Nmat-biology-lecture-notes

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B I O L O G Y Lecture Notes Cell Types and Cell Structures Prokaryotic Cell • no nucleus • no membrane enclosed organelles • single chromosome • no streaming in the cytoplasm • cell division without mitosis • simple flagella • smaller ribosomes • simple cytoskeleton • no cellulose in cell walls • no histone proteins • example: bacteria Eukaryotic Cell • nucleus • membrane enclosed organelle • chromosomes in pairs • streaming in the cytoplasm • cell division by mitosis • complex flagella • larger ribosomes • complex cytoskeleton • cellulose in cell walls • DNA bound to histone proteins • Example: plant cells, animal cells, fungi, protists Plasma membrane 1. Surrounds Cells 2. Protected by cellulose and protein cell wall in plants Cytoplasm 1. Fluid (Cytosol) and organelles that make up the inside of the cell Nucleus 1. Membranous nuclear envelope 2. Chromosomes of DNA and protein (Histones) Endoplasmic reticulum (ER) 1. Rough ER - Transport of proteins (roughness is the attached ribosomes) 2. Smooth ER – Processing and transport of lipids Ribosomes 1. Attached to Rough ER 2. Site of protein synthesis Golgi Apparatus (Golgi body, Golgi complex) 1. Assembly and editing of proteins Lysosomes 1. Contain enzymes that break down and help recycle large proteins in animal cells Mitochondria 1. Powerhouse - site of ATP synthesis Flagella and Cilia 1. Cell surface projections for movement Microtubules and Microfilaments 1. Structural components of the cell (cytoskeleton) in eukaryotes Vacuoles 1. Large central vacuoles in plant cells contain enzymes and pigments in plant cells Chloroplasts 1. Photosynthetic organelles in plant cells,

containing the chlorophyll pigments Plant Cells  Large, central vacuole  Chloroplasts  Rigid cell wall outside of cell membrane Animal Cells  No large, central vacuole  No chloroplasts  No rigid cell wall Cell Membranes: Structure and Function

Semi-permeable Membranes • Lipid membranes are semi-permeable, also called selectively permeable – Water moves across the membrane freely – Ions (charged particles) do not move across the membrane freely – Many large molecules do not move across the membrane freely Passive Transport • Diffusion – the movement of substances from an area of higher concentration to an area of lower concentration. • Osmosis – the movement of water from an area of higher water content to an area of lower water content. Active Transport • The movement of a substance against the concentration gradient (from lower concentration to higher concentration. • Active transport requires the use of energy. Membrane proteins play an important role in passive and active transport

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Very large taken in by endocytosis

molecules

may

be There are two types of carbohydrates:  The simple sugars  Glucose, sucrose, fructose (and many others)  The complex carbohydrates  Carbohydrates that are made of long chains of sugars  Starches, cellulose, glycogen

Exocytosis secretes substances

 All carbohydrates are made up of units of sugar (also called saccharide units).  Carbohydrates that contain only one sugar unit are called monosaccharides.  Disaccharides have two sugar units bonded together.  For example, common table sugar is sucrose (below), a disaccharide that consists of a glucose unit bonded to a fructose unit. Complex carbohydrates are polymers of the simple sugars.  In other words, the complex carbohydrates are long chains of simple sugar units bonded together.  For this reason the complex carbohydrates are often referred to as polysaccharides.  Starch (below) is a polymer of the monosaccharide glucose (n is the number of repeating glucose units and ranges in the 1,000's). Starches and cellulose are complex carbohydrates used by plants for energy storage and structural integrity.  Glycogen, another polymer of glucose, is a polysaccharide used by animals to store energy. Both starch and glycogen are polymers of glucose.  Starch is a long, straight chain of glucose units, whereas glycogen is a branched chain of glucose units.  Proteins are polymers of amino acids.  Amino acids all have the general structure:  The R in the diagram represents a functional group that varies depending on the specific amino acid in question.

When 2 amino acids bond together, water is released as the carboxyl end of one amino acid bonds to the amine end of the adjacent one forming a peptide bond, as illustrated below. Biochemistry CHEMICAL BONDS Covalent bonds form between atoms of nonmetals by sharing of electrons - Molecules bond covalenty Ionic bonds form between oppositely charged ions after the transfer of electrons - Salts bond ionically Organic Molecules Organic molecules are molecules composed of carbon and hydrogen, and often containing other elements such as phosphorus, sulfur, oxygen and nitrogen. Organic molecules are the molecules of life and are built around chains of carbon atoms that are often quite long. There are four main groups of organic molecules that combine to build cells and their parts: carbohydrates, proteins, lipids, and nucleic acids.

