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156 Cards in this Set
- Front
- Back
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Nucleoside?
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Nucleotide precursor
Base attached to 1' C of ribose without a phos 5' end |
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Nucleotide?
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Nucleic acid subunit ribose with 5' phoshporylated carbon base bound to 1' carbon
Phosphates added make mono, di, adn tri phos |
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Deoxynucleotide
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Modified nucleotide taht lacks the 2' OH groub of its ribose moieyty
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Charges on uracil?
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2
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Charges on thymine?
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2
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Charges on cytosine?
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3
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Charges on guanine?
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3
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Charges on adenine?
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2
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What is the 3" group of ribose
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OH
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What is te 5' group of ribose?
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Me
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Where does energy for phosphodiester bond come from?
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Triphosphate hydrolysis
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What holds nucleotides together?
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Phosphodiester bonds
3 OH to the -5-Phosphate |
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How is nucleotide polymerization done.
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5' phosphate is added to the 3 OH of the preexisting so it increases in the 5'-3' direction
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What is the orientation of the strand?
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5'-3'
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Difference between DNA and RNA?
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DNA is
1) Longer 2) Double stranded 3) DNA lacks 2' OH -Keeps it from being recognized by RNAase 4) DNA is methylated |
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What is hybridization?
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Annealing two strands from opposite sources.
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What is antisense RNA?
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RNA with a sequence complimentary to a DNA or RNA. Antisense will form a double helix the RNA/RNA stongest then R/D and then D/D
Usually made in lab as a proble |
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How many bp per turn are shown in ribbon model?
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10bp
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Major groove?
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This is where DNA binding proteins bind.
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What is charge of DNA? and why?
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Negative due to phosphodiester bonds
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What is the normal orientation of DNA?
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B DNA
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What is the orientation of RNA:RNA helix
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A DNA.Z
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What is left handed double helix that may be involved in repression of gene expression
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Z DNA
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What is karyotype?
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Physical representation of all mitotic chromosomes.
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What is euchromatin?
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Transcriptionally active chromatin.
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Chromatin?
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DNA plus protein. All DNA is bound by protein.
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What is the most abundant protein of chromatin?
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Histones
THe mass of histones = mass of DNA |
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How many types of histones are there?
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6 H2A, H2B, H3, H4 make ocatmeric core. H1 binds the linker region between the octamers.
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What allows histones to bind to DNA?
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They have regions rich in lysine and arginine.
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What is core DNA?
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DNA wrapped around an octomer.
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What is second most abundant class of chromatin proteins?
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Scaffold proteins.
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What do scaffolds do.
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Tie solenoids together to form condensed mitotic spindles. and to maintain super coiling.
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What is mitotic chromosome?
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The chromosomal condensation during prophase that involves solenoid tangling in complex patterns to from cthe
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What is nucleosome?
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histone octomer and associated DNA with out linker regions.
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How do histones bind to DNA
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they are rich in lysine and arginine.
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Metacentric?
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Central centromeres
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Submetacentric?
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Off center
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Acrocentric
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Towards teh end
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Telocentric
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at the ends (does not occur in human.s.
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What is largest chromosome?
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1
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What is smallest chromosome?
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22
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What are acrocentrics important to?
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Robertsonian Translocations.
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What is the make up of telomers?
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GT rich sequences with few genes.
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What is repeat sequence for humans?
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AGGGTT
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d
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fb
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What are three sequence classes?
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Highly repetitive
Intermediate Rare |
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What percentage of DNA encodes proteins?
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5%
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What is highly repetitive sequence?
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Up to maillion copies per genome
Only 3% of genome |
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What is intermediate
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hundred-thoussands per genome
>45% of genome |
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What is rare?
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One copy per genome
>50% |
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Highly repetitive function and locations?
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Centromeres and telomeres
Structural not functional tandem arrays of short sequences |
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Intermediative sequences function and location?
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Degenerate retrotransposons
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What is transposons?
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Sequences capable from moving form one location in genome to another
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What is retrovirus?
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Parasitic DNA molecules capable fo moving from one cell to another with the use of an RNA intermediate
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Retrotransposons
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Transposons that move through RNA intermediates. DNA sequences are transcribed into RNA which is then reversed transcribed back into DNA to be reinserted into a chromosome.
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What is the most common retrotransposon sequence?
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Alu. Alu transposition can cause tumorgenesis.
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What are the function intermediate sequence class genes?
BELL! BELL! |
rRNA(250 copies), tRNA (1300), 5S-rRNA (2000) and histones (87).
These are house keeping genes! |
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Where are most functional genes found?
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Rare sequences.
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T/F all gene families contain only rare sequences?
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True
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What % of protein encoding genes belong to families?
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50%
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Clustered gene families?
