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BIS 101: Midterm 2_Kliebenstein
UC Davis
98
Biology
Undergraduate 4
11/08/2018

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Term
Repressor
Definition
*Binds DNA called the silencer to regulate transcription
*bound by silencer to regulate transcription
Term
Sigma Factor
Definition
*Initiates transcription by attracting RNAP to the +1 location
*initiates transcription by binding the CAT and TATA boxes
Term
Ubiquitin
Definition
Small protein added to the end of a protein to target it for degradation
Term
Topoisomerase
Definition
*Part of both replication and DNA packaging to help keep DNA from being too wound up
*enzyme in DNA synth, no new strands of nucleic
Term
Alternate Splicing
Definition
Can change how many proteins are encoded by a gene
Term
mi/siRNA, siRNA
Definition
Small RNA that targets specific mRNAs for degradation
Term
Ligand/ Kinase
Definition
Something that can interact with a protein to change its activity
Term
RHO
Definition
*Helps to stop transcription
*when RNA Pol falls off
Term
Release Factor
Definition
Helps to stop translation
Term
Proteasome
Definition
Degrades specifically tagged proteins
Term
RNA Polymerase/ primase
Definition
Makes RNA that is complementary to DNA (for replication)
Term
activator
Definition
Binds DNA called the enhancer to regulate transcription
Term
TBP
Definition
*transcription binding protein
*initiates transcription by binding TATA boxes in euks
Term
E3 Ligase
Definition
specifically tags proteins with other proteins for degredation
Term
Splicing
Definition
*process of remiving RNA from mRNA in euks
Term
does NOT recognize stop codon to allow translation termination
Definition
tRNAS
Term
does recognize stop codon to allow translation termination
Definition
release factor
Term
Processes that ensure there are few mistakes when DNA Is replicated
Definition
selection of the correct base by hydrogen bonding between the DNA and new base
Term
has free phosphate ends (no ester link)
Definition
*separated DNA inside bubble
Term
DNA polymerase 1
Definition
*key enzyme for synthesizing DNA
*BIOCHEM FUNC:
5'- 3' DNA polymerase
5' - 3' exonuclease
3' - 5' exonuclease
Term
Enzymes in DNA synthesis w/ no capacity to create new strands of DNA
Definition
Primase
Topoisomerase
Helicase
Term
Enzymes in DNA synthesis that can create new strands of nucleic acid
Definition
DNA polymerase 1
DNA polymerase 3
Primase
Term
Trp Operator
Definition
*a specific DNA sequence that is bound by proteins
Term
involves protein for direct function
Definition
ribosome
ligase
Term
compound involved in tRNA formation
Definition
ATP
CTP
GTP
UTP
Term
compound involved in DNA replication
Definition
ATP
CTP
GTP
TTP
UTP
Term
compound involved in miRNA formation
Definition
ATP
CTP
GTP
UTP
Term
Nucleosome
Definition
*allows packaging of DNA
*allows the cell to control transcription of DNA
Term
DNA polymerase
Definition
*required to remove incorrect bases during replication (3' - 5' exonuclease)
*required to remove RNAs during replication (5' - 3' exonuclease)
Term
Prevents strong expression of Lac Operon
Definition
*PRESENT: glucose
ABSENT: CAP-cAMP

