General Biology BI 102, Fall 2014 CRN 22608 Instructor: Bill Thomas (Instructor website under Thomas, William) Email: thomasw@linnbenton.edu
Learning Objectives Week 1 Properties of life The 3 domains of life Archaea, Bacteria, Eukarya Biological Themes Evolution, Flow of Energy, Cooperation, Structure Determines Function, Homeostasis Scientific process Unifying Theories of Biology Cell Theory, Gene Theory, Theory of Heredity, Theory of Evolution Atoms: Structure and properties Electron shells and orbitals How are ions formed? The types of bonds: ionic, covalent, hydrogen bonds (and van der Waals forces) Biological importance of the special properties of water Become familiar with the terms hydrophilic and hydrophobic and understand their biological importance Understand the basics of the ph scale Logarithmic Lower Higher = Acidic Basic Learn the four main types of biological macromolecules and their components What is a monomer? Two reactions: dehydration synthesis and hydrolysis Which requires energy input? Which releases energy? Understand the basics of protein structure (primary, secondary, etc.) See how the structure of a macromolecule determines its function
Introductions Syllabus First-day business Read safety instructions in lab packet for Thursday McGraw Hill Connect resources http://connect.mheducation.com/class/w-thomas-bi-102-lbcc-fall-14-1 LearnSmart: Objective: Familiarize yourself with material we will be covering in class Homework: Weekly Activity LearnSmart and online homework together make up 10% of your grade don t forget about them!
Hands-on lab experience Course Objectives DNA extraction, genetics, electrophoresis! Gaining a better understanding of biological systems Cell structure and function Genetics and heredity Evolutionary processes Understanding the scientific method Scientific inquiry Impact of cell biology on your life Photo : Frank Wojciechowski
The Domains of Life Historically, life was grouped into three kingdoms. Modern taxonomy divides life into three domains textbookofbacteriology.net
The six kingdoms of life
What is Life? What qualifies something as living versus nonliving? Consider these points complexity movement response to stimulation Are these properties unique to living things? A life-defining property must be exclusive to living things
Properties of Life 1. Cellular organization all living things are comprised of at least one cell 2. Metabolism all living things process energy which is used to power other processes 3. Homeostasis all living things maintain relatively stable internal environments to optimize conditions for metabolism and other processes
Properties of Life 4. Growth and reproduction all organisms have the capacity for growth and reproduction 5. Heredity all organisms pass genetic information to future generations from parents to offspring Does this possess the properties of life?
The Organization of Life Living things function and interact with each other on many levels The organization of life is a hierarchy of levels of increasing size cellular organismal populational
Figure 1.4 Levels of organization: cellular level Alternative example: 1. Atoms (C, H, N, O, S) 2. Molecule (amino acid) 3. Macromolecule (protein; e.g., actin) 4. Organelle (Cytoskeleton) This level of organization is where we will spend most of our time!
Figure 1.4 Levels of organization: organismal level
Figure 1.4 Levels of organization: populational level On which of these three levels (cellular, organism, population) do you think evolution takes place?
The Organization of Life At higher levels of the living hierarchy, new properties become apparent that were absent at the lower levels These emergent properties result from the interaction of diverse but simpler components Many higher order processes that are hallmarks of life are emergent properties metabolism consciousness
Biological Themes: Evolution Evolution is genetic change in a species over time The mechanism for evolution is natural selection The diversity of life is explained by evolutionary processes
Biological Themes: Flow of Energy All living things require energy Energy from the sun flows through the living world Organisms acquire energy differently How much energy is available determines how many and what kinds of organisms can live together in an ecosystem biology.tutorvista.com
Biological Themes: Cooperation As energy and other resources are limiting, many organisms have evolved cooperation as a means of survival Symbiosis describes when two species live in direct contact
Biological Themes: Structure Function Structure Determines Function Evolution favors structures that function in an adaptive manner Many structures are specialized for a particular function tiger.towson.edu naturedocumentaries.com
Biological Themes: Homeostasis Homeostasis is a physiological condition of steady-state The internal environment of organisms is relatively stable Organisms act to control their internal environments so that the complex processes of metabolism function efficiently
Scientific Investigation Scientists systematically conduct experiments to evaluate hypotheses about observed phenomena You ve probably used the scientific method without realizing it! What s missing from this experimental design? Copyright 2011 Pearson Education, Inc.
