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General biology review

by: Sierra Mongeon

General biology review BIOS 111

Sierra Mongeon
GPA 3.96

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About this Document

Hi everyone! Here is a general review of basic biology and biochemistry that I think will really benefit you all moving forward in this class, especially with the units we are currently studying. I...
Dr. Kenneth Nickerson
Biology, Microbiology, general biology, biochemistry
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This 13 page Bundle was uploaded by Sierra Mongeon on Friday February 12, 2016. The Bundle belongs to BIOS 111 at University of Nebraska Lincoln taught by Dr. Kenneth Nickerson in Spring 2016. Since its upload, it has received 51 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.


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Date Created: 02/12/16
A review of general biology for BIOS 213 Chemistry-what makes up cells?: Atoms: smallest component of a pure substance w/ properties of that substance -can’t be divided w/o losing those properties -combine to form molecules Parts of an atom: nucleus (protons +, neutrons 0), electron field (electrons,e-) If # protons=# electrons, no net charge Atomic number: # protons Atomic Weight: # protons+# neutrons Isotope: # of neutrons differ in atoms of same element Electron configuration: outermost (valence) energy level has to have 8 e- to be stable. **This is why atoms react with other atoms; to achieve 8 valence e- When they react, they form Chemical Bonds: Ionic: One atom takes electrons from another atom, and they become charged particles called ions (ionic bond forms ions) Covalent: electrons are shared between atoms. One atom usually “wants” electrons more than the other one, resulting in polarity. These bonds are stronger and more common. Hydrogen bonds: Hydrogen (H) atom is bonded covalently to a larger Oxygen or Nitrogen atom. However, the sharing is unequal (polar), and a slight positive charge forms on the H atom while a slight negative charge forms on the larger O or N atom. Positive and negative charges attract, but since the charge is only partial, a bond doesn’t form. Rather a “bridge” forms. -Clear diagrams of this concept can be found online (I can’t put them in the notes for copyright reasons!) **Hydrogen bonds and polarity are responsible for giving water its distinct properties!** Distinctive Properties of Water 65-75% all cells are H20! (So we are basically cucumbers with anxiety) But water is the universal solvent for many molecules, and the medium in which almost all biological reactions occur!!* So what makes it special? 1. Polarity- remember those Hydrogen bonds? A water molecule has a slightly negatively charged part (the O atom)and two slightly positively charged parts (the H atoms). Therefore, water can form hydrogen bonds with itself. 2. It takes a great deal of energy to separate water molecules thanks to these H bonds, so water is a great temperature buffer, meaning it resists change in temperature. This is why our body temperature remains so constant. 3. Because of its polarity, it is the universal solvent for any molecule that would dissociate into ions. 4. Density: when it gets colder, it expands (becomes less dense). It is most dense in its liquid form. This is why ice floats! The ice on top of a frozen lake insulates the organisms below. It is because of ice that aquatic life is able to survive the winter. 5. It plays a part in just about every chemical reaction that takes place in an organism, either as a reactant (actively reacting) or as a product (what’s produced). Chemical reactions: Endothermic and Exothermic Endo=in Exo=out Therm=energy -requires energy input to form bonds, and energy is released when bonds break **can also be called exergonic or endergonic, but meaning is the same** Making bonds=absorbs energy=endothermic Breaking bonds=releases energy=exothermic Molarity Atomic #= # of protons. Can be found on periodic table. Atomic weight= # of protons + # neutrons in an atom (measured in amu’s-atomic mass units) Molecular weight=sum of atomic weights of all atoms in a molecule (amu) A mole of a substance is that substance’s molecular weight expressed in grams