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121 Cards in this Set

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What is the structure of Chromatin?
Negatively charged DNA looped TWICE around nucleosome cores - forms NUCLEOSOME BEADs
What does a Nucleosome core consist of?
2 each of +charged:
H2A
H2B
H3
H4
What ties nucleosomes together in a string?
H1
So the only histone that is NOT in a nucleosome core is:
H1
What happens to Chromatin during Mitosis?
It CONDENSES into mitotic CHROMOSOMES
What is the condensed chromatin during periods of transcription INACTIVITY called?
Heterochromatin
What is EUchromatin?
Less condensed and Transcriptionally ACTIVE
What are the PURINES?
Pur As Gold
-Adenine
-Guanine
What are the PYRIMIDINES?
CUT the PY
-Cytosine
-Uracil
-Thymine
How are the purines different from pyrimidines?
Purines - 2 rings

Pyrimidines - 1 ring
What makes Uracil?
Deamination of cytosine
Which nucleotide has a ketone?
Guanine
Which nucleotide has a methyl?
Thymine
What nucleotide bonds are strongest? Why?
G-C; they have 3 OH bonds
What does DNA with high GC content exhibit?
High melting temps
What are the 5 "ingredients" that contribute the structural components of Purines?
-Glycine
-Glutamine
-Aspartate
-CO2
-N10-Formyl-THF
And how many rings do the purines have?
2
And what are the purines?
Adenine and Guanine
And what 3 amino acids are necessary for making purines?
GAG
Gly, Asp, Glutamine
What are the Pyrimidines made up of?
Carbamoyl phosphate
Aspartate
And how many rings do the Pyrimidines have, and what are the pyrimidines?
1 ring
CUT the py
Cytosine, Uracil, Thymine
What exactly is a nucleotide?
Base + Phosphate + Ribose
How are bases linked?
By 3'-5' phosphodiester bonds
What is a TRANSITION?
Substitution of a Purine for purine / or Substitution of a Pyrimidine for Pyrimidine
How do you remember what a Transition is?
TransItion is Identical
What is a TransVersion?
ConVersion of a Purine to Pyrimidine or vice versa.
What are the 4 big features to note about the Genetic Code?
-Unambiguous
-Degenerate/Redundant
-Commaless, nonoverlapping
-Universal
What does UNAMBIGUOUS mean?
A codon really means what it means - a specific AA
What does Degenerate mean?
More than one codon may imply the same amino acid
What is one amino acid that only has ONE corresponding codon however?
Methionine
What does Commaless mean?
Reading bases to determine AA sequence starts at a FIXED point and is CONTINUOUs; it doesn't overlap or skip around.
What does Universal mean?
The genetic code is conserved and is used by all organisms
What are 4 exceptions to the genetic code being universal?
-Mitochondria
-Archaebacteria
-Mycoplasma
-Some yeasts
4 types of DNA MUTATIONS that can occur:
-Silent
-Missense
-NONSENSE
-Frameshift
What is the order of severity of DNA mutations?
Worst = Nonsense
Med = Missense
Least = Silent
Why are Nonsense mutations so severely damaging?
They STOP DNA reading - too early
What is a silent mutation?
Substution of only one aa
Where do silent mutations often occur?
At the 3rd position of a codon - the tRNA wobble site.
What is a Missense mutation?
When there IS a different AA replaced, but it is structurally similar so not too bad.. conservative.
What does a Frameshift mutation cause?
Misreading of all nucleotides downstream
What is the usual result of a Frameshift mutation?
Truncated protein
What type of genome has multiple origins of replication?
EUKARYOTIC
What genome has just one single origin of replication?
PROKARYOTIC
Where does Eukaryotic DNA replication START?
At AT-rich CONSENSUS SEQUENCES
Where does Prokaryotic DNA replication start?
At a single site
How does Prokaryotic DNA replication progress from that single origin?
