bio113 Flashcards
(140 cards)
1
Q
Pleiotropy
A
Where a single gene has multiple effects on the phenotype it is said to be pleiotropic
2
Q
Polygenic Inheritance
A
Where a single trait is determined by multiple genes
3
Q
Epistasis
A
When one gene masks or modifies the expression of another gene it is said to be epistatic to that gene
4
Q
3 ways to identify chromosome
A
length
banding pattern
placement of centromere
5
Q
acrocenctric
A
centromere very close to the end
6
Q
polyploidy
A
extra whole sets of chromosomes
7
Q
aneuploidy
A
some additional or missing chromosomes
8
Q
trisomy and an example
A
trisomy is one extra chromosome and an example is downsyndrome
9
Q
Cytogenetics
A
Study of chromosome structure and function.
10
Q
Karyotyping Process
A
Collect blood (10-20 ml). Stimulate mitosis using phytohaemagglutinin. Incubate cells (2-3 days). Halt mitosis in metaphase using colcemid. Lyse cells with hypotonic solution. Fix, stain (Giemsa), and arrange chromosomes by size.
11
Q
Chromosome Classification
A
Metacentric: Centromere in center. Sub-metacentric: Centromere slightly off-center. Acrocentric: Centromere very close to one end. Chromosomes identified by length, banding pattern, centromere placement.
12
Q
Polyploidy
A
Additional whole chromosome sets. Examples: Triploid (3n), Tetraploid (4n). Common in plants (e.g., cultivated banana, 3n=33); rare in animals.
13
Q
Aneuploidy
A
Additional or missing chromosomes. Types: Monosomy: Missing one chromosome. Trisomy: Extra chromosome. Example: Trisomy 18 (47, XX, +18).
14
Q
Non-disjunction
A
Failure of chromosomes or chromatids to separate during meiosis. Occurs: Meiosis I: Homologous chromosomes. Meiosis II: Sister chromatids. Common, leads to ~50% human conceptions being aneuploid.
15
Q
Down’s Syndrome (Trisomy 21)
A
Karyotype: 47, XX/XY, +21. Characteristics: Distinct facial features, short stature, learning disabilities. Heart defects, increased risk of leukemia and Alzheimer’s. Risk factor: Maternal age.
16
Q
Screening for Down’s Syndrome
A
Methods: Blood tests (specific protein markers). Ultrasound (nuchal pad thickness). Amniocentesis and karyotyping.
17
Q
Turner’s Syndrome (XO)
A
Karyotype: 45, XO. Characteristics: Phenotypically female, sterile. Lack mature sexual organs; secondary characteristics develop with estrogen replacement therapy. Incidence: 1 in 2500 live female births.
18
Q
Klinefelter’s Syndrome (XXY)
A
Karyotype: 47, XXY. Characteristics: Essentially male phenotype, sterile. Some female traits, tall stature. Treated with testosterone therapy. Incidence: 1:500-1000 live male births.
19
Q
Sex Determination
A
Determined by presence or absence of Y chromosome: Turner’s Syndrome (XO): essentially female. Klinefelter’s Syndrome (XXY or XXXY): essentially male.
20
Q
Chromosome Structural Changes
A
Types: Deletions, translocations. Identified precisely by chromosome ‘address’ (banding pattern).
21
Q
Cri-du-chat Syndrome (Deletion)
A
Deletion: Short arm of chromosome 5 (5p-). Characteristics: Cat-like cry (larynx/glottis abnormality). Wide face, saddle nose, intellectual/physical disabilities. Incidence: ~1 in 50,000 live births.
22
Q
Prader-Willi Syndrome
A
Deletion: Long arm chromosome 15 (15q1.12), paternal chromosome. Characteristics: Poor infant feeding, obesity, diabetes, poor sexual development in males. Due to genomic imprinting (maternal or paternal gene silencing).
23
Q
Chronic Myelocytic Leukaemia (CML) (Translocation)
A
Cause: Reciprocal translocation between chromosomes 22 and 9, creating the Philadelphia chromosome. Result: BCR-ABL fusion gene (oncogene) stimulates excessive white blood cell production. Characteristics: High white blood cell count. Common in middle-aged/elderly individuals. Accounts for 15-20% leukemia cases.
24
Q
Mendel
A
Established principles of heredity (dominant/recessive traits).
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Miescher
Discovered nucleic acids ('nuclein') from nuclei in white blood cells (pus from bandages).
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Darwin
Developed the theory of natural selection and evolution from a common ancestor.
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Griffith's Transformation Experiment
Used two strains of Streptococcus pneumoniae: S strain (pathogenic, with capsule) and R strain (harmless, no capsule). Heat-killed S + live R strain → mice died (live S found in blood), proving existence of a 'transforming principle.'
