ACTUAL REVIEW FINAL EXAM 1

What is the role of DNA?

information storage

What is the role of RNA?

intermediate, ribozymes, regulation

What is the role of protein?

perform work

What is the central dogma of molecular biology?

(Replication/Repair) DNA to(Transcription) RNA to (Translation) Protein

What is the experiment that concluded that a genetic material exists?

Griffith, Transformation Experiment with mice; smooth vs. rough Strep bacteria

What was the experiment done by Avery, MacLeod, and McCarty?

Transformation Experiment with cultured cells; smooth vs. rough Strep bacteria

What was the conclusion of the Transformation Experiment with cultured cells; smooth vs. rough Strep bacteria?

DNA is the genetic material

What was the experiment done by Hersey and Chase?

32P-labeled DNA vs. 35S-labeled protein in bacteriophages, followed radioactivity

What did the 32P-labeled DNA vs. 35S-labeled protein in bacteriophages, followed radioactivity experiment conclude?

DNA is the genetic material

What are the properties of the genetic material?

replication of self, storage of information, expression of information, variation through mutation

What property of genetic material explains DNA  DNA?

Replication of Self

What property of genetic material explains Stability, low mutation rate?

Storage of Information

What property of genetic material explains Gene Expression (Transcription + Translation)?

Expression of Information

What property of genetic material explains Evolution is possible?

Variation through Mutation

What are the features of genetic code?

Continuous, Unambiguous, Degenerate, Nonoverlapping, Universal

What feature of genetic code explains Uninterrupted, commaless, collinear?

Continuous

What feature of genetic code explains Only one amino acid per codon?

Unambiguous

What feature of genetic code explains Can have >1 codon per amino acid?

Degenerate

What feature of genetic code explains Nucleotides not reused in an mRNA?

Nonoverlapping

What feature of genetic code explains Almost all life uses the same code?

Universal

What cannot be explained by DNA alone?

Epigenetics

What are ways gene expression patterns can be controlled in a heritable fashion?

Histone Marks, DNA Methylation, Cytosolic Proteins and RNAs

What are features of histone marks?

Acetylation, Methylation, Phosphorylation, Ubiquitin marks, Reader, Writer, Eraser proteins for each of those marks, Direct effect is heterochromatin or euchromatin, Indirect effect is transcription off/on, respectively, Includes X-chromosome inactivation/Barr Bodies

What are features of DNA methylation?

+ methyls at promoter turns off transcription, - methyls at promoter turns on transcription, Includes Genomic Imprinting

What are features of cytosolic proteins and RNAs?

Transcription factors (proteins) and Noncoding RNAs

What DNA elements are located probably in euchromatin and produce regulatory RNAs, rRNAs, or tRNA?

Noncoding RNA Gene

What DNA elements are located at the hetero-/euchromatin border and stops the spread of heterochromatin?

Barrier/Insulator

What DNA element may be far from promoter and activates a promoter?

Enhancer

What DNA element is at/near transcription start site and is where transcription starts?

Promoter

What DNA element is a the ends of chromatin and protects coding genes from degradation?

Telomere

What DNA element is the middle of chromosome and where sister chromatids are joined?

Centromere

What DNA element is interspersed in genome and where DNA replication starts?

Origin of Replication

What DNA element is usually heterochromatin and are repetitive DNA like centromeres and telomeres?

Satellite DNA

What DNA element is interspersed in genome and is repetitive DNA; may be expressed, may be able to move?

Transposon

What DNA element is site of gene duplication and allows mutation accumulation, may produce regulatory RNAs?

pseudogene

What RNA element is located in cytosol and is the protein-coding message; part of ceRNA networks?

mRNA

What RNA element is between exons, in anticodon and is the non-coding sequence that is removed to get mature RNA?

intron

What RNA element is 5’ and 3’ termini of mRNA and is site of regulatory protein binding?

UTR

What RNA element is in nucleus and Cajal bodies and is part of the spiceosome?

snRNA

What RNA element is in the nucleolus and Cajal bodies and is a chemical modification of other RNAs, can become mi/piRNA?

snoRNA

What RNA element is in the nucleus or cytosol and degrade or prevent transcript?

siRNA

What RNA element is in the cytosol and inhibit translation (note hairpin shape!); part of ceRNA networks?

miRNA

What RNA element is in the nucleus and silence transposons by DNA methylation?

piRNA

What RNA element is in various locations and does various things like (e.g., signal, decoy, guide, scaffold archetypes); part of ceRNA networks?

lncRNA

What RNA element goes from Nucleolus  Cytosol and part of ribosome?

rRNA

What RNA element is in the cytosol and carries amino acids to ribosome and contains anticodon?

tRNA

What RNA element is in the cytosol and are circular exons and part of ceRNA networks?

circRNA

What RNA element is in the cytosol and is part of the ceRNA networks?

