BMSC 220

tasnimjaisee's version from 2017-10-24 17:20

Lecture 2 pt1

Question Answer
HookeCoined the term "cell" through cork cross sections
Leeuwenhoekviewed “animalcules” in pondwater & teeth bactera; differentiaed types
GlycolosisLactic Acid --> 2ATP
Lactic acid chemical formulaC3H6O3

Lecture 2 pt2

Question Answer
most complex prokaryotecyanobacteria
simplest eukaryotesYeast
Are volvoxes prokaryotes or eukaryotes?Eukoryotes
Plant cells are organized into three main tissue systemsground tissue - dermal tissue - vascular tissue
Human 5 main tissue systemsEpithelial, Connective, Blood, Nervous, Muscle
Fibroblastsfill the spaces between organs and tissues in the body
How often does E. Coli divide?20 mins
Bright-field microscopylight passes directly through - Requires cells killed
Phase contrast and DICConverts thickness into image without staining - live cells
Confocal microscopeDifferent of layers
Transmission electron microscopyimage on a fluorescent screen
Scanning electron microscopyelectron beam reflects off sample surface- coated with metal

Lecture 3

Question Answer
Carbohydrates characteristic5 and 6 carbon sugar
Lipids characteristicpolar vs. nonpolar parts
What type of sugars are ribose?pentose sugar
Is glycogen Branched or unbrached of A or B ?Branched A
Is starch Branched or Unbrached of A or B ?unbranched A
Cellulose and chitin: Branched/Unbranched of A/B?unbranched B
are triacylglycerols soluable in water?No
are phospholipids soluable in water?Both
Structure of triacylglycerols3 fatty acids linked to a glycerol
Structure of phospholipid2 fatty acids linked to a 1 phosphate, bound to carbon in glycerol
Purine typesAdenine and Guanine
Pyramidines typesCytosine and Thymine
Nucleosidesnitrogenous base linked to the ribose or deoxyribose sugar
Nucleotidesphosphate group, and are the basic building block of RNA and DNA
Phosphate group is attached to what and which charge?5’ carbon of deoxyribose and carries a negative charge
Hydroxyl group on 3’ carbon will attach to?phosphate group of the Next nucleotide in the DNA strand
Phosphodiester bonds form between?5' phosphate of one nucleotide and the 3' hydroxyl of a sugar
Structure of amino acidsSide chain - H - Carboxyl - H3N+

Lecture 4

Question Answer
Nuclear LaminaProvides strcutural support; Lamin proteins
Outer membrane is continuous with the ______________________endoplasmic reticulum
The inner membrane has proteins that bind the __________________Lamina
Coined the term GenesJohannsen
Coined the Linkage groupsMorgan
TranscriptionRNA molecule from a DNA template
Translationpolypeptide chain from an mRNA template
Exonssegments of protein-coding sequence [and 5’ and 3’- untranslated regions (UTRs)].
Introns (or intervening sequences)segments of non-proteincoding sequences.
RNA splicingjoining of exons in a precursor mRNA molecule
~35% of human genome is?Introns
Only 10% (on average) of a typical genes sequenceexons
micro RNAs (3)fold into hairpin structures - cleaved by nucleases (Dicer) - become double stranded.
Second smallest genome of known cellsMycoplasma genitalium
Chromatin has about ____ protein as DNAtwice as much
basic structural units of chromatin, and consist of DNA+histonesNucleosomes
Types of histonesH1, H2A, H2B, H3, H4
Proteins containing a high proportion of the basic amino acids, arginine and lysineHistones
Nucleosome core particles147 bp DNA wrapped around octamer of two molecules each of histones H2A, H2B, H3, and H4
Chromatosome166 bp + histone H1
EuchromatinDecondensed - transcriptionally active interphase chromatin
Heterochromatincondensed - transcriptionally inactive chromatin - highly repeated DNA sequences.
Constitutive heterochromatinDNA that is not transcribed in any cell type (EX. DNA sequences at centromeres)
Facultative heterochromatinnot transcribed in the cell being examined but may be transcribed in other cell types
Acetylation of specific lysine groups on the tails of histone proteins...neutralize the positive charge of those lysines
Histone acetyltransferases (HAT)adding acetyl groups
Histone deacetylases (HDAC)remove acetyl groups
CENP-Arequired for assembly of kinetochore
sequences at the ends of eukaryotic chromosomes - stability of linear chromosomes - aging & reproductionTelomeres
Telomere DNA sequencesrepeats of a simple-sequence DNA with clusters of G residues on one strand
Messenger RNAs (mRNAs)templates for protein synthesis
Transfer RNAs (tRNAs)align amino acids along the mRNA template
Semiconservative replicationwould produce two copies that each contained one of the original strands and one new strand
increased organism complexity = ?increased genome size

