1'Knowledge: arrange, define, duplicate, label, list, memorize, name, order, recognize, relate, reca

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BLOOM'S TAXONOMY
Benjamin Bloom (1956)

• - Developed a classification of levels of
  intellectual behavior
• important in learning.
• Found that gt 95 of the test questions students
  encounter
• require them to think only at the lowest
  possible
• level...the recall of information.

1.Knowledge arrange, define, duplicate, label,
list, memorize, name, order, recognize, relate,
recall, repeat, reproduce state. 2.Comprehension
classify, describe, discuss, explain, express,
identify, indicate, locate, recognize, report,
restate, review, select, translate, 3.Application
apply, choose, demonstrate, dramatize, employ,
illustrate, interpret, operate, practice,
schedule, sketch, solve, use, write. 4.Analysis
analyze, appraise, calculate, categorize,
compare, contrast, criticize, differentiate,
discriminate, distinguish, examine, experiment,
question, test. 5.Synthesis arrange, assemble,
collect, compose, construct, create, design,
develop, formulate, manage, organize, plan,
prepare, propose, set up, write. 6.Evaluation
appraise, argue, assess, attach, choose compare,
defend estimate, judge, predict, rate, core,
select, support, value, evaluate.
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Central Dogma of Biology
DNA
RNA
Protein
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5 TCA 3
5
DNA Replication

• - Models of DNA replication
• (semi-conservative and semi-discontinuous)
• - 5 to 3
• - Origin of replication
• Bidirectional, unidirectional and rolling circle
  replication
• (leading vs. lagging)
• - Enzymes and proteins important for DNA
  replications
• (helicases, SSBs, topoisomerases, and DNA
  polymerases)

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The Bare Bones of Transcription
Bacteria (E. coli) - RNA synthesis is 5 to 3
AUG RNA polymerase holoenzyme core sigma
(specificity factor, part/whole) Promoter -35
and -10 regions (and UP for rRNA
genes) Initiation, elongation, and termination
(rho-dependent and -independent
Regulation lac (/-), trp, lytic/lysogenic
Eukaryotes More factors and complex
promoters RNA polymerase I, II, III for rRNA,
mRNA, and tRNA/5S transcripts Sequence-specific
DNA-binding proteins Activators (Modular domain
structure for activators ) and enhancers
(position- and orientation-independence)
Repressors and silencers Pre-initiation
complex binding to DNA and to factors
pre-bound TFIID - TBP TAFs, Mediators Order of
assembly Promoter escape/clearance Control of
pre-initiation and sometimes elongation Extra-cell
ular signals and transcription Chromatin is
generally repressive - modification and remodeling
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a-Helix Recognizes DNA Major Groove
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The Central Dogma
DNA
Double-stranded
Precursor RNA
mRNA
Protein
cDNA
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The Bare Bones of RNA metabolism or biogenesis
In eukaryotes Primary transcripts are generally
processed/modified 5 capping, splicing, 3 end
formation/poly(A) tailing, base modification,
editing, RNA export and import, localization,
decay, and mRNA translation.
Splicing nuclear pre-mRNA splicing (cis and
trans) - two trans-esterifications Splicing
signals 5 SS, branchpoint, polypyrimidine-tract/
3 SS Splicing factors U snRNAs/snRNPs,
splicing factors (U2AF), regulators (SXL, PTB
(hnRNPs) and ASF/SF2 (SR proteins) Alternative
splicing - generation of molecular diversity
and developmental control Positive and negative
regulation of splicing RNA can be catalyst
self-splicing of group I and II introns tRNA and
rRNA processing
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Eukaryotic mRNAs are capped at the 5 end
Pol II
CH3-pppN
U6 snRNA
Pol III
Fig. 15.3
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The Bare Bones of Translation
- 5-3 direction on mRNA and N to C terminus
protein synthesis - Genetic code triplet, fixed
start and stop, non-overlapping, degenerate,
wobble (isoaccepting tRNAs), (almost) universal
- mRNA features Bacteria - Shine-Dalgarno
sequence, and AUG Eukaryotes - mRNA cap, First
AUG, and Kozak sequence versus internal
ribosome entry site (IRES)
- Components Bacteria - 70S ribosome with
30S and 50S subunits Eucaryotes - 80S
ribosome with 40S and 60S Small subunit -
Codon recognition and mRNA binding Large
subunit - Peptidyl transferase, GTPase stimulation
- Initiation factors (ribosome recruitment)
IF1, 2, 3 (bacteria) eIF3, 2, 4F, 1, 1A, 5,
5B (eucaryotes)
- Elongation factors (Translocation) EF-Tu,
EF-Ts, and EF-G
- Termination factors RF1 (UAA, UAG), RF2 (UAA,
UGA) plus RF3 (bacteria) eRF1 (UAA, UAG,
UGA) plus eRF3 (eucaryotes)
- Ribosome release EF-G and RRF (bacteria)
- tRNAs
- Ribosome is a ribozyme

• Regulation Heat shock response (bacteria)
• Growth factor response and iron response
  (eucaryotes)

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Chess board positions used in memory experiments.
Recall by chess players by level of expertise.
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Karmaneya vadhikarste maa Phaleshu Kadachana Maa
Karmphal heturbhu maa te Sangotsva karmani
Your freedom is only in the field of action, and
not in the field of bringing about the fruits of
action. Never take yourself as the cause of
bringing about a karma- phala (situation), and
never resort to a life of inaction.
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codons dNTPs include The to 3 should student
mRNA the of processing DNA basics replication RNA
know and translation These that DNA the DNA in a
5 direction using 5 to Transcription RNA
involves polymerase DNA and generates RNA in a
duplicates direction 3 requires is translated
generating by the ribosome C NTPs polypeptides
terminal in an N to polymerase involving tRNA
(promoter) double-stranded and transcription
direction
The student should know the basics of DNA
replication, transcription, RNA processing, and
translation. These include that DNA polymerase
duplicates the double-stranded DNA in a 5 to 3
direction using dNTPs. Transcription involves RNA
polymerase and DNA (promoter), generates RNA in a
5 to 3 direction, requires NTPs. mRNA is
translated by the ribosome generating
polypeptides in an N to C terminal direction,
involving tRNA and codons.
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