Prep101 - Bio 200 Equation Sheet(Lasko Fagotto Biology 200...

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Unformatted text preview: Bio 200 Equation Sheet (Lasko / Fagotto) Biology 200 is a challenging course containing lots of material and requires a full understanding of the course content Start studying early to be well prepared for the exam It is impossible to memorize all the information without understanding it Do not only rely on lecture notes – create a summarized version of notes to study with by using lecture notes, class notes and the text book The exam style is multiple choice - many questions will not be straight forward but will require the application of different parts of the course It is important to do as many practice questions as possible to be comfortable with approaching exam questions MACROMOLECULES: PROTEINS, NUCLEIC ACIDS, CARBOHYDRATES AND LIPIDS Key Terms Coiled coil Polypeptide motif α helix Tertiary β-pleated Structure sheets Quaternary Helix-loopStructure helix Purines Ca2 Zinc Finger Pyrimidines Nucleotide Ribonucleic Acid (RNA) Deoxyribonucleic acid (DNA) Lipid membranes composed of phospholipids that are amphipathic. Have hydrophobic tail and hydrophilic head Carbohydrates : Have the general formula (CH2O)n o Monosaccharides are linked together via a glycosidic bonds forming polysaccharides o Sugars can also branch forming huge polymers Proteins : Consists of one or more polypeptide that have a defined 3-D structure and have diverse biological functions o Peptides have covalent bonds between the amino group from one amino acid with the carboxyl group of adjoining amino acid o There are 20 different amino acids differing by their R group Nucleic Acids: macromolecules composed of a long chain of monomers known as nucleotides. o Nucleotides consist of : a Pentose Sugar, 5-C sugar either deoxyribose or ribose, a nitrogenous base either a purine or pyrimidine and a phosphate group o o o Nucleotides are joined through 5’-3’ phosphodiester linkage DNAs stores all genetic information in genes 2 categories of RNA : Structural (tRNA, mRNA, rRNA) and catalytic TRANSCRIPTION Key Terms Primary transcript Capping Poly (A)tail Alternative splicing Operon repressors Activators mutations Enhancers Protein-coding region Pre-Initiation Complex Transcription factors TATA-BOX Regulatory Sequences Promoterproximal elements Deletion analysis Repression domain DNA-binding Domain Homeodomain proteins Zinc-Finger proteins Leucine Zippers Basic helix-loop-helix proteins (bHLH) enhancesome Transcription a process by which the polymerization of ribonucleotides is guided by complementary base pairing with DNA producing an RNA transcript of a gene Occurs in 3 steps : o Initiation : RNA Polymerase binds consist of multiple subunits, DNA denatures, 2 ribonucleotides are aligned, release of the σ subunit ends initiation o Elongation : Transcription bubble is formed o Termination: RNA sequences that signal the end of elongation coded by DNA. Terminator sequence stops RNA Polymerase Promoter is essential for transcription. Prokaryotes and eukaryotes have different polymerases Prokaryotes regulate gene transcription via operons and Two-component regulatory systems Eukaryotic gene regulation is much more complex - each gene has its own promoter unlike operons Eukaryotic transcription factors bind the promoter and other regulatory sequences regulating gene expression. o The DNA binding domain of transcriptions factors contain a variety of motifs that bind specific DNA sequences o Different combinations of factors can form dimmers which bind different regulatory sequences enhancing or inhibiting transcription POST-TRANSCRIPTIONAL GENE REGULATION Key Terms Capping Polyadenylation RNA-Binding Domains hnRNP Proteins RNA recognition motif(RRM) RGG box KH motif Cleavage Splicing Spliceosomes Self-Splicing Alternative Splicing RNA Editing Nucleocytoplasmic export Nuclear localization signals (NLS) Nuclear Export Signal (NES) SR proteins Exon-Junction complex (EJC) Eukaryotic transcripts go through several processes before becoming mRNA o 5’ capping o Poly A (tail) o Alternative splicing RNA processing occurs in the nuclei and only mRNA is exported out to be translated All post transcriptional modifications have multiple steps and different enzymes are involved which must be known