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General Biology Week 2 Notes

by: Selen Nehrozoglu

General Biology Week 2 Notes 01:119:115

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Selen Nehrozoglu

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These notes cover lectures 3-4.
General Biology I
Dr. Gregory Transue
Class Notes
monosaccharides, polysaccharides, disaccharides, glucose, lactase, lactose, sugar, sucrose, fructose, Eon, era, age, period, Epoch, protocells, eukaryotes, prokaryotes, cellulose, starch, Biology, GenBio, Oparin-Haldane, Abiogenesis, Miller-Urey, Iron-Sulfur, Self-Replication, DNA, RNA, chitin, Carbohydrates, amino, hydroxyl, carboxyl, carbonyl, Sulfhydryl, Phosphate, ATP, Methyl, carbon, Hydrocarbon
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This 12 page Class Notes was uploaded by Selen Nehrozoglu on Sunday September 18, 2016. The Class Notes belongs to 01:119:115 at Rutgers University taught by Dr. Gregory Transue in Fall 2016. Since its upload, it has received 8 views.


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Date Created: 09/18/16
Lecture 3 I. Biological importance of Carbon  In organic compounds, carbon is bonded to hydrogen or another carbon  Carbon backbone: a basic skeleton of the structure of a carbon. Can vary in four ways o Length o Branching o Double-bond position o Presence of rings  Skeleton properties affect molecular geometry  Recall: valence electrons dictate bonding properties o Hydrogen carries 1 valence electron o Oxygen carries 2 valence electrons o Nitrogen carries 3 o Carbon carries 4 A. Hydrocarbons  Organic molecules composed of carbon and hydrogen  Nonpolar, uncharged, nonionic  Hydrophobic (hates water)  Can contain functional groups  If you were to replace one or more hydrogen, properties would become very different. The overall molecule would be different B. Functional Groups  Chemical groups that replace hydrogen in hydrocarbons  Affect chemical properties of molecule  Often dictate function of hydrocarbon  Key to molecular function  We mentioned replacing hydrogen in a hydrocarbon. We replace that hydrogen with functional group  7 Key functional groups o Hydroxyl  Hydrogen bonded with oxygen: -OH or HO-  When attached to a hydrocarbon, they become alcohols, words end in -ol  Polar, hydrophobic o Carbonyl  Carbon double bonded to oxygen: C=O  There are 2 types of carbonyl groups:  Carbonyl located at end: aldehyde  Carbonyl located in middle: ketone  Polar, hydrophilic, but not as polar as other molecules  General rule: not all polar molecules are equally polar o Carboxyl  Carbon double-bonded to oxygen and single-bonded to hydroxide: can be written as -COOH  Acetic acid, gives vinegar its sour taste +  Can release pr+tons, aka H , which makes it acidic  Note: H is called proton because it is Hydrogen without its negatively charged electron. Because hydrogen has only one proton and one electron, without its electron it is just a proton  Polar, hydrophilic, important part of amino acids, makes them acidic o Amino  Nitrogen single-bonded to two hydrogens  Proton acceptor, base, has positive charge  Important component of amino acids o Sulfhydryl  Sulfur bonded to hydrogen: written as -SH  Important in some protein structures  Close to, but not entirely polar o Phosphate  -PO H 4 2  Can release one or both hydrogen ions; exists both ionized and unionized  Acidic, hydrophilic, found in phospholipids and nucleic acids o Methyl  Written as -CH3  C bonded  Nonpolar, hydrophobic  In DNA, affects gene expression II. Biological Macromolecules A. Macromolecules  Large molecules formed by thousands of atoms  Polymers: produced by making monomers: identical or similar building blocks  Polymers are formed via dehydration reaction, and broken via hydrolysis o Dehydration reaction: synthesizing a polymer o Removes a water molecule (H O)2 forming a new bond o A short polymer and an unlinked monomer come together, removing a water molecule to form a larger polymer o Enzymes: dehydrogenases  Hydrolysis: breaking down polymer o Adding a water (H 2) molecule o Enzyme: hydrolases o Opposite of dehydration reaction B. Carbohydrates  Polymers  Made of C, H, and O  Have an approximate ratio of one carbon, two hydrogens, and one oxygen: CH 2  Monomers are sugars  Very hydrophilic  Sugars tend to end with “ose” like “glucose” and “fructose” and “sucrose”  Monosaccharides o Simple sugars o Classified by  Number of carbons  Location of carbonyl group, whether it’s an aldehyde or ketone o Glucose is the most common monosaccharide  It is an aldehyde: C6H12 2  It has both linear and ring form, they go back and forth spontaneously  Can form isomers (molecules with same chemical formula but different structure): alpha and beta glucose due to the different ways the ring can close  Disaccharides o Formed via linkage of 2 monosaccharides o Formed by dehydration reaction, results in covalent bond called glycosidic linkage o Common disaccharides  Maltose: glucose + glucose, this is sugar fermented to