Exam Four Notes PDF

Preview

Summary

These are notes for most of the topics covered before the fourth and final exam in this course. The professor at this time was William Adams....

Description

Exam Four  





 



Gene expression = DNA directs the synthesis of proteins Two universal steps o Transcription o Translation The genetic code is shared by (almost) all life on earth o Example: Fluorescent jellyfish protein can be accurately transcribed and translated in fish and cats Gene Expression Outline o Easing in: basic principles of transcription and translation o Transcription in detail o RNA processing in Eukaryotes o The genetic “code” o Translation in detail o Mutation Genes are nucleotide sequences, hundreds or thousands of nucleotides long The central dogma o DNA  RNA  PROTEIN o DNA = A polymer of nucleotides (A, T, G, C) in a specific order o  = A process of going from one “language” to another in 2 fundamental steps o Protein = A polymer of amino acids (e.g. alanine, glycine, etc.) in a specific order o When a single pre-mRNA molecule is made in one of your cells, how much information does it contain?  The genetic code for one allele from one chromosome o Which cells in the albino donkey have the albino mutation?  All of its cells Transcription in detail o Initiation  Figure out where to start reading DNA and actually begin making mRNA  Upstream of the gene is a promoter (the start here signal)  Whole promoter = several dozen nucleotides  RNA polymerase = reads one strand of DNA and builds the mRNA  Once RNA polymerase binds, it can only synthesize RNA in a 5’ to 3’ direction. Which of the two DNA strands shown here will it “read” as it makes RNA?  Bottom one  With transcription factors in place, RNA polymerase can now bind DNA at the right place to begin transcription of the gene o Elongation  Make the full length mRNA transcript  RNA polymerase untwists DNA, makes mRNA (A can sometimes be matched with U instead of T)  RNA has the base Uracil (U) instead of Thymine (T)

 





RNA has the sugar Ribose instead of Deoxyribose send nudes Summary of Elongation  RNA polymerase untwists and separates 10-20 base pairs of DNA at a time  This opens space for RNA nucleotides to come into the site of mRNA synthesis  base pairing of RNA nucleotides with the DNA template  RNA polymerase catalyzes the addition of correct nucleotides onto the 3’ end of the RNA molecule  RNA polymerase moves along, the new RNA molecule peels away from the DNA, and the helix re-twists o Termination  Strop transcribing; mRNA completed  Bacteria: termination sequence  Eukaryotes: a bit more complicated enzymes that cut the transcript free another enzyme “chases” RNA polymerase RNA processing in Eukaryotes o Average human pre-mRNA transcript length: 27,000 nucleotides o Average human protein: 400 amino acids  requires only 1200 nucleotides o Before RNA transcripts leave the nucleus, they are modified  Alteration of ends  Cutting out some of the middle  This offers the cell a way of controlling when and where protein is produced o Cutting out some of the middle: RNA splicing o Any mutation that alters splicing can cause a different protein, or different form of a protein to be produced o Alternative splicing occurs normally for more than half of our protein-coding genes o But incorrect splicing can lead to serious problems o The sequence of DNA that codes for a eukaryotic protein is not a continuous sequence o Some introns are “self-splicing”  catalyze their own excision The Genetic Code o Nucleotides: A, T, G, and C in DNA (A, U, G, and C in RNA) o Amino Acids  20 are commonly used by most organisms o The genetic code consists of 3 letter codons:  Sequence of 3 nucleotides = specification of amino acid  Each triplet is called a codon o Analogy with English language: using just 26 letters we can make thousands of words  Using just 4 nucleotides, DNA can make 64 different codons o Some notes on Codons  When we say “codon” we are referring implicitly to the RNA triplets





 

