Biology notes from September 26 - October 5
Biology notes from September 26 - October 5 BIOB 160
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This 16 page Class Notes was uploaded by Alice Giem on Sunday October 2, 2016. The Class Notes belongs to BIOB 160 at University of Montana taught by Art Woods in Fall 2016. Since its upload, it has received 8 views. For similar materials see Principles of Living Systems in Biology at University of Montana.
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Date Created: 10/02/16
September 26, 2016 Chapter 53- Basics of Population Ecology *Go to health sciences 114! Not natural sciences building **Mastering Bio due Thursday Questions about a population A population is a group of individuals of a single species living in the same general area o How big is it? Using the Mark-Recapture method Scientists capture, tag, and release a random sample of individuals (s) in a population Marked individuals are given time to mix back into the population Scientists capture a second sample of individuals (n), and note how many of them are marked (x). The logic: The number of marked animals caught the 2 ndtime (x)/ the total number of animals caught the 2 ndtime (n) = the number marked the first time (s)/ the total population size (N) x/n =s/N N=sn/x o How are individuals dispersed within it? Patterns of dispersion Environmental and social factors influence the spacing of individuals in a population In a clumped dispersion, individuals aggregate in patches A clumped dispersion may be influenced by resource availability and behavior A uniform dispersion is on in which individuals are evenly distributed It may be influenced by social interactions such as territoriality the defense of the area around the individual In a random dispersion, the position of each individual is independent of other individuals It occurs in the absence of strong attractions or repulsions o What’s the demography of the population? Demography is the study of the vital statistics of a population and how they change over time Death rates and birth rates are of particular interest to demographers A life table is an age-specific summary of the survival pattern of a population It is best made by following the fate of a cohort, a group of individuals of the same age The life table of Belding’s ground squirrels reveals many things about this population A survivorship curve is a graph showing the number or proportion of individuals surviving to each age for a given species or group. There are 3 species specific survivorship curves Type 1 curve (humans) low probability of death until age is high Type 2 curve is a straight line because predation doesn’t focus on age Type 3 curve is high death rate in the beginning and then it flattens out when you reach a high enough age. For species with sexual reproduction, demographer often concentrate on females in a population Ecologists use many approaches to estimate the A reproductive table, or fertility schedule o How does the number of individuals change over time? Population size is the result of an interplay between processes that add individuals to a population and those that remove them. Births and immigration add individuals to a population Deaths and emigration remove individuals from a population September 28, 2016 *Mastering Bio due Thursday before midnight Exponential vs Logistic growth curve Tow idealized models of population growth The exponential model describes population growth in an idealized, unlimited environment Change in population size = births + immigrants entering population – deaths – emigrants leaving population Simplify by ignoring immigration and emigration; then a population’s growth rate equals birth rate minus death rate. Exponential Growth The population growth rate can be expressed mathematically as Delta(N)/Delta(t) = B-D Where Delta(N) is the change in population size, Delta(t) is the time interval, B is the number of births, and D is the number of deaths Births and deaths can be expressed as the average number of births and deaths per individual during the specified time interval B = bN D = mN Where b is the annual per capita birth rate, m (for mortality) is the per capita death rate, and N is population size The population growth equation can be revised by substituting and rearranging Delta(N)/Delta(t) = bN-mN substitute Delta(N)/Delta(t) = (b-m)N Where b and m are per capita rates Now define the per capita rate of increase R= b-m Substitute Delta(N)/Delta(t) = rN Zero population growth (ZPG) occurs when the birth rate equals the death rate (r=0) Change of population size can now be written as Delta(N)/Delta(t) = rN Instantaneous growth rate can be expressed as dN/dt = r_inst*N where r_inst is the instantaneous per capita rate of growth Exponential population Exponential