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[BIOL 190] - Midterm Exam Guide - Comprehensive Notes for the exam (42 pages long!)

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Biology Courses
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BIOL 190
Meier Deanna

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USD BIOL 190 MIDTERM EXAM STUDY GUIDE find more resources at Tuesday, September 6, 2016 Bio 190- Lecture 1 (Fundamental Concepts in Biology) Themes in the Study of Biology - All forms of life share common properties - Properties of life include: • Order- highly ordered structure that typifies life - symmetry, ex. repeated segments of the body, parts of the body - some organisms look like blobs of nothing —> microscope reveals cells lined up in order • Reproduction- ability of organisms to reproduce their own kind - bacteria simply dividing through mitosis (use fission) -> reproduce themselves - sexual reproduction and behaviors involved before they can reproduce —> much higher diversity (genes from two different organisms) Growth and Development- consistent growth and development controlled by • inherited DNA - once they are born or cells divide, they change. - larvae —> very first stage for a lot of organisms (look very different from the adult) • Energy processing- use of chemical energy to power an organism’s activities and chemical reactions - plants use energy of the sun, humans eat chemical energy to make ATP to fuel our processes • Response to the Environment-ability to respond to environmental stimuli - homeostasis- state an organism needs to be in to survive • Regulation-ability to control an organism’s internal environment within limits that sustain life - also refers to homeostasis - if they go out of the state and cannot quickly adapt, they will parish. ▯1 find more resources at find more resources at Tuesday, September 6, 2016 • Evolutionary adaption- adaptions evolve over many generations as individuals with traits best suited to their environments have greater reproductive success and their traits to offspring - requirement of being alive - organism is subject to changes In life’s hierarchy of organization, new properties emerge at each level - Biological Organization • Biosphere-all the environments on Earth that support life • Ecosystem- all the organisms living in a particular area and the physical components with which the organisms interact - Forest, desert, etc. • Community- the entire array of organisms living in a particular ecosystem • Population- all the individuals of a species living in a specific area(community) - not regularly interacting with other species/populations Pop A., Sp. A Pop.B, Sp. A • Organism-an individual living thing • Organ system-several organs that cooperate in a specific function • Organ-structure that is composed of tissues and that provides a specific function for the organism • Tissues-a group of similar cells that perform a specific function • Cells- the fundamental unit of life - most of life is single-celled • Organelle-a membrane-bound structure that performs a specific function in a cell ▯2 find more resources at find more resources at Tuesday, September 6, 2016 - student microscope is here and up • Molecule- a cluster of small chemical units called atoms held together by chemical bonds • Atom- fundamental unit of substances Cells are the structural and functional units of life - Cells are the level at which properties of life emerge - A cell can: • regulate its internal environment - have membranes that can choose what comes into the cell and what passes through and gets expelled • take in and use energy - convert energy within them and send it out - receive energy from somewhere else in the body - eat something -> digest -> absorption-> other cells absorb • respond to its environment - environment too watery or too saline —> release water or take in water • develop and maintain its complex organization - designed to keep the organelles in a certain area and keep things organized • give rise to new cells - constantly undergoing mitosis • Two basic types of cells: - Prokaryotic cells • first to evolve - on Earth for a very long time before eukaryotic cells evolved • simpler • usually smaller than eukaryotic cells ▯3 find more resources at find more resources at Tuesday, September 6, 2016 • genetic material is loosely arranged • only single celled • found in Bacteria and Archaea - Eukaryotic cells • contain membrane-enclosed organelles, including a nucleus containing DNA • found in plants, animals, and fungi more complex, larger, have more going on • • can be single or multi celled Living organisms interact with their environment, exchanging matter and energy - Living organisms interact with their environments which include: • other organisms, physical factors - sunlight, water, finding an area to reproduce, temperature, natural barriers - In most ecosystems: • organisms compete for all those resources • plants- producers that provide the food - photosynthetic- use sun as their initial energy source (plants) - chemosynthetic- bacteria • consumers- eat plants and other animals ▯4 find more resources at find more