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Avery's Experiment
Identified the 'transforming principle' as DNA by demonstrating it was resistant to proteases, lipases, RNases, insoluble in ethanol (not carbohydrate), and positive for DNA-specific (Dische) test.
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Hershey-Chase Experiment
Labelled bacteriophage protein with ^35S and DNA with ^32P. DNA (^32P) entered bacterial cells; proteins (^35S) did not. Confirmed DNA as genetic material definitively.
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Chargaff's Rule
Erwin Chargaff analysed base composition across species. Found that adenine = thymine (A=T) and cytosine = guanine (C=G). Provided evidence for complementary base pairing.
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Structure of DNA
Composed of nucleotides with three components: Pentose sugar (deoxyribose), Phosphate group, Nitrogenous base (A, T, G, C). DNA strands form a sugar-phosphate backbone.
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Nitrogenous Bases
Purines: Adenine (A), Guanine (G) - double-ring structures. Pyrimidines: Cytosine (C), Thymine (T) - single-ring structures.
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DNA Double Helix (Watson-Crick Model)
Two antiparallel strands form double helix. Diameter of helix: 2 nm. 10 base pairs per turn; each turn 3.4 nm long. Base pairs 0.34 nm apart.
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Base Pairing Specificity
Hydrogen bonding ensures specific pairing: A pairs with T (2 hydrogen bonds). G pairs with C (3 hydrogen bonds).
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DNA Replication (Semi-Conservative Model)
Proposed by Watson & Crick; each DNA strand acts as a template. After replication, each new DNA molecule consists of one original strand and one new strand.
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Meselson-Stahl Experiment
Labelled parental DNA with heavy nitrogen (^15N). DNA replicated in presence of lighter nitrogen (^14N); produced intermediate-density DNA, confirming semi-conservative replication.
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DNA Polymerase
Synthesizes DNA strands in the 5'→3' direction. Requires single-stranded template, nucleoside triphosphates (dNTPs), and a primer with a free 3' hydroxyl. Possesses proofreading ability to correct errors.
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Leading and Lagging Strands
Leading strand: Continuous synthesis toward replication fork (5'→3'). Lagging strand: Discontinuous synthesis, forming Okazaki fragments, away from replication fork; fragments later joined by DNA ligase.
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Key Enzymes in DNA Replication
Helicase: Unwinds DNA helix. Single-strand binding proteins: Prevent strands from re-annealing. Primase: Synthesizes RNA primer. DNA Polymerase III: Extends DNA strands. DNA Polymerase I: Removes RNA primers and replaces them with DNA. DNA ligase: Joins Okazaki fragments on lagging strand.
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Alkaptonuria
Autosomal recessive condition causing dark urine due to accumulation of homogentisic acid.
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Homogentisic acid oxidase
Enzyme whose defect causes Alkaptonuria.
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One gene-one enzyme hypothesis
Concept established by Beadle and Tatum that links genes to enzymes.
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Neurospora crassa
Haploid bread mould used by Beadle and Tatum to identify auxotrophic mutants.
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Pulse-chase experiments
Experiments showing RNA moves from nucleus to cytoplasm.
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Transcription
Process where RNA polymerase synthesizes mRNA from DNA.
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Translation
Process where mRNA is translated into protein.
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Triplet codons
Three bases per codon that encode amino acids.
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Redundant genetic code
Multiple codons can specify one amino acid.
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Specific genetic code
Each codon specifies only one amino acid.
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Start codon
AUG (methionine), signals translation start.
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Stop codons
UAA, UAG, UGA, signal translation termination.
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Universality of the Genetic Code
Genetic code nearly identical across organisms, indicating common evolutionary ancestry.
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RNA vs. DNA
RNA contains ribose sugar, is single-stranded, and has Uracil; DNA has deoxyribose, is double-stranded, and has Thymine.
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Initiation of Transcription
RNA polymerase binds DNA, no primer needed.
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Elongation in Transcription
RNA polymerase unwinds DNA and synthesizes mRNA in the 5' → 3' direction.
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Termination of Transcription
RNA polymerase reaches terminator sequence, releasing mRNA.
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One Gene-One Polypeptide Hypothesis
Revised concept acknowledging proteins can be multi-subunit.
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Central Dogma of Molecular Biology
Information flow in cells: DNA → RNA → Protein.
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Codons reading frame
Codons are read in the correct 'reading frame' to encode proper protein sequence.
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Experimental proof of the Genetic Code
Proven by Crick and Brenner using artificial mRNA (UUU codon = phenylalanine).