population growth results in a J-shaped curve. The rate of increase is constant, but the population accumulates more individuals per unit time when it is large than when it is small. The J-shaped curve of exponential growth characterized some rebounding populations. For example, the elephant population in Kruger National Park, South Africa, grew exponentially after hunting was banned Logistic Growth The logistic model describes how a population grows more slowly as it nears its carrying capacity Exponential growth cannot be sustained for long in any population A more realistic population model limits growth by incorporating carrying capacity Carry capacity (K) is the maximum population size the environment can support Carrying capacity varies with the abundance of limiting resources In the logistic population growth model, the per capita rate of increase declines as carrying capacity is reached The logistic model starts with the exponential model and adds an expression that reduces per capita rate of increase as N approaches K dN/dt = r_inst*N((K-N)/k) The inflection point is the point in logistic growth when the growth rate is the highest but it is also the point at which the growth rate starts to slow down. Population Cycles Some populations undergo regular boom-and-bust cycles Lynx populations follow the 10-year boom-and-bust cycle of hare populations Global human population The human population increased relatively slowly until about 1650 and the began to grow exponentially Birth rates have been coming down since about 1960 so that’s why it technically isn’t exponential growth. The birth rate is going down so r is going down as well September 30, 2016 Dr. DeAnna Bublitz is the new professor. Next Exam is October 21 . st New Mastering Bio due on Wednesday Chapter 4 – Carbon The backbone of life (on Earth…) Versatile! Valence of four carbon can make 4 bonds can be 3-dimensional Can form long chains, elaborate branching Double bonds can give rigidity to compounds Isomers – compounds with the same number of atoms but vary in structure vary in function Side group diversity – diversity in function Organic Compounds Compound – molecule made of 2+ elements Organic compound – molecules containing carbon, produced by living organisms o Cam be simple – methane: CH_4 o Can be incredible complex – hemoglobin: C_2952H_4664O_832N_812S_8Fe_4 Word “organic” just means that they all have carbon o Comes from the study of vitalism o Earth + water + air + fire + “Life force” o Friedrich Wohler – fist proof that organic compounds can be made from inorganic elements Natural organic compounds o Vitamin C (ascorbic acid) in an orange o Alcohol form naturally fermenting fruit Synthetic compounds o Vitamin C (ascorbic acid) made from glucose o Alcohol made from ethane and steam Naturally derived o Alcohol from human controlled fermentation Valence Carbon has 6 electrons – 4 are in the outer shell Atoms “need’ 8 electrons to complete the outer shell o Octet rule Carbon can bond with up to 4 different atoms Allotrope- different physical forms of an element (all carbon molecules that are just in different structures) o Diamond-not actually formed from coal o Graphite o Lonsdaleite o Buckminsterfullerene o Fullerite o C_70 o Amorphous carbon o Carbon nanotube Carbon and bond formation Generally forms covalent bonds – share electrons for strong bonds Different bonds = different structure Carbon is small: 6 protons, 6 neutrons, 6 electrons Small shape = can form bonds and take on shapes that bulkier atoms cannot Carbon can make ring structures which is very important in formation of hormones and such For ionic compounds, the formula represents the ratios of elements Compounds formed by ionic bonds are called salts Salt has been incredibly important in human history! It is the most important electrolyte in our bodies Salt preserves food Our nerves fire using sodium channels Salt was very rare in many areas of the world Salt was one oft he most valued commodities. It was a HIGHLY valued trade item and led to development of “salt roads” since 2000 BC Places that had monopolies on salt become fabulously wealthy “salary” comes from the Latin word “salarium” “salt wars” throughout history Venice was originally founded on salt making Carbon bonds – long chains No limit to the number of atoms in a carbon chain Basis for many of our basic biomolecules o Polysaccharides (complex carbohydrates) Starch - plants Glycogen - animals Cellulose – plants for cell walls o Fatty acids A fat molecule with a glycerol “head” and 3 energy-rich hydrocarbon fatty acid “tails” Hydrocarbons Molecules made of only carbon and hydrogen Few in living organisms o Fatty acids – hydrocarbon tails Examples – petroleum, methane, ethane Release large amount of energy Really long powerful Petroleum and natural gas