Ex. Glucose molecule molecular weight is 180 amu 1 mole of glucose is 180 grams 1 M=1 mole of solute/Liter solute=what’s dissolved in the solvent (example: salt dissolved in water) Acids and Bases Acids: substances that dissociate into H+ ions in water Ex. HCl  into H+ and Cl- ions Bases: Substances that dissociate into OH- (hydroxide) ions in water Ex. NaOH into Na+ and OH- ions Salts: still dissociates into ions when dissolved in water, but these ions are not H+ or OH- Ex. NaCl Na+ and Cl- pH: “potential of Hydrogen” pH scale: shown below lower #= more acidic higher #=more alkaline (basic) The pH scale diagram can be found online very easily! (sorry I can’t put it in the notes because of copyright reasons, but I recommend looking it up!) -organisms are EXTREMELY SENSITIVE to even small changes in pH- So…many biological systems use buffers! Buffers: prevent drastic pH changes by replacing strong acids and bases with weaker ones that don’t break into as many H+ or OH- ions Organic Molecules *-contain carbon, hydrogen, oxygen and nitrogen -the carbon forms a “skeleton”, which the other atoms are covalently bound to. -most C are bonded to H atoms, but other functional groups with specific properties may be attached. Terms to know: Monomer- (mono=one) the “building block” of an organic molecule, the simplest unit that still contains the properties of that type of molecule. If you were building a wall, the monomer would be one of the bricks. Polymer- monomers join to form polymers. using the wall analogy, the polymer would be the entire wall, made out of all the bricks Dehydration synthesis: This is how monomers join to form polymers! One monomer loses an H atom, and the hydroxyl group (OH) of another monomer is lost and the two combine to form a water molecule. Dehydration means water is being lost Hydrolysis: the opposite of dehydration synthesis! A water molecule is added to the polymer, and it separates the two monomers again. Isomer: not related to the building of a molecule! It means: two or more molecules that have the same chemical formula, but are structured differently. An example of this is the carbohydrates glucose, fructose, and galactose. Both have the same chemical formula C6H12O6, but different physical structures and chemical properties. Carbohydrates-“hydrated carbon” -saccharides=sugar -these are the sugars and starches Functions: structural component of cell walls/membranes/DNA, fuel cells with energy -made of C, H, O atoms. **Ratio of H to O atoms is 2:1 Monomer=monosaccharide Example: glucose Disaccharide=2 monosac. bound together Polysaccharide=multiple monosac. (can be 10’s or 100s!) Ex. Glycogen, cellulose Lipids Functions: structure and functional unit of cell membranes, energy storage **non polar and insoluble in water** Simple lipids Triglycerides: glycerol molecule with 3 fatty acid chains attached (Diglycerides/monoglycerides=2 or 1 fatty acid chain) Fatty acid=carbon skeleton with attached hydrogen atoms Saturated=no double bonds, MAXIMUM amount of H atoms possible -solid at room temp., no “kinks”, stick together more easily Unsaturated=double bonds, liquid at room temp, “kinks” in the chain so they can’t be as tightly packed Complex lipids **Phospholipids-phosphate group+glycerol+sat. fatty acid chain+unsat. fatty acid chain -polar hydrophilic (water loving) head-phosphate group faces water -nonpolar, hydrophobic fatty acid “tails” forms a bilayer (double layer) with tails facing in and heads facing out, which is the main structural component of a cell membrane -other complex lipids are waxes and glycolipids, which are also found in cell membranes Steroids (yes, these are lipids!) -interconnected carbon rings -structural component of cell membranes (cholesterol) -keep the phospholipids from sticking together, preserves fluidity of membrane Ex of steroid= Hormones (estrogen, testosterone) *Proteins -have nitrogen and sometimes sulfur as part of their chemical structure! Unlike other org. molecules Function: 1. enzymes-speed up biochem. Reactions 2. transport proteins 3. muscle contraction (actin and myosin) 4. some hormones 5. antibodies- part of immune defense system 6. structural component of cell membranes Monomer=amino acid Stereoisomer= amino acids exist in either of 