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Week 2 Notes Cresawn

by: Jay Ty

Week 2 Notes Cresawn 140

Marketplace > James Madison University > Biology > 140 > Week 2 Notes Cresawn
Jay Ty
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Here are some of the notes I took for BIO 140 for this week! You should also go to class to hear practice questions, I am not putting her personal questions in these notes. Please remember to go to...
Foundations of Biology I
Kerry Creswawn
Class Notes
Biology, Science, Chemistry, carbon, bonds, Proteins, amino acids, Life Science
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This 7 page Class Notes was uploaded by Jay Ty on Saturday September 17, 2016. The Class Notes belongs to 140 at James Madison University taught by Kerry Creswawn in Fall 2016. Since its upload, it has received 4 views. For similar materials see Foundations of Biology I in Biology at James Madison University.


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Date Created: 09/17/16
9/13/2016 BIO 140 Cresawn Notes I. The pH case of aspirin overdose a. Cell Respiration: How Cells Harvest Energy from Nutrients i. Food (e.g C ???? ???? ) + ????  CO + ???? ???? + ???????????????????????? 6 12 6 2 2 2 ii. Running requires more energy= requires more respiration= produces more carbon dioxide b. Look at the group worksheet, and last week’s notes, for answers in regards to pH and aspirin overdose c. Bicarbonate worked because it brings pH up, and hyperventilation causes a change in pH. II. Chemistry of Life Finale: Could there be life on Mars? Assignment: Read pages 70-76 and 86-87 in chapter 4 and take chapter 4 quiz on Launchpad!! Due at 10am on Thursday! a. Mars Case III. Hydrophobic amino acids (p. 70-76 summary) a. Amino acids that do not readily interact with water or form hydrogen bonds. i. Most hydrophobic amino acids have nonpolar R groups composed of hydrocarbon chains or uncharged carbon rings. 1. Amino acids differ in the R group a. 20 Different R groups: Some b. Non-polar (Hydrophobic) c. Some Polar (Hydrophilic) i. Hydrophilic amino acids consists of: acidic, basic, and polar amino acids. 1. Bases accept protons and are therefore + charged 2. Acids donate protons and are therefore negatively charged d. Some fully charged e. Some even contain sulfur ii. Because water molecules in the cell form hydrogen bonds with each other instead of with the hydrophobic R groups, the hydrophobic R groups tend to aggregate with each other. 1. Their aggregation is also stabilized by weak van der Waals forces in which asymmetries in electron distribution create temporary charges in the interacting molecules, which are then attracted to each other. a. Ex: This tendency for hydrophilic water molecules to interact with each other and for hydrophobic molecules to interact with each other is what usually leads to oil droplets in water. 2. This is also the reason why most hydrophobic amino acids tend to be buried in the interior of folded proteins, where they are kept away from water. iii. Amino acids with polar R groups have a permanent charge separation, in which one end of the R group is slightly more negatively charged than the other. 1. Polar molecules are hydrophilic, and they tend to form hydrogen bonds with each other or with water molecules. iv. The R groups of the basic and acidic amino acids are highly polar. 1. At the pH of a cell, the R groups of the basic amino acids gain a proton and become positively charged, and protons of the acidic amino acids lose a proton and become negatively charged. 2. Because the R groups of these amino acids are charged, they are usually on the outside surface of the folded molecule. 3. The charged groups can also form ionic bonds with each other and with other charged molecules in the environment a. This ability to bind another molecule of opposite charge is one important way proteins associate with each other or with other macromolecules (such as DNA). v. Glycine 1. Different from the other amino acids because its R group is hydrogen, exactly like the hydrogen on the other side of the α carbon a. It is not asymmetric b. Nonpolar c. Small enough to tuck into spaces where other R groups would not fit. i. The small size also allows for freer rotation around the C–N bond 1. R group does not get in the way of the R groups of neighboring amino acids. 2. Glycine increases the flexibility of the polypeptide backbone 2. All of the other amino acids have four different groups attached to the α carbon and are asymmetric. vi. Proline 1. Also different 2. Its R group is linked back to the amino group. a. Linkage creates a kink or bend in the polypeptide chain and restricts rotation of the C–N bond, i. Imposes constraints on protein folding in its vicinity (opposite of glycine) vii. Cysteine 1. Makes a special contribution to protein folding through its –SH group. a. When two cysteine side chains in the same or different polypeptides come into proximity, they can react to form an S–S disulfide bond, i. Covalently joins the side chains. ii. Disulfide bonds are stronger than the ionic interactions of other pairs of amino acid iii. Forms cross-bridges that can connect different parts of the same protein or even different proteins. 1. This property contributes to the overall structure of single proteins or combinations of proteins. IV. Polymers (p. 70-76 summary) a. Polymers of amino acids share a chemical feature common to individual amino acids i. The ends are chemically distinct from each other. ii. A polymer of amino acids connected by peptide bonds is known as a polypeptide. iii. Typical polypeptides produced in cells consist of a few hundred amino acids. iv. Protein is often used as a synonym for polypeptide 1. Amino acids that are incorporated into a protein are often referred to as amino acid residues. 