Because water is lost, the process is called:  Condensation synthesis, or…  Condensation polymerization When many amino acids bond together to create long chains, the structure is called a protein (it is also called a polypeptide because it contains many peptide bonds).  Proteins are large molecules that may consist of hundreds, or even thousands of amino acids.  Proteins are important in cell structure, as enzymes, which speed up reactions in the body, and as antibodies which fight infection.

Carbohydrates No part of this material may be reproduced in any form without asking permission. This is for the exclusive use of St Louis Review Center.

Fats Fats are a sub-group of compounds known as lipids that are found in the body and have the general property of being hydrophobic (meaning they are insoluble in water). Other lipids include waxes, and steroids, such as cholesterol. Fats are also known as triglycerides, molecules made from the combination of one molecule of glycerol with three fatty acids.

Fats are concentrated forms of energy storage  -9 calories per gram Fats are components of cell membranes Enzymes: A Cell’s Catalysts • • • •

Catalyst: A substance that speeds up a chemical reaction without itself being changed Enzyme: A biological catalyst that is usually a protein Substrate: The reactant(s) upon which an enzyme has its action Product: A substance that results from a chemical reaction

Photosynthetic Reactions 1. Light dependent reactions 2. Light independent reactions (Calvin Cycle) Light Reactions Light dependent reactions take place in the thylakoid membrane, with the pigment chlorophyll absorbing sunlight

Catalysts Lower Activation Energy

Enzyme-Substrate Interaction

1. Energy from sunlight breaks water into H+, oxygen (O2) and electrons (e-). 2. H+ and e- are used to produce energy carrying molecules NADPH and ATP Light Independent Reactions Light independent reactions occur in the stroma The Calvin (C3) Cycle

Enzyme Inhibition

Enzymes are… • Essential to all forms of life • Not “used up” by the reaction that they catalyze • Specific to the reaction that they catalyze Photosynthesis Chloroplast Structure

  

CO2 enters the leaf through the stomates ATP and NADPH (from the light reactions) power the creation of three carbon chains ADP and NADP+ return to the light reactions in the thylakoid to be “recharged”

Formation of Glucose 3-carbon chains from the C3 cycle join to form the six carbon molecule, glucose (or other molecules required by the plant)

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Cellular Respiration Aerobic and Anaerobic Metabolism Glycolysis takes place in the cytoplasm

Glycolysis Simplified

Oxygen is the terminal (final) electron acceptor  Oxygen is needed only in the very LAST step of cellular respiration! ½ O2 + 2H+ + 2e-  H2O Aerobic Respiration C6H12O6 + 6O2 → 6CO2 + 6H2O + 38 ATP

If oxygen is available (aerobic), then pyruvate enters the Krebs cycle If oxygen is not available(anaerobic), then pyruvate undergoes fermentation

 The Krebs cycle and electron transport take place in the mitochondria  The Krebs cycle and electron transport maximize ATP yield  38 ATP vs. 2 ATP for fermentation Anaerobic Respiration (Alcohol Fermentation) C6H12O6 → 2 CH3CH2OH + 2 CO2 + 2 ATP glucose ethyl alcohol carbon dioxide Alcohol fermentation takes place in yeast and some bacteria, and yields only the 2 ATP produced in glycolysis. Cell Reproduction

The Krebs cycle takes place across inner membrane space (matrix) of the mitochondrion

Major Events in Mitosis

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Mitosis = division of the cell nucleus and its contents Cytokinesis = the division of cell cytoplasm into two identical daughter cells Chromatin = the combination of DNA and histone proteins

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Diploid = Two copies of each chromosome, one paternal, one maternal

Chromosome Structure 1 – Chromatid 2 – Centromere 3 – Short arm 4 – Long arm Telomeres  Do not code for genes  Keep ends of chromosomes from sticking to each other  Prevent loss of genes

The Cell Cycle

Binary Fission  The primary method of reproduction for prokaryotes  Does not require a mate  Is asexual reproduction  Does not increase the variation in a population No part of this material may be reproduced in any form without asking permission. This is for the exclusive use of St Louis Review Center.

Mitosis and Meiosis Compared

Karyotypes A karyotype is the characteristic chromosome complement of a eukaryote species.

Central GROWTH

APICAL GROWTH

Meiosis

HUMAN MALE

 Gametes = sex cells (eggs, sperm)  Homologous chromosomes = paired chromosomes (maternal and paternal) that have the same genes  Haploid = Having only one copy of each chromosome (as opposed to diploid, which has two copies of each) Meiosis I Produces Diploid Cells

HUMAN FEMALE Heredity Law of Segregation • Organisms inherit two copies of each gene, one from each parent • Organisms donate only one copy of each gene in their gametes • Two copies of each gene segregate, or separate, during gamete formation Segregation and Inheritance

Meiosis II Produces Haploid Cells

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In pea plants: The allele for violet flower color (B) is dominant The allele for white flower color (b) is recessive CF - An Autosomal Recessive Trait

Sex-Linked Traits

Because X-linked traits are traits that are predominant sex-linked traits, for our purposes: Sex-linked = X-linked

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Blood-Type Genetics Blood types are the result of the presence (or absence) of antigens (molecules) on the surface of the individual’s red blood cells. These fall into two groups:  A, B, O blood type  Rh factor  The gene for antigen A and the gene for antigen B are CODOMINANT.  Both traits are expressed completely when the gene for A is inherited from one parent and the gene for B is inherited from the other parent.