2 forms/configurations, which are mirror images of each other. D and L- D is right handed, L is left handed **amino acids found in proteins are most often the L form** -D isomers occur in bacteria cell walls and antibiotics Amino acids “link” together via peptide bonds, forming a polypeptide chain ( I will cover this more in my next posting of notes over ribosomes and protein synthesis) Protein structure-4 levels 1. Primary structure=the sequence of amino acids (like beads on a necklace) 2. Secondary= the folding and twisting of the polypep. chain into either a helix or pleated sheet -held together by H bonds 3. Tertiary=the unique three-dimensional shape of the protein Most proteins stop here, but some have 4. Quaternary=how 2 or more polypep. chains join to make one functional protein Shape=function. If a protein loses its shape (denatures) it can no longer perform its function. Denaturation can occur w/ high temperatures, pH values, or salt conc. Nucleic Acids DNA-deoxyribonucleic acid RNA- ribonucleic acid Monomer=nucleotide Nucleotide=simple sugar, phosphate group and nitrogenous base Bases form pairs: -in DNA, bases are A, T, C, G AT CG -in RNA, bases are A,U,C, G AU CG DNA=genetic material of an organism. RNA=3 types-tRNA, mRNA, rRNA (will be covered more in upcoming notes) Adenosine Triphosphate(ATP) -the principal energy carrying molecule of all cells! -3 phosphate groups=ATP When ATP is “used”, the third phosphate group splits off and it becomes ADP (what’s left) and Pi (the phosphate that splits off) -The reaction goes in the reverse direction to replenish the ATP supply Body tissues-what are organ systems made out of? Muscle -3 types: skeletal, cardiac, smooth **myo=muscle Skeletal: attached to bones (skeleton) -controlled by conscious thought (voluntary) -striated (stripes) -multinucleate: multiple cells in a fetus combined to form one fiber (myofiber) -arranged in bundles of fibers Cardiac: heart muscle -short, branched, striated, involuntary (can’t control with thought) -connected via intercalated discs, which connect physically and electrically; heart muscle is all connected and forms a continuous “fabric” stimulation of one cell triggers wave of contraction across entire heart Smooth muscle: no striations (appears “smooth under microscope) -found in the ducts and tubes of the body (digestive system, blood vessels, reproductive system, etc.) -arranged circularly (forms a lumen/cavity) or longitudinally (linearly) -involuntary Nervous Tissue -neurons (nerve cells)-generate and conduct electrical impulses -parts: cell body, axon, dendrites body: nucleus, the “brain” of the cell axon: conducts impulses away from cell body (axon=away) dendrites: conduct imp. to cell body -neuroglial cells -that support and repair the neurons, chemically and physically Epithelium -Covers and lines body surfaces, supports and binds organs. Also forms glands -Basement membrane=what binds epithelium to the organ -Characterized by cell arrangement and shape -Arrangement: simple (one layer thick) or stratified (multiple layers, cells upon cells) -Shape: squamous (“fried egg”-flat and irregular), cuboidal (like a cube) and columnar (column shaped) **Table 1.3 in textbook lists all the types, their functions and locations** Glands=secretory structures, classified by how they secrete Exocrine= secrete through ducts Endocrine=do not have ducts Connective Tissue 4 types: connective tissue proper, cartilage, bone, blood matrix=what surrounds the main structural cells Connective tissue proper: what you think of when you think “connective tissue” Types: loose (areolar), dense regular, dense irregular, adiposedifferent -except for adipose, these tissues contain collagen fibers-strong, flexible, support the tissue Adipose tissue- fatty tissue, made of adipocytescells who’s cytoplasm is stretched around a globule of fat. Synthesize, store, and break down fat. Cartilage: made of chondrocytes. Can be elastic cartilage or fibrocartilage Bone: made of osteocytes surrounded by calcium salt and mineral matrix Blood: liquid, “connects” organ systems by transporting nutrients/taking away waste Organ systems 1. Integumentary=skin, hair nails 2. Nervous=brain, spinal cord and other nerves 3. Endocrine=hormone secreting glands 