Cleavage and polyadenylation occurs in the same process Splicing occurs at introns and alternative splicing can lead to different proteins from the same transcript o At introns/exon border there are is short consensus sequences o The splice reaction occurs in two transesterfication steps Most splicing occurs via spliceosomes which contain several small nuclear ribonucleotide proteins (snRNPs) and have a specific series of steps RNA Editing :The sequence of pre-mRNA is altered and mRNA sequence is different than the genomic DNA sequence o Deamination reactions changes A to I and C to U Nucleocytoplasmic export of RNA- ONLY fully spliced mature mRNA gets exported to the cytoplasm for translation o Different proteins and receptors allow transport through the nuclear pore Protein import Nuclear Localization Signal (NSL) o Proteins that are destined for the nucleus have a specific sequence o NSL is recognized by specific proteins that orchestrate import through the nuclear pore Nuclear Export Signal (NES) o Proteins can exported through the nuclear pore by recognition of the nuclear export signal o Specific proteins recognize the NES and orchestrate export We’ve helped over 50,000 students get better grades since 1999! Need help for exams? Check out our classroom prep sessions - customized to your exact course - at RNA POST-TRANSCRIPTIONAL REGULATION II Key Terms Phosphorylation Ferrtin Transferrin receptors (TfRs) MicroRNAs RNA Interference mRNA stability effects how long mRNA persists and therefore the amount of protein translated o degradation of the poly(A) tail over time leading to decapping and degradation of mRNA by exonucleases o AUUUA in the 3’UTR sequence decreases the ½ life of mRNA Cytoplasmic Polyadenylation and mRNA Translation: Some mRNA must undergo polyadenylation in the cytoplasm to become translationally active o They have a Regulatory sequence that control translation are usual found with the UTR at the 3’ or 5’ end o Sequence-specific translational-control proteins can bind to the 3’UTR of an mRNA and function in a combinatorial manner and in most cases repress translation o Phosphorylation allows translation to occur RNA Interference: dsRNA on the 3’end of a target will silence the whole gene while dsRNA on the 5’ end only target the region it hybridizes with o miRNA is formed by the processing of ≈70-nt pre-RNA that has a hairpin structure with a few mismatched base pairs in the stem o siRNA are produced by cleavage of long dsRNA (RNAi) Iron regulation : Iron levels are kept at equilibrium through Transferrin receptors (TfRs) which mediate iron uptake and through ferrtin an intracellular iron binding protein. A brief overview : o stability of TfRs mRNA and Ferrtin mRNA is regulated by iron concentrations o TfR mRNA have Iron Response Elements(IRE) that contain the AU-rich degradation signals at the 3’ end o Ferrtin mRNA has 5’ Iron Response Elements(IRE) o Control of mRNA for both occurs through IRE-binding protein(BP) and iron levels control mRNA levels of each through binding of this protein DNA REPLICATION Key Terms RNA primer primase DNA Replication bubble Replication fork Okazaki fragments Restriction polymerase T-antigen helicase RPA Phosphodiester bonds Complementary base-pairing endonuclease MCM Helicases Topoisomerase DNA replication is a semi-conservative process where newly synthesized DNA contains a parental and daughter strand. o Synthesis occurs in the 5’ to 3’ direction o RNA primer is required which is added by primase o DNA polymerase proofreads and removes any mistakes: DNA pol δ make less mistakes that DNA pol α o During elongation, RNA primers is removed by DNA pol δ o DNA pol δ (not DNA pol α) fills in the gap O DNA ligase seals the 3’ OH and 5’ PO4 nicks by catalyzing the formation of phosphodiester bonds O DNA pol δ is responsible for the majority of replicating strand elongation O Multiple enzymes and protein complexes are involved In Eukaryotes there are multiple Origin sites of replication and replication occurs bidirectionally Many amino acids have more than one tRNA and many tRNAs can bind more than one amino acid o rRNAs are found in the ribosome which catalyzes the formation of a polypeptide chain A ribosome is the site of translation o Composed of a small subunit and a large subunit o Recognizes translation initiation start