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Dihybrid Crosses • The inheritance pattern of one trait will not affect the inheritance pattern of another • Independent assortment occurs during meiosis • For a single human gamete, the possible ways chromosomes may assort is astounding: 223 = 8,388,608 possible combinations

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DNA: Structure and Replication

Transformation: Robert Griffith (1928)

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Translation Translation is the process by which protein is made from an mRNA template

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A mutation is a change in an organism’s DNA – Silent mutations are changes that do not result in a change to the organisms phenotype – Mutations that occur in germ cells (sperm, eggs) are passed on to offspring – Mutations in somatic (body) cells may be harmless, or may result in disease such as cancer

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British naturalist Charles Darwin (1809 –1882) “The theory of Natural Selection”

Lamarck and Darwin French naturalist Jean-Baptiste de Lamarck (1744-1829) “The theory of Acquired Traits”

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Gene Pool • All of the genes of a population of organisms –

Organisms that are the most successful at reproducing contribute most to the gene pool

Evolution • Any change in the frequency of any allele within a gene pool – Populations undergo evolution – Individuals do not undergo evolution Factors Affecting the Allele Frequency • Mutation – Especially important for organisms with short generation times • Migration – Movement of organisms into or out of the population • Genetic Drift – Random change in allele frequencies – Occurs mostly in small, isolated populations • Selection – Environmental pressures – Competition – Climate change • Nonrandom mating – Preferences in selection of a mating partner

• Speciation is the evolution of new species through time • Speciation occurs most rapidly in a small population Mechanisms of Speciation • Artificial Speciation – New species have been developed by man • Intentional mutations • Cross breeding • Genetic engineering • Natural Speciation by Isolation of Small Populations – Geographical Isolation • Geographical barriers separate two populations • Mountain ranges • Deep canyons • Bodies of water – Ecological Isolation • Organisms of two populations require different habitats

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Behavioral Isolation – Changes in habits that identify one population with another • Mating rituals • Methods of communication Seasonal Isolation – Reproductive cycles do not coincide • Plants that flower at different times • Animals that mate or nest build at different times Mechanical Isolation – Physical characteristics that keep organisms from interbreeding • Difference in size • Difference in reproductive anatomy • Inability of sperm to penetrate the egg

The Hardy-Weinberg Equilibrium Hardy-Weinberg Equilibrium “Allele and genotype frequencies in a population tend to remain constant in the absence of disturbing influences” Disturbing influences: non-random mating mutations selection limited population size random genetic drift gene flow migration In Reality… The conditions for Hardy-Weinberg equilibrium are never met in nature.  There are always some disturbing influences in nature  Hardy-Weinberg equilibrium can be approximated in the lab  It has usefulness as a model for studying real populations

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Photosynthetic organisms – Capture energy from sunlight, CO2 and H2O – Most producers are photosynthetic • Chemosynthetic organisms – Capture energy from chemical compounds in the surroundings • Herbivores – Eat only plants and fungi • Omnivores – Eat both plants/fungi and animals • Carnivores – Eat only animals • Detrivores – Eat dead organic matter • Decomposers – Break down organic matter into simpler compounds • Trophic Structures – Manner in which energy moves through an ecosystem – Each ecosystem has its own unique trophic structure • Producers – Autotrophs (Photosynthesizers, Chemosynthetic organisms) • Primary consumers – Herbivores and omnivores that eat producers • Secondary consumers – Carnivores and omnivores that eat herbivores • Tertiary consumers – Carnivore eats another carnivore • Decomposers and Detrivores – Consume decaying producers and consumers Food Chain  Energy is lost in each step up a food chain  Only 10 percent of the energy from one level on the food chain is available to the next level Food Webs • Many consumers and decomposers have more than one food source • Movement of energy occurs in complex webs rather than in simple chains Energy pyramids show the reduction of available energy at each higher trophic level •

ECOLOGY • the study of the interactions among living things and their surroundings – Eco: (from Greek oikos, meaning “house”) • Organism – An individual living thing • Population – A group of the same species living in the same area • • Community – A group of different species that live together in one area • Ecosystem • – All of the organisms (biotic) as well as the climate, soil, water, rocks and other nonliving things • (abiotic) in a given area • Biome – A major regional or global community of organisms, usually characterized by the climate conditions and plant communities of the region