Fig.1.5 The scientific process
Stages of a Scientific Investigation The scientific process has six stages 1. Observation science begins with careful observation of natural phenomena 2. Hypothesis scientists make an educated guess that might be true often scientists formulate multiple ideas about a phenomenon; these are called alternative hypotheses
Stages of a Scientific Investigation 3. Predictions if a hypothesis is correct, then specific consequences can be expected 4. Testing scientists conduct experiments to attempt to verify predictions made by hypotheses
Stages of a Scientific Investigation 5. Controls experiments usually employ a parallel design scientists use a control to assess the influence of potential factors, called variables conditions stay the same in the control in comparison to the variable condition 6. Conclusion a hypothesis that has been tested and not rejected is tentatively accepted
The Experiments of Francesco Redi Copyright 2011 Pearson Education, Inc.
Scientific Method in Action
Theory and Certainty The term theory means different things to different audiences To scientists A theory represents certainty and is a unifying explanation for a broad range of observations To the general public A theory implies a lack of knowledge or guess
Theory and Certainty Scientists acceptance of theory is provisional the possibility always remains that future evidence will cause a theory to be revised The process of science is not just trialand-error but involves judgment and intuition
Four Theories Unify Biology as a 1. The Cell Theory Science 2. The Gene Theory 3. The Theory of Heredity 4. The Theory of Evolution
The Cell Theory All organisms are composed of at least one cell The cell is the most basic unit of life All cells come from preexisting cells
The Gene Theory Genetic information is encoded in molecules of deoxyribonucleic acid (DNA) Genes encode specific proteins The proteins encoded by an organism s genes determine what it will be like in terms of form and function
The Theory of Heredity Genes are passed down generations as discrete units Mendel s theory of heredity gave rise to the field of genetics Chromosomal theory of inheritance located Mendelian genes on chromosomes
The Theory of Evolution All living organisms are related to one another in a common tree of descent The six kingdoms of life are grouped into three domains Theory of evolution explains the unity and diversity of life
The Theory of Evolution Charles Darwin attributed evolution to natural selection Organisms best able to respond to the challenges of living will leave more offspring, thus their traits become more common in the population Scientists have been able to identify changes in individual genes that are responsible for differences among individuals
Figure 1.13 The theory of evolution
Figure 2.2 Basic structure of an atom
An atom is characterized by the number of protons it has or by its overall mass Atoms - Properties atomic number the number of protons in the nucleus Why not the number electrons? mass number the number of protons plus neutrons in the nucleus electrons have negligible mass www.chemistry.wustl.edu
Organic Table 2.1
Electrons Electrons determine the chemical behavior of atoms These subatomic components are the parts of the atom that come close enough to each other in nature to interact Electrons are associated with energy Electrons have energy of position, called potential energy Electrons occupy energy levels, or electron shells, of an atom, which are actually complex, three-dimensional volumes of space called orbitals orbitals are where electrons are most likely to be found
Electron Shells & Energy As electrons move to a lower energy level, closer to the nucleus, energy is released Figure 2.3 The electrons of atoms possess potential energy Moving electrons to energy levels farther out from the nucleus requires energy
Electron Shells & Orbitals Electron shells have specific numbers of orbitals that may be filled with electrons atoms that have incomplete electron orbitals tend to be more reactive atoms will lose, gain, or share electrons in order to fill completely their outermost electron shell these actions are the basis of chemical bonding
Ions Ions atoms that have gained or lost one or more electrons
Isotopes Isotopes atoms that have the same number of protons but different numbers of neutrons most elements in nature exist as mixtures of different isotopes
Isotopes & Radioactivity Some isotopes are unstable and break up into particles with lower atomic numbers this process is known as radioactive decay Radioactive isotopes have multiple uses dating fossils medical procedures Figure 2.7 Using a tracer to identify cancer
Molecular bonds A molecule is a group of atoms held together by energy in the form of a chemical bond There are 3 principal types of chemical bonds 1. Ionic 2. Covalent 3. Hydrogen van der Waals forces are a kind of weak chemical attraction (not a bond) that come into play when atoms are very close to each other
Ionic compounds Ionic bonds involve the attraction of opposite electrical charges Molecules comprised of these bonds are often most stable as crystals Fig. 2.8(a) The formation of ionic bonds in table salt
Molecules Covalent bonds Covalent bonds form between two atoms when they share electrons The number of electrons shared varies depending on how many the atom needs to fill its outermost electron shell Covalent bonds are stronger than ionic bonds because they are directional
H H Single covalent bond H C H H C H H Methane gas (CH 4 ) H O O O Oxygen gas (O 2 ) O Double covalent bond
Polar molecules Some atoms may be better at attracting the shared electrons of a covalent bond This creates tiny partial negative and positive charges within the molecule, now called a polar molecule Polar covalent bonds form when the shared electrons of a covalent bond spend more time in the vicinity of a particular atom What is this important polar molecule?