4. Skeletal=bones 5. Muscular=muscles 6. Circulatory=heart, blood vessels, and lymphatic vessels 7. Immune/Lymphatic=lymph nodes, bone marrow 8. Respiratory=lungs, airways 9. Urinary=Kidneys, bladder, ureters, urethra 10. Digestive=Mouthanus, liver, pancreas, gall bladder 11. Reproductive=gonads, external genitalia Cell Biology Components: plasma membrane, cytoplasm, organelles, nucleus Plasma membrane=phospholipid bilayer + associated proteins/molecules (see lipids notes) Selectively permeable (only lets certain thigns in or out. Organized in the “fluid mosaic model”-always changing shapes/positions, flexible Cytoplasm-watery component of cell. Contains cytoskeleton-complex network of microtubules and microfilaments-helps cell hold its shape while remaining flexible Organelles: “miniature organs” 1. Lysosomes: the “stomach”, contains digestive enzymes 2. Mitochondria: “powerhouse”, produce ATP (energy) 3. Ribosomes: “protein factories”, combine amino acids into proteins a. RNA made from DNA, transported to ribosome (mRNA), ribosome “reads” the code (tRNA) and combines amino acids in the correct order. 4. Endoplasmic reticulum: smooth and rough. Site for enzyme reactions a. Rough: has ribosomes on surface b. Smooth: doesn’t have ribosomes 5. Golgi Apparatus: “the mail delivery system” packages and prepares materials for transport outside of cell, and then transports them 6. Centromeres: function in cell division Nucleus- the cell’s “brain Contains DNA-genetic material which codes for proteins DNA in nucleolus (miniature nucleus, inside nucleus) codes for rRNA which forms ribosomes Chromatin-DNA molecules that condense to form chromosomes Mitosis=cell division Cell grows, organelles and DNA replicate, things are divided equally between the mother and daughter cell, and pinches in half -DNA condenses into chromosomes which are pairs of chromatids containing identical DNA. These split and one from each pair goes into each cell. Most cells are diploid (46 chromosomes). Sex cells are haploid (23 chromosomes) -Haploid=half -sex cells divide via Meiosis, which begins with mitosis, but then cell divides again so 4 cells are produced. Each cell contains half the chromosomes of the mother cell. Genetics: terms to know Genes: regions of DNA that code (via RNA) for amino acids DNA is a double-stranded helix, RNA is single stranded Genome=all genes in an individual Alleles: alternate forms of the same gene, can be dominant or recessive. Form pairs in an individual that are homozygous (2 of the same allele) or heterozygous (both different) Dominance: if dominant allele present, the trait associated with that gene will appear instead of the recessive gene. Recessive genes only express themselves when they are in a homozygous pair with each other -the genetic code is made of “words” called codons=3 nitrogen bases. Each codon stands for 1 amino acid! -“start” codon=AUG. this signals to the ribosome to start the chain of amino acids. -“stop” codons=tell ribosome to stop the amino acid chain Replication: chromosomes replicate, becoming an identical pair of sister chromatids which are pulled apart during anaphase of the cell cycle so that one of the chromatids goes into each cell Crossing over: the “arms” of two chromosomes literally cross over each other, which allows some genes to be re-combined. This increases genetic diversity. Protein synthesis 3 types of RNA- mRNA, tRNA, rRNA rRNA=what the ribosomes are made out of mRNA= messenger RNA. created from the DNA molecule, which serves as a “template”. Travels from the nucleus of a cell to a ribosome. The carrier of the genetic code to the place where it can actually be used! tRNA= translation/transfer RNA, “reads” and interprets (translates) the codons and brings the correct amino acids to the ribosome to be linked together via peptide bonds -A chain of amino acids=polypeptide chain Enzymes and Energy-how do cells get energy? Enzyme-usually a protein, speeds up a biological reaction (catalyzes it). Name of enzyme usually ends with suffix “-ase” -Each enzyme has its own specific shape, as does the molecule it reacts with (the substrate). They fit together like a “lock and key”so that an enyme doesn’t react with the wrong molecule -the substrate has an “active site” where the