Producers must comprise most of the mass of the biotic part of an ecosystem – This is the ONLY place where energy (solar) enters the ecosystem Energy is always lost in the form of heat, so energy transfers are no more than 10% efficient Each trophic level must be supported by a 10/1 energy ratio below it

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Interactions in Ecosystems

Habitat • All of the biotic and abiotic factors in the area where an organism lives Ecological niche • All of the physical, chemical, and biological factors that a species needs to survive, stay healthy, and reproduce – Food – Abiotic conditions – Behavior Competitive Exclusion • When two species are competing for the same resources, one species will be better suited to the niche, and the other species will be pushed into another niche or become extinct • Invasive species may outcompete organisms that are native to a particular region Predation • The process by which one species captures and feeds upon another – Heterotrophs can prey on autotrophs and other heterotrophs • Prey outnumber predators • Increasing numbers of prey promote increases in predator populations Symbiosis • A close ecological relationship between two or more organisms of different species that live in direct contact with one another – Mutualism – Commensalism – Parasitism Mutualism • An interspecies interaction in which both species benefit – Flowers and pollinating insects – Humans and intestinal E. coli – Clown fish and anemones No part of this material may be reproduced in any form without asking permission. This is for the exclusive use of St Louis Review Center.

Commensalism • A relationship between two organisms in which one receives an ecological benefit from another, while the other neither benefits or is harmed • Many ecologists believe that commensalism is rare, and that most such relationships are probably subtle mutualism or parasitism Parasitism • A relationship in which one species benefits while the other is harmed. • Many parasites have complex lifecycles involving more than one host

Changes in Population Size • Growth factors – Immigration: individuals moving into a population – Births • Shrinking factors – Emigration: individuals moving out of a population – Deaths

Populations and Growth Population Dispersion

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Succession

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Deserts can be cold or hot – Antarctica is a cold desert • Nocturnal animal life in hot deserts • Plants are well adapted to short water supply Temperate Deciduous Forests • Deciduous forests of mid-latitude regions • Cold winters and hot summers • Abundant rain and snowfall • Wide variety of animal life Temperate Rain Forests • Cold winters and hot summers • Abundant rain and snowfall • Conifers (redwood, firs, pines, spruce) retain their needles. – Needles conserve water in dry summer and shed snow in cold winter • Wide variety of animal life Taiga (Boreal Forests) • Coniferous (Evergreen) Forests • Found at high elevations and/or far northern latitudes • Snow accounts for most of the precipitation • Animals are adapted to long, cold winters Tundra • Areas with continuously frozen ground (permafrost) • Near polar regions • Small plants limited by frozen soil and prolonged dark season • Animals adapted to extreme cold; birds often migrate •

Regions of the world with similar physical environments Named for most conspicuous types of vegetation Climate factors  Rainfall (precipitation)  Temperature  Altitude  Latitude • Boundaries are indistinct Six Major Biomes • Tropical Rain Forests • Grassland – Tropical/Subtropical Grassland – Temperate Grassland • Desert • Temperate – Temperate Deciduous Forest – Temperate Rain Forest • Taiga • Tundra Tropical rain Forests • Equatorial lowlands • Constant temperature and abundant rainfall all year long • Many arboreal animals • Few terrestrial animals Tropical and Subtropical Grassland • Warm temperatures throughout the year • Well defined dry season and rainy season • Large herbivores • High grasses • Scattered trees and shrubs Temperate Grassland • Hot, humid summer and cold winter • Precipitation as winter snow and heavy spring and summer rain • Short and tall grasses; trees found only near streams • Wide variety of animal life – Large herbivores – Smaller animals build burrows Deserts • Identified by lack of precipitation • • •

Invasive Species  Introduced species: any organism that was brought to an ecosystem as the result of human actions  Invasive species: A species that takes advantage of an unoccupied niche, or that successfully out-competes native species ----• Bioaccumulation is the process by which substances not readily broken down or excreted can build up and be stored in living tissue (usually in fatty tissue.) • Biomagnification, also known as bioamplification, is the process by which substances become more concentrated in the bodies of consumers as one moves up the food chain (trophic levels). FACTORS AFFECTING BIOACCUMULATION 1. Some chemicals bind to specific sites in the body, particularly in fat tissue, prolonging their stay 2. Chemicals that are immediately eliminated do not bioaccumulate. 3. Duration of exposure is also a factor in bioaccumulation. Most exposures to chemicals in the environment vary continually in concentration and duration, sometimes including periods of no exposure. 4. Bioaccumulation varies between individual organisms as well as between species. Large, fat, long-lived individuals or species with low rates of metabolism or excretion of a chemical will bioaccumulate more than small, thin, short-lived organisms. -Thus, an old lake trout may bioaccumulate much more than a young bluegill in the same lake.

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