make beer  Sucrose: glucose + fructose, found in table sugar  Lactose: glucose + galactose, milk sugar  Broken down by lactase  Many people stop producing lactase after infancy, they are unable to break down lactose which makes them lactose intolerant  Polysaccharides o Polymer composed of hundreds of thousands of monosaccharides o 2 main functions in cells  Energy Storage  Structure o Function determined by:  Type of monomer  All of the monomers tend to be identical  Position of glycosidic link  How bond is oriented between each monomer  Affects stability  Starch o Main carbohydrate storage molecule o Comprised of α -glucose subunits o Tends to be unbranched  Glycogen: animal storage polysaccharide o Also comprised of α -glucose subunits o Glycogen granules found in muscle tissue o Is larger and has more branches than starch o Reserves are stored in muscles and liver  Cellulose: Structural polysaccharide o Most abundant organic compound on earth o Uses β – glucose subunits; require different enzymes to break compared to α -glucose linkages o Very few organisms can digest cellulose o In diet, cellulose is fiber  Found in fruits and veggies and fiber one bars!  Fiber isn’t really digested. We can ingest it, but we don’t digest; it just goes straight down into the bowels o There are tons of cellulose out there  Starch vs Cellulose o Cellulose is larger than starch and tends to be more branched o Starch contains 1-4 linkage of α-glucose monomer o Cellulose contains 1-4 linkage of β-glucose monomer o This means that the linkage between adjacent monomers is different, so it requires different enzymes to break o There are very few enzymes that can break down cellulose. Termites, fungi, and some snails can  Structural polysaccharide: chitin o Monomer: N-acetyl glucosamine o Made up of β-glucose monomers with N-containing group o Chitin is very strong. These make up  Arthropod exoskeletons  Fungi cell walls o Carbohydrates summary  Made from carbon, hydrogen, and oxygen  They have sugars as their monomers  For storage and structure C. Lipids  Macromolecules  Diverse, hydrophobic, NOT polymers. They are the ONLY classes of biological molecules that are not polymers  Do not dissolve in H2O, as mentioned before they’re hydrophobic  Dissolve in nonpolar substances  Fats: Most abundant lipid o Energy storage contain 9 calories/gram o Carbs/proteins contain 4 calories/gram o Structure: glycerol +1, 2, or 3 fatty acids o Glycerol molecule is a 3-carbon alcohol (we can tell because the word “glycerol” ends in -ol), has 3 hydroxides  Has three places for a fatty acid to bond  Ester linkage  Fat synthesis o Dehydration reaction o Not forming a polymer, but using dehydration reaction to form a fat  Fat structure o Triacylglycerol (triglyceride) main storage form of fat glycerol + 3 fatty acids  Saturated fatty acids o Each carbon is bonded to the highest possible number of hydrogens that can fit o Tend to be solid at room temperature o Come from most non-fish animals  Unsaturated fatty acids o Structure: double bonds in hydrocarbon chain, fewer hydrogens than maximum capacity o Are either monosaturated or polysaturated o Double bonds create kinks in molecules, which lead to less dense packing o Tend to be liquid at room temperature o Most plant and fish fat is unsaturated, ex. olive oil o BUT: opposite orientation creates a linear fatty acid, allowing fewer hydrogens  Phospholipids o Structure: Glycerol + 2 fatty acids + phosphate groups (+ another group) o Amphipathic: has hydrophobic and hydrophilic regions  Fatty acid “tails” are hydrophobic, while the “head” is hydrophilic o Phosphate  Steroids o Three 6-carbon rings and a single 5-carbon ring all based on the one backbone o Differ in functional groups o Example: cholesterol, sex hormones o Cholesterol: membrane component precursor to other steroids, will get modified into things like testosterone  Lipids summary o Often extremely hydrophobic o Involved in Storage, structure, signaling D. Proteins  Polymers  Monomers = amino acids  Amino Acids (AA’s) all have the same basic structure: H H O H N C C OH amino group Carboxyl Group R Side chain  The R group varies, depending on what it is, it dictates the properties of the AA in different ways  20 Common Amino Acids: Fig. 5.12 in textbook. You don’t have to memorize this, but it’s good to have o Nonpolar AA’s have a hydrocarbon side chain, and are yellow in fig. 5.12 o Polar AA’s have hydroxyl groups and are green o Charged AA’s are acidic (pink) or basic (purple)  Essential Amino Acids o Humans cannot make these; they need to be provided in diet or else humans will suffer malnutrition  Peptide bonds o AA’s are joined by peptide bonds, between their carboxyl and amino groups o Form via dehydration reaction  Polypeptides o Hundreds of AAs joined in linear sequence by peptide bonds  4 levels of organization to protein structure – Hierarchy o Primary Structure: Linear sequence of AA’s joined by peptide bonds in polypeptide chain o Secondary Structure: H bonds at regular intervals