Lecture 5

Question Answer
DNA replication must have a high degree of ____ to ensure that the accuracy of replication is compatible with the low frequency of errors that is needed for cell reproductionfidelity
multisubunit enzymes that catalyze the synthesis of DNADNA polymerases
All polymerases synthesize DNA only in which way?5 to 3 direction (therefore, read DNA template in the 3 to 5 direction) .
DNA polymerases can add a new deoxyribonucleotide only to a preformed primer strand (3’-OH) that is ____ ____ to the templateHydrogen bonded
Primase-enzyme that synthesizes short fragments of RNA(3-10 nucleotides)
Exonuclease-enzyme activityhydrolyzes (degrades) DNA or RNA molecules from their ends
RNase H- exonucleasedegrades the RNA strand of RNA-DNA hybrids in eukaryotes
DNA ligase-enzymeseals breaks in DNA strands following replication
Helicases-enzymes in replication forkcatalyze the unwinding of parental DNA
Single-stranded DNA-binding proteins in replication forkstabilize the unwound single-stranded template DNA
Topoisomerasescatalyze reversible breakage and rejoining of DNA strands to relieve torsion caused by DNA unwinding
How can toposiomerase help in the mpact of unwinding a two stranded rope attached at it’s base?Unwinding parental DNA - Twisting strands ahead of replication
How can toposiomerase help in the mpact of unwinding double-stranded circular or attached DNA Molecule?Transient break serving a swivel to allow free rotation of DNA strands
Origins of replication (ori)serve as binding sites for the protein complex that initiates the replication process
autonomously replicating sequence (ARS)origin of DNA replication in yeast
Origin recognition complex (ORC)recognizes core sequence and bind to it to initiate formation of replication bubble - 6 subunit complex
DNA polymerase cannot replicate the extreme5-end of linear DNA molecules
Telomerase (2)maintains the ends of eukaryotic chromosomes - possesses reverse transcriptase activity
How is a protective loop made?3’ overhang attaches to the DNA strand
Somatic cells do not contain enough telomerase for indefinite replications?No, therefore as we age, telomeres become shorter
usually less than ___ errors during replication10^9
Simple free energy differences in hydrogen bonding between correct and incorrect bases1/100-1/1000 incorrect
Active selection of correct base by polymerase based on the conformation of the expected base1/10^5 -1/10^6 bases incorrect
Proofreading by polymerase1/10^7 - 10^8 bases incorrect
DNA repair mechanisms ___ fidelity (increases/decreases)increases
Replication origins in other eukaryotic cells less well defined at DNA sequence level, and may involve unique aspects of chromatin ____ rather than a specific ____structure - sequence

