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Biology 1001A
Tom Haffie

Lecture11 endosymbiosis: symbiosis in which one organism lives inside the other, the two typically behaving as a single organism cyanobacteria: blue-green algae, a group of photosynthetic bacteria containing blue photosynthetic pigment lateral gene transfer: the movement of genes over millions of years from the mitochondria or chloroplast to the nucleus reactive oxygen: chemically-reactive molecules containing oxygen, highly reactive due to the presence of unpaired valence shell electrons, form as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling, it takes 4 electrons to go from oxygen to water origin of endomembrane system: - endomembrane system is a collection of inter-related internal membranous sacs that divide into functional and structural compartments called organelles - major membrane components are: the nuclear envelope, the ER, the Golgi complex - infolding of the plasma membrane is believed to be responsible for the evolution of all these structures - in the cell lines leading from prokaryotes to eukaryotes, pockets of the plasma membrane may have extended inward and surrounded the nuclear region origin of mitochondria and chloroplasts: - prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells, forming a mutually advantageous relationship called a symbiosis - and over time the host cell and the endosymbionts became inseparable parts of the same organism - descendants of ancient free-living prokaryotes evidence supporting theory of endosymbiosis - morphology: the form or shape of both mitochondria and chloroplasts is similar to that of a prokaryotic cell - reproduction: a cell cannot make a mitochondria or a chloroplast, just like free-living prokaryotic cells, mitochondria and chloroplasts are derived only from preexisting mitochondria and chloroplasts, both divide by binary fission which is how prokaryotic cells divide - genetic information: mitochondria and chloroplasts contain their own DNA, which code for proteins essential for the organelle’s function - transcription and translation: both contain a complete transcription and translational machinery, including a variety of enzymes and the ribosomes necessary to synthesize the proteins encoded by their DNA - electron transport: both can generate energy in the form of ATP through the presence of their own electron transport chains factors driving development of early eukaryotic cells - earliest prokaryotes were anaerobic, barely making enough ATP 1 - cyanobacteria evolved: oxygenic photosynthesis, producing oxygen, huge amount of oxygen started to accumulate in the atmosphere, could use oxygen as the terminal acceptor in electron transport chain - prokaryotes that undergo aerobic respiration make huge amounts of ATP why eukaryotic cells can be larger and more complex than prokaryotic cells - bigger because they have increased energy production - most have hundreds of mitochondria means it can be bigger - much more complex, have more genes evidence for lateral gene transfer from organelles to nucleus - proteins still do the same thing but is now in the nucleus - the product of the gene is the same but the location of the gene has shifted to the nucleus - if ancestor had gene in the mitochondria, but the present cell has it in the nucleus then it is obvious that lateral gene transfer occurred general idea about how lateral gene transfer is detected - look at the species in the mtDNA and nDNA - one that is only in the mtDNA stays in the mitochondria - one that is in both is in the process of gene transfer - one that is in nDNA, gene transfer has already taken place and is only in the nucleus genome now rubisco structure and assembly from components code by different genomes - most abundant on the planet, giant molecules, have 8 large subunits (LSU) and 8 small subunits (SSU) - requires two genomes, small is coded in the nucleus and large is coded in the chloroplast so lateral gene transfer occurred for one of these but not the other - coordinate expression of these units is required various reactive oxygen species and how they are made - oxygen ions, peroxides - form as a natural byproduct of the normal metabolism of oxygen - highly reactive due to the presence of unpaired valence shell electrons - product of water splitting - takes 4 electrons to reduce a molecule of oxygen to water - but if oxygen only accepts one electron, superoxide is made and if only 2 electrons are accepted, hydrogen peroxide is made (very reactive molecules that can mess with your DNA) possible reasons why genes have moved to the nucleus from organelles - who’s the boss: gives nucleus control of overall cell activities - metabolic processes must be integrated