Codons are read in the 5’ to 3’ direction, because that is how they are read by the translation machinery  Codons don’t overlap (300 nucleotides encode 100 codons) Translation in Detail o The structure of tRNA o The ribosome  Initiate  Elongate  Terminate o The ribosome  Facilitates the coupling of mRNA codons with tRNA anticodons  Provides a physical site for translation in which all the participating molecules find their proper spatial arrangement  Catalyzes formation of peptide bonds  Made out of RNA (rRNA) o All those RNA molecules  RNA = ribonucleic acid  Pre-mRNA = the RNA transcript produced initially during transcription in eukaryotes  mRNA = messenger RNA = the (processed) RNA transcript molecule that will actually be translated  tRNA = transfer RNA = the RNA molecule that brings amino acids to the ribosome  rRNA = ribosomal RNA = RNA that forms the structure of the ribosome o Initiation of translation  Small ribosomal subunit binds both mRNA and initiator tRNA then “scans” for start codon  correct reading frame Viruses o Nucleic acids gone rogue Viral Structure o Viruses are:  Particles that infect cells  Nucleic acids with protein coats  Nucleic acid contains instructions for making more virus particles  Obligate intracellular parasites o Most have a well-defined host range o Viruses are not considered to be living things o How does a virus do its business?  First, a virus enters the cell  the cell manufactures viral proteins AND copies of virus’ genome  Second, the virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, etc.  Third, the assembly of new viruses occurs w/in the cell







 Finally , new virus particles break out of the cell Animal viruses o Two key variables used to classify viruses that infect animals:  Is the genome made out of DNA or RNA?  Is it single-stranded or double-stranded? o Many viruses that infect animals have a membranous “envelope” derived from host cell o Viruses have many ways of parasitizing the host cell’s machinery How viruses make us sick o Damage or kill cells (with enzymes) o Cause infected cells to produce toxins o Envelope proteins that are toxic o However, MOST symptoms and most of the damage to the body comes from your own immune system o The immune system detects virus-infected cells and mounts an inflammatory response  Infected cells kill themselves by apoptosis  Fluids, immune cells accumulate in tissues to clean out dead cells (inflammation)  Fever, mucus, soreness are all caused by the strong inflammatory response  Death can result from uncontrolled inflammation o We can’t take antibiotics to cure ourselves of viral infections because viruses use our own cellular machinery o Vaccines are effective in preventing viral illnesses because vaccines teach your immune system how to recognize specific viruses o Vaccines are the greatest public health triumph of medical science in the 20th century The origin of new viruses and H1N1 o Most newly emerging pathogens are viruses, especially RNA viruses o Most that are new to humans come from animal reservoirs (wild or agriculture) o Emergence of new pathogens often associated with changes in human ecology include: exotic trade, agriculture, bushmeat, and population density and travel o Wen newly acquired from animals, most pathogens are NOT highly transmissible between humans at the beginning (lucky for us lol) o Humans are infected by three main groups of influenza viruses:  Influenza A  Influenza B  Influenza C o Most of what we hear about and are vaccinated for, including 2009 H1N1  Influenza A o What does H1N1 stand for?











 

Naming convention referring to two proteins in viral envelope of influenza type A viruses  These proteins are called Hemagglutinin and Neuraminidase  There are 16 types of “H” and 9 types of “N” in birds  Only 3 types of H (1,2,3,) and 2 types of N (1,2) are common in humans  A scare several years ago in far eastern Asia involved the jump of H5N1 influenza virus from birds to humans o How do different viruses get mixed up?  Reassortment: Possible when multiple virus types infect the same individual host and get into the same cell  Think “viral sex” o In reasserting influenza viruses:  Replication in host cell  production of separate genetic segments (“mini chromosomes”)  Assembly of new viruses  possible to put together elements from different viruses  Result = novel combinations of influenza genetic elements in newly made virus Mutation = any change in a DNA sequence but… o Where do mutations come from?  Damage to the DNA molecule (toxins, carcinogens, etc.)  Errors in DNA replication o How do mutations affect gene expression? Suppose a mutation in DNA caused a stop codon to appear prematurely in an mRNA transcript. What effect would this have? o Cause a shortened version of the protein to be produced (i.e., a version with fewer amino acids) Today’s feature: muscular dystrophy o Multiple types, all part of a group of inherited conditions  Duchenne muscular dystrophy is caused by an X-linked recessive allele o Some types of MD are caused by mutations causing early stop codons in a specific protein (dystrophin) Substitution – Switching one nucleotide for another can cause a different amino acid to be attached o Nucleotide-pair substitution: missense Substitution – Switching one nucleotide for another can cause no change in the protein o Nucleotide-pair substitution: silent Insertions or Deletions – Inserting an extra nucleotide, or deleting a nucleotide causes a frameshift o 3’ G T A C G G C C A T T G C 5’  The mRNA transcript from this sequence would be: 5’ C A U G C C G G U A A C G 3’ o How do we know what “reading frame” to use, that is, where to start translating the mRNA and how to break it into codons?