site o Has catalytic activity linking amino acids to form polypeptide Translation occurs in three defined and which must be known o Formation of the Pre-initiation complex and translation initiation o Translation elongation o Translation termination Polysomes allow simultaneous translation of an mRNA by multiple ribosomes increasing efficiency of protein synthesis Protein degradation occurs through a series of steps leading to a ubiquitin tag and cleavage by proteosomes o w TRANSLATION Key Terms tRNA mRNA rRNA Ribosomes AminoacyltRNA synthetase Wobble MethionyltRNAi Met Pre-initiation complex Internal ribosome entry site (IRES) P site E site A site Polysomes Ubiquitin Proteosome Translation is a cytoplasmic process in which mRNA transcripts are translated into a polypeptide sequence by ribosomal machinery Different RNA’s have different roles in translation Three ribonucleotides of an mRNA make a codon and carries the transcribed genetic sequence o mRNAs have three reading frames usually only is read and codes for a protein tRNA has an amino acid attached to its 3’ end by aminoacyl-tRNA synthetase and has an anticodon sequence o Methionyl- tRNAi Met : has a different structure than regular tRNA that binds methionine o The AUG start codon is recognized by tRNAiMet CHROMATIN AND CHROMOSOMES Key Terms Chromatin Nucleosome Core proteins Linker protein Histone Solenoid Protein scaffold MARs SARs Heterochromatin Euchromatin Acetylation Centromeres Telomeres Gene Silencing Hypoacetylated Hyperacetylation DNA is compacted into the nucleus by an ordered chromatin structure which also can regulate gene transcription and expression DNA in the interphase state is complexed with proteins this DNA-protein complex is called chromatin The smallest unit of chromatin is the nucleosome which is associated with histones Solenoid is a coiling of nucleosome filament into a higher-order, thicker filament Protein scaffold is a higher order of compaction of solenoids associated with Scaffold-associated proteins (SARs) and matrix attachment protein (MARs) During cell division Chromosomes appear which are a the most compact organization of chromatin Histones can be acetylated and deacetylated : charges are altered, altering the level of compaction of chromatin o Deacetylation tight chromatin structure o Acetylation loose chromatin structure Our Course Booklets - free at prep sessions - are the “Perfect Study Guides.” Need help for exams? Check out our classroom prep sessions - customized to your exact course - at regulates transcription; genes found in tight chromatin cannot be transcribed : Gene silencing i.e. yeast mating type o Complexes can bind leading to deacetylation and acetylation suppressing and activating gene transcription Heterochromatin is more condensed areas, Euchromatin less condensed areas Stable inheritance of chromosomes during cell division requires a centromeres, two telomeres and multiple origins of replication o Centromeres bind microtubules and are important for chromosome separation o Telomeres are added to prevent shortening of chromosomes after each replication round o MOLECULAR TECHNIQUES Key terms Gel Electrophoresis DNA Sequencing Polymerase Chain Reaction (PCR) RT-PCR DNA Cloning Vector Plasmid Bacteriophage YAC BAC Transformation Shotgun Cloning FISH SDS-Gel Transient Transfection Stable Transfection Western Blots Probes Ligation Oligonucleotide Klenow fragments Transgene Knock Out Knock In Dominant negative Knock down Microarray Yeast twohybrid Molecular techniques are a very important part of this course and are the fundamental basis of many of the questions on the exam Understand the practical application as there is a wide array of questions that can be asked. You likely will be asked to apply a practical technique to a situation as well as know what is involved in each technique Look through lecture notes and the text book and ensure you have a full understanding if a technique was applied to a given experiment or what it can be used for cDNA libraries Screening Recombinant Transient Transfection Stable Transfection Western Blots Probes Restriction Cutting Transformation Shotgun Cloning cDNA libraries Screening Recombinant Protein Chips GENE STRUCTURE AND FAMILIES Key Terms Genes Mutations Retrotransposons Pseudogenes Transposable Elements Retrovirus Exon shuffling Alu