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Bio 1361H First Exam Review

by: gypsgirl

Bio 1361H First Exam Review 1361H

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About this Document

Covers all of Ch. 1-7, 26, and 33 In order of when we learned the chapters
Introduction to Biological Sciences
Marc H. Hanke
Study Guide
Biology, Viruses, Bacteria, prokaryotes, eukaryotes, cells
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This 10 page Study Guide was uploaded by gypsgirl on Thursday September 22, 2016. The Study Guide belongs to 1361H at University of Houston taught by Marc H. Hanke in Fall 2016. Since its upload, it has received 59 views. For similar materials see Introduction to Biological Sciences in Biology at University of Houston.


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Date Created: 09/22/16
Honors Bio 1361 First Exam Review Ch. 1- Biology and the Tree of Life - What Does It Mean That Something Is Alive?  Five characteristics of an organism:  Cells- made of cells  Replication- able to replicate itself  Evolution- have gone through evolution and still capable of doing so  Information- ability to obtain and process it  Energy- ability to acquire and use it  Cell Theory- all organisms are made of cells and all cells come from pre-existing cells  Theory of Evolution- how and why organisms evolve, single common ancestor for all  Chromosome Theory of Inheritance- genes are found on chromosomes and patterns of inheritance are determined by actions of chromosomes during meiosis - Life is Cellular  Cell theory defines the fundamental structural unit in all life - Life Evolves  Theory of evolution says that all organisms have a common ancestor  Natural selection- well-tested explanation of why species change over time and why they are extremely well adapted to their environments - Life Processes Information  Chromosome theory of inheritance says genes are found on chromosomes  Chromosomes have a molecules of DNA (the hereditary information)  Genes, consisting of specific segments of DNA, are located on the chromosomes  Code for products in the cell  Central Dogma- flow of information from DNA to RNA to protein  Organisms highly different in how they obtain and use energy - Tree of Life  Theory of evolution says all organisms are part of a genealogy of species and all species trace back to a single common ancestor  Biologists analyzed sequences in an array of genetic material found in all cells to construct this idea  Based on similarities and differences in molecules  Has three lineages/ domains:  Bacteria  Archaea  Eukarya - Doing Biology  Is a hypothesis-driven and experimental science Ch. 2- Water and Carbon: The Chemical Basis of Life - Building Blocks of Chemical Evolution: Atoms, Ions, and Molecules  The shared or transferred electrons in chemical bonds give atoms full valence shells and usually higher stability  Covalent Bond- electrons shared equally (nonpolar) or unequally (polar) - Properties of Water and the Early Oceans  In order for life to exist in water, chemical reactions must take place  Polar, bent, two polar covalent bonds  Affects hydrogen bonding in polar molecules; similar electrical attractions in ions; causes solutes to dissolve in water  Can absorb heat and cohere to other water molecules is caused by its ability to hydrogen bond  Spontaneously dissociates into H+ (hydrogen ions or protons) and OH- (hydroxide ions)  pH- concentration of H+ in solution; altered by acids and bases; stabilized by buffers - Chem Reacstons, Energy, and Evolution  1 step of chem evolution- creation of small organic compounds from simple molecules (ex. H2 and CO2)  Chem reactions- breaking bonds, rearranging atoms, forming new bonds  Involves either the potential energy from bonds of reactants or kinetic energy from external sources (ex. thermal energy)  Energy- many different forms; can’t be created or destroyed; one form can transform into another - Models for Chemical Evolution  Suggested that external sources of energy (ex. sunlight or lightning) drove chem reactions b/w simple molecules to make higher potential energy molecules; energy in form of radiation/ electricity was changed into chem energy  Prebiotic Soup and Surface Metabolism Models- supported by lab experiments to synthesize organic molecules in early Earth environment - Importance of Organic Molecules  Carbon- foundation of organic molecules; its valence allows for construction of complex molecule shapes  Organic molecules- critical for life, possess versatility in chem behavior thanks to presence of functional groups Ch. 3- Protein Structure and Function - Amino Acids and Polymerization  Have central carbon joined to an amino group, hydrogen atom, carboxyl group, and R-group  Structure of R-group changes chem reactivity and solubility of amino acids  Amino acids connected by peptide bonds b/w carboxyl group of one and the amino group of another - What Proteins Look Like  Primary structure- sequence of amino acids, responsible for most of its chem