Chapter 5: Genetics Flashcards
4 RNA nucleotides
- Nucleotide (triphosphate), nucleoside (no phosphate)
1a. Purines: double ringed->Adenine (NH2) and guanine (O)
1b. Pyramidines: single ringed->uracile (O) and cytosine (NH2) - If DNA…thyamine instead of uracile (Thyamine looks like uracile + methyl)
Genetic code
- Unambiguous: each codon can code for only 1 amino acid
- Degenerate/redundant: 1 amino acid can have been translated by up to 6 codons (6 codons-> 1 amino acid)
- Universal: all organisms have same codon amino acid pairing
Important codons to know
- Stop: UAA, UGA, UAG
- Start: AUG
Central dogma of biology
- States that genetic info can be transferred between DNA and DNA, between DNA and RNA, between RNA and RNA or from RNA to protein
Gene
- Segment of DNA that code for RNA
- Genes are regulatory sequences of DNA: meaning that they increase or decrease the expression of a gene
Genome
- An organisms complete set of DNA: (nuclear genome: 23 chromosomes/linear and mitochondrial genome: 1 chromosome/circular)
- Single copy dna (scDNA): genes that code for proteins in humans
Components of genome
- Coding DNA sequence (CDS/exons) only accounts for 1.5% of genome…many other parts (introns, and ncRNA)
- Moderately repeating sequences/transponons: DNA a sequences that can move from one location to another in genome (45%)
2a. Long interspersed elements (LINE): contain genes for reverse transcriptase and endonuclease
2b. Short interspersed elements (SINE): no protein coding genes but co opt proteins from LINE and host cell - Highly repeatitive sequences/ simple sequence repeats (SSR)/satellite DNA: are centromeres an telomeres
Single copy vs repetitive sequences
- Single-copy DNA is a unique sequence that code for proteins and undergoes transcription. These are found in exons or the euchromatin
- Repetitive DNA is the sequence that has repeated sequences of nucleotides in the DNA and that don’t code for proteins.
Bacterial vs eukaryotic genome
- Bacteria: polycistronic, colinear, mostly single copy, mostly protein coding
- Eukaryotic: monocistronic, noncolinear, half single copy, mostly non coding
DNA replication overview
- During S phase
- Semiconservative: each daughter double strand contains one strand from parents and one new one
- Replication is bidirectional: has 2 replication forks
DNA replication: initiation
- Starts at the origin (eukaryotes have multiple on linear chromosome ; prokaryotes have one on circular chromosome)
- Eukaryotes have origin of replication complex (ORC) that binds each origin
- ORC recruits helicase that unwinds DNA double helix (breaks H bonds) via ATP hydrolysis which creates 2 replication forks
3a. Replication forks are bidirectional: leading strand is 3’->5’ and lagging strand is 5’->3’ Leading strand (3’->5’): easy - RNA primer is added via DNA primase
DNA replication: elongation
- Organisms
1a. Bacteria: Polymerase 3 binds to site of primer and adds new base pairs complementary to the strand during replication
1b. Eukaryotes: Polymerase alpha, beta, and epsilon does so - Strands
2a. Leading strand: easy because replication occurs in 5’->3’ direction
2b. Lagging strand: binds multiple primers and DNA polymerase adds DNA called Okazaki fragments to strands between primers (discontinuous)
DNA replication: Termination
- Exonuclease removes all RNA primers and these primers are replaced w bases
- Another exonuclease proofreads
- DNA ligase joins Okazaki fragments
- Telomerase catalyzes synthesis of more telomeres
DNAP
- Proofreader using 3’->5’ exonuclease activity for accuracy
- Fidelity of replication: determined by accuracy of base selection (DNAP is highly specific)
- If a base is in tautomeric form: DNAP may mismatch base pair which may cause replication to hault for a bit during elongation
MMR: mismatch repair
- Complex process involving several proteins that identify, excuse and replace entire section of strand during elongation
Important types of RNA
- MRNA (messenger RNA): carries code dictating amino acid
