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What makes Uracil?
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Deamination of cytosine
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Which nucleotide has a ketone?
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Guanine
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Which nucleotide has a methyl?
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Thymine
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What nucleotide bonds are strongest? Why?
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G-C; they have 3 OH bonds
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What does DNA with high GC content exhibit?
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High melting temps
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What are the 5 "ingredients" that contribute the structural components of Purines?
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-Glycine
-Glutamine -Aspartate -CO2 -N10-Formyl-THF |
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And how many rings do the purines have?
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2
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And what are the purines?
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Adenine and Guanine
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And what 3 amino acids are necessary for making purines?
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GAG
Gly, Asp, Glutamine |
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What are the Pyrimidines made up of?
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Carbamoyl phosphate
Aspartate |
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And how many rings do the Pyrimidines have, and what are the pyrimidines?
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1 ring
CUT the py Cytosine, Uracil, Thymine |
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What exactly is a nucleotide?
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Base + Phosphate + Ribose
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How are bases linked?
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By 3'-5' phosphodiester bonds
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What is a TRANSITION?
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Substitution of a Purine for purine / or Substitution of a Pyrimidine for Pyrimidine
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How do you remember what a Transition is?
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TransItion is Identical
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What is a TransVersion?
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ConVersion of a Purine to Pyrimidine or vice versa.
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What are the 4 big features to note about the Genetic Code?
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-Unambiguous
-Degenerate/Redundant -Commaless, nonoverlapping -Universal |
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What does UNAMBIGUOUS mean?
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A codon really means what it means - a specific AA
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What does Degenerate mean?
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More than one codon may imply the same amino acid
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What is one amino acid that only has ONE corresponding codon however?
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Methionine
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What does Commaless mean?
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Reading bases to determine AA sequence starts at a FIXED point and is CONTINUOUs; it doesn't overlap or skip around.
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What does Universal mean?
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The genetic code is conserved and is used by all organisms
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What are 4 exceptions to the genetic code being universal?
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-Mitochondria
-Archaebacteria -Mycoplasma -Some yeasts |
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4 types of DNA MUTATIONS that can occur:
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-Silent
-Missense -NONSENSE -Frameshift |
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What is the order of severity of DNA mutations?
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Worst = Nonsense
Med = Missense Least = Silent |
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Why are Nonsense mutations so severely damaging?
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They STOP DNA reading - too early
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What is a silent mutation?
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Substution of only one aa
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Where do silent mutations often occur?
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At the 3rd position of a codon - the tRNA wobble site.
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What is a Missense mutation?
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When there IS a different AA replaced, but it is structurally similar so not too bad.. conservative.
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What does a Frameshift mutation cause?
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Misreading of all nucleotides downstream
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What is the usual result of a Frameshift mutation?
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Truncated protein
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What type of genome has multiple origins of replication?
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EUKARYOTIC
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What genome has just one single origin of replication?
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PROKARYOTIC
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Where does Eukaryotic DNA replication START?
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At AT-rich CONSENSUS SEQUENCES
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Where does Prokaryotic DNA replication start?
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At a single site
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How does Prokaryotic DNA replication progress from that single origin?
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BIDIRECTIONAL synthesis - thus producing a LEADING strand and LAGGING strand
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On which strand is DNA synthesis DISCONTINUOUS in prokaryotes? What does this create?
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The LAGGING strand - creates OKAZAKI fragments
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What enzymes make nicks in the DNA helix to relieve supercoils during DNA replication and synthesis?
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DNA topoisomerases
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What makes an RNA primer on DNA?
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Primase
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What is the primer necessary for?
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DNA polymerase III initiation of replication
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So what enzyme does the bulk of the work in DNA replication?
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DNA pol III
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What is the direction of synthesis and special function of DNA pol III?
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5'->3' synthesis
3'-5' exonuclease proofreads! |
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What does DNA Pol I do?
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Degrades RNA primers and fills in the gap with DNA
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How does DNA Pol I excise RNA primers?
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With 5'-3' exonuclease activity
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What seals DNA?
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Ligase
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What takes over when DNA Pol III misses a mistake despite its proofreading activity?
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DNA repair mechanisms!
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What are 3 SS DNA repair mechanisms?
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-NT excision repair
-Base excision repair -Mismatch repair |
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What are the 2 steps in Nucleotide Excision repair?
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1. SPECIFIC ENDONUCLEASES excise the oligonucleotide containing damaged bases
2. DNA pol and Ligase fill the gap |
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In what disease are Nucleotide Excision repair genes mutated?
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XERODERMA PIGMENTOSA
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How does Mismatch repair work?
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By the RECOGNITION of Unmethylated, Newly synthesized strings
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In what disease are DNA Mismatch Repair genes mutated?
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HNPCC - hereditary nonpolyposis colorectal carcinoma
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What is the only mechanism of DNA repair of DOUBLE stranded DNA?
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Nonhomologous end joining
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In what direction are both DNA and RNA synthesized? Why?
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5'-3' - the polymerase requires a 5'OH for the incoming NT's 5' phosphate to attach.
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In what direction does PROTEIN synthesis occur?
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ALSO 5'-3'!
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What is the way in which AA's are linked in protien synthesis?
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N'term to C'term
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What are 3 types of RNA, which is largest, smallest, and most abundant?
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Massive = mRNA
Rampant = rRNA Tiny = tRNA |
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What has multiple vs one type of RNA polymerase; proks or euks?
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Euks have 3 types of RNA pol
Proks only have 1 |
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What are the 3 types of RNA pols in eukaryotes?
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RNA pol I - makes rRNA
RNA pol II - makes mRNA RNA pol III - makes tRNA |
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How does RNA polymerase differ from DNA polymerase?