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Small percentage of gene families
Differe from tandem repears since sequences are not identical not as contigiousm and not necessarily oriented in same direction |
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Where are the alpha and beta globin genes located?
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Alpha are clustered on chromo 16
Beta are clustered on 11 |
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What are psuedogenes?
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Genominc sequences similair to expressed genes but which have been mutated so they no lnger express a gene product
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Where do pseudogenes come from?
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Crossing over.
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What is the only example of a cluster gene family that is in the intermediate class?
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Histones.
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What is thalassemias?
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Defective alpha or beta globins. With severe cases rbc dies in bone marrow, resulting in thinned bone cortex, fractures and distortions of the head, Marked enlargement of liver and spleen, with death within a decade.
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What makes histone mRNA unique?
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No introns
never polyadenylated |
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What cells undergo DNA replication
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Only dividing cells
Non-dividing cells blocked in Go do not progress to S phase |
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What is translation?
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Protein synthesis
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Where do prokaryotes replicate DNA?
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Cytoplasm
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When does DNA replication occur?
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S phase
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What is direction of DNA replication?
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5'-3' direction
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What is proofreading
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3'-5' exonuclease that removes mistakes
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What five things are required to replicate DNA
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1)DNA Polymerase
2)Deoxyribonucleotides (dNTPs) 3)Primer 4)Magnesium 5)Template |
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What is a primer?
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A strand with a free OH grouip at the terminal nucleotide
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What is the direction of DNA replication
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5-3
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Which DNA polymerases can proof read?
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Gamma and Delta
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What is the proofreading enzyme of DNA rep
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3'-5' exonuclease activity.
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T/F eurkaryotic ORIs replicate simulataneously?
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True
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What is replicon?
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A region of a eukaryotic chromosome that is replicated as aunit from one central ori
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What is a Helicase?
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An enzyme that unwinds DNA this is one of the first factors to bind an ORI, where it serves to ppen the double helix so the SNA pol can replicate the strand.
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What is the last protein to bind during DNA replication?
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Helicase
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Are SSBs part of the DNA replication apparatus?
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No!
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WHat is DNA clamp?
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Ring like protein that wraps around DNA to stabilize the assoication of the replication apparatus. Without the clamp Pol delta could only produce short stretches
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What replicates the leading strand?>
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POL DELTA
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What does Primase do?
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Makes short stretch of RNA that serves as a primer fo the short strand
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What enzymes remove RNA primers from lagging strand?
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RNAase
DNA polymerase Beta DNA ligase |
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T/F does helicase induce supercoiling?
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True
as a consequence of unwinding |
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Topoisomerase does what?
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Restore DNA to proper level of supercoilin
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What fills in gaps afters RNA primers have been removed
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DNA polymerase Beta
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What does DNA ligase do?
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This enzyme binds any free 3' OH and 5' phosphates of DNA. IN replication it seals the nicks between okazaki frags left by Pol Beta
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What removes the primers?
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RNAase
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Why is telomerase important?
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Ther is no upstream template
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T/F RNAase, DNA ligase, and Pol B are house keepers and do more than just fill in and fix RNA segments
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TRUE
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Describe Telomerase?
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Doesnt just fill in gaps it elongates telomeres by reverse transcription using RNA.
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T/F do cancers cells have elevated telomerase activity?
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True
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What controls what genes are expressed since every cell has the same genese?
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Hierarchies of gene regulation
A reticulate netword of regulatory mechanisms interacts to control when and where genes are expressed. |
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At what level is gene expression regulated?
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At every level
pre-transcriptional, transcriptional, post transcriptional, translational, post translational |
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Does double inhibition allow for activation?
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YEs
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RNA Pol I transcribes?
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rRNA
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RNA Pol II transcribes?
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mRNA
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RNA Pol III transcribes?
BELL! BELL! BELL! BELL! |
tRNA
5S-RNA snRNA |
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What is the most abundant form of RNA?
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rRNA at 90%
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Describe upstream and down steam for mRNA transcription.
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5' is upstream
3' is downstream During transcription new RNA strand is synthesized in the 5'-3' direction. so downstream is direction of transcription and upstream is region in front of gene. |
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Describe numbering system.
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Transcription starts at +1
Upstreams negator Down stream positive |
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When orienting in reading mRNA strand.
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3'-5' is the strand that is viewed it is the non read strand
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What is the promoter?
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The entire upstream region that determines wherter gene is activated or not.
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What is minimal promotor?
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Drives low level constitual epression.
Part of teh promoter most proximal upstream region Regulation and full expression is done by the promoter |
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What is enhancer?
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A region of DNA that regulates transcription liek a promoter but can be moved relative to the gene it controls
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What are distinguishing characteristics of an enhancer?