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mRNA
Messenger RNA, carries genetic info from DNA to ribosomes.
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tRNA
Transfer RNA, adaptor molecule linking amino acids to mRNA codons.
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rRNA
Ribosomal RNA, combines with proteins to form ribosomes, catalyzing protein synthesis.
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tRNA Structure
About 80 nucleotides long. Cloverleaf shape that folds into an L-shaped molecule. Anticodon pairs with codon on mRNA. Amino acid attachment at 3' hydroxyl end.
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tRNA Specificity
Each tRNA binds a specific amino acid determined by its anticodon. Example: tRNA anticodon UAC binds AUG codon, carrying only methionine.
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Aminoacyl-tRNA Synthetase
Enzyme that attaches amino acids to their corresponding tRNAs. Specific enzyme for each amino acid (20 total). Two-step process: ATP hydrolyzed, amino acid joins AMP. Amino acid transferred from AMP to the correct tRNA.
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Genetic Code and Wobble
61 amino acid codons but only 40-45 tRNAs. Wobble effect: Flexibility at the 3rd base of the codon allows one tRNA to recognize multiple codons.
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Ribosome Structure
Made of rRNA and proteins. Two subunits: Large and small. Three binding sites for tRNA: A-site, P-site, E-site. Moves along mRNA in 5'→3' direction, synthesizing proteins N-terminus to C-terminus.
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Protein Synthesis Stages
Initiation: Ribosome assembles at start codon (AUG). Elongation: Amino acids added sequentially, forming peptide bonds. Termination: Synthesis ends at stop codon (UAA, UAG, UGA), protein released.
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Initiation (Translation)
Small ribosomal subunit binds mRNA near 5' end. Initiator tRNA (carrying methionine) binds AUG codon. Large subunit binds, placing initiator tRNA in P-site. Requires GTP hydrolysis and initiation factors.
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Elongation Cycle
Aminoacyl-tRNA enters A-site, pairs with mRNA codon (GTP hydrolysis). Peptide bond formation catalyzed by ribozyme activity (peptidyl transferase). Translocation: ribosome moves forward one codon, ejecting empty tRNA from P-site (GTP hydrolysis).
72
Termination of Translation
Occurs when stop codon reaches A-site. Release factor enters A-site, polypeptide released after water addition. Ribosome subunits dissociate (requires GTP hydrolysis).
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Protein Synthesis (Prokaryotes vs. Eukaryotes)
Prokaryotes: Coupled transcription and translation (no nucleus). Eukaryotes: Transcription (nucleus) separate from translation (cytoplasm); proteins trafficked to organelles.
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Targeting Proteins to Endoplasmic Reticulum (Eukaryotes only)
Signal peptide directs proteins to ER. Signal Recognition Particle (SRP) binds peptide, pauses translation. SRP docks ribosome at ER; translation resumes, protein enters ER, signal peptide cleaved.
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Mutations: Definition and Types
Permanent DNA changes: Chromosomal mutations (large-scale, gene position/number). Point mutations (single nucleotide changes).
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Types of Point Mutations
Base pair substitutions: Silent (no amino acid change), Missense (amino acid substitution), Nonsense (premature stop codon). Insertions/deletions: Frameshift mutations, severe effects on protein function.
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Causes and Repair of DNA Mutations
Spontaneous mutations: DNA replication errors (e.g., base tautomerism). Induced mutations: Chemical (base analogues, alkylating agents, intercalating agents) and physical agents (ionizing radiation, UV radiation). Repair mechanisms: e.g., Nucleotide Excision Repair (NER), correcting DNA damage like UV-induced thymine dimers.
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Single Gene Disorders
Disorders caused by mutations in a single gene.
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Modes of Inheritance
Autosomal (chromosomes 1-22), Sex-linked (X or Y chromosome); Each can be dominant or recessive.
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Autosomal Recessive Inheritance
Only homozygous individuals affected. Carriers (heterozygotes) asymptomatic. 25% risk for carrier parents to have affected child.
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Cystic Fibrosis (CF) Overview
Autosomal recessive disorder, affects secretory epithelia. Most common life-shortening genetic disorder among Northern Europeans. Frequency: Carrier frequency 1/25, disease frequency ~1/2500 births.
82
Molecular Basis of CF
Caused by mutations in CFTR gene (codes for chloride channel). Most common mutation: ΔF508 (deletion of phenylalanine at position 508). Leads to defective chloride transport; mucus thickens.
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CF Symptoms and Treatment
Symptoms: Thick mucus accumulation, chronic bronchitis, recurrent infections. Treatments: Antibiotics, daily mucus clearance, precision medicines targeting specific mutations, potential gene therapy.