in polypeptide among nearby AA’s  R groups are not involved  2 types:  α: helix, flexible, elastic  β: Pleated sheet, strong o Tertiary Structure: Interactions between R groups within same polypeptide, can lay across large distances  Result in specific 3D shape  Many types of interactions possible: H bonds, ionic bonds, hydrophobic interactions, covalent bonds, disulfide bonds o Quaternary Structure  Interaction between 2 or more polypeptides  Ex: collagen-fibrous protein made of 3 polypeptides coiled like rope  Hemoglobin – globular protein made of four polypeptides  Not usually needed  Effects of protein unfolding o Denaturation: loss of protein’s native structure. When they lose their structure, they lose their function o Can be caused by pH change, added salt concentration, or high temperature o Renaturation: bringing the altered protein back to its original structure  Protein functions: o Structure o Signaling o Enzymes o Defense o Transport E. Nucleic Acids  Polymers of nucleotides  2 Classes: DNA and RNA  Store and transmit genetic information Lecture 4 – The Origin of Life There are many hypotheses on how life on earth was formed The earliest fossil evidence traces back to 3.7 billion years ago (bya) I Abiotic Synthesis The first life on earth had to develop from non-living organic molecules. This process is called abiogenesis These molecules had to form spontaneously. This is known as abiotic synthesis. F. Requirements for abiotic synthesis  Low free O 2 o We need low molecular oxygen (O )2to break chemical bonds o Oxygen is reactive, so it can inhibit organic compounds such as amino acids o On the other hand, oxygen’s valence shell can only allow two bonds. Therefore, it is not conductive to building o To build biological molecules, we need low 2  Energy source o In order to form biological molecules, bonds need to be made o Making bonds requires energy. The energy used to make these bonds came from:  Sun  Meteors  Volcanoes: The only energy source out of the three that did not come from outside earth  Chemical building blocks o What is needed to sustain life:  Liquid water is needed in an aqueous environment  Dissolved inorganic materials  Atmospheric CO , 2 O2 CO, H , 2 2  Notice how all of these molecular compounds include hydrogen, oxygen, nitrogen, and carbon (HONC), the four most important elements for life  Maybe NH , 3 S2 CH , 4e don’t know for sure if these contributed to the creation of life on earth, but there are theories  Time o These processes take time o Because there is no life, all reactions are spontaneous at this point. Any reaction that occurs just happened because something bumped into something else. o The earth was formed 4.6 bya. However, life (or evidence thereof) was formed 3.7 bya G. Abiotic Synthesis Hypothesis  There are two general ideas about how life started o Oparin-Haldane  This hypothesis was proposed by A.I. Oparin and J.B.S. Haldane independently  It proposes that life first formed near earth’s surface  The conditions of early earth favored spontaneous formation of inorganic molecules  This has been since tested out. 2 famous tests:  1953: Miller-Urey experiment o Recreated early earth atmosphere, simulating lightning as an energy source o Found amino acids and other organic compounds o Flaw: Used reducing atmosphere, while newer data on early earth shows that the atmosphere was neutral rather than reducing  Recent developments o The experiment was repeated under many conditions, many organic molecules were produced  DNA/RNA nucleic acids and bases  All amino acids  Several lipids and sugars  ATP if phosphate was added: ATP is a chemical source of energy, so lightning or the sun or meteors would not be needed as an energy source if there was ATP  All original samples were reanalyzed o Iron-Sulfur  Hypothesis: organic molecules form and accumulate at hydrothermal vents  Hot CO 2 CO, iron, and nickel were released in the form of sulfur to help facilitate reactions  Hot springs produce precursors to biological molecules  This could be a possible environment where early life could accumulate  Was recently tested by creating mini-ocean with artificial hydrothermal vents o Nobody is sure which hypothesis is true, but both may have been occurring simultaneously III. Abiogenesis Steps of abiogenesis, or life from non-life 2. Formation of 3. Formation of 4. Appearance of 1. Abiotic synthesis oforganic molecules protocells self-replication monomers A. Abiotic Synthesis of monomers B. Formation of macromolecules  Can form on clay or rock surfaces because they have pits/depressions where particles can form  Neg2+ive ion2+bind monomers  Zn and Fe catalyze polymerization  Examples of spontaneous polymerization o Drop solutions of AAs onto hot rocks, get polypeptides o Montmorillonite: Type of clay used to test spontaneous polymerization C. Formation of protocells  Vesicles: fluid-filled compartments surrounded by membrane-like structure. They form from lipids in water  Protocells: aggregates of abiotically produced organic