BIDIRECTIONAL synthesis - thus producing a LEADING strand and LAGGING strand
On which strand is DNA synthesis DISCONTINUOUS in prokaryotes? What does this create?
The LAGGING strand - creates OKAZAKI fragments
What enzymes make nicks in the DNA helix to relieve supercoils during DNA replication and synthesis?
DNA topoisomerases
What makes an RNA primer on DNA?
Primase
What is the primer necessary for?
DNA polymerase III initiation of replication
So what enzyme does the bulk of the work in DNA replication?
DNA pol III
What is the direction of synthesis and special function of DNA pol III?
5'->3' synthesis
3'-5' exonuclease proofreads!
What does DNA Pol I do?
Degrades RNA primers and fills in the gap with DNA
How does DNA Pol I excise RNA primers?
With 5'-3' exonuclease activity
What seals DNA?
Ligase
What takes over when DNA Pol III misses a mistake despite its proofreading activity?
DNA repair mechanisms!
What are 3 SS DNA repair mechanisms?
-NT excision repair
-Base excision repair
-Mismatch repair
What are the 2 steps in Nucleotide Excision repair?
1. SPECIFIC ENDONUCLEASES excise the oligonucleotide containing damaged bases
2. DNA pol and Ligase fill the gap
In what disease are Nucleotide Excision repair genes mutated?
XERODERMA PIGMENTOSA
How does Mismatch repair work?
By the RECOGNITION of Unmethylated, Newly synthesized strings
In what disease are DNA Mismatch Repair genes mutated?
HNPCC - hereditary nonpolyposis colorectal carcinoma
What is the only mechanism of DNA repair of DOUBLE stranded DNA?
Nonhomologous end joining
In what direction are both DNA and RNA synthesized? Why?
5'-3' - the polymerase requires a 5'OH for the incoming NT's 5' phosphate to attach.
In what direction does PROTEIN synthesis occur?
ALSO 5'-3'!
What is the way in which AA's are linked in protien synthesis?
N'term to C'term
What are 3 types of RNA, which is largest, smallest, and most abundant?
Massive = mRNA
Rampant = rRNA
Tiny = tRNA
What has multiple vs one type of RNA polymerase; proks or euks?
Euks have 3 types of RNA pol
Proks only have 1
What are the 3 types of RNA pols in eukaryotes?
RNA pol I - makes rRNA
RNA pol II - makes mRNA
RNA pol III - makes tRNA
How does RNA polymerase differ from DNA polymerase?
-No proofreading function
-Can initiate synthesis without a primer!
What inhibits RNA pol II? So what would be the result?
a-Amanitin! Mushroom toxin
-Result would be no mRNA
What is the mRNA initiation codon in DNA?
AUG
What does AUG code for in EUKARYOTES?
Methionine
What does AUG code for in PROKARYOTES?
Formyl-methionine; fMET
what are the 3 mRNA STOP codons?
UGA you go away
UAA you are away
UAG you are gone
What are the 3 components of Gene Expression Regulation?
-Promoters
-Enhancers
-Operators
What is the PROMOTER?
Where RNA polymerase and other Trscrpn factors bind to DNA UPSTREAM from the gene locus to be transcribed
What is the promoter in eukaryotic DNA then?
The AT-rich sequence upstream the intended gene
What are the 2 special components of the AT-rich promoter?
TATA and CAAT boxes
What do promoter mutations commonly result in?
DRAMATIC decreases in the amount of gene transcribed!
What is an ENHANCER?
A stretch of DNA that ALTERS gene expression by binding transcription factors
Where is an Enhancer located with respect to the gene for which the enhancer regulates its expression?
May be CLOSE to the gene, FAR from the gene, or even WIHTIN THE GENE!
So promoters will be ____, where enhancers can be ____:
Promoters = UPSTREAM

Enhancers = ANYWHERE
What is an Operator?