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Autosomal Recessive - Sickle Cell Anaemia (SCA)
Frequency: 1/625 in Afro-Caribbean/Afro-American populations. Mutation: Single nucleotide substitution (glutamic acid replaced by valine) in haemoglobin β-chain.
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Consequences and Treatment of SCA
Effects: Sickle-shaped red blood cells cause anaemia, joint pain, frequent infections. Treatments: Regular blood transfusions; cure via bone marrow transplant.
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Heterozygote Advantage in SCA
Carriers (heterozygotes) show resistance to malaria, maintaining allele frequency in malaria-endemic regions. Example of heterozygote advantage (fitness benefit for carriers).
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Autosomal Dominant Inheritance
Heterozygotes display disease phenotype. 50% chance affected parent transmits disease to offspring. Dominance often from haploinsufficiency or toxic protein production.
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Huntington's Disease (HD)
Autosomal dominant disorder; late-onset brain degeneration. Symptoms: Jerky movements, personality changes, progressive disability. Caused by CAG repeat expansions (36-125 repeats) in the HD gene.
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Familial Hypercholesterolaemia (FH)
Autosomal dominant condition; incomplete dominance (haploinsufficiency). Symptoms: High blood cholesterol, early heart disease, cholesterol deposits in tissues. Molecular cause: Lack of functional LDL receptors, resulting in cholesterol accumulation.
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Sex-Linked (X-linked) Recessive Inheritance
Mostly affects males (XY), females typically carriers. Carrier mother has 50% chance affected son, 50% chance carrier daughter. Affected father transmits gene to all daughters (carriers), but not to sons.
91
Haemophilia (A & B)
X-linked recessive bleeding disorder due to defective clotting factors. Haemophilia A: Factor VIII deficiency (1/5000 males). Haemophilia B (Christmas disease): Factor IX deficiency (1/30,000 males). Symptoms: Excessive bleeding, joint damage; treatable with clotting factor replacement.
92
Duchenne Muscular Dystrophy (DMD)
Most common lethal genetic disorder in males (1/3500 males). Cause: Mutation in large dystrophin gene on X chromosome (Xp21.2). Symptoms: Progressive muscle wasting; death typically by age 20 due to cardiac or respiratory failure. Treatment: Currently incurable; potential gene therapies under investigation.
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FASTQ
is a format specialised for storing raw sequencing data
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FASTA
•Each sequence is described by exactly 2 or more lines.
(Defline + sequence)One of the most common format for sharing nucleotide and amino acid sequences
95
Fluid Mosaic Model
Describes membranes as fluid structures with a mosaic of proteins embedded or attached.
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Membrane Fluidity and Lipid Movement
Phospholipids move laterally rapidly (~2 µm/s), but rarely flip-flop. Membrane fluidity is crucial for function and depends on lipid composition (unsaturated fatty acids enhance fluidity).
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Cholesterol's Role in Membrane Fluidity
Cholesterol acts as a temperature buffer: Reduces fluidity at high temperatures. Prevents tight packing and maintains fluidity at low temperatures.
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Hop Diffusion of Membrane Proteins
Proteins move slower than lipids. 'Hop diffusion' (Kusumi, 2001): Proteins restricted by actin cytoskeleton fences, periodically hopping to new regions.
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Mosaic Nature of Membranes
Integral proteins: Span entire membrane. Peripheral proteins: Attached loosely to integral proteins. Lipid-anchored proteins: Covalently attached to membrane lipids (e.g., GPI anchors).
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Membrane Carbohydrates
Short oligosaccharides (<15 sugars), highly diverse. Attached to proteins (glycoproteins) or lipids (glycolipids). Serve as cell-surface markers (e.g., blood group antigens).
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Membrane Asymmetry
Inner and outer surfaces differ in: Lipid composition, Associated proteins (integral/peripheral), Carbohydrate attachment (exterior surface only).
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Membrane Functions
Compartmentalization (cells, organelles), Selective permeability (small/non-polar pass easily; large/polar/charged need transport proteins), Cell-cell recognition (glycoprotein markers), Enzymatic activity, signal transduction, cell adhesion, attachment to cytoskeleton/ECM.
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RNAseq
•allows you to look at all genes and determine affected gene networks•Disease•Drug•Mutation
done as bulk
captures the transcriptome for individual cell
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FASTA
a commonly used simple format for nucleotide/amino acid sequences and little else
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pdb
format is used to store information on protein structure
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E. coli genome
Single circular, double-stranded DNA molecule. ~4.6 million base pairs, ~4500 genes. Compacted into the nucleoid, which occupies much of the cell volume.
