Exam 2 Notes PDF

LECTURE 1: Transformation: - No cell to cell - Not all bacteria can do it - Only competent - Due to polymorphism - One alive (the transforming) and one dead (the material that is being taken) Conjugation: - Requires cell to cell interaction - Both cells must be...

LECTURE 1: Transformation: - No cell to cell - Not all bacteria can do it - Only competent - Due to polymorphism - One alive (the transforming) and one dead (the material that is being taken) Conjugation: - Requires cell to cell interaction - Both cells must be alive - Three types: - F conjugation - HFr conjugation - F\* conjugation (sexduction) **Plasmids are circular extrachromosomal DNA, present in prokaryotes and SOME unicellular EUKARYOTES** **Episomes: independent DNA that can reversibly bind chromosomes (suspected to be the origin of viruses)** F conjugation: - F stands for fertility plasmid - Phosphodiester bond is broken - F+ remains F+ - F- becomes F+ - F+ = donor cell - F- = recipient - Occurs between homologus chromosomes - NO RECOMBINATION - Between the plasmid and genophore of the recipient cell - Because they don't have the same genes HFr conjugation: - **Most recombination** - The HFr stays HFr - And the F- usually stays F- - Full HFr is not transferred - F factor follows the recipient cell because it has been intergrated into the bacterial chromosome - More time = more bacterial chromosome transferred F' conjugation: - The donor comes off with a part of it's own chromosome - If the plasmid satys, then the chromosome is a diploid for whichever gene - F' stays f' - F- becomes f' - May produce a merozygote - Partially diploid when plasmid is inside Tranduction: - Generalized and specific - Requires a viral factor - Transfer of DNA from one Cell to another via a viral vector - Viruses that specialize on bacteria = bacteriophage - First virus found = tobacco mosaic - Virion = fully formed viral partied Lytic cycle: (bacteriophage) virulent viruses (generalized) 1. Attachment 2. Genetic material insertion 3. Transcription and translation 4. Virion assembly 5. Lysis of viruses and release Lysogenic: (specific) Same as lytic but the virus incorporates its own genetic material into the host chromosome If the host cell is a prokaryote: prophage If the host cell is a eukaryote: provirus END OF LECTURE 1 LECTURE 2: - infective encephalopathies that lead to inevitable fatalities - If PrPc and PrP Sc are together in the golgi, they stay together in the golgi and they don't come out of the golgi due to them being stuck together and they die there Chromosomal variations: - Centromere contains - Heterochromatin - Tightly packed DNA (inactive) - Less than 10 % of human chromatin - Heterochromatin has 2 types - Constitutive: - Permanent - In Centromere and telomeres - Facultative - Reversible - Recognized by LINE seuqnces - Its structure changes depending on the cell cycle - Euchromatin - Loosely packed DNA (active) - 90% of human chromatin **DNA is maximally condensed in metaphase** - Types of chromatids: - Metacentric - 1,3,16,19,20 - Submetacentric - P = short arm - Q = larger arm - X chromosome - Acrocentric - P = very small arm - Q= very big arm - Sattelite regions - rRNA genes - 13,14,15,21, & 22 and Y chromosome - Telocentric - Not in humans **Karyotypes are numbered according to their sizes (largest to smallest)** **Chromosome \#23 = sex chromosome** - G Banding: - Distinguishes areas that are A & T rich by exposing the chromosome to Giemsa stain - R banding - Reverses light - Shows areas rich in C & G - Q banding - Quinacrie mustard and looking at it under UV light - Shows heterochromatins **Ideograms: gives the locations of the genes** 13q12.2 13= which chromosome Q = which arm Karyotypes: - Requires metaphase cells - Any pop of dividing cells could be used - Lymphocytes can be induced to proliferate to provide a metaphase cells source - RBCs can't be used **Mutations:** **Point mutations: base pair** **Chromosomal mutation: parts *(rearrangements)* or entire chromosome (*number changes)*** Somatic = non-sexual Germ cells = sex cells Chromosomal rearrangements: - Balanced - Normal complement of genetic material - Unbalanced - Addition or missing genetic material - Unstable rearrangements can't be inherited - Stable rearrangements can be inherited Types of rearrangements: - Duplications - Unbalanced - Stable - Unequal crossing over at prophase 1 - If centromere is changed = unstable - Types: - Tandem: - Adjacent - Displaced - Not adjacent - Reverse duplication - Reversed and duplicated - ABCDE = normal - ABABCDE= tandem - ABCDEAB = displaced - ABBACDE= reverse duplication - Can cause phenotypic effects - Imbalance in gene product that affected development - Dosage effect - Duplicated may assume 3 roles: - Extra functional - New function - Loses function (pseudogenes) - Deletions - Unbalanced - Stable - Loss of chromosomal segment - Chromosomal breakage - Unequal crossing over during metaphase 1 - Heterozygous individuals may experience: - Gene imbalance - Pseudodominance - Deletion of dominant allele - Two copies may be needed for normal expression - AKA haploinsuffiency - Deletion on chromosome 5 p arm causes: Cri-du-Chat syndrome - Inversions - Balanced - May be stable or unstable - Depends on the presence and alteration of centromere - Inverses the actual chromosome (end of lecture 2) - Can include the centromere - Pericentric - Decrease in fertility by 50 % because of diploinsufficiency (deletion) - Not including the centromere - Paracentric - Can lead to abnormal gametes if it is a heterozygous inversion - Decrease in fertility by 50 % - If two inversions are