Pseudogene transcript

(1) Initiation – DNA sequences (BRE, TATA box, INR, DPE), TFIID/B/A/F/E/H, Mediator, Histone Readers/Writers/Erasers/remodeling, Activator @ Enhancer, RNA Pol II (2) Promoter-Proximal Pausing – NELF, DSIF (+/-PO4 ), P-TEFb (3) Elongation – RNA Pol I/II/III, pDSIF, FACT, NAP1, Topoisomerases, PARPs (4) RNA processing – CBC, 5’cap; Group I, Group II, spliceosomal, Archaeal/tRNA intron splicing; alternative splicing; PAP, PABP, CPSF, CstF, 3’ PolyA tail (5) Termination – Torpedo vs. Allosteric models

Transcription

(1) Initiation – bind small subunit + eIF1/2/3/4F/6, tRNAi -Met enters @ P site, scanning of 5’ UTR, large subunit binds (role of eIF5) (2) Elongation – A/P/E sites of ribosome, eEF1A/1B/2 (3) Termination – eRF1/3 (4) Protein folding – chaperone proteins (5) Quality controls – cap/tail check, NMD, UPR

Translation

What are activator/enhancer combo; histone density; DNA methylation; TF’s/elongation factors/termination; siRNA, piRNA, lncRNA action?

Transcriptional Control Availability

What are Reversible covalent modifications (e.g., phosphates)?

Transcriptional Control Activity

What are 5’ cap, splicing + 3’ tail (QC#1), alternative splicing; miRNA, siRNA, snRNA, snoRNA, lncRNA, ceRNA networks?

RNA processing availability

What are Irreversible covalent modifications (i.e., proteolytic activation)?

RNA processing activity

What are compartmentalization?

Location control availability

What are Heteroallostery/Effectors?

Location control activity

What are 5’ cap, splicing + 3’ tail (QC#1); eIFs/eEFs/eRFs?

translational control availability

What are Homoallostery/Cooperativity?

translational control activity

What are NMD (QC#2); cap and tail prevent?

mRNA degradation availability

What are Cofactors and/or Coenzymes?

mRNA degradation activity

What are proteasome and UPR?

Protein degradation availability

What are Isozymes/Isoforms

Protein degradation activity

What are eEF1A, eEF2, and eRF3?

GTPases

What GTPase has Codon-anticodon interaction as a GAP and eEF1B as a GEF?

eEF1A

What macromolecule does NMD degrade?

Nucleic acid (mRNA)

What is NMD’s degradation cue?

Splicing-related proteins present OR 3’ UTR too long

What is NMD’s reason to degrade?

“Bad” RNA makes bad protein (quality control)

What macromolecule does siRNA degrade?

Nucleic acid (mRNA)

What is siRNA’s degradation cue?

dsRNA

What is siRNA’s reason to degrade?

gene expression regulation strategy

What macromolecule does UPR degrade?

Protein (misfolded)

What is UPR’s degradation cue?

Misfolded protein accumulation

What is UPR’s reason to degrade?

Too many “bad” proteins stress the cell

What macromolecule does Proteasome degrade?

Protein (misfolded, old, regulatory)

What is Proteasome’s degradation cue?

Poly-Ub

What is Proteasome’s reason to degrade?

Protein is: no longer needed, in wrong location, damaged/old, misfolded

What is A part of the whole e.g., A single amino acid is necessary but not sufficient to make a protein?

Necessary but not sufficient

What is Everything that is needed e.g., DNA is both necessary and sufficient to cause transformation from R to Stype Streptococcus?

Necessary and sufficient

What is Can function on its own, but is redundant or unsustainable e.g., an individual copy of a multicopy gene – like rRNA genes – is sufficient but not necessary to make that particular transcript?

Sufficient but no necessary

How many organelles in prokaryote’s cytoplasm?

none

What is prokaryote chromosome structure?

circular

What is prokaryote chromosome compaction?

supercoiling

What is prokaryote genome size?

small

What is prokaryote gene expression timing?

simultaneous

What is prokaryote gene expression location?

cytosol

What is prokaryote helical stress resolution?

Gyrase (Topoisomerase IV)

What is prokaryote transcription?

Promoter = -10/-35 Elements TFs = Sigma Factors Single RNA Pol Many genes, one RNA Rho/hairpin termination

What is prokaryote RNA processing?

Limited splicing

What is prokaryote translation?

Similar Ribosome EFs = EF-Tu/Ts/G

What are the eukaryote organelles in cytoplasm?

nucleus, ER, Golgi, Mitochondria, etc.

What is the chromosome structure in eukaryotes?

linear

What is the chromosome compaction in eukaryotes?

supercoiling + histones

What is the genome size in eukaryotes?

large

What is the gene expression timing in eukaryotes?

sequential

What is the gene expression location in eukaryotes?

nucleus  cytosol

What is the helical stress resolution in eukaryotes?

Topoisomerases I & II

What is the transcription in eukaryotes?

Promoter = BRE, TATA, INR, DPE TFs = TFIIB/D/E/F/H RNA Pol I/II/III One gene, one RNA Torpedo/allosteric termination

What is the RNA processing in Eukaryotes?

5’cap, 3’ PolyA tail, 4 types of splicing

What is the Translation in eukaryotes?

Similar Ribosome EFs = eEF1A/1B/2

What is primary effects?

Direct action