1.

Topoisomerase: responsible for relieving tension caused by supercoiling

a. I nicks one strand; is able to induce OR relax supercoiling
b. II nicks both strands to undo knots; can ONLY relax supercoiling
2. Histone proteins
a. H2A 2 molecules in nucleosome core
b. H2B 2 molecules in nucleosome core
c. H3 2 molecules in nucleosome core
d. H4 2 molecules in nucleosome core
e. H1 linker protein: interactions lead to secondary structure of
histones (30nm solenoid fiber)
3. Non-histone proteins (scaffolds): third level of chromatin condensation
4. POT-1 (protection of telomerase-1): protects the single-stranded molecule in
the bubble caused by displacement of the double-stranded molecule by t-
loop
5. TRF-1/2: responsible for creating the t-loop structure of a telomere
6. Shelterin: name for protein complex that is involved in telomeres
7. Dna: proteins involved in replication initiation in prokaryotes
a. A: binds to 9mer sites in oriC: causes DNA to bind around it, leading
to loosening of strands at 13mer
b. B: helicase: unwinds further
c. C: binds but then is released; pretty much useless?
8. RNA polymerase (primer): lays down primer for the intuition of the leading
strand and for the lagging strands Okazaki fragments
9. Nucleosome assembly protein 1 (NAP-1) brings histones into nucleus
during replication due to need for double the number of histones
10. DNA Pol III:
a. Beta subunit: clamps the molecules to the DNA
b. Catalytic Core:
i. Alpha subunit: actual polymerase
ii. Epsilon subunit: proofreading subunit
1. Exonuclease: ability to cut from the end of a nucleic acid
iii. Gamma: holds everything together
iv. Delta: who knows
11. Single-stranded binding proteins: bind to single stranded molecules after
helicase unwinds them: prevents reannealing
12. DNA Pol I: chews out RNA primers and adds nucleotides
13. DNA ligase: joins the Okazaki fragments (phosphodiester bond)
14. Tus proteins: involved in termination in prokaryotes: bind to Ter sites
prevent growing forks from moving past termination point
15. DNA Pol:
a. Epsilon: lagging strand synthesis
b. RNA primer (primase): creates primers for initiation of leading
strand; okazaki fragments
c. Alpha: elongates primers
d. Delta: lagging strand: synthesizes the rest of the Okazaki
fragment
e. Ribonuclease: removes RNA (not Pol I)
16. Replication Protein A: equivalent to Single stranded binding proteins in
prokaryotes
17. PCNA clamp: clamps the Pol to the DNA molecule
18. CAP-1/NAP-1: chromatin-assembly factor/nucleosome-assembly factor-1:
responsible for bringing in more histones due to the double demand from
replication
19. Telomerase: creates telomeres by repeating sequence
20. Holoenzyme: core enzyme required for transcription in prokaryotes
a. Sigma factor: provides specificity by being specific to certain
promoter
21. Rho: involved in transcription termination in prokaryotes: binds to rut site
(G+C rich) and then when RNA pol is stalled at stem-loop, zooms past it and
causes detachment of mRNA from DNA
22. TFIID: Binds to RNA Pol II in eukaryotes to initiation transcription
23. RNA Pol II: polymerase involved in eukaryotic transcriotion
24. FACT: chaperone protein that holds nucleosome when RNA polymerase goes
past it and then replaces it
25. ASFI: same as FACT
26. ___-methyl transferase: series of enzymes associated with the formation of
the 5 Guanine cap at the beginning of transcription
27. Endonuclease: an enzyme with the ability to cut the middle of a nucleic acid
strand
28. Exonuclease: an enzyme with the ability to cut at the end of a nucleic acid
strand
29. Poly(A) polymerase: protein involved in the formation of the Poly(A) tail
a. Cell will transcribe past the end point: allows for AAUAA to be
released from ribosome, which is cleaved by endonuclease and signals
the Poly(A) polymerase to synthesize the tail
30. snRNP: involved in intron splicing during RNA processing
a. U1: binds to the exon 1 intron site
i. Binds to U2 to form the circular intron form
b. U2: binds to branch point A
c. U4/6: last part of complex: brings everything together
d. U5: binds to the exon 2-intron site
31. RNA-binding deaminase: deaminates the C to form U
32. Editosome: cleaves the RNA wherever it doesnt match with gRNA to allow
for the addition of Us during RNA editing
33. RNA ligase: once Us have been added in RNA editing forms phosphodiester
bond to relink the mRNA
34. Terminal U transferase: adds U to cleavage point during the insertion of U
(using gRNA)
35. Aminoacyl-tRNA synthetase: charges tRNA with amino acid
36. Initiation Factor:
a. 2: binds to the f-met tRNA
b. 3: binds to the 30s ribosome subunit to promote binding to the Shine-