 Some kind of “start” signal in the mRNA sequence o How do we know what “reading frame” to use, that is, where to start translating the mRNA and how to break it into codons?  Some kind of “start” signal in the mRNA sequence  The first codon (AUG) establishes the start point and the reading frame Gene regulation: Turning genes on and off when needed o Which of the following types of cells in your body has a gene for eye color?  All of the above (eye cells only, toe cells, gametes only, brain cells) o Why do genes need to be regulated?  Every cell in our body has the same genome (set of genes)  However, our body consists of trillions of cells and millions of distinct cell types  What makes a skin cell different from a liver cell? o Why not express all your genes in every cell?  It would be impossible to have differentiated structures/organs  Within one cell, not all of that cell’s functions are needed all the time  Waste of energy/molecules to express genes whose products are not needed  Some functions are mutually exclusive; two enzymes may have opposite functions o Examples: different cell types within a human  Muscle cells express muscle actin and myosin  Hair and nail cells express keratin  Blood cells express hemoglobin o How can a cell do this, with no “brain” or “intelligence” directing it?  Molecules can act as signals by directly influencing transcription o Tryptophan synthesis in E. coli: a specific example meant to illuminate general principles  Turning multiple genes “on” and “off” in concert  Doing so at the appropriate times o Turning all 5 genes “on” and “off”  All 5 genes are clustered together  Single promoter serves all 5 genes  one big transcription unit  One long mRNA is translated into 5 polypeptides o In bacteria, how could one long mRNA be translated into five polypeptides?  The mRNA is punctuated with stop and start codons signaling where one polypeptide stops and the next begins Gene Regulation o Transcriptional regulation is the most important level of gene regulation  It is the main on/off/dimmer switch  It determines whether a gene is turned on/off and at what level (i.e. how much protein is ultimately expressed)





The first step in transcription is binding of transcription factors (proteins) to the promoter of the gene  Enhancers: additional regulatory sequences  In addition to the promoter, an additional regulatory sequence, called an enhancer, is generally involved  An enhancer for a specific gene tends to be located far from the gene  For transcription factors to bind the enhancer and the promoter at the same time, the DNA between the enhancer and the promoter bends  Cells are ultimately different from each other because they have different transcription factors  Combinations of TFS are essential for gene regulation  There are only several thousand TFs but millions of cell types o Cells are defined by the combinations of TFs they have  An enhancer often has around 10 control elements  The same individual control element may be used in the regulation of many different genes o Different cell types will have some of the same TFs present, but not all o Cells acquire their unique set of TFs during development  Controlling Blood sugar  Normal human blood sugar levels: 70-100 mg/dL  So when you eat a donut, there’s a temporary surge in blood sugar o Need to return to normal to keep tissues and organs working properly o Part of homeostasis  Two aspects of homeostasis in this example o Release of insulin  next term o Make more insulin (get ready for next donut)  gene regulation problem  What would need to happen in order for a healthy adult human to make more insulin? o “Turn on” expression of the insulin gene in cells in the pancreas  Given what you know about eukaryotic gene regulation: To turn on expression of the insulin gene in pancreatic cells, what would be needed? o The right combination of transcription factors to promote expression of the insulin gene General principles for turning on genes and getting the right tissues in the right places o Embryonic development as a process of cell division and gene regulation  Zygote (one cell)  developed animal (many cells, multiple cell types, 3-D arrangement)