with whats going on in the rest of the cell by the nucleus - reactive molecules: organelles are home of some reactive molecules - things have to be safe (in the nucleus) so you wouldn’t want genes near reactive molecules (they oxidize the DNA and cause mutation) - reactive oxygen species (ROS) 2 - they can recombine in the nucleus to repair mutations and create new genes that could become more useful, you can’t do that in the organelles - there is no other way to fix mutations once they are double stranded possible reasons why certain genes have not moved to the nucleus from organelles - proximity some proteins are highly hydrophobic and cannot survive the journey from nucleus to mitochondria/chloroplast - codons: some codons mean different thing sin organelles, so maybe when you move them over they can not be expressed properly in the nucleus - they haven’t move yet - products are needed in abundance locally and are too hard to transfer from the cytoplasm - if proteins degrade we can rapidly reproduce them - whatever mechanism is used to transfer them doesn’t work for those genes - not easily synthesized and transported because they are more hydrophobic Lecture12&13 mRNA: a single-stranded molecule of RNA that is synthesized in the nucleus from a DNA template and then enters the cytoplasm, where its genetic code specifies the amino acid sequence for protein synthesis tRNA: a small RNA molecule, consisting of a strand of nucleotides folded into a clover- leaf shape, that picks up an unattached amino acid within the cell cytoplasm and conveys it to the ribosome for protein synthesis rRNA: RNA that is fundamental structure element of ribosomes promoter: the site to which RNA polymerase binds for initiating transcription called promoter proximal elements UTR: untranslated region, refers to either of two section on each side of a coding sequence on a strand of mRNA, if found on the 5’ side (called 5’ UTR) or if found on the 3’ end (3‘ UTR) terminator: specific DNA sequence for the gene that signals the end of transcription of a gene, terminators are common for prokaryotic genes codon: each three-letter word (triplet) of the genetic code anticodon: three-nucleotide segment in tRNAs that pairs with a codon in mRNAs termination factor (release factor): a protein that recognizes stop codons in the A site of a ribosome translating an mRNA and terminate translation operon: a cluster of prokaryotic genes and the DNA sequences involved in their regulation operator: a DNA regulatory sequence that controls transcription of an operon repressor: a regulatory protein that prevents the operon genes from being expressed CAP (catabolite activator protein): transcriptional activator that exists as a homodimer in solution, two cAMP molecules bind dimeric CAP with negative cooperativity and function as allosteric effectors by increasing a protein’s affinity for DNA cAMP (cyclic AMP): in a particular signal transduction pathways, a second messenger that activates protein kinases, which elicit the cellular response by adding 3 phosphate groups to specific target proteins. cAMP functions in one of two major G protein-coupled receptor-response pathways lacZ: encodes the enzyme beta-galactosidase, which catalyzes the converion of the disaccharide sugar, lactose, into the monosaccharide sugars, glucose and galactose (z- no activity ever) lacY: encodes a permease enzyme that transports lactose actively into the cell lacI: a gene that encodes the Lac repressor, its nearby but separate from the lac operon (I- stands for non inducible) allolactase: disaccharide similar to lactose, inducer of the operon positive control: genes are expressed all the time, cells are always looking for glucose negative control: binding of repressor reduces expression, the expression goes down (has nothing to do with the lactose) inducible expression: a gene whose expression is either responsive to environmental change or dependent of the position of the cell cycle constitutive expression: a gene that is transcribed continually compared to a facultative gene which is only transcribed as needed quorum sensing: used to coordinate their gene expression according to the local density of their population basic mechanism of transcription and translation in proks vs. euks - proks: RNA polymerase synthesizes an mRNA molecule that is ready for translation on ribosomes - no nucleus, that means that as soon as a message begins to be produces, that message can begin to be translated by ribosomes - transcription and translation occur at virtually the same time in proks - euks: RNA polymerase synthesizes a precursor-mRNA (pre-mRNA molecule) that has extra segments that are removed by RNA procession to produce a translatable mRNA, that mRNA exits