formation o Ocean 300-400 million years ago Tiny sea plants and animals died and were buried on the ocean floor. Over time they were covered by layer of silt and sand o Ocean 50-100 million years ago Over millions of years, the remains were buried deeper and deeper. The enormous heat and pressure turned them into oil and gas o Today We drill down through layer of sand, silt, and rock to reach the rock formations that contain oil and gas deposits Isomers Molecules with the same chemical formula but different structure Structural isomers o Structural isomers have the same chemical formula o Require breaking bonds and reorganizing structure Ex. Glucose and fructose Same formula but different arragements Geometric isomers o Moving where the side chains are based on a double bond o Geometric isomers have same chemical formulas, but different in their spatial arrangement on either side of an inflexible double bond. “cis” means same side (of the double bond) top +top “trans” means opposite side (of the double bond) top + bottom o Geometric isomers and your eyes… Retinal- the visual pigment in the rods that allow detection of photons Retinal undergoes a conformational change when it is hit by a photon The cis-isomer is primed and ready to detect photons When photons trigger the conformational change to the trans-form this triggers your nerves to fire to your brain. However, the trans-forms cannot detect any more incoming photos. They are called “bleached” or “fatigued”. It takes ATP to “recharge” them into cis-form Enantiomers o Enantiomers – isomers that are mirror images o Different spatial arrangement around a carbon “handedness” L vs D isomers (R and S) Amino acids that make up our proteins have L and D isomers Functional groups Hydroxyl o -OH o Alcohols, names usually end in -ol o Polar as a result of the electronegative oxygen atom drawing electrons toward itself o Attracts water molecules, helping dissolve organic compounds such as sugar Carbonyl o Ketones: if carbonyl group is within a carbon skeleton o Aldehydes: if carbonyl group is at the end of the carbon skeleton o Sugars can be aldoses or ketoses o Polar side group Interact with other polar molecules o Acetone- the simplest ketone o Propanol – an aldehyde Carboxyl o Combination of a hydroxyl and a carbonyl group o Carboxylic acids or organic acids o Acetic acid, which gives vinegar its sour taste o Has acidic properties – can donate hydrogen ions Amino o Amine o -NH_2 o Glycine- both an amine and a carboxylic acid, compounds with both groups are called amino acids o Accts as a base – can pick up a hydrogen ion from the surrounding solution Amino acids R = side group In most living organisms, L-isomer is used exclusively Chiral – non-symmetric molecule Sulfhydryl o -SH Thiols o Ethanethiol o 2 sulfhydryl groups can interact to help stabilize protein structure o We will see that the shapes of proteins are maintained by many kinds of bonds. o Disulfide bridges between thiols are strong covalent bonds that “weld” the structure together Phosphate o Organic phosphates o Gives a negative charge to the molecule it is attached to o Can transfer energy between organic molecules o key to all energy used by living organisms Methyl Side groups give molecules much of their specificity and function Shape Charge Solubility Chemical reactions Importance of functional groups Ethane C_2H_6 o Hydrocarbon will kill you if ingested; exploded when missed with air Ethanol C_2H_5OH o Alcohol in beer and wine Acetic acid C_2H_3OOH o Vinegar Glycine C_2H_2NO_3 o The simplest amino acid; building block of proteins October 3, 2016 Covalent vs ionic bonds Ionic- o Formed when two atoms exchange an electron – one donates an electron, the other accepts o Weaker bod o Important in regulating pH Compounds with hydrogens – acids Compounds with hydroxyls – bases Covalent – o Formed when tow atoms share an electron in their outer shell o Stronger bond o Majority of bonds that carbon forms Building block of life… Monomers – single units, smaller molecules that build Polymers – larger molecules comprised of monomers Macromolecules: o Carbohydrates o Fats o Proteins o Nucleic acids Polymer synthesis Monomers linked together polymer o Dehydration vs hydrolysis reaction o This reaction occurs with all of the monomers we will discuss Polymer Enzymatic hydrolysis Monomers absorbed into bloodstream Moved to cells where they are needed Reassembled via dehydration reaction Carbohydrates Function o Primary energy source o Energy storage o Building block for cell structure, especially in plants Classification o Carbonyl group – ketose or aldose o Size of carbon skeleton (3-7 carbons) o Arrangement of atoms around the carbons SUGAR Monosaccharide – monomer, simplest sugars o Glucose o ribose/deoxyribose o Fructose o Galactose Isomers – molecules