Delgado sequence
37. EF-Tu: elongation factor that is bound to tRNAs in the cell and brings it to the
A site of the ribosome
38. EF-Ts: recharges the EF-Tu with GTP
39. Peptidyl transferase: forms bond between amino acid in tRNA in P site and in
A site
40. EFG: promotes translocation of the ribosome/mRNA complex during
translation
41. Release Factor: when ribosome encounters stop codon, this is what replaces
the tRNA and binds to it, prompting release of ribosomal complex,
polypeptide and mRNA
a. 1: UAA, UAG
b. 2: UAA, UGA
42. Eukaryotic Release Factor (eRF): release factor in eukaryotes
43. Photolyase: repairs damage from thymine dimers: locates and then breaks
the internucleotide bond
44. Glycosylase: repairs mismatch: specific to each base pair; excises but doesnt
break phosphodiester bond in mismatch repair
45. AP Endonuclease: removes the sugar-phosphate in mismatch repair
46. Phosphodiesterase: breaks phosphodiester bonds in mismatch repair
47. LexA: SOS genes inhibitor; bound to promoter
48. RecA: binds to ssDNA complex breaks LexA allows for SOS to be
expressed when cell is shocked
49. UVR: repair thymine dimers when UV damage is too severe for photolyase
a. A: complex of A and B locate the thymine dimer and then A is release
b. B: nicks the 3 end of the area; replaced by Pol I and then by ligase
c. C: nicks the 5 end
d. D: helicase: unwinds and removes the nucleotides;
50. Mut: involved in mismatch repair
a. S: binds to mismatch
b. L: binds with MutH
c. H: endonuclease: cleaves at nearest GATC (either 3 or 5)
d. U: DNA helicase II: together with exonuclease removes strand
from mismatch to nick
e. DNA polIII repairs gap and Ligase seals
51. Lambda integrase: involved in the integration of lambda DNA into the
bacterial cell
52. LacI: lac repressor: binds to the operator sequence and prevents RNA pol
binding
53. Beta-galactosidase: converts lactose into its monomers
54. Allolactose: inducer: binds to LacI and allosteric shift causes removal from
operator allows transcription
55. cAMP: lac operon positive control: is produced when there is low glucose,
and thus, low ATP binds to CAP to then have the complex bind to the
promoter and enhance transcription initiation rate
56. CAP: binds to cAMP to enhance the transcription of lac in the absence of
glucose
57. Leader polyeptide: in trp operon; nonfunctional protein that requires trp in
its translation and stalls ribosome on sequence 1 so 2 and 3 can bind and
transcription can continue
58. CI: lambda repressor: coded for by PRM and invreased by PRE
59. Cro: promotes lytic cycle by downregulating CI
60. CII: when stabilized, allows transcription of PRE otherwise, degraded by
FtsH
61. CIII: stabilizes CII
62. FtsH: degrades CII
63. N: binds to nut sites to prevent rho-dependent termination at Tr and Tl sites
in lambda
64. Tra/Tra2: sex lethal genes: alternative splicing: if exon 3 is spliced out, then
Tra will form a functional protein (in females, basically) if both Tra and Tra2
are present female
65. Transcription Factor: any protein that binds to DNA to regulate transcription
66. Activator: binds to enhancer sequence and bends DNA around it so activators
are physically present at promoter
67. Coactivator: presence needed for TF to activate transcription
68. DNA-binding domain: parts of TF that binds to DNA-binding domain
69. Activation domain: involved in actual activation
70. Zinc-finger motif: 2 Cys and 2 His interact around Zn to form a finger that sits
on DNA
71. Helix-turn-helix: 3 alpha helices that turn around each other
72. Gal4/Gal80: UAS Gal 4 is TF but Gal80 makes it inactive form by binding to
activation site
73. Dicer: cleaves the double-stranded RNA into smaller RNA to form RISC
74. HAT: add acetyl to histones to open it
75. HDAC: deacetylizes histones to condense it
76. MeCP2: methylates CpG island to silence genes
77. pRB: tumor suppressor gene that binds to transcription factor E2F, holding it
in check
a. phosphorylated by cyclin/cdk
78. p53: checks that cell is healthy enough to divide
a. Cell-arrest pathway
i. proteins that repair DNA damage phosphorylate and activate
p53 activate p21 synthesis
1. p21 downregulates CDK
2. pRB remains bound to E2F no transcription of target
genes
b. Apoptic pathway:
i. Very high p53 activation: increased synthesis of BAX
downregulation of BCL-2
1. Normally represses apoptosis: absence cell
destruction
79. pAPC: tumor suppressor
a. B-catenin in young cells binds to signal protein and acts as
transcription factor involved in cell growth
b. Cell ages: pAPC binds to and degrades B-catenin, downregulating cell
growth
c.