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Exam #1 Study Guide

by: Hannah White

Exam #1 Study Guide BIOS 1700

Hannah White

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Study guide covering chapters 1,2,3,4,5
Biological Sciences I: Molecules and Cells
Soichi Tanda
Study Guide
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This 12 page Study Guide was uploaded by Hannah White on Monday September 19, 2016. The Study Guide belongs to BIOS 1700 at Ohio University taught by Soichi Tanda in Fall 2015. Since its upload, it has received 6 views. For similar materials see Biological Sciences I: Molecules and Cells in Biological Sciences at Ohio University.

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Date Created: 09/19/16
Friday, September 9, 2016 Exam #1 Study Guide Chapter 1 (sections 1.1, 1.2, and 1.3) - Scientific Method • Observation: - Questions we have about the world around us - “What is going on when this happens?” • Hypothesis: - Possible answers to explain what is going on • Prediction: - What will happen if you hypothesis is correct? • Experiment: - Test for each hypothesis; all variables must be the same, except for one (the independent variable) - If your results support your hypothesis multiple times, you get a theory - If your results disprove your hypothesis, you must come up with a new hypothesis Theory: • - A general explanation for whats going on - Where do living organisms come from • Living must come from living • MUST know the Redi Experiment - Redi hypothesized that maggots must come from flies and are not spontaneously generated. - Three jars containing raw meet. The first jar was open to the air. The second jar had a gauze cover and the third jar was sealed. 1 Friday, September 9, 2016 - The results showed that maggots only appear in the jar open to the air. The presence of maggots in the open air jar and the absence of maggots in the other two jars supported that maggots come from flies (life comes from life). - This allowed Redi to reject the hypothesis that life can be spontaneously generated. • Must know the Pasteur experiment - Pasteur hypothesized that if microbes could be generated spontaneously, then they should be able to appear in sterilized broth without any microbes present. - Pasteur used two flasks. One with a straight neck, and the other with a swan (bent) neck. He heated the broth in each flask and effectively killed all the microbes in them. After being left alone in the open air. The flask with the straight neck contained microbes and the swan neck flask contained none. - The presence of microbes in the straight-neck flask and the absence of microbes in the swan neck flask supported the hypothesis that microbes come from other microbes and are NOT spontaneously generated. • These experiment demonstrate the scientific method because they were constant, repeatable, only one variable was changed and had the same outcome each time. - Central Dogma of Molecular Biology • DNA is transcribed into RNA and RNA translates for proteins • A cell, like an egg, can be seen with the naked eye or may need to be seen with a microscope like a skin cell - Differences between Eukaryotic and Prokaryotic cells • Eukaryotic: Contain a nucleus and membrane bound organelles • Prokaryotic: Do NOT contain a nucleus - Cell is simplest unit of life; Information in the cell is stored in DNA (nucleic acid) - Plasma membrane separates cell from its environment - Metabolism is a set of chemical reactions that build and break down macromolecules to harness energy 2 Friday, September 9, 2016 Chapter 2 (section 2.5) - Four major groups of biological macromolecules • DNA and RNA - Monomer: Nucleotides Polymer: Nucleic Acid - Phosphodiester bond between OH of one nucleotide and the OH of another • Proteins - Monomer: Amino acids Polymer: Proteins/Peptide chains - Peptide bonds between carboxyl group and amino group - Read N-terminus (Amino group end) to C- terminus (carboxyl group) • Carbohydrates - Monomer: Simple sugars Polymer: Carbohydrate/Polysaccharides - Contain isomers (same formula different structure) - Polysaccharides from through 1-4 (OH) glycosidic bonds - Found mostly in cyclic form • Lipids/Fatty Acids - Defined by physical properties Hydrophobic - Hydrocarbon chains with a carboxyl group on the end - Saturated: no double bonds, long; higher melting point - Unsaturated: double bonds, kinked; lower melting point - Hydrophobic vs. Hydrophilic • Hydrophobic = water fearing • Hydrophilic = water loving - Charged or polar molecule react with water - Stability of Fatty Acids • Stack together through Van der Waals forces to become stable 3 Friday, September 9, 2016 • Stability depends on length of the chain and the number of double bonds Chapter 3 (All sections) - DNA is the genetic material • Frederick Griffith Experiment - Griffith