properties  Secondary structure- created by interactions b/w C=O and N-H groups in same peptide-bound backbone, stabilized by hydrogen bonds  Tertiary structure- interactions b/w R-groups (also R-groups and peptide-bound backbones), stabilizes complete polypeptide into 3D structure  Complete proteins have several polypeptides joined together  Quaternary structure- combo of polypeptides - Folding and Function  Folding is spontaneous  Folded shape is important for its function  Proteins have to bind to other molecules and ions to have active conformation  Improperly folded proteins are bad, certain kinds can cause deadly infectious diseases - Diverse Protein Functions  Function in catalysis, defense, movement, signaling, structural support, and transport of materials  Can have diverse functions b/c they have diverse structures and chem properties  Catalysis is done at enzymes’ active sites  Have unique chem properties and certain shapes and sized that are specific to substrates Ch. 4- Nucleic Acids and the RNA World - What is a Nucleic Acid?  Nucleic acids-polymers of nucleotide monomers (contain a sugar, phosphate group, and nitrogenous base)  RNA- ribonucleotide monomers  DNA- deoxyribonucleotide monomers  Ribonucleotides- hydroxyl (-OH) group on 2’ carbon  Deoxyribonucleotides- hydrogen (-H) group on 2’ carbon  Polymerize when condensation reactions join nucleotides together by phosphodiester linkages  Are directional- have a 5’ and 3’ end; new nucleotides are added on 3’ end - DNA Structure and Function  Primary sequence- series of linked nucleotides  Secondary structure- two DNA strands running in opposite directions and twisted into a double helix; stabilized by hydrogen bonds, hydrophobic interactions, and van der Waals interactions  Tertiary structure- twisting of double helices into supercoils or wrapping around proteins  Extremely stable- why it’s good to store genetic info (in the form of base sequences)  Copied by complementary base pairing- occurs between A-T and G-C pairs - RNA Structure and Functions  Primary structure- sequence of linked nucleotides  Secondary structure- variety of configurations  Including short regions of complementary base pairing formed by double-helical stems and unpaired loops  Tertiary structure- secondary folded into complex shapes by complementary base pairing  Versatile and can work as an information carrier and a catalyst - First Life Form  RNA World Hypothesis- researchers are trying to synthesize ribozymes in lab  Ribozymes- catalyze reactions for the production of nucleotides  May have preceded the evolution of RNA replicase Ch. 5- An Introduction to Carbohydrates - Sugars as Monomers  Monosaccharides- organic compounds containing a carbonyl group and multiple hydroxyl groups  Typical formula- (CH2O)n n= # of “carbon-hydrate” groups  Aldose or ketose configurations  Aldose- aldehyde sugar; carbonyl group at end of molecule  Ketose- ketone sugar; carbonyl group within carbon chain  Spatial arrangement of functional groups shows differences in molecular structures and functions for monosaccharides that have the same molecular formula  Can form ring structures that differ from one another in placement of hydroxyl group even if they are molecules of the same monosacchride - Structure of Polysaccharides  Monosaccrides- covalently bound to each other by glycosidic linkages  Join hydroxyl groups together  Don’t always form an uniform, single backbone  Numerous hydroxyls in monosaccharides allow glycosidic linkages to form at various sites and new strands to branch from chains  Types of monomers and geometries of glycosidic linkages b/w monomers distinguish polysaccharides from others  Common ones: starch, glycogen, cellulose, chitin, and peptidoglycan  Peptidoglycan- sugar monosaccharides and short chains of amino acids - What Do Carbohydrates Do?  Structure correlates with function  Cellulose, chitin, and peptidoglycan- function in support; monosaccharide monomers joined via (beta)-1,4-glycosidic linkages; strong and flexible fibers/sheets that resist hydrolysis  Oligosaccharides- function as specific signposts or id tags; diverse geometry and composition of constituent sugar residues  Starch and glycogen- function as energy storage; made of glucose molecules joined via (alpha)-glycosidic linkages- readily hydrolyze to release glucose for creation of ATP and materials for building new molecules Ch. 6- Lipids, Membranes, and the First Cells - Lipid Structure and Function  Largely hydrophobic compounds thanks to their high number of nonpolar C-H bonds  3 main types of lipids:  Fats- store chem energy  Steroids- key component of cell membranes  Phospholipids- key component of cell membranes  Hydrocarbon chains- length and degree of saturation have profound effect on physical properties  All have hydrophobic region  Amphipathic lipids possess distinct hydrophilic region that has polar and charged groups  Phospholipids have a polar, charged head and nonpolar tail  Nonpolar tail typically has fatty acids or isoprenoids - Phospholipid Bilayers  Spontaneously assemble into bilayers; serve as physical barrier b/w internal and external environment  Small nonpolar molecules usually move directly across bilayer easily; ions cross rarely  Permeability and fluidity depend on temperature, concentration of cholesterol, chem structure of lipids present (ex. saturation status and length of hydrocarbon chains)  Phospholipids w/ longer or saturated tails form dense, highly hydrophobic interior that lower bilayer permeability (relative to phospholipids containing shorter or unsaturated tails) - How Molecules Move Across Lipid Bilayers  Diffusion- random movement of ions or molecules owing to thermal energy  If membrane separates solutions of different concentrations or charges, passive transport creates net directional movement of solutes across membrane that makes environment on both sides to be more similar  This spontaneous process driven by increase in entropy  Osmosis- diffusion of water across membrane in response to concentration gradient - Proteins Alter Membrane Structure and Function  Permeability of lipid bilayers altered greatly by membrane proteins  Channel proteins- provide pores for membrane that have very regulated closed and open conformations; facilitate diffusion of certain solutes into and out of the cell  Carrier proteins- undergo conformational changes; facilitate diffusion of specific molecules into and out of cell  Pumps- use energy to actively move ions or molecules in single direction; often against electrical or chemical gradient  Selective permeability of phospholipid bilayers and specificity of transport proteins make it possible to make an environment inside cell that is radically different from exterior one Ch. 26- Bacteria and Archaea - Why Do Biologists Study Them?  Most abundant organisms on Earth; found in every habitat sampled  Very small, prokaryotic cells; most unicellular  Distinguished by their different kinds of membrane lipids and cell walls and their different transcription machinery  Bacteria- play role in animal digestion, bioremediation, and production of antibodies  Cause some of most dangerous human diseases (ex. plague, syphilis, botulism, cholera, and tuberculosis) - How Do Biologists Study Bacteria and Archaea? Enrichment cultures- used to grow large amounts of bacterial and archaeal cells that proper under certain conditions Metagenomic analysis- study bacteria and archaea that can’t be cultured by DNA extraction directly from environment and then sequencing and characterizing DNA fragments Info obtained used to id biochemical processes and organisms that are placed on the tree of life Analyzed DNA from samples from different parts of the human body (ex. mouth and intestine); discovered microbiomes containing large numbers of diverse species of prokaryotes - What Themes Occur in Diversification of Bacteria and Archaea? Genetic variation achieved by:  Transformation- uptake of DNA from environment  Transduction- transfer of DNA from one cell to another one via a virus  Conjugation- direct transfer of DNA from one cell to another one Metabolic diversity and complexity- aspects of bacteria and archaea  Morphological diversity and complexity- aspects of eukaryotes Wide variety of inorganic and organic compounds containing high potential energy; may serve as electron donors in cellular respiration Wide array of inorganic and organic molecules containing low potential energy; may serve as electron acceptors in cellular respiration Dozens of organic molecules are fermented Many are phototrophs  Use light energy to create high energy electrons that generate ATP  Water is used as a source of electrons and oxygen gas is generated as a by-product in cyanobacteria  In others, electrons come from somewhere other than water and no oxygen is produced  Use enzymes of the Calvin cycle to reduce CO2 and get building block compounds (that have C-C bonds)  Several biochemical pathways can also break down simple organic molecules into sugars and carbohydrates Play large role in carbon and nitrogen cycling and change global atmosphere, oceans, and terrestrial environments  Thanks to their metabolic diversity Nitrogen-fixing species- provide nitrogen that can be used by many species, including plants and animals - Key Lineages of Bacteria and Archaea Prokaryotes divided into two groups: bacteria and archaea; based on variety of biochemical, morphological, and molecular characteristics  Bacteria- 29 major lineages; including organisms that have major roles in ecosystems as primary producers, decomposers, and parasites  Archaea- 5 major lineages; thought to exist only in extreme environments but are actually widespread Ch. 7- Inside the Cell - Bacterial and Archaeal Cell Structures and Functions  2 basic cellular designs:  Prokaryotes- absence of a nucleus  Eukaryotes- presence of a nucleus  Most prokaryotes have:  Ribosomes  Cell Wall  Plasma Membrane  Interior Cytoskeleton  Nucleoid  Many possess:  Flagella  Fimbriae  Internal Membrane Structures (some of which