Hydrogen bonding Hydrogen bonds are weak electrical attractions between the positive end of one polar molecule and the negative end of another each atom with a partial charge acts like a magnet to bond weakly to another polar atom with an opposite charge the additive effects of many hydrogen bonding interactions can add collective strength to the bonds Example?
Electrons Big Picture Electrons can be energized ; this energy can be used by cells to do work The number of electrons and the way they are shared by atoms give molecules biologically important properties: Charge: the charge on an ion restricts its movement in a cellular environment, can be used in transport Polarity: polar molecules interact with ions and other polar molecules, are repelled by nonpolar molecules Nonpolarity: nonpolar molecules repel polar and charged molecules, hide from water
Polarity of Water Water can form hydrogen bonds Hydrogen bonding confers on water many different special properties
Unique Properties of Water Why is this important? Evaporative cooling
Hydrophilic vs. Hydrophobic High polarity In solution, water molecules tend to form the maximum number of hydrogen bonds hydrophilic molecules are attracted to water and dissolve easily in it these molecules are also polar and can form hydrogen bonds hydrophobic molecules are repelled by water and do not dissolve these molecules are nonpolar and do not form hydrogen bonds
Figure 2.14 How salt dissolves in water
Water Ionizes The covalent bond within a water molecule sometimes breaks spontaneously H 2 O OH - + H + Water Hydroxide Hydrogen This produces a positive hydrogen ion (H + ) and a negatively charged hydroxide ion (OH - )
Figure 2.15 The ph scale The amount of ionized hydrogen from water in a solution can be measured as ph The ph scale is logarithmic, which means that a ph scale difference of 1 unit actually represents a 10-fold change in hydrogen ion concentration
Acids & Bases Pure water has a ph of 7 there are equal amounts of [H+] relative to [OH-] Acid any substance that dissociates in water and increases the [H + ] acidic solutions have ph values below 7 Base any substance that combines with [H + ] when dissolved in water basic solutions have ph values above 7
Biological ph The ph in most living cells and their environments is fairly close to 7 proteins involved in metabolism are sensitive to any ph changes Organisms use buffers to minimize ph disturbances a buffer is a chemical substance that takes up or releases hydrogen ions Blood is an example of a biological buffer
Organic Molecules Carbon is the basis of all organic molecules Carbon core has attached groups of atoms called functional groups The functional groups confer specific chemical properties on the organic molecules
Macromolecules Macromolecules are actually assembled from many similar small components, called monomers the assembled chain of monomers is known as a polymer There are four types of macromolecules: 1. Proteins 2. Nucleic acids 3. Carbohydrates 4. Lipids
Fig. 3.3 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Monomer: Amino acid H H N CH 3 C C H O OH Ala Ala Val Val Ser Polymer: Polypeptide Monomer: Monosaccharide H HO CH 2 OH O H OH H H OH Polymer: Starch (a) Protein Alanine (c) Carbohydrate H OH Monomer: Nucleotide O O P O O (b) Nucleic acid CH 2 H H H H OH O C C H H NH 2 C N C N H O P G C P T A P P P P P T A P G A C T P P P P P A P P Polymer: DNA strand Monomer: Fatty acid (d) Lipid O H H H H H H H H H H H H O C C C C C C C C C C C C H H H H H H H H H H H Polymer: Fat molecule Which of these monomers is polar? What does that mean for the polymer/macromolecule?
Dehydration synthesis All macromolecules are assembled the same way A covalent bond is formed between two subunits by removing a hydroxyl group (OH) from one subunit and a hydrogen (H) from another subunit Because this amounts to the removal of a molecule of water (H 2 O), this process is called dehydration synthesis
Figure 3.4(a) Dehydration synthesis
Figure 3.4(b) Hydrolysis Which process releases energy: dehydration synthesis or hydrolysis?