- TRNA (transfer RNA): translates genetic code from nucleotides to amino acids
- RRNA (ribosomal RNA): catalyze formation of peptide bonds
- MiRNA (microRNA): regulates gene expression by inhibiting translation or promoting degradation of mRNA
- SnRNA (small nuclear RNA): Splices introns from mRNA
- SnoRNA (small nucleolar RNA): modifies ribosomal RNA
Transcription overview
- Occurs in nucleus (eukaryotes)
- DdDNA->ssRNA
2a. Transcribed DNA: template strand (3’->5’)
2b. Not transcribed: Coding strand (5’->3’) - Transcription unit: exons, introns and UTRs
Operon (prokaryotes)
- RNA transcripts are transcribed from operons (promotor, operator, transcription unit (polycistronic:carries products for more than 1 gene) and terminator)
- Promotor is where transcription is initiated after DNA polymerase binds
Enhancer and silencers (eukaryotes)
- Regulate sequence when bound by transcription factors
Transcription factors (eukaryotes and prokaryotes)
- Activators and repressors are transcription factors that bind to enhancers and silencers respectively
- Can lead to positive regulation or negative regulation
RNA polymerase
- RNAP: transcribes RNA from DNA
1a. RNAP 1: rRNA
1b. RNAP 2: transcribes mRNA
1c. RNAP 3: transcribes tRNA - RNAP 2 binds to the TATA box within the promotor
Transcription: DNA->pre-mRNA
- Initiation: RNA polymerase binds to promotor on template strand
1a. Template strand (3’->5’): identical to DNA replicated
1b. Coding strand: complementary to DNA strand and exact same as pre-mRNA made (except U and T) - Elongation
2a. RNA polymerase builds mRNA by adding complementary base pairs except A->U to template strand (3’ -> 5’) in 5’ to 3’ direction
2b. RNA transcript is identical to coding strand except - Termination: RNA polymerase crosses termination site
The lac operon
- Jacob Monod model of open: regulation of prokaryotic gene expression
The trp operon
- Promote biosynthesis of amino acid trp
- If trp is present, the trp operon is turned off which blocks transcription of trp open
- If no trp, operon is not repressed and structural genes are transcribed…and trp is synthesized
Transcriptional ground state
Epigenetics regulation to DNA
- Histone acetylation (=active): acetyl added to lysine which loses charge and unable to interact w DNA backbone=loosens DNA=euchromatin=high gene expression
- Histone deacetylation: removes acetyl so lysine is charged=interacts tight w DNA=heterochromatin=no gene expression
- DNA methylation (=mute): adds methyl to cytosine =DNA tight=heterochromatin=low gene expression
- Demethylation: DNA loose=euchromatin=high gene expression
Post transcriptional processing: Pre mRNA -> mature mRNA
- 5’ cap added: 7-methylguanosine cap
- 3’ Poly A tail
- Pre-mRNA splicing: splice out introns
- Now mRNA exits nucleus
Protein synthesis: activation of tRNA
- Before translation, each tRNA is covalently bound to its amino acid
- A mature tRNA has 4 arms: acceptor (amino acid) arm, anticodon arm, D arm and T arm
Translation: mRNA->protein
- Initiation
1a. Ribosome subunits get together
1b. TRNA carries UAC and methionine to 5’ end of mRNA by recognizing 5’GTP and it walks to 3’ direction until it recognizes a AUG and translation starts at P complex - Elongation
2a. New codon goes to A site and tRNA binds at that site with the codons anticodon
2b. Peptide bond then forms which connects amino acids together and transfers methionine from first tRNA to second tRNA in A site
2c. Empty tRNA then exits via E site
2d. A site is exposed and cycle repeats - Termination: When stop codon in mRNA (UAA, UGA, UAG) enters A site
Protein synthesis: PTM folding /processing
- New polypeptide chain needs to fold to its native conformation: primary, secondary, tertiary and quaternary structure
- Next they undergo processing:
2a. Proteolysis: activation by polypeptide cleavage
2b. Phosphorylation: of S, T, Y
2c. Glycosylation: add sugar
2d. Acetylation: affect stability
2e. Methylation: affect protein-protein interactions
2f. Ubiquitination: degradation
2g. Prenylation: add lipid to anchor to membrane
