Exam 2- Fxns and Dysfunction in Genomic Regulation Flashcards
Central dogma of molecular biology
- DNA to RNA via transciption
- RNA to protein via translation
- DNA replication via mitosis
meiosis
-transfer of genetic information from parent to offspring
exclusive carrier of information from DNA to protein
mRNA
RNA virus
- can be reverse transcribed into DNA using reverse transciptase
transcription vs translation
- transcription is DNA to RNA (same language)
- translation if RNA to protein (different language)
structure of DNA
- DNA is double stranded and antiparallel
- strands connected by hydrogen bonds between nucleotides
- strands are polar with a 5’ and 3’ end
- sugar-phosphate backbone forms major and minor grooves
Hydrogen bonds between nucleotides
- G to C has 3 H-bonds
- A to T has 2 H-bonds
importance of condensation of mitotic chromosomes
- mitotic chromosomes are condensed to prevent physical damage to DNA when cells are separated and DNA is passed on to daughter cells
DNA packaging
- DNA is wrapped around histone octamer using hydrogen bonds to form nucleosomes
Histone proteins
- 20% of histone proteins AA residues are Lys or Arg (have NH+ group)
- Lys and arg are targets of PTM
- histone proteins are highly conserved across species
nucleosome
- basic unit of chromosome packing
- each nucleosome core consists of a complex of 8 histone proteins
histone octamer
- protein around which DNA is wound
- protein + DNA= chromatin
euchromatin
- lightly packed form of chromatin
- often under active transcription
- most active part of genome
- 92% of human genome is euchromatin
heterochromatin
- very condensed chromatin
- seemingly genetically inactive
- highly concentrated at centromeres and telomeres
- very few active genes, those that are presents are resistant to gene expression
- position effect: activity of a gene depends on relative position on the chromosome
What information is found on chromosomes?
1) genes (encoding proteins and RNA molecules)
2) interspersed DNA that does not contain genes (regulatory information, “junk” DNA)
year watson and crick describe the double helical structure of DNA
1953
year nirenberg, khorana and holley determin the genetic code
1966
February 2001
the sequence of the human genome (human genome project) was announced, it was only 90% completed, finished in 2004
percentage of DNA sequence in exons (protein coding sequences)
1.5%
microRNA
1) precursor folds back on itself using H bonds
2) Dicer moves along double stranded RNA and cuts it into shorter segment
3) 1 strand of the small segments is degraded and the other associates with a complex of proteins
4) bound miRNA wan base-pair with any target mRNA that contains a complementary sequence
5) miRNA either induce degradation of mRNA or block translation of mRNA
Coding sequences of DNA and RNA
- exons
- they are spliced together out of mRNA
Start/end sequences of introns
intron mRNA sequences start with GT and end with AG 99% of the time
Histone deacetylation
- actively represses gene expression
- deacetylated chromatin is very compact and transciptionally repressed
Histone acetylation
- actively promotes gene expression
- acetylated chromatin is open and transciptionally active
- mediated by binding of transcription factors
nuclear receptor signaling
- lipophilic ligands (cholesterol derivatives) pass through the PM and nuclear membrane to bind to the DNA and cause transciptional modifications
Post translational modifications of histones
- alter histone interactions with DNA and nuclear proteins
- histone protein tails are the target of multiple PTMs
- most PTM focus on lysine and arginine residues
DNA methylation
- methy groups added to DNA by methyl transferase
- changes activity of DNA sequence
- represses gene transcription when at promoter
PTM phosphoylation
often occurs at serine or threonine residues
CpG Islands and Methylation
- CpG islands in promoter acquire abnormal hypermethylation
- silences gene
- can be inherited by daughter cells
Hypomethylation
- chromosomal instability
- loss of imprinting
nucleoside analog inhibitors
- DNA polymerase requires a primer with a free 3’ -OH to begin processing
- nucleoside analog inhibitors lack a 3’ -OH group and act as drugs that inhibit DNA replication i.e. cytarabine, acyclovir for herpes virus, and AZT for HIV
DNA replication is..
- semiconservative
- bi directional with replication fork
- semi- discontinuous (continuous leading strand synthesis, discontinuous/segmented lagging strand synthesis)
Okazaki fragments
segments of DNA from lagging strand during DNA synthesis
DNA helicase
- pries apart the helix/unwinds DNA during synthesis
- binds and hydrolyzes ATP
Single-stranded DNA binding protein
- binds cooperatively to exposed ssDNA
- helps stabilize unwound DNA and straightens DNA
- prevents formation of hairpins
topoisomerase
- relieves over-wound supercoils
- like untangling old phone cord
- pharmaceutical drugs that target/inhibit DNA topoisomerase are used as anti-cancer agents (harm integrity of genome- lead to apoptosis)
DNA ligase
It has three general functions: It seals repairs in the DNA, it seals recombination fragments, and it connects Okazaki fragments
DNA polymerase
are enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA.
Ionizing radiation (x-rays)
can damage DNA by:
- DNA strand breaks
- chemical modification of bases
- DNA and proteins form cross-links
nonionizing radiation (UV light)
- can create pyrimidine dimers or 6-4 cross linkages between 2 pyrimidines (thymine dimers)
spontaneous DNA damage
- caused by endogenous agents
1) depurination of Adenosine and guanine by removal of their bases (hydrolysis of N-glycosyl linkage)
2) deamination of adenine/guanine/cytosine to generate hypoxanthine/xanthine/uracil - can result in base deletion or substitution
Thymine modifications
- formation of thymine dimers
- 6’-4’ covalent linkages of thymine bases
intercalation
substance inserts itself in between DNA bases and damages DNA (thalidomide)
direct repair
- enzymatic repair
- damage repaired: pyrimidine dimers, O6-methylguanine
base excision repair (BER)
Damage repaired: single-base mismatches, nondistorting alterations (i.e depurination)
nucleotide excision repair (NER)
- damage repaired: chemical adducts that distort DNA( pyrimidine dimers, BPDE-guanine adducts, cisplatin adducts)
- associated disorder: Xeroderma pigmentosum
mismatch excision repair (MER)
- damage repaired: mismatched base in daughter strand
- associated disorder: Hereditary nonpolyposis colorectal cancers
recombination repair/ homologous recombination
- damage repaired: double-strand breaks, interstrand cross-linking
- associated disorder: BRCA 1/2 breast cancer
transcription coupled repair (TCR)
- damage repaired: stalled RNA polymerase during transcription (not replication)
- associated disorder: Cockayne syndrome
Xeroderma pigmentosum
phenotype: skin CA, UV sensitivity, neurological abnormalities
process affected: nucleotide excision repair
Hereditary nonpolyposis colorectal cancer
process affected: mismatch repair
Hereditary nonpolyposis colorectal cancer
process affected: mismatch repair
-inherited in an autosomal dominant manor
cockayne syndrome
Phenotype: developmental and neurological delay, photosensitivity, and progeria
process affected: transciption coupled repair
- if DNA is not repaired then this leads to early cell death
BRCA associated breast CA
phenotype: breast, ovarian and prostate CA
process affected: repair by homologous recombination
- BRCA genes are tumor suppressor genes