Lecture 6

Question Answer
RNA polymerases are the principal enzymes responsible for RNA synthesisTranscription
Unlike DNA polymerase, RNA polymerases do not require a ___ ___ to initiate RNA synthesisprimer sequence
Fundamental differences of eukaryotes relative to prokaryotes with respect to gene expressionChromatin - Nucleus compartments - RNA Processing - Nuclear RNA polymerases (l, ll and lll)
RNA polymerase IrRNA: ribosomal RNA: 5.8S, 18S, 28S
RNA polymerase IImRNA: messenger RNA (also miRNA, snRNA)
RNA polymerase IIItRNA: transfer RNA (also 5S-RNA, snRNA)
make up well over 90% of the total RNA (by mass) in any given cellrRNAs and tRNAs (RNA polymerases I and III)
relatively small number of genes transcribed at very high levelsrRNAs and tRNAs (RNA polymerases I and III)
Product of large number of different protein coding genesmRNA RNAp ll
BREupstream of TATAA - binding site for TFIIB
DCE, MTE, DPEdownstream of INR - binding sites for some TAFs
DNA sequence elementspecific functional property with respect to regulation of transcription of that particular gene has been ascertained
Cis-acting DNA sequencespromoter and enhancer elements - regulate expression of genes
Basal or core promoterGenes transcribed by RNA polymerase II contain core promoter elements, including the TATA box and an initiator (Inr) DNA sequence
Upstream promoter and enhancer elements are the same ____Functionally
Herpes simplex virus thymidine kinase gene promotercontains a relatively simple promoter with a TATAA sequence, and two upstream promoter sites known as “GC box”
SV40 enhancer can function in any orientation, and in any position relative to..the core promoter
plasmid DNArepresents a method by which to introduce recombinant DNA into a cell
How does DNA sequence being randomly insert into the genome?Stable transfection with a plasmid
Reporter geneEncodes an easily assayed enzyme - Replace normal gene sequence adjacent to gene promoter
Retrovirus/LentivirusRandom insertion of DNA - Plasmid includes sequence from retrovirus that allows cells to continue transfecting other cells
CRISPR/Cas9Cas9 nuclease and a CRISPR RNA strand target changes of DNA into a genome
Hsp70/eGFPReporter gene expression in transgenic zebrafish
General transcription factorstranscription from all polymerase II promoter - Formation of the transcription initiation complex
gene-specific transcription factorsbind to promoter and enhancer elements of one or a small number of different genes, and direct activity of the general transcription factors
TATA boxregulatory DNA sequence in the promoters of eukaryotic genes - transcribed by RNA polymerase II
TBP-associated factors, or TAFs, are proteins associated with ___ in the general transcription factor, ____TBP - TFIID
___ subsequently associates with TFIID at the core promoter, followed by recruitment of RNA polymerase and ___TFIIB - TFIIF
DNA sequences that are downstream from the start of transcriptionexons, introns, stop
DNA sequences that are upstream from the start of transcriptionInr, TATA box, proximal promoter sequences
enhancersbinding sites for gene specific transcription factors that modulate activity of the basal transcription complex
Gene specific transcription factors work by?Modifying transcription initiation rate by the basal transcription complex
What specifies the amount of transcriptional initiation by RNA pol II?combination of transcription factors interacting at a specific gene’s promoter/enhancer sequences
DNA-affinity chromatographyisolate transcription factors based on their binding to specific DNA sequences in order to study them further
Steroid hormone receptors and homeodomain proteins as?transcription factors
Steroid hormone receptorsZinc finger domain - Transcription factors that regulate gene transcription in response to hormones such as estrogen and testosterone
Homeodomain proteinscontain a helix-turn-helix DNA binding domain - play critical roles regulating gene expression in embryonic development
coactivatorsModify chromatin structure
2 general mechanisms of action of transcriptional activatorsInteract with mediators and general transcription factors - Interact with coactivators
coactivatorsChromatin structure modification
Mediatorbinds to the preinitiation complex - key role in linking the general transcription factors to the gene-specific transcription
DNA loopingAllows transcription factors bound to a distant enhancer
Release of RNA polymerase from the basal complex to initiate transcription requires?the phosphorylation and helicase activities of TFIIH
Gene expression in eukaryotic cells is regulated by?repressors as well as by transcriptional activators
Gene expression functions by?Blocking binding of transcriptional activator to sequence - Repress mediator - Interact with co-repressors
Prokaryote, E. coli preferred energy and carbon sourceglucose
Prookaryote, E. coli preferred energy and carbon sourceglucose; other sugars used when it is low
Regulation of the lac operon are controlled by2 DNA loci-O & i gene (repressor)
When lactose is present what does the allolactose do?Inactivates the repressor and allows transcription of the lac operon
Glucose repression occurs through?A-ketoglutarate
What does A-Kutogluterate inhibit the production of?cAMP
When glucose is low, how do the levels of a-ketoglutarate react?they decrease
When a-ketoglutarate levels decrese what happens to cAMP?cAMP→CAP→DNA→RNA Polymerase→LAC operon
immunoglobulin heavy chain enhancer contains ____ functional sequence elements within 200 bp9
What does SP1 recognize?GC
What does CBTF recognize?CCAAT
Purification of transcription factor Sp1 by DNA-affinity chromatographyGC box DNA column - Sp1 addition→Other proteins flow through - Salt buffer→Pure Sp1
methylated histone H3Marks nucleosome devoid DNA
Chromatin remodeling factors canslide nucleosomes along DNA - change nucleosome conformation - eject histones from DNA
Histone acetylationacetyl groups to specific lysine residues in histone tails
histone acetylation results in?transcriptionally permissive chromatin
DNA methylation: FunctionsPrevent transposon movement - Inactivate genes involved in development
What is a binding site for the enzyme complexes required for mRNA processingC-Terminal domain of RNAp2