PRESENT:glucose
PRESENT:glucose catabolite
Term
Promotes strong expression of Lac Operon
Definition
PRESENT:CAP-cAMP
ABSENT:glucose
Term
Tryptophan operator
Definition
*same box w/ promoter
Term
RNA polymerase bound when transcription bubble opens
Definition
*same box w/ promoter
*one before
Term
Stop codon RNA seq in same read frame as AUG
Definition
*promoter box
*protein ORF 2
*after ORF 2
Term
Ribosome binds @ translation start
Definition
*promoter
*ORF 1
Term
elements that regulate RNA of mRNA accumulation (euk terminates E)
Definition
*all
Term
Sigma factor bind to allow RNAP to start transcription bubble and allow 1st base to be incorpoarted into RNA
Definition
*before promoter
Term
RHO terminators
Definition
*all besides b4 promoter
Term
Functional ATG
Definition
*ORF 1,2
Term
Ribosome binds @ translation end
Definition
*ORF 2
*after ORF 2
Term
Functional Trp codons
Definition
ORF 1,2
Term
Stop codon RNA seq in diff read frame as AUG
Definition
*all besides b4 promoter
Term
Minimal size for functional RNA (B-D)
protein 100 AA
Definition
*310
Term
Euk transcrip vs prok
Definition
*euk trancripts have a cap structure that is 3' - G - 5' - PPP - 5'N
*introns in all euk transcripts marked by sequences at 5' and 3' ends of introns
Term
tRNAs exit ribo
EPA Translation
Definition
*below E
Term
tRNAs enter ribo
EPA Translation
Definition
*under A
Term
tRNAs ANY exit ribo
EPA Translation
Definition
*under E
*under A
Term
@ start translation, where tRNA w/ AA chain
EPA Translation
Definition
*under P
Term
@ end translation, where tRNA w/ AA chain
EPA Translation
Definition
*under P
Term
during translation, tRNAs w/ AA
EPA Translation
Definition
*under P
*under A
Term
during translation, tRNAs w/o AA
EPA Translation
Definition
*under E
*under P
Term
Scans region A to find start codon
EPA Translation
Definition
*3oS ribosome
Term
Components bound to allow initiation
EPA Translation
Definition
initiation factor (bound prior)
16S RNA
30S Ribosome
Term
Information contained ensure tRNA has correct AA attatched
EPA Translation
Definition
tRNA synthetase
tRNA
Term
Information contained ensure tRNA adds correct AA to growing chain
EPA Translation
Definition
tRNA synthetase
Term
part of translation uses only RNA/ protein in some form
EPA Translation
Definition
*recognition of shine delgarno
*recruitment of next tRNA
*termination
*growth of polpep chain
Term
provides E for translation
EPA Translation
Definition
GTP
Term
The Lac Operator
Definition
a specific DNA seq bound by protein
Term
Involves RNA for func
Definition
tRNA
Ribosome
Okazaki
rRNA
Term
How DNA Pol 1 minimizes errors in DNA replication
Definition
*selection of correct base by H bond betweenn DNA and new base
*3'-5' exonuclease mediated proffreading activvity
Term
Parts of diagram w/ no RNA
Definition
*outside buble DNA strand
Term
Why Okasaki
Definition
*DNA synt only goes 5'-3'
*DNA synth bidirectional
Term
Rho sequence
Definition
*a specific RNA proteins bound by protein
Term
Involves only protein for activity
Definition
*ligase
Term
Small Pitch
Definition
*ability to bend w/o crack
Term
Lrg Pitch
Definition
*ability to bend w/o crack
*largest pocket for transcription factors to interact w/ new bases
Term
Ribbons
Definition
*diester
*bonds critical hold DNA together
*deoxy ribose
*key info in bond histones
Term
Nucleic Acid
Definition
*Hbond
*N
*bonds critical to hold DNA together
*transcript fact trying to access DNA pol
*aromatic rings
Term
i
Definition
*repressor
i, i- = inducible transcrip
i-, i-= always transcrip
is = never transcrip

is > i+ > i-
Term
p
Definition
*promoter
*no p = no o
* p- = never transcrip

p+ > p-
Term
o
Definition
*operator
* oc = always transcrip
oc, oc = >is, always transcrip
o= bind repressor (no lact)

o+ > oc
Term
prioity
Definition
p > o > i > z,y
Term
[image]
Definition
B
E
Term
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Definition
A
E
Term
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Definition
D
E
Term
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Definition
E
Term
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Definition
D
E
Term
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Definition
B
C
Term
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Definition
A
D
Term
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Definition
A
B
C
D
E
Term
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Definition
B
E
Term
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Definition
A
C
E
Term
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Definition
D
E
C
Term
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Definition
C
Term
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Definition
A
B
Term
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Definition
C
D
Term
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Definition
A
B
D
Term
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Definition
E
Term
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Definition
C
Term
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Definition
Term
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Definition
Term
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Definition
Term
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Definition
Term
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Definition
Term
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Definition
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Definition
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Definition
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Definition
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