saw that nonvirulent bacteria, when injected into a mouse, did not make the mouse sick. Virulent bacteria that was killed by heat does not cause the mouse to become sick as well. But when the two strands are mixed, the injected mouse becomes sick and dies. The bacteria collected from the dead mouse contain the virulent strain of bacteria. - Griffith concluded that nonvirulent bacteria can be transformed into virulent bacteria by an unknown molecule in the virulent cells. • Unknown molecule carries the traits for virulence from virulent strand to nonvirulent strand. • Avery, Macleod, and McCarty Experiment - Wanted to identify the molecule responsible for transforming nonvirulent bacteria into virulent bacteria as Griffith saw. - Prepared an extract from virulent bacteria that was shown as being able to transform nonvirulent bacteria. Separated the extract into six different flasks. In the first flask nonvirulent DNA was added to show it can be transformed. - In the next four flasks RNase (flask 2), Protease (flask 3), Lipase (flask 4) and Carboase (flask 5) were added to a mixture of virulent and nonvirulent bacteria. The results of each of these tests were the same: the nonvirulent was transformed into virulent. However, in the last test, DNase was added to flask 6 which contained virulent and nonvirulent bacteria. The result of this test showed nonvirulent bacteria only. - This shows the DNA is the molecule responsible for transforming nonvirulent bacteria into virulent bacteria. DNA is the genetic material. - DNA structure Nitrogenous bases are complementary to one another • - A=T (two hydrogen bonds) G=C (three hydrogen bonds) 4 Friday, September 9, 2016 • Two strands that form an antiparallel double helix • Run 5’ to 3’ and is synthesized in that direction as well. • Always write complementary pairs in the 5’ to 3’ direction - DNA vs. RNA • DNA contains the bases A, T, G, C • RNA contains the bases A, U, G, C - U just replaces T in RNA - Transcription • Transcription occurs in the 5’ to 3’ direction • Proteins involved - RNA Polymerase ll: creates mRNA strand from DNA strand - Transcription Factors: Proteins involved in transcription • Strands and regions - Template Strand: The strand of DNA that RNA Polymerase ll reads to create an mRNA strand. Can be either strand of DNA - Non-template Strand: Strand of DNA not being used to create mRNA - Promoter: TATA box; at 5’ end - Enhancer: Site for specific transcription factors such as activators and repressors • Processing (only occurs in eukaryotes) - Splicing: removing of introns and connecting of exons • Regular: All introns are removed and all exons are spliced together in order - i.e ABCD Alternate: All introns are removed and certain exons are spliced together • - i.e ABD - 5’ Cap: Cap is added to the 5’ end of the mRNA for protection during transportation from nucleus to cytoplasm 5 Friday, September 9, 2016 - Poly A Tail: Poly A tail is added to the 3’ end of mRNA by polyadenylation - Through looping of DNA, transcriptional activator proteins, mediator complex, RNA Poly II, and general transcription factors are brought into close proximity, allowing transcription to begin. - Prokaryotes vs. Eukaryotes • In Prokaryotes, transcription and translation occur in the cytoplasm - Energy for Polymerization • Energy to add a nucleotide to a nucleic acid comes from each nucleic acid’s nitrogenous base. So thymine uses TTP and guanine uses GTP and so on. Chapter 4 - R-Groups If R group is hydrophobic then that amino acid will be folded into the middle of the • protein away from water • If R group is hydrophilic then that amino acid will be outwards toward the water • Special R- Groups - Glycine H • • Super flexible - Proline • R-group connected to amino group • NO flexibility • Kinked due to double bond - Cysteine • S-S Disulfide double bond • Unique role in tertiary structure • Replacing one amino acid can create an entirely new protein 6 Friday, September 9, 2016 - Protein Structures • Primary: Sequence of amino acids • Secondary: Results from interactions between amino acids - Alpha Helix: connect via hydrogen bonds - Beta Sheet: connect via hydrogen bonds • Tertiary: 3D shape made by interactions between R groups Quaternary: Results from interactions of different peptide chains • - Hodomer-two identical proteins in a protein complex - Tetramer- two different proteins in a protein complex • Hydrophobic and Hydrophilic - Hydrophilic regions of a protein must fold around the hydrophobic regions of the protein. - Translation • Eukaryotic - Small subunit of ribosome comes to the 5’ cap on mRNA - Met (protein that is always coded for the start codon) and tRNA attach - Search for AUG codon • Found closest to the 5’ end - A charged tRNA enters the A site from the end of ribosome - Peptide bond is formed at the P site - The used or uncharged