resources at Tuesday, September 6, 2016 • decomposers- recyclers, changing complex matter into simpler mineral nutrients - Dynamics of ecosystems include two major processes: • recycling of chemical nutrients - where are nutrients found? • in the soil, in our bodies when we die - who recycles nutrients? • the Earth • One-way flow of energy through an ecosystem - what is the source of energy entering an ecosystem? • sunlight - What do producers do to energy entering an ecosystem? • convert it into chemical energy using photosynthesis - How does energy leave the ecosystem? • waste heat Evolution, the Core and Theme of Biology and This Class The unity of life is based on DNA and a common genetic code - All cells have DNA, the chemical substance of genes Deoxyribonucleic Acid —> blueprint for what everything is supposed to look like, • act like, etc. - Genes unit of inheritance that transmits information from parents to offspring • • grouped into very long DNA molecules called chromosomes - every species has a set number of chromosomes ▯5 find more resources at find more resources at Tuesday, September 6, 2016 • control the activities of a cell - creating proteins - A species’ genes are coded in the sequences of the four building blocks (alphabet of DNA) making up DNA’s double helix • All forms of life use essentially the same code to translate information stored in DNA into proteins (nucleotide sequences) - Adenine - Thymine - Cytosine - Guanine • The diversity of life arises from differences in the DNA sequences - so many combinations, lengths that apply to the diversity The diversity of life can be arranged into three domains - Diversity is the hallmark of life 1.8 million species identified • - million are arthropods (crabs, lobsters, insects, etc) • Actual number of species likely 10 to 100 million - many are in extreme locations so hard to find - a lot are insects or bacteria that we can’t see - Taxonomy names species and classifies them into a system of broader groups Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species • - previously started at Kingdom, but Domain was added - developed by Linnaeus in the 1800s ▯6 find more resources at find more resources at Tuesday, September 6, 2016 - helps us to keep track of life • Species: unique type of organism - can produce viable living offspring - Three Domains • Bacteria are the most diverse and widespread prokaryotes - typical rod shape Archaea are prokaryotes that often (but not always) live in Earth’s extreme • environments - different from bacteria in structure, but pretty similar • Eukarya have eukaryotic cells and include: - single-celled protists • there are some multi cellular algae - multicellular fungi, animals, and plants Evolution explains the unity and diversity of life - The history of life, as documented by fossils, is a sage of a changing Earth • 4.5 billion years old • inhabited by an evolving cast of life forms - some that died the second they were introduced - some have lived for millions and millions of years - Evolution accounts for life’s dual nature of: • unity • diversity Homework: Observe traits in 1 organism Why is/are the trait/s unique? What survival advtange may the trait/s provide? ▯7 find more resources at find more resources at Tuesday, September 6, 2016 Do you observe variation in the trait/s within the same individual organism? Evolution explains the unity and diversity of life - In 1859, Charles Darwin published the book On the Origin of Species by Means of Natural Selection • Theory of evolution: species living today are descendants of ancestral species via “descent with modification” - modifications must be beneficial to be passed on (changes from the ancestor) • Natural selection is a mechanism for evolution - Natural selection was inferred by connecting two observations • Individuals in a population have varying traits, many of which are passed on from parents to offspring - characteristics/traits are different (heritable traits-those that can be passed on through DNA) • A population can produce far more offspring than the environment can support - From these observations, Darwin inferred: • individuals with heritable traits best suited to the environment are more likely to survive and reproduce than less well-suited individuals • an increasing proportion of individuals will have the advantageous traits • the result will be evolutionary adaption, the accumulation of favorable traits in a population over time ▯8 find more resources at find more resources at Thursday, September 8, 2016 Bio 190-Lecture 2 A few chemical groups are key to the functioning of biological molecules - Organisms are made up of organic molecules • Carbon-based molecules - An organic molecule has unique properties that depend on • size and shape • group of atoms (functional groups) attached to it Cells make up a huge number of large molecules from a limited set of small molecules - Four classes of molecules important to organisms: • carbohydrates, proteins, lipids, and nucleic acids • can be very large molecules=macromolecules • Monomers (one) and Polymers (many) - Monomer is a subunit that makes up polymers that are aka macromolecules - Monomers link together to form polymers through dehydration reactions • removal of water - Polymers are broken apart by hydrolysis • addition of water (lyse-to break apart) - All biological reactions of this sort are mediated by enzymes • Which class of molecule are most enzymes part of? ▯1 find more resources at find more resources at Thursday, September 8, 2016 - proteins! Monosaccharides are the simplest carbohydrates - Carbohydrates- small sugar molecules (monomers) to large polysaccharides (polymers) - Sugar monomers are monosaccharides • glucose and fructose- fuels for cellular work - Monosaccharides (one sugar) can be hooked together to form: • more complex sugars • disaccharides (ex. sucrose) • polysaccharides (ex. starch, glycogen, chitin) Twomonosaccharidesarelinkedtoformadisaccharid e - two monosaccharides (monomers) can bond to form a disaccharide - the disaccharide maltose is formed from two glucose monomers Polysaccharides are long chains of sugar units - Starch • used by plants for energy storage - Glycogen • used by animals for energy storage - Cellulose • forms plant cell walls • most abundant molecule on earth - Chitin • used by insects and crustaceans to build an exoskeleton • hard substance, storage and structural carbohydrate ▯2 find more resources at find more resources at Thursday, September 8, 2016 Fats are lipids that are mostly energy-storage molecules - Lipids • water insoluble (hydrophobic, or water-fearing) compounds - hydrophobic (water-fearing) vs. hydrophilic (water-loving) • important in long term energy storage • contain twice as much energy has a polysaccharide • consist mainly of carbon and hydrogen atoms • Subunits? - don’t technically have subunits - just have 2 parts that come together; don’t get bigger by putting other parts together - Lipids differ from carbohydrates, proteins, and nucleic acids • not huge molecules • not built from monomers - Four types: • Fats - A fat is a large lipid made from two kinds of smaller molecules: • glycerol • fatty acids - contains one glycerol linked to three fatty acids via a dehydration reaction - fats aka triglycerides because of their structure - unsaturated fats has a kink in it’s structure • not saturated with as many hydrogens - saturated fats—> has the most amount of hydrogens and does not have the double bond • Phospholipids ▯3 find more resources at find more resources at Thursday, September 8, 2016 - structurally similar to fats (2 fatty acids attached to the glycerol) - major component of all cells - cluster into a bilayer • helps to maintain homeostasis - semipermeable membrane • hydrophilic heads • hydrophobic tails • Waxes - lipids with long fatty acid tails - tails are bonded to alcohols or C rings - Firm due to tightly packed molecules • beeswax • line outside of plants • line skin and hair • Steroids - lipids in which the carbon skeleton contains four fused rings - no fatty acid tails - very useful for regulation within hormones - ex. cholesterol • common component of animal cell membranes • starting material for making steroids, including sex hormones Proteins are made from amino acids linked by peptide bonds - Proteins • involved in nearly every dynamic function in your body ▯4 find more resources at find more resources at Thursday, September 8, 2016 • very diverse, each with a specific structure and function • form polypeptides, long chains of amino acids - Proteins are composed of differing arrangements of just 20 amino acid monomers • R groups vary - A protein’s specific shape determines its function • most important role for proteins is as enzymes: - can be reused - serve as metabolic catalysts - regulate the chemical reactions within cells - are absolutely necessary for many chemical reactions to occur DNA and RNA are the two types of nucleic acids - gene- unit of inheritance - genes consist of DNA, a type of nucleic acid • deoxyribonucleic acid • inherited from an organism’s parents • provides directions for its own replication (self-replicates) and does so through the cell cycle (mitosis) • programs a cell’s activities by direction the synthesis of proteins • does not build proteins directly • works through an intermediary, ribonucleic acid (RNA) - DNA is transcribed into RNA - RNA is translated into proteins Nucleic acids are polymers of nucleotides - DNA and RNA are composed of monomers called nucleotides - Nucleotides have 3 parts: ▯5 find more resources at find more resources at Thursday, September 8, 2016 • five-carbon sugar • phosphate group • a nitrogenous base (determines the sequence of the DNA) - DNA nitrogenous bases: • adenine (A) • thymine (T) guanine (G) • • cytosine (C) - RNA nitrogenous bases: • also has A, C, and G • but instead of T, it has uracil (U) The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits - DNA specifies traits by dictating protein synthesis - Transcription is the synthesis of RNA under the direction of DNA • mRNA: messenger RNA - contains the code that will be read by tRNA to bring in the right amino acids to create the protein • tRNA: transfer RNA - tRNA brings to the ribosomal RNA • rRNA: ribosomal RNA - site of the creation of the protein - Translation is