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-No proofreading function
-Can initiate synthesis without a primer! |
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What inhibits RNA pol II? So what would be the result?
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a-Amanitin! Mushroom toxin
-Result would be no mRNA |
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What is the mRNA initiation codon in DNA?
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AUG
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What does AUG code for in EUKARYOTES?
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Methionine
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What does AUG code for in PROKARYOTES?
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Formyl-methionine; fMET
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what are the 3 mRNA STOP codons?
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UGA you go away
UAA you are away UAG you are gone |
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What are the 3 components of Gene Expression Regulation?
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-Promoters
-Enhancers -Operators |
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What is the PROMOTER?
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Where RNA polymerase and other Trscrpn factors bind to DNA UPSTREAM from the gene locus to be transcribed
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What is the promoter in eukaryotic DNA then?
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The AT-rich sequence upstream the intended gene
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What are the 2 special components of the AT-rich promoter?
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TATA and CAAT boxes
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What do promoter mutations commonly result in?
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DRAMATIC decreases in the amount of gene transcribed!
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What is an ENHANCER?
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A stretch of DNA that ALTERS gene expression by binding transcription factors
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Where is an Enhancer located with respect to the gene for which the enhancer regulates its expression?
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May be CLOSE to the gene, FAR from the gene, or even WIHTIN THE GENE!
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So promoters will be ____, where enhancers can be ____:
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Promoters = UPSTREAM
Enhancers = ANYWHERE |
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What is an Operator?
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The site where NEGATIVE regulators bind - repressors
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What would an enhancer that was located WITHIN the gene being regulated be an example of?
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An INTRON
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What are INTRONS?
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INtervening DNA that does not get translated into any useful protein product.
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What are the DNA segments that contain actual genetic info that codes for protein?
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Exons
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What happens to Introns?
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Get spliced out
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What does the fact that Introns get spliced out allow for?
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Alternative splicing - production of different proteins in different tissues!
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What is the first step in mRNA splicing?
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Primary RNA transcript combines with snRNPs to form SPLICEOSOME
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What happens after the spliceosome forms?
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A LARIAT-SHAPED INTERMEDIATE is formed
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What does the formation of the lariat-shaped intermediate allow for?
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Precise removal of the intron and then joining of the two exons that were flanking the intron.
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What happens in EUKARYOTES immediately after DNA transcription?
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RNA PROCESSING
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Where does RNA processing occur? Why?
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In the nucleus - only PROCESSED RNA can be TRANSPORTED out of the nucleus
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What are the 3 steps of RNA processing in eukaryotic nuclei?
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1. Capping of 5' end
2. Polyadenylation of 3' end 3. Splicing out of introns |
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What is the 5'cap?
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7-methyl-G
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What is the 3' end addition?
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200 adenylates (polyadenylates)
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What is the INITIAL primary RNA product prior to processing called?
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Heterogenous nuclear RNA - hnRNA
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What is the processed, Capped/tailed transcript called?
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Messenger RNA - mRNA!!
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Why does mRNA have to get out the nucleus?
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So protein can be made!
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What RNA carries amino acids for protein synthesis?
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tRNA - teeny RNA
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What are the 4 characteristic features of tRNA?
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-75-90 amino acids
-Cloverleaf structure -Anticodon end (recognizes mRNA) -3' Aminoacyl end (carries AA) |
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What is on all tRNA's 3' end - in both euks AND proks?
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CCA with a high % of chemically modified bases
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And where is the Amino Acid bound to tRNA?
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At the 3' end
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What enzyme accomplishes 'Charging' of tRNA - addition of the amino acid?
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Aminoacyl-tRNA synthase
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But what enzyme checks to make sure it's the RIGHT amino acid before charging actually happens? How?
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Aminoacyl-tRNA SYNTHETase - hydrolyzes incorrect bonds
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So the 2 things responsible for accuracy of amino acid selection by tRNAs are:
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-Aminoacyl tRNA synthetase
-Binding of charged tRNA to the codon for which it is complementary |
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What sites in the mRNA codon actually have to have accurate base pairing for a peptide bond to form?
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ONly the first 2 sites
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What is the 3rd site of the mRNA codon?
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Wobble
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What does the tRNA wobble position allow for?
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Different mRNA codons encoding the same tRNA/AA
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What are the 3 general phases of Protein synthesis?
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1. Initiation
2. Elongation 3. Termination |
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What molecules help Initiation?
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IFs - initiation factors
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What do IFs do?
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Help assemble the 30S ribosomal subunit with the initiator tRNA
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When are IFs released?
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When the mRNA and ribosomal subunit assemble together
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What are the 3 sites on the ribosome for protein synthesis? What is the function of each?
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A = Aminoacyl-tRNA binds here
P = Peptide bond forms here E = Empty tRNA sits here as it Exits |
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What catalyzes the Peptide bond formation at the P site? How?
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Peptidyltransferase - transfers the growing polypeptide to the AA in the A site.
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How does the empty uncharged tRNA get into the E site?
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The Ribosome moves 3 nt's down toward the 3' end, which moves the peptidyl-RNA to the P site, and empty tRNA to the E site.
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What is Termination?
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The release of completed protein from the ribosome, and dissotiation of the ribosome.
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3 types of posttranslational modifications of protein:
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-Trimming
-Covalent alterations -Proteasomal degradation |
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What is TRIMMING?
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Removal of N- or C-terminal pro-peptides from ZYMOGENS to generate mature proteins
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What are 3 types of covalent alterations that can be done to proteins after translation?
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-Glycosylation
-Phosphorylation -Hydroxylation |
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How is Proteasomal degradation triggered?
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When ubiquitin is attached to defective proteins as a tag for their destruction.
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