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APrep101: BioBiochem > Chapter 5: Genetics > Flashcards

Chapter 5: Genetics Flashcards

1
Q

4 RNA nucleotides

A
  1. Nucleotide (triphosphate), nucleoside (no phosphate)
    1a. Purines: double ringed->Adenine (NH2) and guanine (O)
    1b. Pyramidines: single ringed->uracile (O) and cytosine (NH2)
  2. If DNA…thyamine instead of uracile (Thyamine looks like uracile + methyl)
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2
Q

Genetic code

A
  1. Unambiguous: each codon can code for only 1 amino acid
  2. Degenerate/redundant: 1 amino acid can have been translated by up to 6 codons (6 codons-> 1 amino acid)
  3. Universal: all organisms have same codon amino acid pairing
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3
Q

Important codons to know

A
  1. Stop: UAA, UGA, UAG
  2. Start: AUG
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4
Q

Central dogma of biology

A
  1. States that genetic info can be transferred between DNA and DNA, between DNA and RNA, between RNA and RNA or from RNA to protein
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5
Q

Gene

A
  1. Segment of DNA that code for RNA
  2. Genes are regulatory sequences of DNA: meaning that they increase or decrease the expression of a gene
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6
Q

Genome

A
  1. An organisms complete set of DNA: (nuclear genome: 23 chromosomes/linear and mitochondrial genome: 1 chromosome/circular)
  2. Single copy dna (scDNA): genes that code for proteins in humans
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7
Q

Components of genome

A
  1. Coding DNA sequence (CDS/exons) only accounts for 1.5% of genome…many other parts (introns, and ncRNA)
  2. 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
  3. Highly repeatitive sequences/ simple sequence repeats (SSR)/satellite DNA: are centromeres an telomeres
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8
Q

Single copy vs repetitive sequences

A
  1. Single-copy DNA is a unique sequence that code for proteins and undergoes transcription. These are found in exons or the euchromatin
  2. Repetitive DNA is the sequence that has repeated sequences of nucleotides in the DNA and that don’t code for proteins.
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9
Q

Bacterial vs eukaryotic genome

A
  1. Bacteria: polycistronic, colinear, mostly single copy, mostly protein coding
  2. Eukaryotic: monocistronic, noncolinear, half single copy, mostly non coding
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10
Q

DNA replication overview

A
  1. During S phase
  2. Semiconservative: each daughter double strand contains one strand from parents and one new one
  3. Replication is bidirectional: has 2 replication forks
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11
Q

DNA replication: initiation

A
  1. Starts at the origin (eukaryotes have multiple on linear chromosome ; prokaryotes have one on circular chromosome)
  2. Eukaryotes have origin of replication complex (ORC) that binds each origin
  3. 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
  4. RNA primer is added via DNA primase
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12
Q

DNA replication: elongation

A
  1. 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
  2. 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)
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13
Q

DNA replication: Termination

A
  1. Exonuclease removes all RNA primers and these primers are replaced w bases
  2. Another exonuclease proofreads
  3. DNA ligase joins Okazaki fragments
  4. Telomerase catalyzes synthesis of more telomeres
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14
Q

DNAP

A
  1. Proofreader using 3’->5’ exonuclease activity for accuracy
  2. Fidelity of replication: determined by accuracy of base selection (DNAP is highly specific)
  3. If a base is in tautomeric form: DNAP may mismatch base pair which may cause replication to hault for a bit during elongation
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15
Q

MMR: mismatch repair

A
  1. Complex process involving several proteins that identify, excuse and replace entire section of strand during elongation
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16
Q

Important types of RNA

A
  1. MRNA (messenger RNA): carries code dictating amino acid
  2. TRNA (transfer RNA): translates genetic code from nucleotides to amino acids
  3. RRNA (ribosomal RNA): catalyze formation of peptide bonds
  4. MiRNA (microRNA): regulates gene expression by inhibiting translation or promoting degradation of mRNA
  5. SnRNA (small nuclear RNA): Splices introns from mRNA
  6. SnoRNA (small nucleolar RNA): modifies ribosomal RNA
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17
Q

Transcription overview

A
  1. Occurs in nucleus (eukaryotes)
  2. DdDNA->ssRNA
    2a. Transcribed DNA: template strand (3’->5’)
    2b. Not transcribed: Coding strand (5’->3’)
  3. Transcription unit: exons, introns and UTRs
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18
Q

Operon (prokaryotes)

A
  1. RNA transcripts are transcribed from operons (promotor, operator, transcription unit (polycistronic:carries products for more than 1 gene) and terminator)
  2. Promotor is where transcription is initiated after DNA polymerase binds
19
Q

Enhancer and silencers (eukaryotes)

A
  1. Regulate sequence when bound by transcription factors
20
Q

Transcription factors (eukaryotes and prokaryotes)

A
  1. Activators and repressors are transcription factors that bind to enhancers and silencers respectively
  2. Can lead to positive regulation or negative regulation
21
Q