2. Peptide chains fold to make the functional protein 3. “The collection of proteins within a cell determines its health and function. Proteins are responsible for nearly every task of cellular life, including cell shape and inner organization, product manufacture and waste cleanup, and routine maintenance. Proteins also receive signals from outside the cell and mobilize intracellular response. They are the workhorse macromolecules of the cell and are as diverse as the functions they serve”. – Scitable 4. Over 8 million sequenced proteins (many more not yet sequenced) are divided into: a. 25,000 different families b. Based on structure c. And function 5. b. Structures i. Primary structure 1. The sequence of amino acids in a protein a. The sequence of amino acids ultimately determines how a protein folds. b. Usually represented by a series of three-letter or one-letter abbreviations for the amino acids c. Determines the secondary and tertiary structures ii. Secondary structure 1. Formed by local interactions between stretches of amino acids in a protein a. Results from hydrogen bonding in the polypeptide backbone b. Nearby amino acids interact by hydrogen bonds in 1 of 2 ways i. One way creates an alpha helix ii. Another creates a beta sheet 1. We see these in ßAPP iii. Tertiary structure 1. Formed by the longer-range interactions between these secondary structures and in turn support the overall three-dimensional shape of the polypeptide a. Results from interactions with the amino acid side chains b. Determines function because it is the three-dimensional shape of the molecule that enables the protein to serve as structural support, membrane channel, enzyme, or signaling molecule. c. When the multiple secondary structures interact, more folding occurs d. Tertiary structure is depending on interactions between the R groups; and the sequence of R groups is different in every protein iv. Quaternary structure 1. The resulting ensemble after some proteins are made up of several individual polypeptides that interact with each other a. Formed by polypeptide subunits coming together i. Polypeptide subunits may be identical or different ii. When multiple tertiary structures (subunits) come together iii. Ex: hemoglobin v. Denaturing 1. The unfolding of proteins by chemical treatment or high temperature a. Disrupts the hydrogen and ionic bonds holding the tertiary structure together. b. The proteins lose their functional activity. c. Mutant proteins contain an amino acid that prevents proper folding i. Leads to proteins often being inactive or not functioning properly vi. Mutation 1. A change in the sequence of a gene. a. Mutations affecting proteins occur at random in regard to their effects on protein function i. Some affect the amino acid sequence (what we focus on) ii. Most mutations that impair protein function will be eliminated 1. If the function of the non-mutant protein contributes to survival and reproduction, the individuals carrying these mutations will leave fewer offspring than others. iii. Mutations that do not impair function may remain in the population for long periods because their carriers survive and reproduce in normal numbers 1. A mutation of this type has no tendency to either increase or decrease in frequency over time. iv. Individuals that carry the occasional mutation that improves protein function will reproduce more successfully than others. 1. Enhanced reproduction leads to the mutant gene encoding the improved protein to gradually increase in frequency and spread throughout the entire population. V. The Case of Chris Benoit a. Twice recognized by the World Wrestling Entertainment as the world heavyweight champion, Canadian Professional Wrestler, Chris Benoit, was booked to win his third championship the weekend of his death (2007). i. Instead, that weekend he killed his wife and strangled his seven year-old son to death, and then hung himself using cords from a weight machine. ii. Medical examiners concluded that the elevated testosterone levels in Benoit’s body (probably prescribed to remedy deficiencies resulting after prior steroid abuse) did not contribute to his violence. 1. Nowinski believed that he knew the cause: repetitive head injuries. 2. Benoit and other athletes suffer in contact sports that result in Chronic Traumatic Encephalopathy (CTE). a. Needs to be tested... 3. Most CTE occurs in boxers, but also in professional football players. iii. Ten percent of retired pro-football players suffer from depression, the same as the general population. 1. Is this strong enough evidence? b. Basics of Experimental Design i. What question do you want to answer? ii. What would you want to measure in order to answer that questions? iii. The answer to this question is your DEPENDENT variable iv. What types of groups do you want to compare? v. The group that you are “changing” is the experimental group vi. The other group, that you’re not changing is the “control” c. Concussions and CTE i. Study of more than 2,500 former NFL players by the Center for the Study of Retired Athletes at UNC found that cognitive impairment, dementia, and depression rose proportionately with the number of concussions they had sustained (Guskiewicz et al,. 2003, 2005, 2007). Those who had sustained 3 or more concussions were more likely to experience “significant memory problems” and 5 times more likely to develop mild cognitive impairment 1. Impact: when the head slams into a hard surface, the skull stops abruptly, while the brain, floating in cerebral fluid, continues to move and is shaken and sometimes bruised. 2. Along with other damage, one result is that a nerve cell protein called ß-Amyloid Precursor Protein (ßAPP) is cut into pieces called ß-amyloid peptides which aggregate in neurons forming toxic plaques–what does all that that mean? This protein is also implicated in Alzheimer’s disease


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