CELL BIOLOGY

Ribose Sugar contain OH group at 2nd position

Deoxyribose Sugar doesnt contain OH group at 2nd position
Purines: 2 rings [Adenosine(A), Guanine (G), Xanthine, Hypoxanthine, Uricacid]
- A is identified by NH3 group.
Pyrimidines: 1 ring [C, U, T]
- U precursor of both C & T [C contains NH2 & T contains CH3]
- Amination of U C [deamination of C gives U]
- Methylation of U T [demethylation of T gives U]
% Purines = % Pyrimidines
[ % of A = % of T(or % of U), % of G = % of C]
A-T double bond, G-C triple bond

B DNA Watson Crick DNA, Rt. handed, 10 base pair (bp) per turn, sugar PO4
Z DNA GC rich, Lt. handed
Denaturation occurs by heat & Renaturation occurs by cooloing
Supercoiling more twisting
- DNA gyrase (topoisomerase-2) negative supercoiling (remove positive)
- Topoisomerase-1 positive supercoiling (remove negative)
Histone Protiens (Lysine & Arginine) - +ve charged
H2A, H2B
H3, H4 - form octamer DNA wound around the outside of octamer

H1 linker DNA found b/w nucleosomes to help package them into solenoid like
structure (30 nm)
Without H1 (10 nm fibers) sensitive to Endonucleases [10 nm fibers are first
fibers to destroyed in apoptosis]
Basic PH decrease Histone activity fibers susceptible to endonucleases

Sequences are always specified as 5 3

DNA & RNA Synthesis:

Similarities: Always synthesize in 5 3
Template 3 5
Newly synthesize strand is complementary & anti-parallel to
template strand.
Differences: DNA contains T, RNA contains U
DNA Polymerase (DNAP) require primers [RNAP doesnt]
DNAP proof read (check error) [RNAP doesnt]
RNA is anti-parallel & complementary to DNA template strand; RNA is
identical to DNA coding strand (except U substitutes for T in RNA)

DNA Replication: [Prokaryote Pro, Eukaryote Eu]

- Recognition of origin of replication: dna A protein in Pro; unknown in Eu
- Unwinding of DNA double helix: Helicase [in both]
 - Stabilization of unwound template strand single stranded DNA-binding
protein (SSB) [in both]
- Synthesis of RNA primers Primase [in both]
- Synthesis of DNA Leading strand DNAP3 in Pro; DNAP in Eu
Lagging strand DNAP3 in Pro; DNAP in Eu
- Removal of RNA primers DNAP1 (5 3exonuclease activity) in Pro;
unknown in Eu
- Proof Reading DNAP3 (3 5exonuclease activity) in Pro
DNAP (&) (3 5exonuclease activity) in Eu
- Joining of Okazaki fragments DNA Ligase [in both]
- Removal of positive supercoiling DNA gyrase (topoisomerase-2) [in
both]
- Synthesis of telomeres Telomerase in Eu; not require in Pro

Telomerase: work at 5 end as reverse transcriptase, contain a short RNA

template complementary to DNA telomere sequence.
snRNA (small nuclear RNA): participate in splicing mRNA (remove introns)
Ribosomes: 70s (30s & 50s) in Pro; 80s (40s & 60s) in Eu
tRNA: Acceptor arm carry AA [amino acid]; Anti-codon arm anti-codon
complementary & anti-parallel to codon in mRNA.
mRNA: code for various AA
rRNA: structural form of ribosomes
RNA: tRNA smallest speices; mRNA & hnRNA largest species. On
electrophoresis smallest species migrate farthest.

farthest

Synthesis of RNA (Transcription):

- Gene region: may be polycistronic (in Pro) & very little spacer (non-
coding) DNA b/w gene (in Pro). Always monocistronic (in Eu) &
large spacer (non-coding) DNA b/w gene. Gene have exons & introns.
- RNA Polymerase: core enzyme 2 [in Pro]
RNAP1 rRNA (nucleolus) [28s, 18s, 5.8s]
RNAP2 mRNA, snRNA (nucleoplasm) [in Eu]
RNAP3 tRNA, 5s rRNA (nucleoplasm)
- Initiation of transcription:

