Genomics

Organizations of the human genome

Gene expression and regulation
DNA methylation Inactive for transcription (eg: X chromosome of mammalian)
Histone acetylation loosen nucleosome shape Easier transcription
Transcription control
Non-coding DNA/ Control elements regulates DNA transcription
Proximal CE: Close to promoter
Distal CE: Enhancers Sites bounded activators in order to loop the DNA bringing a specific promoter to the initiation complex
Transcription factor (Activator) Enhance RNA polymerase and promoter interaction
Transcription factor (Repressors) Bind to operator to repress transcription
Genes of related function are scattered over different chromosome Usually share similar regulatory sequence even though have individual promoter
Translational control
Duri g i itiatio regulatory protei a i d to leader
Protein factors can initiate translation simultaneously

RNA 5 Block ribosome attachment

DNA structure and function REVIEW MACROMOLECULES

Instability of the human genome:
Replication REVIEW MACROMOLECULES
DNA Mutation
Type
Synonymous mutation
Missense mutation
Nonsense mutation
Frame shift mutation

Feature
Nucleotide change to different codon but codes same amino acid
Does not affect product functioning
Nucleotide change to different codon which codes different amino acid
May or may affect product functioning
Nucleotide change to different codon which is a stop codon
Inactive gene product, truncated protein
Addition or deletion of nucleotide change in reading frame Incorrect AA coded
Inactive gene product

DNA repair
Only biomolecule DNA is repaired, others are replaced
Prevent cancer, cell senescence and apoptosis does not affect future generation
Repair types
Direct Reversal of Base damage
Single
Base excision repair
strand
Damage
Nucleotide excision repair

Mismatch repair

Double
strand
breaks

Non-Homologous end
joining
Homologous end joining

Damage type
Mostly alkylation
Single nucleotide
Alkylation, oxidation, deamination, hydrolysis
2-30 bases
Dimer induced by uv

Mismatch bases during DNA replication

(Non-Damage)
Failed proof reading
Ionizing radiation and certain chemical DNA
breaks Ends lose nucleotide
Detects by protein Ku

Translesion
synthesis

Mechanism
Glycosylation without breaking DNA backbone
Glycosylase Recognize and remove base Apurinic/apymidinic base
AP endonuclease removes AP site
DNA polymerase + DNA ligase--> Fills the gap
XPC protein Recognize thymine dimers
XPB and XPD protein Strand separation
DNA nuclease Incision
DNA helicase Removes entire oligonucleotide
DNA polymerase Fills gap
DNA ligase Ligates the new DNA fragment
Parental strand is methylated
Repair enzymes remove and replace non-methylated strand
Direct joining between DNA with loss of 1 or more nucleotide
Alters DNA by deletion or short insertion
Homologous recombination
Uses undamaged chromosome as template
DNA segment moves from one DNA molecule to another

Relationship between genes and proteins REVIEW MACROMOLECULES

a) Structure and function of proteins
b) Protein folding and conformation
c) Transcription into RNA
d) mRNA translation into proteins
Molecular pathology- Identifying human disease genes
Karyotyping
Displays of i dividuals hro oso es etaphase
Preparation: Blood (lymphocyte) add colchicine CentrifugationDiscard supernatant, mix cell with KCl Fixate cell on slide
Can discover gene disease from banding pattern
Type of staining
Preparation
Banding pattern
G Banding
Digestion with trypsinGiemsa stain
Dark bands AT
Light bands GC
R Banding
Heat with phosphate bufferGiemsa stain
Dark bands GC
Light bands AT
Q banding
Quinacrine
Dark bands AT
Light bands GC
C banding
Alkaline denaturation wash Renatured Giemsa stain
Dark bands Constitutive heterochromatin