are considered organelles) - Eukaryotic Cell Structures and Functions  Usually larger and more complex than prokaryotic ones  Have multiple specialized organelles that organize the cytoplasm and enable the cell to grow larger  Common organelles:  Nucleus- hold the cell’s chromosomes; control center or “brain of the cell”  Endomembrane System- group of diverse, interrelated organelles; synthesize, process, sort, transport, and recycle materials; include:  Endoplasmic Reticulum (ER)  Golgi Apparatus  Lysosomes  Vacuoles  Endosomes  Perixisomes- where key reactions take place; often result in generation of toxic by-products  Specialized enzymes in them disarm the by-products after they are created  Mitochondria and chloroplasts- extensive internal membrane systems where enzymes that aid in ATP generation and photosynthesis are located - Putting the Parts Together  Cells have a very organized interior  Presence and quantity of organelles define function of cell  Activity in cell shows the dynamic nature of life; organelles and cytosolic proteins are constantly doing stuff  Most of what is known about cells is from advances in cell imaging and cellular component isolation techniques - Cell Systems 1: Nuclear Transport  Traffic across nuclear envelope happens through nuclear pore complexes (the gatekeepers)  Small molecules passively diffuse through nuclear pore complexes  Larger molecules require a nuclear localization signals to get them through by nuclear transport proteins - Cell Systems 2: The Endomembrane System Works Cargo  Molecules synthesized in the ER transported as cargo to Golgi apparatus and then to either other organelles or outside the cell  Products are sorted by their molecular “zip code” to be put in specific vesicles in order to leave the Golgi apparatus  Membrane and cytosolic proteins deliver the packages to their locations  Lysosomes- made of enzymes and membranes that created and processed through the endomembrane system; involved in recycling materials by autophagy, phagocytosis, and receptor-mediated endocytosis - Cell Systems 3: Dynamic Cytoskeleton  Extensive systems of fibers that provide:  Structural support for organizing organelles and other parts of the cell  Paths for moving organelles and intracellular structures  Cellular locomotion by flagella, cilia, or cell crawling  Dynamic; actin filaments and microtubules- polarized (have different ends, plus and minus)  Plus sides have higher growth rates than minus ends  Motor proteins move along actin filaments and microtubules via chem energy found in ATP  Myosin motor proteins move toward the plus ends of actin filaments  Kinesin moves along microtubules toward the plus ends  Dynein moves down microtubules toward the minus ends  In absence of cilia and flagella in eukaryotes, dynein motors move microtubules to create forces that bend the structures and allows the cells to swim Ch. 33- Viruses - Why Do Biologists Study Viruses?  Shaped the evolution of organisms b/c they transfer genetic information; serve as agents of natural selection by illness and death  Specialists- different types infect particular species and types of cells - How Do They Study Them?  Most have a protein capsid, either icosahedral or helical; some are covered by a membranous envelope  Genomes exhibit major diversity  Genetic material may have one or more molecules of DNA or RNA, either double or single stranded  Entry into host cells depends on certain interactions b/w viral proteins and virus receptors (molecules on the host cell’s surface)  Viral genome is released into the cytosol by uncoating  Use the host cell’s substrates, biosynthetic machinery, and chem energy to create viral proteins and replicate the viral genome  Enveloped- exit cell via budding  Naked- exit via lysis, killing the host cell  Some may enter a dormant phase  Don’t produce virions, just coexist with the host and transmit genetic material to daughter cells when the cell divides - What Themes Occur in Diversification of Viruses?  Origin of Viruses:  Escaped gene sets from cells  Products of degenerated cellular parasites  Coevolved with cells in RNA world  Continue to evolve  Factors that increase rate of evolution:  Errors during genome application  Genomic reassortment  Many diseases are caused by viruses transmitted from one host species to another - Key Lineages of Viruses  Vary in how their genomes are replicated and transcribed to produce mRNA, morphology, and nature of their genetic material Additional Info for the Exam - First Page 5 definitions @ 3 points each 1 short answer @ 9 points  4 sentences if you know your stuff 1 “fun and informative” table @ 9 points  Ch. 6 1 short answer* @ 12 points  Subject to change 1 long essay @ 25 points  Ch. 2-6, find common topics discussed throughout that you can write about 30 multiple choice questions @ 1 point each  Focus on macromolecules’ structures and functions Identify them How they are made  What happens when they join together


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