Molecular Genetics Flashcards
Organization of DNA
- 3.3 billion base pairs
- 20,000 - 25,000 protein coding genes
- 20,000 - 25,000 non-coding genes (produce functional RNA)
- not random; some areas are gene-rich and some are gene-poor
Mitochondrial DNA
- circular molecule containing 37 genes
- some mitochondrial-related DNA present in nuclear DNA
DNA Structure
- consists of 3 key parts: nitrogenous base, deoxyribose sugar, phosphate group
- 4 nitrogenous bases: pyrimidines - C and T, purines - A and G
- molecule is 30 angstroms wide
- one full turn of DNA is 34 angstroms long and consists of 10 nucleotides, each 3.4 angstroms apart
- major groove is 24 angstroms long
- minor groove is 10 angstroms long
- strands of DNA are antiparallel and run in 5’ - 3’ direction
DNA Compaction
- DNA coils around histone octamer to form a nucleosome; “beads on a string”
- nucleosomes coil around one another to form a solenoid structure
- solenoids from loops and coils known as chromatin (interphase DNA)
- chromatin condenses into chromosomes during mitosis
DNA Replication
- 3 key features: semi-conservative, semi-discontinuous, bidirectional
- starts at replication origin and terminates at the telomeres
- involves several proteins: helicase, single strand binding proteins, sliding clamp, topoisomerase, DNA polymerase, primase, and ligase
- leading strand (3’ - 5’) replicated continuously
- lagging strand (5’ - 3’) replicated discontinuously through Okazaki fragments
- telomeres not usually preserved in somatic cells, which contributes to aging (senescence); in cells that do preserve telomeres, rely on telomerase to finish replication process and create single stranded end that protects DNA from degradation
Transcription
- generates mRNA molecule from DNA as part of the process to form a protein
- takes place in the nucleus and involves key proteins and regions of DNA: RNA polymerase II, transcription factors, promoter region, promoter activator sequences (enhancers)
- initiation of transcription starts at TATA box with binding of transcription factors
- RNA pol II binds and synthesizes RNA molecule
- mRNA extensively processed and modified
- 5’ end of mRNA is capped so molecule is stable, can be transported out of nucleus, and recruited to ribosomes
- introns spliced out via lariat formation by spliceosomes
- cleavage and polyadenylation of 3’ end to protect mRNA from degradation and help transfer it to cytoplasm
Translation
- process that converts mRNA into protein
- process requires ribosomes, tRNA, and amino acids
- takes place in 3 phases: initiation, elongation, and termination
- initiation of translation starts with recognition of start site (AUG)
- elongation involves polymerization of polypeptide
- termination is end of protein synthesis
DNA Regulation/Modification
- epigenetics (reversible changes that are heritable)
- DNA methylation
- imprinting
- histone modifications/variants
- environment and lifestyle
- RNA interference (form of mRNA degradation)
Mutations
- most mutations found within protein coding regions
- mutations affecting splicing, transcription, and other regulatory processes account for 10-20% of single gene mutations
- originate from errors introduced during DNA replication or from failure to properly repair DNA damage
DNA Repair
- types of problems to be fixed: wrong base inserted, base removed from backbone, damage to base (oxidation, deamination), cross-links (T-T dimers), double stranded breaks
- 6 repair mechanisms: 3’ - 5’ exonuclease proofreading, mismatch repair, base excision repair, nucleotide excision repair, non-homologous end joining, homologous repair
Primase
synthesizes RNA primers on template strands for DNA polymerase to attach to and continue synthesizing
Ligase
joins nucleotides together by forming phosphodiester bonds
Ligase
joins nucleotides together by forming phosphodiester bonds
RNA polymerase II
directs synthesis of RNA in 5’ - 3’ direction using DNA as a template; does not require a primer
Transcription factors
required for transcription initiation and recruitment of RNA pol II
Promoter region
provide specificity and determine how much RNA/protein made
Enhancers
modulate transcription from a distance; can be upstream, within, or downstream of a gene and are bound by specific proteins to regulate gene expression
Spliceosomes
large RNA-protein complex comprised of snRNPs
Isoforms
different proteins formed from the same gene as a result of alternative splicing of the same mRNA molecule
Amino acids
- basic building block of proteins and contain amino group (N-terminus), carboxyl group (C-terminus), and R side chain that specifies the type
- 20 amino acids in total
tRNA
- intermediary molecules that transfer amino acids to growing peptide chain during translation
- each amino acid has at least one specific tRNA
Ribosomes
- orchestrate process of translation by recognizing mRNA and initiating translation, recognizing tRNAs, and catalyzing peptide bonds
- made up of rRNA which comes from short arms of acrocentric chromosomes and chr 1
- contain 2 subunits: 40S and 60S
Nonsense mediated decay
- mechanism used by cells to decrease production of truncated proteins
- does so when it encounters a premature stop codon upstream of an exon junction complex
- cap of mRNA cleaved and mRNA molecule degraded
Features of the Genetic Code
- linear and read in non-overlapping triplets (codons)
- degenerate because most amino acids are specified by more than one codon
- unambiguous (AUG is always met, UUU is always phe)
- nearly universal between eukaryotes and prokaryotes (except mitochondria)
Silent mutation
alters codon but does not result in change in amino acid at that position of protein
Missense mutation
- ~50% of disease-causing mutations
- single nucleotide substitution that changes the coding strand of gene to specify a different amino acid
Nonsense mutation
- ~10% disease-causing mutations
- point mutation that causes replacement of normal codon with one of three stop codons
Frameshift mutation
- alters reading frame
- abnormal splicing: ~10-20% of disease-causing mutations
- insertions/deletions: ~30% of disease-causing mutations
Dynamic mutation
involves amplification of a simple nucleotide repeat sequence and often leads to genetic anticipation
Mutation effects
- loss of function
- gain of function
Mutation effects
- loss of function
- gain of function
3’ - 5’ exonuclease proofreading
exonuclease activity in DNA pol that proofreads the growing strand and fixes incorrectly incorporated bases
Mismatch repair
- used if proofreading does not catch a mutation
- repair enzyme complex removes mispaired base, DNA pol fills in gap, ligase seals nicks
Base excision repair (BER)
- occurs when purine or pyrimidine is damaged
- damaged based removed, DNA pol fills in gap, ligase seals nicks
Nucleotide excision repair (NER)
- occurs when bigger, bulky lesions distort double helic
- section of DNA surrounding lesion removed, DNA pol fills in gap, ligase seals nicks
Non-homologous end joining
- broken DNA ends are aligned and rejoined by DNA ligase
- can result in loss of nucleotides or lead to deletions, inversions, translocations
Homologous repair
- repair process that uses sister chromatids as templates for repair of damaged DNA strands usually after DNA replication occurs
- involves strand displacement, ligation, branch migration, and duplex separation for accurate repair without loss of information