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Plasmids
Small, circular DNA molecules independent of the bacterial chromosome. Often carry beneficial genes (e.g., antibiotic resistance). Can be transferred between bacteria.
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Bacteriophage Types
Lytic (virulent): Infect, replicate, and lyse host cell. Temperate (lysogenic): Can integrate into host genome and replicate passively.
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Transformation
Uptake of naked DNA from environment.
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Transduction
Transfer via bacteriophage.
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Conjugation
DNA transfer through direct contact via sex pilus.
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Generalised Transduction
Any gene transferred; occurs with virulent phage.
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Specialised Transduction
Specific genes near integration site transferred; occurs with temperate phage.
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Transformation in Bacteria
DNA from lysed cells taken up by competent bacteria. Incorporated into genome by homologous recombination.
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F factor
A plasmid that enables bacteria to form sex pili and transfer DNA. Donor (F⁺) → Recipient (F⁻) via cytoplasmic bridge. Recipient becomes an exconjugant.
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Hfr Cells
Hfr (high frequency recombination) cells: F factor integrated into chromosome. Transfers chromosomal genes to F⁻ cell, leading to recombination.
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Constitutive genes
Always expressed (e.g., housekeeping genes).
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Regulated genes
Expressed only under specific conditions.
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Repressible Operon
Usually on; turned off when repressor is activated by corepressor (tryptophan).
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Inducible Operon
Usually off; turned on when inducer (lactose) inactivates the repressor.
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trp Operon Regulation
Negative regulation. High tryptophan: activates repressor → binds operator → transcription blocked. Low tryptophan: repressor inactive → transcription proceeds.
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lac Operon Regulation
Negative & positive regulation. No lactose: active repressor binds operator → transcription off. Lactose present: repressor inactive → transcription possible (if glucose is low).
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Positive Regulation in lac Operon
cAMP-CRP complex enhances RNA polymerase binding. High cAMP (when glucose is scarce): lac operon activated. Low cAMP (high glucose): lac operon minimally expressed.
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Operon
Cluster of functionally related genes under coordinated control. Includes: Promoter, Operator, Structural genes. Controlled by regulatory genes producing repressors.
125
F+ / F−
Donor / recipient cells in conjugation.
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Hfr
High recombination donor.
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Repressor
Protein that blocks transcription by binding operator.
128
Polycistronic mRNA
Single mRNA encoding multiple proteins (typical of prokaryotes).
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Repetitive DNA - Interspersed
Scattered throughout genome. Units 100-10,000 bp, e.g., Alu elements (~300 bp) make up 5% of the genome. Often closely related but not identical.
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Repetitive DNA - Tandemly Repetitive
Repeats in sequence (e.g., microsatellites, minisatellites). Found in centromeres and telomeres. Can contribute to disorders (e.g., Huntington's disease).
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Chromatin Structure Overview
DNA + histone proteins = chromatin. Enables 10,000-fold compaction. Two forms: Euchromatin: Loosely packed, active. Heterochromatin: Densely packed, silent.
132
The Nucleosome
Basic unit of chromatin: ~200 bp of DNA wrapped around a histone octamer. Histones are positively charged and bind negatively charged DNA.
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Higher-Order DNA Packing
Nucleosomes fold into 30 nm fibres, loop into domains, then further compact during mitosis/meiosis. Maintains gene accessibility during interphase.
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DNA Methylation
Adds methyl groups (-CH₃) to DNA. Silences genes (inactivates transcription). Basis of genomic imprinting.
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Histone Acetylation
Adds acetyl groups (-COCH₃) to histones. Activates gene expression by loosening DNA-histone interaction. Reversible and regulates chromatin openness.
136
RNA Polymerases in Eukaryotes
Pol I: rRNA, Pol II: mRNA, Pol III: small RNAs (e.g. tRNA).
137
Promoters and the TATA Box
Promoter: Region upstream of gene where transcription starts. TATA box: Key promoter element (~10-35 bp upstream), where TBP (TATA-binding protein) binds to initiate transcription.
138
Preinitiation Complex Assembly
TFIID binds TATA box. TFIIA, TFIIB join. TFIIF brings RNA Pol II. TFIIE and TFIIH complete the complex.
139
Enhancers and Specific Transcription Factors
Enhancers: Distant DNA elements that increase transcription. Activators/Repressors bind to control elements, influencing RNA polymerase activity. Work through DNA looping and protein recruitment.
140
Post-Transcriptional Modifications
5' capping, 3' polyadenylation, and splicing of introns. Alternative splicing allows a single gene to encode multiple proteins (e.g., Dscam gene → 30,000 isoforms).
