Genetics Unit 2

• very stable, not reactive, well preservable, 1 molecule (functional unit)
• stores genetic information, allows access to genetic information, replication
• helix allows for energy efficiency, stacking interactions, hydrophobic bases repel water, negative phosphates limit stacking
• 2nm wide, 0.34nm between pairs, 3.4nm for one turn (10 nucleotides)

• pentose sugars and phosphates (base pairs with sugar, hydrogen bonds to form helix)
• A=T
• C triple bond G
• genetic information is held in base pairs, sticking out functional groups are important (stick out in major and minor grooves for access by enzymes, allow sequence specific DNA binding proteins to recognize specific sequences of nucleotides)

transferring genetic information (nonvirulent bacteria with dead virulent bacterial became virulent)

• DNA has thymine but RNA has uracil
• base pairs are in equal amounts
• purines (2 ring, A & G)
• pyrimidines (1 ring, C & T)

• DNA (replication) --> transcription --> translation
• nucleic language into amino acid language

• Adding a methyl for gene regulation to cytosines
• Causes steric hinderence

• overwinding = positive
• underwinding = negative
• extra twists create tension, can flip into left-handed confiruation
• enzymes can flip/open molecule to negative supercoil (right handed) --> better for transcription and replication
• B structure is hydrated and dominant, Z is left handed and has regulatory role

• organized chromosomes
• twisted loops of DNA
• no histones

• better organized chromatids
• electrostatic interaction with histones (hug tightly to stop transcription, acidic addition like acetate)
• high salts cause disassociation
• euchromatin = lightly packed and can be expressed
• heterochromatin = tightly packed and not expressed
• telomeres protect chromosomes by capping end (progressively disappears) --> germ cells can lengthen with telomerase
• lots of "junk" DNA, 97%

• portion of chromosome is doubled (affects gene dosage)
• good if there's a mutation (hemoglobin)

portion results in a loss of genetic information, protein is not produced

• order of genes change 180 degrees (break, flip, reseal)
• no genetic material is lost
• breakpoint in gene may affect protein production

• moves genetic information from one chromosome to another
• reciprocal = two chromosomes involved with swapping
• non-reciprocal = piece breaks off and joins another
• Robertsonian = two short arms fuse and two long arms fuse, one is lost
• Chronic myelogenous leukemia is abnormal blood stem cell differentiation (too many granulocytes) --> chromosome 9 and 22 --> Philadelphia chromosome

• increase/decrease in number of chromosomes due to nondisjunction
• nullisomy = chromosome completely missing (miscarriage usually)
• monosomy = only one copy present
• trisomy = 3 copies of a chromosome
• tetrasomy = 4 copies of a chromosome

• occurs when nondisjunction happens with mitosis
• traits are shown in half of organism

• Trisomy of 21, translocation of 15 and 21
• homologous chromosomes pair together in meiosis I but 3 line up instead of 2 --> 6 types of gametes (2/3 no syndrome but half are carriers)

presence of more than 2 sets of chromosomes (most plants --> evolution)

• consequence of accidents that happened in meiosis or mitosis
• one organism

hybridization between species (chromosomes don't line up properly)

produce viable gametes and reproduce

• All from transcription but not all is translated
• only mRNA is translated, codes for polypeptides
• rRNA make up ribosomes which synthesize proteins
• tRNA have a crucial 3 base sequence (anticodon) and bind to specific amino acids, bringing them to ribosomes
• single stranded, can fold to become double stranded
• easily degraded by RNAse, antiparalell and conplementary to DNA

• DNA sequence (specific) that RNA polymerase can recognize to start transcription
• attaches to binding site to start transcription (+1)
• isn't transcribed but important for orientation
• sigma factor binds (prokaryotes), part of holoenzyme
• positions active site of RNA polymerase in place

• site where RNA polymerase releases from DNA and transcription terminates
• energy used for process is derived from breaking phosphate bonds (ATP)

• RNA polymerase has many subunits, sigma factor directs core RNA polymerase to bind specific promoter
• forms holoenzyme --> capable of non-specific and specific DNA binding
• -10 before transcription site (for orientation)
• promoters share consensus sequence

• affects afinity for RNA polymerase, measure of frequency of transcription initiation
• the more different it is (weaker), the more difficult it is for the sigma factor to recognize it
• synthesized 5'-->3' but read 3'-->5' because 3' side has a free hydroxyl group (two phosphates cleaved off and nucleotides added)

• release of RNA molecule and snaps back to sigma factor, not productive
• complex must break away from promoter and slide down for transcription to be completed
• elongation = core polymerase breaks away from sigma factor and remains in contact through non-specific binding

dependent on two inverted repeats of DNA, causes string of uracils (unstable and causes loop), RNA falls away (formation of hairpin, RNA pauses, DNA snaps back together)

Rho (binding protein, helicase) contacts RNA polymerase at terminator, unwinds RNA/DNA helix, RNA is released, no string of uracils, RatI destroys rest of RNA and stops RNA polymerase