2H. Sulfation: add sulfate
2i. Disulfide bond: cysteine-cysteins
Location of protein synthesis
- Translation begins on free floating ribosome: polypeptide may have signal sequence at N term to direct it to part of cell
1a. If going to ER, Golgi, lysosome or cell membrane: When signal sequence is translated, it is recognized by SRP which haults translation…when it binds SRPR on RER translation continues (cotranslational translocation)
1b. If staying in cytosol will have MTS (mito), PTS (peroxisomes) or NTS (nuclear)
G0 phase (quiescence)
- Cell is metabolically active /not preparing for cell division
- Cells enter here bc damage/stress, specialization/differentiation, age, regular function
Cell cycle
- Interphase
1a. G1: cell grows in size
1b. G1 checkpoint: checks if cell size, nutrient availability, growth factors and integrity if DNA is all good (if not…goes to GO)
1c. S: cell undergoes replication
1d. G2: cells continue to grow and makes proteins for chromosome migration
1e. G2 checkpoint: ensures DNA is free of both damage and errors from replication…and that there is mitosis promoting factor (MPF) - Mitosis
Mitosis
- Prophase: chromosome condense, centrosomes move to poles, mitotic spindle forms, nuclear envelope breaks down
- Metaphase: mitotic spindles align chromosomes which forms metaphase plate…spindles attach to kinetochore at centromere of each chromatid
- Anaphase: chromatid separation/disjunction
- Telophase: reform nuclear envelope
- Cytokinesis: cell splits along cleavage furrow
Meiosis
- Meiosis 1 (2n->n)
1a. Prophase 1: synapses and crossing over occur
1b. Metaphase 1: homologs line up
1c. Anaphase 1: separation of homologous chromosome
1d. Telophase 1: reformation - Meiosis 2 (n->n)
2a. Same steps
Mitosis vs meiosis
- Mitosis: somatic cells, 2 identical cells, diploid->diploid, 1 division
- Meiosis: germ cells, 4 nonidentical cells, diploid->haploid, 2 division
Spermatogenesis vs oogenesis
- Spermatogenesis: spermatogonium (2n), primary spermatocytes (2n), meiosis 1 forms 2 secondary spermatocytes (n), meiosis 2 forms 4 spermatids (n), differentiation makes spermatozoa
- Oogenesis: oogonium (2n), primary oocyte is arrested at prophase 1 (2n), meiosis 1 causes 1 secondary oocyte+ 1 polar body (arrested at metaphase 2), fertilization induces meiosis 2 which completes and the fertilizes zygote is 2n + polar body
Mutation types
- Point mutation
1a. Silent: doesn’t affect amino acid
1b. Missense: changes amino acid, but may or may not affect function
1c. Nonsense: premature stop codon - Insertion/deletion
2a. Frameshift: nucleotides are added or deleted in a number not divisible by 3 causing a change in reading frame
Mutation types
- Point mutation
1a. Silent: doesn’t affect amino acid
1b. Missense: changes amino acid, but may or may not affect function
1c. Nonsense: premature stop codon - Insertion/deletion
2a. Frameshift: nucleotides are added or deleted in a number not divisible by 3 causing a change in reading frame
Chromosomal aberration
- Deletion
- Duplication
- Inversion: portion of chromosome is revrsed
- Translocation: portion of chromosome is moved to another chromosome
- Aneuploidy: diff number of chromosmes
Genetic recombination
- DNA sequences are rearranged but not changed
6 hallmarks of cancer
- Self sufficiency in growth signals
- Insensitivity to anti growth signals
- Evasion of apoptosis
- Limitless replication potential
- Sustained angiogenesis: stimulate formation of blood vessels which provide O2 to cancer cells
- Tissue invasion and metastasis:
6a. Metastasis: when cancer breaks away from primary tumour to make secondary ones: includes invasion, intravastion, extravasation and colonization
Hayflick limit
- Limited number of divisions of a cell
Tumours/neoplasm
- Abnormal mass of cells that grow at a excessive rate and can be benign (noncancerous) or malignant (cancerous)
- Proto oncogenes: genes that can cause cancer via uncontrolled cell growth … oncogene is a proto oncogene that has mutated or is overexpressed