the nucleus through a nuclear pore and is translated on ribosomes in the cytoplasm - transcription and translation are separated by space and time basic structure and function of RNA polymerase and ribosome - ribosomal RNA base pairs with mRNA to help the whole initiation complex form properly - rRNA binds onto mRNA at a sequence called the docking sequence examples of complementary base pairing in gene expression - mRNA: base pair with themselves to create secondary structures whenever it can, it is most thermodynamically stable when paired with itself - tRNA: base pairing is a fundamental part of tRNA structure, giving it it’s L shape - rRNA: base pairs with itself and is catalytic conceptual connections between RNA and DNA polymerase - RNA polymerase synthesizes RNA, but does not need a primer to initiate synthesis 4 - binds to single stranded DNA - does not need to separate the two strands of DNA - DNA polymerase synthesizes DNA, but need a primer in order to initiate synthesis - binds to double stranded DNA - must unwind the DNA before replicating relative location of such DNA sequence “signals” as - promoter: RNA recognizes this and binds there to start transcription (beginning) - 5’ and 3’ UTR: 5’ UTR is before the start codon, and 3’ UTR is after the stop codon - “SD box”: - start codon: after the promoter and 5’ UTR - stop codon: end of translating RNA, stop codon stops translation - transcription terminator: before stop codon, polymerase transcribes right through the terminator, sequence then pairs with itself to make a structure called a hairpin mechanism by which each signal is interpreted, or understood, by the cell - each signal is interpreted by the polymerase characteristics of promoters that require a particular position and direction - must start at the 5’ end, upstream of the gene they are wanted to transcribe change in amino acid coded, given a change in the DNA sequence (and Genetic Code table) base sequence of start and stop codons as RNA and DNA - start: AUG - stop: UAA, UAG, UGA the location of various signals given a diagram of simultaneous transcription/translation in proks - DNA is the long skinny strand - little “beaded chains” coming off that are the ribosomes (beads) and mRNA (strand) - RNA polymerase is little bump located on the DNA - polypeptide pokes out of ribosomes basic structure of lac operon - strand of DNA that goes, lac I, promoter, operator, transcription initiation site, lacZ, lacY, lacA, transcription termination site - lac I (regulatory gene) binds Lac repressor, promoter binds RNA polymerase, operator binds Lac repressor mechanism of action of lac repressor and CAP - lac repressor binding decreases expression (negative control) - is a dimer that bind the DNA at different places in a way that pops out a region so that polymerase cannot transcribe through that loop - this is not a hairpin loop (they are formed from single stranded nucleic acids that pair with themselves) 5 - negative control; when a protein binds DNA causing gene expression to go down - CAP binding increase expression of the operon (positive control) - example of how DNA learns from its environment, proteins are often used as a way of interpreting the environment - CAP binding site is just upstream of the promoter, it attracts the binding of a protein called CAP (catabolic activator protein), stimulates expression of operon - as glucose comes into the cell, levels of cAMP go down (inverse relationship) cAMP is needed for CAP binding - more glucose, the less transcription of lac - dimers of CAP bends the DNA (just upstream of the promoter) which makes it more available to RNA polymerase and stimulates transcription function of lac operon in the presence, and absence of lactose - presence: lac gene are expressed because allolactose binds to the Lac repressor protein and keeps it from binding to the lac operator, allowing RNAP to transcribe the lac genes and thereby leading to high levels of the encoded proteins - absence: repressor binds very tightly to a short DNA sequence just downstream of the promoter near the beginning of the lacZ called the lac operator, which interferes with binding of RNAP to the promoter and therefore mRNA encoding lacZ and lacY is only made at very low levels function of lac operon in the presence, and absence of glucose - presence: when glucose is present, cAMP presence is not high, therefore, CAP-cAMP binding cannot happen as often, so the cell does not digest lactose frequently - absence: cAMP concentration is high, and binding of CAP-cAMP (CAP right before promoter) to the DNA significantly increases the production of beta-galactosidase, enabling the cell to hydrolyze (digest) lactose and release galactose and glucose - if both glucose and lactose