with same chemical formula but different structure High – fructose corn syrup Use natural glucose in corn syrup o Add an enzyme that converts glucose to fructose o Same chemical formula- totally different taste! Glucose C_6H_12O_6 o Most common o Key energy source for many living things Quick source o Circulates as blood sugar o Cellular respiration Disaccharide – 2 monosaccharides o Sucrose (glucose-fructose) o Lactose (galactose-glucose) o Maltose (glucose-glucose) Mono- and di- saccharides Key points – o Simple structures (one or two monomers) o Can be joined to make larger molecules o Can be broken down for fuel Polysaccharides – long chains of monosaccharides o Fuel storage in animals and plants o Bonds between monomers can be broken, releasing energy Monomers can be broken down for more Glycogen – stored in liver/muscle, energy source for animals Starch – stored in plastids, energy source for plants o Structural function Cellulose – cell wall of plants Chitin – cell wall of fungi; exoskeletons Polysaccharides Starch o Long stings of glucose o Some branching o Energy storage for plants Glycogen o Long, branching string of glucose o Energy storage for animals Ccellulose Most abundant organic compound on earth Long strings of glucose with special hydrogen bonds between chains – no branching Form plant cell walls, wood, cotton Enzymes that hydrolyze starch bonds cannot breakdown cellulose o Few organisms can digest cellulose o Symbiont organisms break it down o Still important to consume – stimulates mucus secretion form digestive tract Chitin After cellulose, most common organic material Cell wall of fungi Arthropod exoskeleton Long chains of glucose o Glucosamine = glucose with amine group o Acetyl group o Connect to other molecules Acetyl-amine group = more hydrogen bonding o Stronger polymer Assemble in different patterns = different properties Squids and chitin Intelligent, adorable, soft-bodied invertebrates Beaks meant to kill and dismember prey o Difficult to scratch, dent, or bend o Fracture resistant Twice as strong as most similar manmade material How does a squid use its beak without tearing its own surrounding tissue Made of o Water o proteins o chitin o pigment base is mostly water chitin increases towards tip o gives shape Tip is 60% proteins, 20% pigment Proteins key to rigidity o Histidine o Modified tyrosine Squids and plastic alternative Chitosan – partially deacetylated chitin Making a plastic-like material o Strong o Biodegradable o Nonpetroleum based Chitosan also used to make a fire resistant fabric Refined vs Unrefined carbohydrates Simple vs complex sugars/whole grains vs white grain Complex carbs – fiber indigestible; slows absorption of sugar o Fiber aids mucus secretion from intestines Single carbs – generally mono- or di- saccharides o Quickly utilized by body o Fast sugar spike Processing removes most of the vitamin content and nearly all of the fiber Manufacturer process grains to increase shelf life o Bran has high oil content – can turn rancid Sugar, insulin, and diabetes Food is broken down blood sugar levels go up Pancreas makes insulin o Insulin – hormone that prompts cells to absorb blood sugar Blood sugar levels drop, pancreas makes glucagon o Glucagon – hormone signals liver to release stored sugar Type I diabetes – genetic o Body produces little or no insulin Type II diabetes o Pancreas reduces amount of insulin o Body becomes less responsive to insulin produced o Less glucose taken up, blood sugar stays high Carbohydrates on cells Cell-to-cell interactions need carbohydrates Glycocalyx – glycoprotein layer that covers cells, in particular, endothelial cells o Glycoproteins – proteins with sugar groups attached Glycocalyx – immune system Glycocalyx – bacteria o Capsule or slime layer Continuous layer, attached to cell membrane – capsule Irregular, loosely attached – slime layer o Cell adhesion o Protection from immune cells o Biofilm formation Glycocalyx – fish o Glycoproteins combined with water = slimy mucus on fish o Reduces resistance while swimming o Protection from fungi, bacteria, parasites o Possible functions in wound healing o Enhances gas exchange o osmoregularity – electrolyte balances October 5, 2016 Lipids Structurally divers group of compounds Function o Cell membrane structures o Energy storage o Insulation Structure o Long chains of hydrocarbons (fatty acids, phospholipids) o Ring structure (steroids) Common features – nonpolar, hydrophobic o Hydrophobic – little or no affinity for water (water fearing) o Hydrophilic – affinity for water (water loving) Lipid Groups Fats: glycerol + fatty acids o Triglyceride Glycerol head + 3 fatty acid chains Fatty acid chain Called an acid because of carboxyl group Carbon chains, usually 16-18 carbons long o Importance of fats Important energy source