inherited (which is very rare) and they cross over, nothing happens - Position effect, if the gene is flipped it messes with gene causing phenotypic effects - Temporal: when does it get expressed during the organism's lifespan - If inversed messes up with the whole gene - Spatial: location on the DNA strand - Translocations - Transfer of chromosome segment to a non-homologous chromosome - If it transfers to another homologous chromosome crossing over - May be reciprocal or non-reciprocal - May be balanced or unbalanced - Robertsonian Translocation - 2 acrocentric translocating to form a metacentric or sub metacentric chromosome and a fragment - Robertsonian chromosome contains the two large arms of the acrocentric chromosomes - Most common: - 13q14q and 14q21q - Phenotypic effects: - Position effects - May expose genes to unnecessary regulatory mechanisms - Breaks may occur in the gene that will affect the function - Isochromosomes - Identical arms - Known to affect chromosomes 12 and 21 - Ring chromosomes - Loss of telomeres - Causing sticky ends that adhere to anything or cohere - Known to effect chromosome 20 - Fragile sites: parts of chromosomes hanging by a thread - CCG trinucleotide repeats - Most common cause of inherited mental retardation LECTURE 3: Chromosomal Mutations II: - Aneuploidy: - More or less chromosomes on a certain set - Can arise from - Failure to separate (nondisjunction) - Chromosome loss during meiosis - Types: - Nullisomy 2n -2 (no one can live with this) - Monosomy 2n -1 (45 in a chromosome) - Trisomy 2n+ 1 (47 in a chromosome) - Tetrasomy 2n+ 2 (48 in a chromosome) - Phenotypic effects: - Alters gene dosage (too much or too little) - If it didn't affect sex chromsomes then the offspring will die - X inactivation - Can't have extra chromosome 16 - Older the mother the higher the risk of aneuploidy - Diseases: - Sex chromsomes - Kleinfeher - 2N= 47 xxy - Trisomy, or tetrasomy or more (more xs not the ys) - Development of breasts and smaller gonads - Turner - 2N=45 XO - Monosomy - No bar bodies - X that is turned off isn't fully turned off (end of lecture 3) - Polyploidy - More sets of chromosomes - Two types: - Auto - Same species - multiply - Allo - Different species - Add - Could have different combinations - - Mosaicism - Two different sets of cells from with different genetic makeup - Cells are abnormal \# of chromosomes, some are don't - Happens: - Nondisjunction after zygote forms - More severe when it happens in earlier development - Severity increases the earlier nondisjunction in development is - More severe phenotypic effects LECTURE 4: - Supercoiling - It is a way to package DNA - Most DNA is supercoiled, which means it is not relaxed - Topoisomerase relaxes DNA - +ve supercoil - With the right handed coil - --ve super coil - Opposite to right hand coil - Genophore - Bacterial chromosome - Doesn't have centromere - Found in nucleoid - Not membrane bound - Circular - Associated with proteins - Non-histones btw - Packed in series of loops - Found in: - Cytosol - Nucleoid - Mito - Chloro - Proteins associated with eukaryotic chromosomes - Histones - H1,H2A,H2B,H3,H4 - Nonhistone - Has Structural roles - Scaffold proteins - Genetic roles - Activators - Represores - TF - Polymerases - Chromosome packaging - Nucleosome - Chromatosome - Nucleosome + H1 = chromatosome - 30nm, 300nm and 700nm fiber **How does sugar phosphate backbone interact with histone ?** **Histone tail is +ve sugar backbone is --ve** - Centromere - Location where kinetochores attach - They know where to attach due to the presence of CenH3 - CenH3 = centromere H3 - Heterochromatin - Condensed - No specific sequences - Telomere - Ends - Heterochromatin - Serves as a cap - 5'TTAGG3' - Codes for nothing but exists in hundreds of thousands - (A and T)~m~G~n~3' - M= 1-4 - N= 2 or more - Shortening of chromosome = sign of old age - Types of sequences - Unique - Present only once - 20-50% protein coding gens - Moderately repetitive - Hundred thousand repeats - Tandem repeats - Interspersed repeats - SINES - Short - 11% of human genome - LINES - long - Highly repetitive - Millions - Transposon - Jumping gene - Discovered by mclintock - Damages sequences of coding and promoting regions **What happens to mitochondria during telophase 2? They get divided** LECTURE 5: - Nucleic acid - Heteroploymer of nuclotides - Phosphate - Attached to 5'carbon - pentose sugar - has 5'carbon - nitro base - attached to 1' carbon - OH on 3' carbon - Purine - 2 rings - Pure As Gold - Pyrimidines - 1 ring - CUT the Pi 10 bp for a 360^0^ - Width of DNA - 2nm - Length of 10bp - 3.4nm - Streptococcus pneumoniae (Fredrick Griffith) - Has 3 types - Type I,II and III - Has R and S strains - R = non pathogenic - S= pathogenic - Need dead type III S and Live IIR for the mice to live - Live IIIS will kill them - Single gene mutation - RS or SR - Multiple mutations - types can't change - RNAse and Protease are need to bring back dead IIIS when mixed with IIR (CIELLA DON'T READ ME) - 3'5 - DNA template - Template strand - Non-coding strand - Downstream is always measured from the 3' end - 5'3' - RNA transcript is synthesized - Transcritption= synthesis of RNA molecule using DNA template - Non-template strand - Coding strand - RNA polymerase reads from 5-3 - Promoters - Most important part = consensus part - TATA box - -31 to -26 - Inr - Most common in eukaryotes - CpG island - Prokaryotes - -10 bp - Gene - Segment of DNA that codes for RNA - Includes the promoter, and coding regions - And includes other regions imp for transcription - RNA polymerase - Can only add to 3-OH adds to 53 direction