In Pro In Eu
Promoter (-10) TATAAT & (-35) (-25) TATA & (-70) CAAT
sequence sequence
Sigma initiation subunit Transcription factor (TFIID)
required to recognize promoter bind promoter
 - mRNA synthesis: template strand 3 5; mRNA synthesize in 5 3;
gene sequence specified from coding strand in 5 3; transcription
begins at +1 base.
- Termination of transcription: unknown in Eu.
Stem & loop +UUUU
Stem & loop +rho factor in Pro
- Post-Transcriptional modification: none in Pro
In Eu: in nucleus: 5 cap (7-methyguanine)
3 cap (poly-A sequence)
Removal of introns from hnRNA by snRNA

Synthesis of Protein (Translation):

- Genetic code: Start AUG (methionine)
Stop UAA, UAG, UGA
- Methionine & Tryptophan only one codon
- Remaining AA more than one codon; often differ at base 3. (first two
bases are same) eg.: Leucine CUU, CUC, CUA
- 4 high energy phosphate bond require to insert 1 AA (2 ATP & 2
GTP)
- AA activation: Aminoacyl-tRNA synthase, two high energy bond
(ATP) to link AA to tRNA.
- Initiation: [eIF-2]
In Pro In Eu
30s subunit binds to shine- 40s subunit associates with 5
Dalgarno sequence on mRNA cap on mRNA
Fmet-tRNA1 binds to P-site Met-tRNA1 binds to P-site
GTP required GTP required
- Elongation [eEF-2]: charged aminoacyl-tRNA binds to A site (GTP);
peptide bond forms [peptidyl synthase (50s subunit in Pro)(60s subunit
in Eu)]
- Translocation: GTP required
- Termination: release of protein, protein synthesize in N C direction
- Protein targeting: (not in Pro.) In Eu:
Secreted or membrane protein: N-terminal hydrophobic signal
sequence encoded by First exon of gene. Occur in rough endoplasmic
reticulum (RER). Dolichol phosphate lipid required.
Lysosomal Enzymes: Phosphorylation of mannose in Golgi apparatus.

DNA repair:
- Thymine Dimers (G1): due to UV radiation; Excision endonucleases
recognize & excise it. (This enzyme is deficient in Xeroderma
Pigmentosa) DNAP & DNA Ligase are repair enzymes.
- Mismatched Bases: occurs in G2 phase; deficiency in the ability to
repair mismatched base pairs in DN leads to Hereditary Non-Polyposis
Colorectal Cancer (HNPCC)
 Regulation of Gene Expression:

Prokaryote: Lactose Operon; Attenuation

Lactose Operon:
- Lactose: induce gene expression for lactose metabolism by preventing
the repressor protein binding to operator sequence
- Glucose: repress gene expression for lactose metabolism by decreasing
cAMP in the cell and thus preventing cAMP dependent activator
binding to CAP site (cAMP dependent Activator Protein site).
- In the absence of lactose, repression protein binds to operator protein
& prevent gene expression.

Attenuation: Premature termination of transcription (not possible in Eukaryote

b/c in eukaryote, transcription and translation not occur simultaneously. Both
transcription & translation are independent events in Eu)
- High Histidine: rho-independent terminator to form; RNAP stops
transcription.
- Low Histidine: prevent terminator formation; RNAP continues
transcription & transcription of message produce all enzymes require
for Histidine biosynthesis.

Eukaryote: (regulation of gene expression)

Upstream Promoter Elements:
- TATA box (-25) general transcription factor (TFIID) binds here
- GC rich SP-1 binds here
- CCAAT box (-75) NF-1 binds here
Enhancers: (response elements) activator proteins bind here.
Silencers: repressor proteins bind here.
Transcription factors:
- DNA binding domain:
Zinc fingers (steroid hormone receptors)
Leucine Zippers (cAMP dependent transcription factors)
Helix-turn-helix (Homeodomain protein)
Act ivat ion Do main:
- Binds to other transcription factors
- Recruit chromatin modifying proteins such as histone acetylase (favor
gene expression) or deacetylase (favor inactivate chromatin)
Homeodomain Proteins: control embryonic gene expression & are regulated
by Homeobox (HOX) / homeotic gene & paired box (PAX) gene.

Klein- Waaredenberg Syndrome:

- Mutation in PAX gene.
- Dystonia Canthorum (Lat. displacement of inner corner of eye).
- Pigmentary abnormality.
- Congenital Deafness, Limb abnormalities.