the synthesis of proteins under the direction of RNA - the molecular chain of command • 98% used to be called “junk DNA” ▯6 find more resources at find more resources at Thursday, September 8, 2016 • only 2% of DNA codes for proteins • ENCODE (Encyclopedia of DNA elements) - 18% of DNA regulates the 2% that codes for proteins - 80% of DNA has an active function Genetic information written in codons is translated into amino acid sequences - sequence of nucleotides in DNA provides a code for constructing a protein • requires a conversion of a nucleotide sequence to an amino acid sequence • flow of information from gene to protein based on a triplet code • each amino acid is specified by a codon - 64 codons are possible - some amino acids have more than one possible codon - methionine is always the start codon - Overview of Transcription • an RNA molecule is transcribed from a DNA template • RNA nucleotides are linked by the transcription enzyme RNA polymerase - “ase" —> enzyme • Specific sequences of nucleotides along the DNA mark where transcription begins and ends • the “start transcribing” signal is a nucleotide sequence called a promoter - regions where the process starts and stops (promoters and terminators on DNA) ▯7 find more resources at find more resources at Thursday, September 8, 2016 1.Initiation 2.Elongation 3.Termination TransferRNAmoleculesserveasinterpretersduring translation - Overview of Translation • Transfer RNA (tRNA) molecules function as a language interpreter - convert genetic message of mRNA (codons) into language of proteins (amino acids) • tRNA molecules perform this interpreter task by: - picking up the appropriate amino acid and bringing it to another tRNA molecule - using a special triplet of bases (anticodons) to recognize the appropriate codons in the mRNA - P site- where the tRNA is formed in the ribosome (always on left side) - A site- point of entry for a new tRNA - ▯8 find more resources at find more resources at Thursday, September 8, 2016 Macromolecule Carbohydrate Lipid protein Nucleic Acid subunits monomers glycerol, fatty monomers (amino monomers (monosaccharides) acids, various acids) (nucleotides) others functions in cell fuels activities energy storage everything! drive provides genetic nearly all bodily material functions hydrophilic or hydrophillics hydrophobics can be either backbone phobic *generally hydrophillics, base pairs hydrophobic unique properties huge size-can be large amount of enzymes heritable very long chains energy stored example honey olive oil beef jerky DNA/RNA ▯9 find more resources at find more resources at Tuesday, September 13, 2016 Biology 190- Lecture 3 Evolution: pre-Darwinian Ideas and the Darwinian Revolution - discoveries leading up to Darwin and opposing ideas - the life and discoveries of Darwin - new evidence for evolution - Objective v. Subjective reasoning • objective- based off of facts, testable • subjective- observations that haven’t been tested, feeling way of knowing something, beliefs - Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species • theory of evolution - theory= something that has been tested many times but has not been refuted - theory of evolution by natural selection • Darwin’s ideas had deep historical roots Timeline - 1795- Hutton proposes his principle of gradualism • observed things that he noticed geologically evolved slowly and over time - 1798- Malthus published “Essay on the Principle of Population” • based on human population • humans produce more offspring than the environment can support - 1809- Lamarck published his hypothesis of evolution • organisms change - changes in organism’s life time are passed onto the offspring= not true • Charles Darwin was born in 1809 as well ▯1 find more resources at find more resources at Tuesday, September 13, 2016 - 1812- Curvier publishes his extensive studies of vertebrate fossils • found fossils in various strata • very religious and did not believe in evolution • he believed that fossils were there and catastrophic events destroyed species and then new species would immigrate in - 1830- Lyell publishes Principles of Geology • earth is always changing and earth is aging slowly - 1831-1836- Darwin traveled around the world on HMS Beagle - 1844- Darwin writes his essay on descent with modification • descent with modification —> descendants are the new ones that differ from the ancestral species - 1858- While studying species in the Malay Archipelago, Wallace sends Darwin his hypothesis of natural selection • his theory of evolution was = to natural selection - 1859- On the Origin of Species is published Classification of Species - Pre-Darwinian Ideas • The Greek philosopher Aristotle viewed species as fixed and arranged them on a scala naturae - fixed scale (vertical), where nothing changes • Old Testament holds that species are individually designed by God and therefore perfect • Carolus Linnaeus interpreted organismal adaptations as evidence that the Creator has designed each species for a specific purpose - Found of taxonomy, the branch of biology concerned with classifying organisms - developed th
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