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It has a 5'-3' orientation that can be flipped in a transgenic expression assay. Promoter cant.
Can be down stream and are often great distances from the gene |
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Do genes with tata boxes tend to be expressed at higher or lower levels?
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Higher
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What is the most common start Nucleotide?
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A,
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What is the consensus sequence for the TATA box?
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TATA(A/T)A
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What are TATAless promoters?
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Promoters that lack any sequences similiar to TATA box. Tend to be expressed at low levels
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What are AT rich sequences?
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These regions are weaker. THis may faciliate strand separation during initial transcription
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What is initation complex?
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Cluster of proteins known as transcription factors that ssembles around a promotoer to initiate transcription.
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TBP?
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Protein that binds to TATA box. ACtually binds to minimal TATA box.
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What is CCAAT box?
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The second most common recognition sequence . Raises baseline transcription
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What are the two regions of transcprtion factors?
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DNA binding region
Activating region |
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What are the usually the most variable region in any gene?
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The activation domain
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What is a transcription factor?
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Proteins that bind recogntion sequences to control transcription
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Why can enhancers be flipped and promoters cant?
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Because of thier distance from the start and the minimal promoter
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Helix turn Helix
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two alpha helices are postitioned at right angles to each by a short linker region.
One helix has a basic face which fits in teh major groove |
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Zinc Fingers
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Cysteine and histidine residues are chealated to central zinc ion. These act like fingers wedging themselves in the major grooves.
Three sub famililes |
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Wht are the three sub families of Zinc fingers
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C2H2 zinc finger class. Pair of cystines 2-4 AA apart 11aa linker region and 2 histidines 3-4aa apart
C4 Class- LIke C2H2 minues the histidines C6 Class- Three pairs of cysteines |
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T/F Are RNApolymerases holoenzymes?
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True
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Where are the activatin domains in in HTH?
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It can be on one or both sides of the binding domain
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Whare would a homeobox be found?
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HTH
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Describe Leucine zippers
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Leucine every 7 aa.
With a leucine every two turns Has a scissors grip binding site. Leucines hold together by hydrophobic interactions |
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What three sites are methylated in all mRNAs?
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The 5' Cap
The 2' OH of the first and third nucleotides |
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What is capping?
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Adding a guanosine to the first nucleotide of the primary transcript by an unusual 5'-5' bond
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What splices introns?
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Spliceosomes.
Which are complexes of snRNPs |
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Where is the enzymatic activity of the snRNP located?
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It is located in the RNA not the protein
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What is the final process of mRNA?
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Polyadenylation
Which is adding 20-200 adenosines to the 3' end of the transcript |
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What is the stop sequence that signals poly adneylation?
Does it stop here? |
AAUAAA
No continues for 500-2000bp before Pol II falls off. |
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What cleaves off teh end sequence of mRNA?
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CA
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What genes are not polyadenylagted.
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Histones
genes made with pol I and pol III and that is why they can use to extract mRNA |
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what is needed to make a protein
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tRNA and ribosomes
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how is all the RNA made?
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1) cell has multiple copies of rRNA
2) Transcribes multiple rRNAs off of each gene |
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What are oscar miller feathers?
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When multiple rRNA are produced from the same gene. It looks like a fucking feather
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Ribonucleo proteins?
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proteins that assemble around the rRNA to from the large and small subunits of ribosomes.
There for ribosomes are composes of RNA and protein |
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Nucleous?
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produces rRNA
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Order of rRNA organization
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rRNA gene cluster-->Pre-rRNA-->18s, 5.8S, 28S
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What cells wont have nucleous?
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RBC,
any cells that arnt producing proteins. NERVE AND GLANDS HAVE BIGGUNS |
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Describe rRNA processing?
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Each gene encodes three rRNAs
All transcribed by Pol I as one large RNA molecule known as pre-rRNA. This is cleaved leavein 18, 5.8, adn 28S sequences |
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Where does splicing occur?
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mRNA
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Whata transcribe 5S RNA?
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Pol III the same polymerase that produces tRNAs
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When do ribosonucleo proteins bind?
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After preRNA as the structure is being turned into Ss and this results in large and small ribosomal subunits
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What contributes to small subunit?
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18S
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The tRNA anticodon loop?
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A nucleotide triplet at the apex of the tRNA and it is complimentary to a specific codon of mRNA/ This is how codons specify AAs
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Do rRNA and tRNA promoters have TATA boxes?
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Negator.
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Where are teh promoters for Pol III
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on the gene itself.
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How does Pol III word?
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Recognizing short RNAs with alot of secondary structure
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Where does translation occur?
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In the cytoplasm
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What allows nuclear transport in and out of the nucleus?
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Importins and exportin
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tRNA charging.
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tRNAs have to be bound with specific AAs
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