tRNA exits from the E site - Ribosomal unit moves down the mRNA and elongation continues Elongation includes elongation factors and the use of GTP as the energy • source - Elongation ends at the stop codon • There is no tRNA molecule with a complementary anticodon to the stop codon. So a release factor arrives and splits the ribosomal subunits 7 Friday, September 9, 2016 • Prokaryotic - Shine-Dalgarno sequence is located right before the AUG start codon • Small subunit of ribosome looks for the Shine-Dalgarno sequence - The Shine Dalgarno sequence is in multiple places along the mRNA sequence • The 3’ end of the small ribosomal unit is complementary to the Shine- Dalgarno sequence • Because the Shine- Dalgarno sequence is located in multiple places on the mRNA, translation in multiple spots can occur at the same time. - Multiple proteins are being coded at once - This is a time saving mechanism • What charges tRNA - Aminoacyl tRNA synthetase signals for uncharged tRNA to attach. It also signals for the corresponding amino acid to attach. - There is a specific aminoacyl tRNA synthetase for each amino acid - The enzyme attaches the amino acid to the 3’ end of the tRNA - tRNA is now charged • Monocistronic vs Polycistronic - Monocistronic: One mRNA = One protein • Eukaryotic - Polycistronic: One mRNA= Multiple proteins • Prokaryotic - Codons and Anticodon • Complementary pairs • Antiparallel to one another • Codons on mRNA • Anticodons on tRNA 8 Friday, September 9, 2016 - Specific Codons • AUG start codon • 3 stop codons • Correct reading frame only begins after the start codon • Reading frames depend on which nucleotide you start with Chapter 5 - Phospholipids • Fluidity - Very important for cell function - Fluorescent Recovery After Photobleaching (FRAP) Membrane is labeled with fluorescent molecules, resulting in a uniform • fluorescence over the entire membrane • Laser bleaching occurs • Photobleaching causes a bleached area where there is no fluorescence Fluorescence gradually returns to the bleached area because of the movement • of fluorescent proteins into the area • The return of fluorescence in the bleached area indicated that proteins move in the membrane • Changes in Fluidity - Extensive Van der Waals forces puts phospholipids together but because they are weak, the membrane is able to move - Fatty acids lengths and number of double bonds after the fluidity - Other lipids in the membrane, like cholesterol affect fluidity • Cholesterol makes membrane less fluid at room temp and higher temps, so membrane won’t separate • Cholesterol makes membrane more fluid at colder temps, so the membrane will stay together 9 Friday, September 9, 2016 • Cells want fluidity to be as constant as possible • Composition of Plasma Membrane - Lipid Bilayer • Hydrophilic head • Hydrophobic fatty acid tails - Actively maintains homeostasis - Plasma Membrane Proteins • Integral Proteins: Proteins that are actually in the cell membrane • Peripheral Proteins: Proteins that temporarily associate with either the inside or outside of the cell membrane Channels • - Create Gradients • Receptors - Transportation • Diffusion (Requires NO energy) - Passive movement or simple diffusion • Only oxygen and carbon dioxide can freely pass through the membrane via simple diffusion - Facilitated Diffusion • Channel-Mediated - Based on a concentration gradient; moves high to low • Carrier-Mediated - Based on a concentration gradient; moves high to low • Active Transport - Creates an ARTIFICIAL gradient - Primary Active Transport 10 Friday, September 9, 2016 • Always uses ATP • Example: sodium-potassium pump - Secondary Active Transport • H+ ions are moved outside of the cell through primary active transport to create a charged proton gradient • The charge allows another molecule to move across the membrane • NO energy required - Osmosis • Movement of water across a selective membrane • High solute concentration = low water concentration (concentrated solution) Low solute concentration = high water concentration (dilute solution) • • The plasma membrane has aquaporins which allow water molecules to move across the membrane - Organelles • ER - Makes Proteins and Lipids • Rough: Ribosomes attached • Smooth: No Ribosomes attached • Golgi Apparatus - Modifies, sorts and sends proteins and lipids to their destinations outside of the cell • Secretory Vesicles - Vesicles that bind to the plasma membrane to release their contents into the extracellular space • Lysosomes - Digest undated or degrades molecules in the cell - Sorting Proteins in the Cell 11 Friday, September 9, 2016 • Specific signal in the protein designates its destination either in the cell or being secreted • The signal sequence is added in translation • If not added the protein goes nowhere 12


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