The site where NEGATIVE regulators bind - repressors
What would an enhancer that was located WITHIN the gene being regulated be an example of?
An INTRON
What are INTRONS?
INtervening DNA that does not get translated into any useful protein product.
What are the DNA segments that contain actual genetic info that codes for protein?
Exons
What happens to Introns?
Get spliced out
What does the fact that Introns get spliced out allow for?
Alternative splicing - production of different proteins in different tissues!
What is the first step in mRNA splicing?
Primary RNA transcript combines with snRNPs to form SPLICEOSOME
What happens after the spliceosome forms?
A LARIAT-SHAPED INTERMEDIATE is formed
What does the formation of the lariat-shaped intermediate allow for?
Precise removal of the intron and then joining of the two exons that were flanking the intron.
What happens in EUKARYOTES immediately after DNA transcription?
RNA PROCESSING
Where does RNA processing occur? Why?
In the nucleus - only PROCESSED RNA can be TRANSPORTED out of the nucleus
What are the 3 steps of RNA processing in eukaryotic nuclei?
1. Capping of 5' end
2. Polyadenylation of 3' end
3. Splicing out of introns
What is the 5'cap?
7-methyl-G
What is the 3' end addition?
200 adenylates (polyadenylates)
What is the INITIAL primary RNA product prior to processing called?
Heterogenous nuclear RNA - hnRNA
What is the processed, Capped/tailed transcript called?
Messenger RNA - mRNA!!
Why does mRNA have to get out the nucleus?
So protein can be made!
What RNA carries amino acids for protein synthesis?
tRNA - teeny RNA
What are the 4 characteristic features of tRNA?
-75-90 amino acids
-Cloverleaf structure
-Anticodon end (recognizes mRNA)
-3' Aminoacyl end (carries AA)
What is on all tRNA's 3' end - in both euks AND proks?
CCA with a high % of chemically modified bases
And where is the Amino Acid bound to tRNA?
At the 3' end
What enzyme accomplishes 'Charging' of tRNA - addition of the amino acid?
Aminoacyl-tRNA synthase
But what enzyme checks to make sure it's the RIGHT amino acid before charging actually happens? How?
Aminoacyl-tRNA SYNTHETase - hydrolyzes incorrect bonds
So the 2 things responsible for accuracy of amino acid selection by tRNAs are:
-Aminoacyl tRNA synthetase
-Binding of charged tRNA to the codon for which it is complementary
What sites in the mRNA codon actually have to have accurate base pairing for a peptide bond to form?
ONly the first 2 sites
What is the 3rd site of the mRNA codon?
Wobble
What does the tRNA wobble position allow for?
Different mRNA codons encoding the same tRNA/AA
What are the 3 general phases of Protein synthesis?
1. Initiation
2. Elongation
3. Termination
What molecules help Initiation?
IFs - initiation factors
What do IFs do?
Help assemble the 30S ribosomal subunit with the initiator tRNA
When are IFs released?
When the mRNA and ribosomal subunit assemble together
What are the 3 sites on the ribosome for protein synthesis? What is the function of each?
A = Aminoacyl-tRNA binds here
P = Peptide bond forms here
E = Empty tRNA sits here as it Exits
What catalyzes the Peptide bond formation at the P site? How?
Peptidyltransferase - transfers the growing polypeptide to the AA in the A site.
How does the empty uncharged tRNA get into the E site?
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.
What is Termination?
The release of completed protein from the ribosome, and dissotiation of the ribosome.
3 types of posttranslational modifications of protein:
-Trimming
-Covalent alterations
-Proteasomal degradation
What is TRIMMING?
Removal of N- or C-terminal pro-peptides from ZYMOGENS to generate mature proteins
What are 3 types of covalent alterations that can be done to proteins after translation?
-Glycosylation
-Phosphorylation
-Hydroxylation
How is Proteasomal degradation triggered?
When ubiquitin is attached to defective proteins as a tag for their destruction.