RNA polymerase

A
  1. RNAP: transcribes RNA from DNA
    1a. RNAP 1: rRNA
    1b. RNAP 2: transcribes mRNA
    1c. RNAP 3: transcribes tRNA
  2. RNAP 2 binds to the TATA box within the promotor
22
Q

Transcription: DNA->pre-mRNA

A
  1. 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)
  2. 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
  3. Termination: RNA polymerase crosses termination site
23
Q

The lac operon

A
  1. Jacob Monod model of open: regulation of prokaryotic gene expression
24
Q

The trp operon

A
  1. Promote biosynthesis of amino acid trp
  2. If trp is present, the trp operon is turned off which blocks transcription of trp open
  3. If no trp, operon is not repressed and structural genes are transcribed…and trp is synthesized
25
Q

Transcriptional ground state

A
26
Q

Epigenetics regulation to DNA

A
  1. Histone acetylation (=active): acetyl added to lysine which loses charge and unable to interact w DNA backbone=loosens DNA=euchromatin=high gene expression
  2. Histone deacetylation: removes acetyl so lysine is charged=interacts tight w DNA=heterochromatin=no gene expression
  3. DNA methylation (=mute): adds methyl to cytosine =DNA tight=heterochromatin=low gene expression
  4. Demethylation: DNA loose=euchromatin=high gene expression
27
Q

Post transcriptional processing: Pre mRNA -> mature mRNA

A
  1. 5’ cap added: 7-methylguanosine cap
  2. 3’ Poly A tail
  3. Pre-mRNA splicing: splice out introns
  4. Now mRNA exits nucleus
28
Q

Protein synthesis: activation of tRNA

A
  1. Before translation, each tRNA is covalently bound to its amino acid
  2. A mature tRNA has 4 arms: acceptor (amino acid) arm, anticodon arm, D arm and T arm
29
Q

Translation: mRNA->protein

A
  1. 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
  2. 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
  3. Termination: When stop codon in mRNA (UAA, UGA, UAG) enters A site
30
Q

Protein synthesis: PTM folding /processing

A
  1. New polypeptide chain needs to fold to its native conformation: primary, secondary, tertiary and quaternary structure
  2. 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
31
Q

Location of protein synthesis

A
  1. 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)
32
Q

G0 phase (quiescence)

A
  1. Cell is metabolically active /not preparing for cell division
  2. Cells enter here bc damage/stress, specialization/differentiation, age, regular function
33
Q

Cell cycle

A
  1. 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)
  2. Mitosis
34
Q

Mitosis

A
  1. Prophase: chromosome condense, centrosomes move to poles, mitotic spindle forms, nuclear envelope breaks down
  2. Metaphase: mitotic spindles align chromosomes which forms metaphase plate…spindles attach to kinetochore at centromere of each chromatid
  3. Anaphase: chromatid separation/disjunction
  4. Telophase: reform nuclear envelope
  5. Cytokinesis: cell splits along cleavage furrow
35
Q

Meiosis

A
  1. 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
  2. Meiosis 2 (n->n)
    2a. Same steps
36
Q

Mitosis vs meiosis

A
  1. Mitosis: somatic cells, 2 identical cells, diploid->diploid, 1 division
  2. Meiosis: germ cells, 4 nonidentical cells, diploid->haploid, 2 division
37
Q

Spermatogenesis vs oogenesis

A
  1. Spermatogenesis: spermatogonium (2n), primary spermatocytes (2n), meiosis 1 forms 2 secondary spermatocytes (n), meiosis 2 forms 4 spermatids (n), differentiation makes spermatozoa
  2. 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
38
Q

Mutation types

A
  1. 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
  2. Insertion/deletion
    2a. Frameshift: nucleotides are added or deleted in a number not divisible by 3 causing a change in reading frame
39
Q

Mutation types

A
  1. 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
  2. Insertion/deletion
    2a. Frameshift: nucleotides are added or deleted in a number not divisible by 3 causing a change in reading frame
40
Q

Chromosomal aberration

A
  1. Deletion
  2. Duplication
  3. Inversion: portion of chromosome is revrsed
  4. Translocation: portion of chromosome is moved to another chromosome
  5. Aneuploidy: diff number of chromosmes
41
Q

Genetic recombination

A
  1. DNA sequences are rearranged but not changed
42
Q

6 hallmarks of cancer

A
  1. Self sufficiency in growth signals
  2. Insensitivity to anti growth signals
  3. Evasion of apoptosis
  4. Limitless replication potential
  5. Sustained angiogenesis: stimulate formation of blood vessels which provide O2 to cancer cells
  6. Tissue invasion and metastasis:
    6a. Metastasis: when cancer breaks away from primary tumour to make secondary ones: includes invasion, intravastion, extravasation and colonization
43
Q

Hayflick limit

A
  1. Limited number of divisions of a cell
44
Q

Tumours/neoplasm

A
  1. Abnormal mass of cells that grow at a excessive rate and can be benign (noncancerous) or malignant (cancerous)
  2. Proto oncogenes: genes that can cause cancer via uncontrolled cell growth … oncogene is a proto oncogene that has mutated or is overexpressed

APrep101: BioBiochem (13 decks)

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