Exam # 2 Study Guide Lectures: 15 - 26Lecture 15 (February 23):Mutations:- defects in DNA sequence that change gene function- example: change in coding region for protein- silent mutations don't change amino acids- others might change amino acids (missense mutations), but these amino acids may or may not be critical to the protein- nonsense - change puts in a stop codon, ribosome will read it and release factor will bind - short, one amino acid protein- may or may not still functionNonsense mutations create new stop codons in DNA template for mRNA, make abnormally short proteins:- high % of human genetic diseases- some forms of --cystic fibrosis (ion channel in lung cells)-Duchenne muscular dystropy (scaffolding/cytoskeleton protein)- experiment treatment: drugs that cause ribosome to read through (skip) stop codons- change coding- Frameshift mutations - deletion or insertion of anything other than 3n nucleotides in coding region - causes extensive missense (1 base pair deletion)DNA nucleotide sequence contains information for:- where to bind RNA polymerase- where to bind transcription factors, alter transcription and histones- where to methylate DNA- where to 5' cap and polyadenylate eukaryotic primary RNA signal (bind enzymes to each)- where to splice eukaryotic primary RNA, intron-exon splice sites (bind snRNA of spliceosomes)- where to bind miRNAs- where to start and stop translation of mRNA (start and stop codons, bind initiator tRNA and release factor protein, respectively)- what amino acids to put in protein (codons bind tRNAs)Mutations can remove or create new splice sites in DNA template for mRNA:- example: one form of Progeria (premature aging)- single base substitution makes a new splice site in pre-RNA for Lamin A- mutations can change recognition sites for transcription factor binding- ex. DNA change in operator DNA might block binding of transcription factorDNA arrangements can change gene expression:- The central dogma (DNA to RNA to protein) and chemical evolution - biogenesisSimplifying part of the central dogma - DNA replication via polymerase chain reaction (PCR):- what, at a minimum, do you need to replicate DNA?- uses heat instead of helicase, topoisomerase, to separate DNA strands- use short DNA primers to start amplification in DNA - no primase!- uses DNA polymerase from heat-resistance bacteria, does not denature at high temps.PCR geometrically amplifies DNA between the 2 primers, but need both DNA and a protein (DNA polymerase):- self-replicating molecules- natural selection would operate on self-replicating molecules- system must contain enzymes that can generate many identical enzymes- What would they be?- self-replicating molecules could possibly be RNA - RNA? --can be a template-can be an enzyme - RNA enzyme = ribozyme BIO 151 1st Edition- "RNA World" HypothesisRNA World Hypothesis:- RNA systems that self-replicate in 2 steps- ribozymes can spontaneously cause nucleotides to link together - act as RNA polymerasesSelf-Replicating RNA:- still lots of problems (efficiency of ribozyme, clutter with other molecules, etc.) some think there must have been somethingbefore RNA- getting beyond RNA - hypothesis1) Self-replicating RNA2) RNA acted as template for forming 3) Proteins then aid in replication of RNA4) Make DNA from RNA for storage of info.- Assume early cell has membrane DNA to RNA to protein = something like modern prokaryoteLecture 16 (February 25):Assume early cell has membrane DNA to RNA to protein:- something like modern prokaryote- next big steps: -metabolic diversity how to get energy (photosynthesis, etc.)-prokaryotes to eukaryotesEukaryotes have membrane-bound "organelles":- prokaryotes - 3.4 billion years ago- eukaryotes - 1.3 - 1.8 billion years ago- infolding of plasma membrane to make nucleus, endomembrane?- What about other organelles?Prokaryotes vs. eukaryotes:- eukaryotic cells - most are larger, more complex than prokaryotesSemi-Autonomous organelles:- where most of the ATP comes from in most eukaryotic cells- the energy to make ATP comes from catabolic reactions that are exergonic- ATP hydrolysis provides the energy for cellular processes that are endergonicMitochondria:- in almost all eukaryotes- produce ATP from carbohydrates, fats, etc.Chloroplasts:- in plants and some protists (single-celled eukaryotes)- produce ATP and carbohydrates from sunlight = photosynthesisEndosymbiant:- theory for semi-autonomous organelles- symbiosis - organisms living together in direct and intimate contact- endosymbiant - one living inside (endo) otherEndocytosis: - pinching off captures substance from outside cell"Semi-Autonomous" Organelles:- mitochondria and chloroplasts contain DNA in small circular chromosomes - replicates, transcribed into RNA- have ribosomes that resemble bacterial ribosomes- other biochemical similarities to specific modern bacteria- they reproduce in cells by fission- circular DNA in mitochondrion (mtDNA has transcription units for):-2 bactera-like ribosomal rRNAs-22 transfer RNAs- 13 protein-coding genes, all for components helping to make ATP- all other genes for making mitochondria reside in cells- nucleus - moved from endosymbiant to host over time?Some cells have true bacterial endosymbiants:- Rickettsia bacteria live only inside eukaryotic cells- cause many diseases: typhus, Rocky Mountain spotted fever, etc.- produce energy similarly to mitochondriaNucleus:- chromatin strands of chromosomes- nucleolus - site(s) of rRNA synthesis, assembly of large and small ribosomal subunits- nuclear envelopes - 2 lipid bilayers- inner and outer nuclear envelopes perforated by nuclear "pores"Protein import into nucleus:- import protein - shuttles back and forth in "pore" - more like active transport- nuclear localization (import) signal sequence = amino acid sequence that allows protein to bind nuclear import protein- mRNA export from nucleus: binds export proteins that contain nuclear export signal sequences- different adaptors for ribosome subunits, tRNAsEndomembrane system for secreted and transmembrane proteins, carbohydrates, lipids:- endoplasmic reticulum - Golgi apparatusEndoplasmic Reticulum (ER):- network of membrane-enclosed tubes, discs- continuous with outer nuclear envelope- rough ER has ribosomes, smooth ER does notSmooth ER:- synthesis of many molecules, including some lipids and carbohydrates- storage of substances, including Ca2+ release from ER plays role in muscle contraction, other eventsRough ER:-
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