o Development of a multicellular organism  Involves lots of precise gene expression  Determination Cell committed to its fate  Differentiation: Cell specialization in structure and function, production of tissue-specific proteins  Morphogenesis: Tissues, organs, and organism take shape  Molecules in the early “environment” lead to determination of cell fate requiring that certain genes are “switched on” o Differential gene regulation set up by molecules in the cytoplasm of the zygote o Within one cell type, how can a cell turn on a bunch of genes in a coordinated manner?  Cascading effects of transcription factors  Embryonic precursor cell has the potential to develop into a variety of different cell types o How do you get the right sets of genes turned on in the right places?  Pattern formation: Setting up the body plan  Pattern formation = development of spatial organization of tissues and organs  establishment of major axes  Positional information = molecular cues that tell a cell its location  Two complementary mechanisms of pattern formation  Cytoplasmic Determinants o Before fertilization, when eggs are made o Maternally derived o Seeds of differential gene expression  Inductive signals o Once there are multiple cells o Substance from outside a cell (e.g. signal from nearby cell) influences cell’s gene expression  Given the distribution of cytoplasmic determinants in this zygote (one molecule type on the right, the other on the left), would division along the vertical line or the horizontal line result in the greatest differences in gene expression between the two resulting cells?  A. Vertical Specific examples of getting the right things in the right places o Anterior-posterior axis in fruit flies  “Nurse” cells  provide nutrients, mRNAs, and other substances for development of egg cell (Before fertilization)  Make egg shell  Development of the fertilized egg into a larva  formation and differentiation of body segments  A closer look at the formation of the anterior-posterior axis in the fruit fly: the role of the bicoid gene





Gradients of molecules establish major body axes  Gradient of bicoid protein determines anterior-posterior axis  A mutant fruit fly larva that never had bicoid protein would: Develop two tails and no head o Vertebrate limbs  Mechanisms of induction and pattern formation: the vertebrate limb as an example  The wings and legs begin as bumps of tissue called limb buds  Proper pattern formation requires three axes of specification  1. Proximal-distal (shoulder to fingertip)  2. Anterior-Posterior (thumb to pinky)  3. Dorsal-ventral (knuckles to palm)  Cells in two regions secrete proteins (inducers) providing positional information  1. ZPA (zone of polarizing activity) o Anterior-posterior o ZPA side = posterior = pinky o Other side = anterior = thumb  2. AER (= apical ectodermal ridge) o Proximal-distal o If the AER cells are removed, there will be no limb outgrowth  If the ZPA was experimentally removed from a developing chick embryo’s limb, what would happen? o The limb would develop with two “thumbs” (one on each side of the limb) o Conclusions:  Cells of ZPA secrete proteins (inducer)  Anterior-posterior inducer gradient creates anterior-posterior pattern  What about wings (arms) vs. legs?  Wings vs legs are differentiated based on previous events in histories of respective limb bud cells Evolution and Natural Selection o A. Evolution: Facts and Theories  Evolution  Change over time in a population’s genetic makeup  Descent with modification  Modern forms are not present in the early fossil record  Novel flu viruses have arisen in our lifetimes  Pine beetles are killing susceptible trees and left resistant trees behind  Distinct species of finches are hybridizing and creating new lineages



Patterns  Observations of the natural world  Factual descriptions of change  Processes  Mechanisms that produce a pattern  Hypothesis  A testable, falsifiable explanation for a phenomenon of interest  Theory  A framework of internally consistent ideas used for generating hypotheses  Fact  A piece of info about circumstances that exist or events that have occurred; an actual occurrence o B. Evolution and Natural Selection  Evolution is not natural selection  Evolution = The fact that species and their characteristics change over time  Natural selection  A theory that provides hypotheses about why and how these changes have occurred  Darwin was the first to offer a compelling theory about the process of evolution, and how such a process could produce adaptations  He was not the first to recognize patterns of evolution  Darwin developed two main ideas:  Descent with modification explains life’s unity and diversity  Natural selection is a cause of adaptive evolution  Darwin’s view: Descent with modification produces a branching tree of species  How does natural selection work?  Offspring are overly abundant: populations would increase exponentially if all individuals that were born survived and reproduced  1. Yet many populations remain stable in size  2. Resources (food, mates, etc.) are limited  Only a subset of all individuals will survive and reproduce  3. No two individuals are alike  4. Variation is often heritable  Individuals that happen to have traits conferring survival and reproductive advantages will tend to leave more offspring  Such favorable traits will tend to increase in frequency in a population over time  Challenges to survival and reproduction + heritable variation in traits affecting survival and reproduction = the traits that confer



survival and reproductive advantages will increase in frequency in the population Important points about natural selection





1. Natural selection does not create variants in a population; it can only maintain or eliminate  2. Natural selection can only cause evolutionary change where there is heritable genetic variation: genetic variation ...