are absent, CAP-cAMP is bound and repressor is bound so no transcription takes place possible location of mutation that give rise to a given phenotype - mutation in lacZ, expression of operon, no lacZ but lacY, cell will fill up with lactose, no enzyme to degrade it - in normal glucose causes the CAP to stop binding and stop promoting transcription like it did before - mutation in CAP such that CAP does not bind the DNA so the operon gets induced but not as much as it would, when glucose is added, nothing happens because DNA has no way to sense the glucose because CAP is whacked phenotype that would arise from a given mutation under given conditions - lacI gene to make repressor insensitive to allolactose - promoter of CAP that stops expression - in CAP gene to decrease cAMP binding 6 - lacY gene to decrease activity - lac promoter to increase affinity for RNA polymerase evidence for why the “lac” operon likely didn’t evolve to metabolize lactose - babies are able to digest lactose, but most adults (except white caucasians) are not meant to digest lactose - in nature, they digest some other molecule (that is present in stomachs of mammals) that you do find that contains galactosidase - lac operon did no evolve to digest lactose because most adult mammals do not drink milk once they have aged Lecture14&15 5‘ cap: specially altered nucleotide n the 5’ end of precursor mRNA and some other primary RNA transcripts as found in euks polyA tail: consists of multiple adenosine monophosphate (a stretch of RNA which only has adenine bases) added posttranscriptionally to the 3’ end of a pre-mRNA molecule and retained in the mRNA produced from it that enables mRNA to be translated efficiently and protects if from attack by RNA-digesting enzymes in the cytoplasm pre-mRNA: the primary transcript of a euk protein-coding gene, which is processed to form mRNA snRNP: small ribonucleoprotein particle are a complex of RNA and proteins that combine with unmodified pre-mRNA and various other proteins to form a spliceosome snRNA: a class of small RNA molecules that are found within the nucleus of euk cells spliceosome: complex formed between the pre-mRNA and snRNPs in which mRNA splicing takes place intron: a non-protein-coding sequence that interrupts the protein-coding sequence in a euk gene, they are removed by splicing in the processing of pre-mRNA to mRNA exon: an amino-acid-coding sequence present in pre-mRNA that is retained in a spliced mRNA that is translated to produce a polypeptide alternative splicing: mechanism that joins exons in different combinations to produce different mRNAs from a single gene polysome: the entire structure of an mRNA molecule and the multiple associated ribosomes that are translating it simultaneously signal recognition sequence: a short segment of amino acids to the signal recognition particle binds, temporarily blocking further translation. a single peptide found on polypeptides that are sorted to the ER signal recognition particle: protein-RNA complex that binds to signal sequences and targets polypeptide chains to the ER endomembrane system: in euks, a collection of interrelated internal membraneous sacs that divide cell into functional and structural compartments TATA box: a regulatory DNA sequence found in the promoters of many euk genes transcribed by RNA polymerase 7 histone: a small, positively charged (basic) protein that is complexed with DNA in the chromosomes of euks nucleosome: the basic structural unit of chromatin in euks, consisting of DNA wrapped around a histone core chromatin remodeling: process in which the state of the chromatin is changed so that the proteins that initiate transcription can bind to their promoters methylation: catalyzed by enzymes, regulation of gene expression, tends to silence gene expression acetylation: transfer of acetate onto tail, makes it less positive and makes the DNA tightly packed, making the genes more accessible to transcription epigenetic marks: chemical additions to the genetic sequence enhancer: in euks, a region at a significant distance from the beginning of a gene containing regulatory sequences that determine whether the gene is transcribed at is maximum possible rate silencer: methylation of cytosines in euk promoters inhibits transcription and turns genes off transcription factor: proteins that recognize and bind to the TATA box and then recruit the polymerase miRNA: (microRNA) short ribonucleic acid molecules, on average only 22 nucleotides long and are found in all euk cells ubiquitin: small regulatory protein found in almost all tissues of euks that direct protein recycling proteasome: very large protein complexes inside all euks and archaea and in
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