Proteins Complex macromolecules that are polymers of many subunits called amino acids Figure 3.3(a) Polymers are built from monomers: protein
Amino acids Small molecules with a simple basic structure, a carbon atom to which three groups are added an amino group (-NH 2 ) a carboxyl group (-COOH) a functional group (R) 20 different R groups
Figure 3.6(b) The formation of a peptide bond
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Primary structure Amino acids Protein structure Secondary structure β-pleated sheet α-helix Tertiary structure Quaternary structure
Protein structure: Primary Primary structure the sequence of amino acids in the polypeptide chain This determines all other levels of protein structure Figure 3.7 Levels of protein structure: primary structure Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Primary structure Amino acids
Protein structure: Secondary Secondary structure the initial folding of the amino acid chains Occurs because regions of the polypeptide that are nonpolar are forced together Figure 3.7 Levels of protein structure: secondary structure Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Secondary structure The folded structure may resemble coils, helices, or sheets β-pleated sheet α-helix
Protein structure: Tertiary Tertiary structure the final 3-D shape of the protein The final twists and folds that lead to this shape are the result of polarity differences in regions of the polypeptide Figure 3.7 Levels of protein structure: tertiary structure Tertiary structure Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Protein structure: Quaternary Quaternary structure the spatial arrangement of component polypeptides in proteins comprised of more than one polypeptide chain Figure 3.7 Levels of protein structure: quaternary structure Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Quaternary structure
Figure 3.8 Protein denaturation Heat ph Inactive
Figure 3.9 Protein structure determines function
Nucleic Acids Nucleic acids are very long polymers that store information comprised of monomers called nucleotides Figure 3.3(b) Polymers are built from monomers: nucleic acid
Figure 3.10 The structure of a nucleotide Dehydration reaction Each nucleotide has 3 parts 1. a five-carbon sugar 2. a phosphate group 3. an organic nitrogencontaining base There are five different types of nucleotides information is encoded in the nucleic acid by different sequences of these nucleotides
DNA & RNA There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) RNA is similar to DNA except that it uses uracil instead of thymine it is comprised of just one strand it has a ribose sugar (instead of deoxyribose)
Figure 3.11 How DNA structure differs from RNA
The structure of DNA is a double helix because there are only two base pairs possible Adenine (A) pairs with thymine (T) Cytosine (C) pairs with Guanine (G) the bonds holding together a base pair are hydrogen bonds a sugar-phosphate backbone comprised of phosphodiester bonds gives support The Double Helix
Structure of DNA The hydrogen bonds of the base pairs can be broken to unzip the DNA so that information can be copied each strand of DNA is a mirror image so the DNA contains two copies of the information Having two copies means that the information can be accurately copied and passed to the next generation
Carbohydrates Carbohydrates are used for energy or as structural molecules a carbohydrate is any molecule that contains the elements C, H, and O in a 1:2:1 ratio the sizes of carbohydrates varies simple carbohydrates made up of one or two monomers complex carbohydrates long polymers Figure 3.3(c) Polymers are built from monomers: carbohydrate
Figure 3.14 The structure of glucose
Mono- & Disaccharides Simple carbohydrates are small monosaccharides consist of only one monomer subunit an example is the sugar glucose (C 6 H 12 O 6 ) disaccharides consist of two monosaccharides an example is the sugar sucrose, which is formed by joining together two monosaccharides, glucose and fructose
Polysaccharides Complex carbohydrates are long polymer chains because they contain many C-H bonds, these carbohydrates are good for storing energy these bond types are the ones most often broken by organisms to obtain energy the long chains are called polysaccharides
Carbohydrate storage Plants and animals store energy in polysaccharide chains formed from glucose plants form starch animals form glycogen Some polysaccharides serve structural functions and are resistant to digestion by enzymes cellulose is found in the cell walls of plants chitin is found in the exoskeletons of many invertebrates and in the cell walls of fungi
Lipids Lipids fats and other molecules that are not soluble in water lipids are nonpolar molecules lipids include fats, phospholipids, and many other molecules Figure 3.3(d) Polymers are built from monomers: lipid
Fats Used for long-term energy storage Glycerol fats have two subunits 1. fatty acids 2. glycerol fatty acids are chains of C and H atoms Glycerol contains three carbons and forms the backbone to which three fatty acids are attached How is the energy released? Fatty acids
Figure 3.17 Saturated and unsaturated fats What forces are at work here?
Lipid membranes Biological membranes use lipids phospholipids make up the two layers of the membrane cholesterol (a steroid) is embedded within the membrane Lipids also include oils, other steroids, rubber, waxes, and pigments What properties of phospholipids make them work as a membrane? Figure 3.16 Lipids are a key component of biological membranes
Steroids Lipids that have rings in their structure Structural components of membranes (cholesterol) Signaling molecules (testosterone, estrogen) Testosterone