• multiple types of RNA polymerase
• chromatin must be remodeled (too tightly packed)
• more transcription factors required
• RNA polymerase I --> large rRNAs
• RNA polymerase II --> pre-mRNA, snRNA, snoRNA
• RNA polymerase III --> small rRNA, tRNA, snRNA
• core promoter = part of DNA with sequence elements and has transcription site (downstream is initiator elements, TATA box, TFIIB recognition element)
• regulator promoter (upstream) = not bound by RNA polymerase, held by transcription factors (proteins with specific binding, change structure of RNA polymerase)
• TFIIB binds to TATA box, has TBP
• holoenzyme enters and binds to core promoter (major groove)
• transcription factors held by mediator (physical contact)
• coactivator interacts with holoenzyme -->drives change in RNA polymerase so DNA can open
• enhancer = DNA sequence recognized by transcription factors (not close to core promoter, DNA loops for interaction)

• 3 major regions but two are untranslated
• untranslated region, start codon, stop codon, untranslated region
• ribosome attaches near start codon and begins forming polypeptide chain
• Shine-Dalgarno sequence before start codon

• receives a 5' cap (first part that's synthesized), increases stability
• removal of a phosphate near 5' end, GTP is added and 2 phosphates are cleaved off, methylation near cap
• polyA tail added (polyadenylation), consensus sequence at end that marks cleavage cuts off at 3' end
• enzyme adds string of As, no template required (over 300)
• enzymes bind to protect from RNAse

• specific sequences, cut at 5' end of exon 1, loops around and forma lariat --> removed from exon 2 to form mature mRNA
• branch point = where lariat forms
• splicesome removes introns composed of 5snRNPs (snurps) --> RNA and proteins bind to consensus sites of introns
• alternative splicing --> more advanced --> remove/mix exons

part with a specific function

• make different proteins
• expanded number from limited amount of genes
• multiple cleave sites for different proteins

• subject to intron splicing and base modification
• extra bases to 3' end (amino acid attachment site, CCA, no template)

• 3 rRNAs produced from the same transcript, combines with proteins to form ribosomes
• add methyls or cuts by enzymes to get types

• codon usage is degenerate (redundant) and universal (common ancestor)
• interactions of side chains determine 2nd and 3rd structures of proteins
• 61 codons, 4 nucleotides, 20 amino acids

• ribosome binds close to 5' end of mRNA by start codon
• translocates down and synthesizes polypeptide chain
• ribosome hits stop codon and falls apart
• 1. small subunit binds to shine-dalgarno sequence (16s rRNA)
• 2. initiator factor binds
• 3. binding of 1st RNA (Met) to start codon
• 4. binding of large subunit

adding correct amino acids by aminoacyl tRNA synthetase (20 types)

• matches correct codon with anticodon
• interaction of proteins in cap and ribosome can initiate translation
• comes in 2 subunits, large and small
• small is sequence specific, complementary to consensus sequence (Shine-Dalgarno sequence)
• subunit breaks apart and initiation factors bind to small subunit to prevent rejoining
• tRNA with anticodon comes, base paired with start codon

• eukaryotes have Kozak instead of Shine-Dalgarno sequence
• no tRNA for stop codon, release factor comes and everything disassociates (polypeptide and mRNA released)
• tRNA can be recycled and recharged

• Charging
• Initiation
• Elongation
• Termination

• alteration of structure (chromatin), histones
• regulation of transcription and translation
• mRNA processing and RNA stability
• posttranslational modification (phosphorylation can alter proteins --> negative charge repels)

• helix-turn-helix = 2 alpha helixes with string of amino acids in between (inserted into major groove of DNA), electrostatic interaction, one side interacts with DNA while other binds to backbone
• zinc fingers = alpha helixes with zinc loops, bind as dimers (2 identical proteins)
• leucine zipper = zip together and make domains that hold together, recognition helix inserted into groove

more than one gene linked to a promoter --> more efficient (all can be turned on with equal dosage of proteins)

• DNA sequence that's a binding site for a protein (overlaps promoter, before first gene) --> stops transcription if regulator protein binds (RNA polymerase can't get through)
• transcription repressor (DNA domain), trans acting regulator --> turns genes on/off

• will bind to repressor, change conformation, allow transcription to occur (allosteric hinderence)
• transactivating factors are regulatory proteins that are free to diguse around

• repressors are present
• inducible = substrate is inducer (catabolic)
• repressible = product is inducer (threshold concentration)

• activators present
• eukaryotic
• inducible = substrate
• repressible = product (high concentration, binds and turns off)

• found in bacteria, produces enzymes required to metabolize lactose (disaccharide sugar)
• permease transporter to allow extracellular lactose to get through membrane
• B-galactosidase cleaves lactose and forms glucose and galactose, sometimes allolactose
• want to make enzymes only when lactose is in high concentrations
• relies on repressor lacI (operon is lacO, genes are lacZ, lacY, lacA)
• negative inducible, allolactose is substrate (changes conformation, can't bind to DNA, transcription is on)

• repressor can briefly fall off to allow permease to be produced
• mutation in operator --> repressor can't bind --> transcription can't turn off
• CAP activator will regulate lac operon (if glucose is present) --> can only bind if it's a dimer, goes before the promoter (cAMPs regulate CAPs dimer formation)
• when glucose is transported, shuts off cAMP, can't bind to CAP --> no dimers
• none present, nothing inhibits cAMP and more is created --> binds to CAP --> which binds to DNA so transcription starts (tortional strain on DNA to open)

• lactose present, no glucose
• no lactose, some glucose
• no lactose or glucose
• very low levels of glucose and lactose