macromolecules  Exhibit attributes of living cells o Electrical potential across surface o Absorb materials from environment, causing osmotic swelling. Pressure in the center causes water to move inwards, causing it to grow o Unique internal chemical environment o If they get too large, they divide spontaneously, otherwise they are unstable o While they exhibit attributes of living cells, they are not living; they have no mechanism for heredity D. Self-Replication  In living cells… o Genetic info is stored in DNA o Transmitted via mRNA (do not worry about this term) o Translated into protProtei DNA RNA n o RNA world hypothesis  States that RNA polymers spontaneously appeared  Had two properties  Catalyze RNA synthesis: Self replicating  Catalyze peptide bond formation: Direct protein synthesis  We know RNA is capable of enzymatic formation: Ribozymes: RNA molecules with enzymatic properties  Create RNA  Catalyze RNA polymerization  Made of RNA  Protocells and self-replicating RNA  RNA polymers occur spontaneously within vesicle: the higher osmotic pressure, the larger the vesicle grows  Growing vesicles take up lipids from stable vesicles, freeing RNA from the environment  RNA inside the vesicle gets “rewritten”, vesicle continues to grow, eventually it splits. Goes from mostly monomers on the inside to mostly polymers. When the split happens, no contents are lost, each vesicle continues to grow  Experimental support is done in lab step-by-step, not all at once o What about DNA?  We thought RNA came first; single-stranded (SS)  At some point it became double-stranded (ds): genomes became more stable, which was better for information storage  RNA was replaced by DNA, making the genomes even more stable, RNA was reduced to intermediate roles  Why isn’t life constantly forming? o Living things already exist in places where it might be able to o Anything “useful” gets used up and doesn’t accumulate  Abiogenesis summary Organic Organic Self- Protocells monomers macromolecu form replication form les assemble appears IV. History of Life Age: < milli on year s Epo(my) 10s of my Period: ~10-100 my Era: ~100s of my Eon: > 500 my A. Geologic time scale  Established by study of fossils, radiometric dating  Based on major geologic, climate, and biological events  E.G. mass extinctions often delineate periods  We divide earth’s existence into 4 eons o Hadean (oldest): lots of heat being cycled, named after Hades, Greek god of underworld, not capable of sustaining life o Archaean o Proterozoic o Phanerozoic (most recent): we mention 3 eras within this eon o Table 25.1 in the textbook has more information on this B. First Cells  Stromatolites: columns composed of dead cells  When bacteria die: o They stick together and compress o Become mineralized over time o New cells grow on top of mineralized departments o Layers form, creating fossils  First cells were prokaryotes: they did not have a nucleus o Anaerobic: they lived without the presence of oxygen o Heterotrophic: had to get food from organic molecules that could be found in the environment surrounding them  Autotrophs appeared later o Use energy from the sunlight to make their own food o Advantageous in the sense that they do not need organic molecules from the environment, they are provided the nutrition they need just by standing in the sunlight o Split H2S or something similar to get electrons, Sulfur released instead of O2; this is not quite the same process of photosynthesis that autotrophs use today.  Cyanobacteria came later on o These were the first organisms to do photosynthesis o They obtain electrons by splitting H O 2 o They released oxygen, becoming responsible for atmospheric oxygen  Oxygen revolution: 2.5 bya o Rise in atmospheric O 2ue to oxygenic photosynthesis o Killed off most organisms because they could not handle O 2 o Banded iron formations, accumulated on ocean floor, showed up on surface later on due to the plate tectonics  Then aerobes appeared o Aerobic respiration: utilize2O in breaking down food o Produces high ATP yield o Common today C. Eukaryotes  Cells with membrane-bound nucleus and organelles  Larger, more complex than prokaryotes  Appeared ~ 1.8 bya  Generated through endosymbiosis  Endosymbiosis: o symbiotic relationship in which one organism lives inside another. o Small free-living bacteria become part of larger cells instead of being digested o Free living prokaryotes began living inside larger cells, over time became organelles  Were ingested, survived, then lost their ability to live on their own  First, mitochondria were formed, then plastids later on  Fig. 25.10 of textbook has more o Evidence for endosymbiosis  Mitochondria and plastids have  Double membranes  Similar size to enzymes as ribosomes have to bacteria  DNA, sequences very similar to living bacteria  Organelles divide via binary fission  All eukaryotes have mitochondria. Plastids came later in eukaryotes, and they only exist in some lines D. Origins of multicellularity


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