enzyme binds. When reaction is complete, the active site changes shape and the enzyme no longer fits and is released -Enzyme activity is determined by temperature, pH, and co-factors/co- enzymes Co-factor=usually a metal ion, causes a change in the enzyme that allows it to do its job. Co-enzyme=enzymes that work together ***Most substrates are modified by multiple enzymes before they become the final product. This is known as a metabolic pathway**** Major metabolic pathways: Terms to know: oxidation=atom loses electrons, reduction=atom gains electrons OIL RIG! Oxidation is losing, reduction is gaining The basic overall equation for aerobic respiration: *****Glucose + O2  Carbon dioxide + water**** Glycolysis: The breakdown of 1 molecule of glucose into 2 pyruvate molecules and 2 NADH (substances used in ATP production) and 2 ATP. Occurs in cytoplasm. -direct phosphorylation: produces small #s of ATP (phosphorylation simply means the adding on of a phosphate to an ADP molecule). Krebs Cycle: (a.k.a citric acid cycle), takes place in mitochondria, Aerobic process (requires oxygen), 8 steps -Produces many compounds essential in ATP production, as well as some small amounts of ATP Starts by pyruvate oxidation into Acetyl Co-A and CO2 and NADH 1. Acetyl CoA (enzyme-2 carbons) combines with oxaloacetate (4 carbons) to form citric acid (citrate) 2. Citrate converted to isocitrate by adding and then removing a water molecule 3. Isocitrate releases a CO2 molecule, leaving a-ketoglutamate. NAD+ is also reduced to form NADH. 4. NAD+ is reduced to NADH and a molecule of CO2 is produced as a- ketoglutamate is oxidized. Succinyl CoA is also produced. 5. CoA of Succinyl CoA replaced by phosphate group, which is transferred from ADP to make ATP. Succinate is also produced 6. Succinate is oxidized into fumarate. FAD becomes FADH2 because of the 2 H atoms from succinate oxidation. 7. H20 added to to fumarate producing malate 8. malate oxidized-converted to oxaloacetate.NADH produced Products: 2 CO2, 3 NADH, 1 FADH2, 1 ATP This video really helped me (Khan Academy)! It illustrates glycolysis and the Krebs cycle very well fermentation/pyruvate-oxidation-and-the-citric-acid-cycle/v/krebs-citric- acid-cycle Electron Transport Chain: How a majority of ATP is actually formed, using components formed from the Krebs Cycle. In the mitochondria! (this is why we call the mitochondria the powerhouse of the cell! -protons are pumped (with proton pumps) from mitochondrial matrix (inside mitochondria) to the space between the inner and outer membranes. -remember that a H atom without electrons is just one single proton! (H+=1 proton) - The first proton pump removes protons (H+) from NADH and FADH2, making them NAD+ and FAD2+ (which are used back in the Kreb’s cycle and glycolysis) and sends them to inter- membrane space of mitochondria. The electrons left behind are at a high energy level! -The electrons then “jump” across the cell membrane to 2 other proton pumps Each time they jump, they lose and release some energy. This energy causes the pumps to send out more protons (H+ atoms) into the inter-membrane space, advancing the electron. (notice the accumulation of H+ ions in the inter- membrane space!) -this creates an electrical gradient (positive on outside inter-membrane space, negative on the inside matrix) and also a pH gradient (more acidic on outside, more basic on inside) -H+ want to get back in to the matrix! (remember, diffusion; highlow concentration) -A protein called ATP synthase helps the H+ diffuse back in. As they come in, ATP is synthesized from ADP and Pi using their energy -The H+ that comes back in combines with oxygen and electrons, and a water molecule is produced. (Without this last step, the electron transport chain would stop and we could not aerobically respirate!) The equation; O2 + 4 e- + 4H+  2 H20 **Oxidative phosphorylation: phosphorylation occurs by oxidizing molecules! (taking their electrons) and using the energy to produce ATP. Produces roughly 36-38 ATP molecules for 1 glucose This video illustrates the electron transport chain very well, for us audio/visual learners!! citric-acid-cycle-and-oxidative-phosphorylation/v/electron-transport- chain


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