sequences Transposase Minisatellite Simple Sequence Repeats (SSRs) Microsatellite Paralogs Orthologues A gene is a region of DNA that controls a distinct hereditary character or the entire nucleic acid region that is required to produce a functional protein o Genes can be present in the genome as single copies or there can be found in duplicates or multiple copies Mutations in genes o Mutations in control regions can lead to higher, lower or no expression of that gene o In an exon they can lead to no change, an amino acid substitution, frame-shift or insertion of a stop site o In introns can lead to new splicing sites and altered alternative splicing patterns Gene families : related genes that have been duplicated o Orthologues genes are genes that evolved form a common ancestor in different species through speciation and will have similar function o Paralogs are genes that are related in the same genome through duplication Simple Sequence Repeats :Simple sequence repeats (SSRs) are short sequence that contain short repeats Tandem Repeats: rRNA and snRNA : these genes produce nearly identical copies Minisatellite DNA : composed of tandem repeats units which are 6-100 bp long and are found in centromeres and telomeres Microsatellite DNA are <150 bp repeats are 1-4 bp long and are sometimes found in transcription units Transposons =Mobile elements= Transposable elements are moderately to highly repetitive DNA that can move in the genome and interrupt genes o Know the mechanism of transposons and Autonomous elements and Nonautonomous elements Interdispersed Elements: mobile elements that do not disrupt gene expression but can have crossing over occur as they have similar sequences. Example Alu Autocrine Signalling : The signalling cells respond to a signal they produce themselves Cell Surface Receptors : G protein –coupled receptors, Cytokine receptor, Receptor tyrosine kinases, TGFß receptors, Receptor guanylyl cyclases, Receptor phosphotyrosine phosphatases, T-cell receptors PROTEINS w CELL SIGNALLING Key Terms Endocrine Signalling Paracrine signalling Autocrine Signalling G protein – coupled receptors Cytokine receptor TGF-β receptors Receptor tyrosine Key Terms Chaperone Native conformation Chaperonines Protein Modifications Glycosylation Ubiquitin Specificity Affinity Antibody Enzymes Protein Kinases Phosphorylation Allostery Signal Recognition Particle (SRP) Translocon Crosslinking Cooperativity Know the mechanisms for how protein are targeted for intracellular organelle membranes and secretion pathways The amino acid sequence of a polypeptide dictates how a protein will fold into a 3-D conformation the native conformation Chaperones help proteins fold, know the mechanisms Following synthesis nearly every protein is chemically modified o Alter the activity, lifespan or cellular location The covalent modification of a lysine with a 76residues ubiquitin polypeptide, tags the protein for degradation by a proteosome o Know the ubiquitin pathway and all it’s components Some Neurodegenerative diseases are caused by aggregates of stably folded proteins in an alternative conformation. example Bovine spongiform encephalopathy (BSE) What effects protein-ligand binding Enzymes catalyze the chemical alteration of substrates by lowering the activation energy o Learn PKA and how it catalyzes a reaction Motor proteins convert chemical energy from ATP hydrolysis or electrochemical gradients into mechanical linear or rotary movement What is allostery and cooperativity and how do they alter a enzyme activity of a protein Learn all the different way in which proteins can be regulated Know how different techniques use certain characteristic of proteins to purify them Endocrine Signalling: The signalling molecules are hormones that can act on cells far from the site of synthesis Paracrine signalling : Signalling molecules targets are in close proximity, many diffuse away from the signalling cell , concentrations gradients of the signals invoke different responses in target cells Our Course Booklets - free at prep sessions - are the “Perfect Study Guides.” ...
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This note was uploaded on 12/07/2010 for the course BIO BIOL 200 taught by Professor Frogatto during the Fall '10 term at McGill.

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