Gasoline also made of long hydrocarbon chains Twin as much energy per unit over carbohydrates and proteins Component of cell membranes Insulation Brain function o Saturated fats Usually solid at room temp Most animal fats are saturated Long fatty acid chains are straight Each carbon making 4 individual bonds Can solidify at low temperatures Normal part of diet Too much can lead to build up in arteries o Unsaturated fats Plant oils Trans fats Omega-3 fats Cis-bond in a fatty acid results in a bent chain Mono-unsaturated fatty acids => 1 cis-bond kink Poly-unsaturated fatty acids => 2 or more cis bond kinks There is a double bond where there could be additional hydrogens The carbon chain is not completely saturated with hydrogen Cis double bond causes bending o Cis-bonded fatty acids All unsaturated fatty acids produced in nature has cis-bonds Our bodies have evolved to recognize and breakdown cis- bonded fatty acids These fatty acids also degrade naturally Enzymes and oxygen can interact with the double bonds Breakdown smaller fragments rancid smell of turned oils o Trans-fatty acids They are geometric isomers Trans-fatty acids are not produced in nature We cannot properly digest Even unsaturated, can build up o Partially hydrogenated oils Cis-bonded oils are good for us but can turn rancid after a while Artificial hydrogenation = removes cis double bond and replaces it with hydrogens Makes liquid oils solid Fully-saturated hydrocarbons (like coal and gasoline) last forever – these fats don’t spoil! To avoid oils separating and to increase shelf life, industrial food processors: Hydrogenate unsaturated oils => convert them to saturated or nearly saturated oils Cis-bonded fatty acids high heat, H_2 gas, nickel(catalyst) hydrogenated, fully-saturated fatty acid Process is not 100% - not all double bonds are broken Other can reform Trans-fats are a by-product of this process We can’t process trans-fats well, can lead to major health problems o Omega-3 fatty acids Found in cold water fish, some seeds Good fats! Polyunsaturated fats Multiple double bonds Essential fatty acids We need them but cannot make them Have to acquire through diet Docosahexaenoic Acid (DHA) Very important omega 3 fatty acid High levels in some fish and plant oils We can synthesize if we ingest smaller omega 3s in our diet Important structural component of the brain o Structure and function o Central nervous system development o Retina development o Turnover in brain is fast o Lack of DHA linked to may cognitive disorders o Fats and diet Fats are not inherently bad – the type and amount make the difference Heart disease is not linked to high-fat diets “Mediterranean diet” is high in fats and considered one of the healthiest diets Heart disease is linked to diet high in saturated and trans-fatty acids Body cannot effectively breakdown trans-fats Synthetically made form industrial processing o Soap! Not all fats leave grease stains Treat oils with a strong base = detergents Fatty acids chain dissociates form glycerol head Hydrophobic hydrocarbon tail Hydrophilic head group Fats are insoluble in water Saponification reaction Fat + lye (NaOH) Glycerol + sodium salt of long chains of fatty acids (soap) What happens when you wash stuff? Micelle – group of molecules oriented by hydrophobicity Hydrophobic ends will be attracted to the grease or anything non-polar Hydrophilic end will be attracted to the water So the head will be in the water and the tail will be in the grease and that will then break up the o Fat facts Viscosity of cell membranes depend on composition of fatty acid portions of phospholipids High saturated content => rigid, stiff membrane High unsaturated content => fluid, flexible membranes Temperature dependent If cells are really hot, membranes should have more saturated fatty acids If cells are really cold, membranes should have more unsaturated fatty acids How do organisms cope with large temperature ranges? Homeoviscous adaptation o During the summer – high amount of saturated fatty acids in core and extremity cells o During the winter – high amount of saturated fatty acids in core cells but high amount of unsaturated fatty acids in extremity cells o Organisms actively manage the fatty acid composition of membranes to maintain appropriate viscosity (or stiffness) Phospholipids o Major component of cell membranes o Similar chemistry as soap molecules o Form bilayers because of hydrophilic/hydrophobic characteristics o 1. Take a triglyceride fat o 2. Replace one of the fatty acid chins with a phosphate group Steroids o Structure – carbon skeleton with four fused rings Different functional groups attached to rings Affect function o Cholesterol Component of cell membranes Precursor to making: Vitamin D Estrogen Testosterone
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