Bio Exam 1

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10 Unifying Themes in Biology

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Evolution, Emergent Properties, Interaction with the Environment, Structure/Function, the Cell, Heritable Information (DNA), Regulation/Homeostasis, Unity and Diversity, Scientific Inquiry, Science Tech & Society

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Evolution

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Change through time. Natural selection=non random agent of change. Random forms of change= genetic drift, mutations, and gene flow. The organizing paradigm of biology. Charles Darwin introduced natural selection in the Origin of Species suggesting that individuals would eventually die off if not equipped to survive in certain environments, meaning eventually the better/stronger are breeding with the better/strong.

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Emergent Properties

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Molecule, organelle, cell, tissues, organ, organisms, populations, communities, ecosystems. Arrangement and interaction of parts as complexity increases.

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Interaction with the Environment

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Producers extract energy from the environment (like plants), consumers obtain energy and nutrients by eating other organisms. Decomposers are consumers that obtain nutrients from dead organisms and organic wastes

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STRUCTURE/FUNCTION

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Form fits function. Guide to anatomy of life at all its structural levels. Birds wing bones have honeycomb interior structure that is strong yet light weight. Shape of bird's wing bones and structure of their bones make flight possible. The mitochondrion has a structure with many folds to increase its surface area in order to facilitate higher production of ATP

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The Cell

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An organisms basic unit of structure and function. The activities of an organism are all based on the activities of cells. Every cell has DNA, genetic information.

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Heritable Information (DNA)

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DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring. Genes encode information to build other molecules in the cell, especially proteins.

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Regulation/Homeostasis

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In feedback regulation, out put or product of a process regulates the process itself by either inhibiting an enzyme or stimulating the production of that enzyme.

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Unity and Diversity

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Enormous variety of life. Prokaryotes are composed of bacteria and archea(found in extreme conditions) groups. The DNA in prokaryotes is not separated from the rest of the cell by the nuclear envelope. Bacteria are the most diverse and widespread of the prokaryotes. Everything that isn't archea or bacteria is a eukaryote. Eukaryia is divided into polyphyletic protist, fungi, plantae and anamalia groups. Many similarities between organisms evident on all levels of biological hierarchy.

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Scientific Inquiry

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(Be able to diagram scientific method)

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Science, Technology, and Society

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Science is rarely perfectly objective, but observations and experiments are expected to be repeatable and hypotheses testable and falsifiable.

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What is Science?

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Observation, identification, description, experimental investigation, and theoretical explanation of phenomena. Questions in science limited by the scientific method, some questions can not be directly or indirectly observed

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What is Biology?

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Scientific study of life. Application of mathematics, chemistry, and physics to living systems. Molecular biologists use chem, plant physiologist may use physics in their studies of water pressure in plants. Microbiology, physiology (plants), zoology (animals), mycology (fungi), astrobiology (study of possible life on other planets)

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Observations

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Initial experience that leads to a question. Collection of preliminary data

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Hypothesis

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Pattern or generalization. A tentative causal explanation. Need in depth observations in order to make

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Predictions

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Based on hypothesis, tests are conducted to see if they are accurate. One hypothesis can have multiple predictions

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Test

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A good test includes a control group (tests carried out in "normal" conditions to compare the results to) an independent variable (the variable that is changed in the experiment) and the resulting dependent variable (what is measured in the experiment and what is predicted to change) In addition to control groups treatment groups are necessary in order to manipulate the independent variable.

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Results

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Either expected or unexpected. If expected results occur, then the method returns to the predictions. If unexpected results occur, the method returns to the hypothesis

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Why start with Chemistry in a Biology Class?

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Biology is the study of life at many levels. Macroscopy (ecosystems) and microscopy (cells) have many chemicals and chemical properties

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Primary Elements in Living Organisms

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Four main elements: oxygen, carbon, hydrogen, nitrogen. Remaining notable elements: phosphorus, sulfur, calcium, potassium

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Electrons Have the Energy--how does this help explain the four different bonds: Covalent, Ionic, Hydrogen, and Van der Waals?

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Covalent bonds: Atoms share electrons. Carbon-hydrogen bonds are non polar and store much energy. Can share 1, 2, or 3 atoms with another atom. Ionic bonds: Electrons are transferred, either creating a negative charge if gained or a positive charge if lost. Positive and negative charged ions=ionic bond. Hydrogen bonds: Weak bonds between atom with slight positive charge and an atom with slight negative charge. Van der Waals: Weak interactions between nonpolar covalent bonds. Dipole moment created when positive and negative exist on 2 different ends, creating polar interaction for a femtosecond. At any given moment electrons can be scattered asymmetrically creating transient positive and negative charges allowing the molecules to adhere to one another

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What is the significance of polarity in covalent bonds?

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The significance of polar covalent bonds is one atoms exerts more of a pull on an electron resulting in a partial charge separation and can lead to hydrogen bonding

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Water's life supporting qualities

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Cohesion, Temperature Moderation, Ice Floats, a great Solvent

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Cohesion

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Water molecules stick closely together as a result of hydrogen bonding, making water more structured than other liquids. Cohesion contributes to the transport of water and dissolved nutrients against gravity in plants. Water is pushed and pulled through plants by evaporating through the leaf and hydrogen bonds cause water molecules leaving through the veins to tug on molecules from farther down and the upward pull is transmitted through the water conducting cells all the way to the roots. Also leads to high surface tension due to H-bonds

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Temperature Moderation

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Water is excellent at regulating temperature. Earth's water supply causes temperature to stay within limits that permit life. A large body of water can absorb heat and keep coastal area temperatures mild and predictable. Evaporative cooling removes heat from the earth and from organisms

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Ice Floats

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Density of solid less than the density of the liquid. If ice sunk, lakes would freeze solid. Insulates liquid below it so life can exist underneath it. Water is most dense at 4 degrees celsius.

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Solvent

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Versatile solvent due to its polarity. Ions and polar molecules will readily dissolve in water as it forms spheres of hydration or hydrations shells around the molecule

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High Specific Heat

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Water has very high specific heat due to hydrogen bonding. Heat must be absorbed to break hydrogen bonds and is released when hydrogen bonds form. Water does not change temperature easily because investment of heat first has to break hydrogen bonds before increasing kinetic energy of the molecules

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High Heat of Vaporization

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When molecules move fast enough they overcome attractions of other molecules in the liquid and evaporate. Heating liquid increases rate of evaporation.

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Sphere of Hydration

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When water begins to interact with a solute and coats it with water molecules. In this way large molecules like proteins can dissolve in water if they have ionic polar regions which attract the water molecules

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pH Scale

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pH is the concentration of H+ ions in a solution. The greater the H+ the lower the pH. Interior of living cells have a pH of 7. 0=acidic, 7=neutral, 14=basic

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Carbon Diversity

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Carbon has molecular diversity because of its length, branching and ability to form double and triple bonds varying in length and shape.

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Ring and Linear Structures

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Linear molecules diffuse across membranes easier than bulkier ring structures. In aqueous solutions, monosaccharides form rings.

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Isomers

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Same chemical formula, different structures. Geometric isomers cis= same side. trans=opposite sides. Hands are isomers

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Macromolecules

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Carbohydrates, lipids, nucleotides, proteins

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Primary Functions of Lipids

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Energy storage, coatings, membrane structure

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Monosaccharides

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One sugar unit, water soluble, sweet taste.

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Disaccharides

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Two monosaccharides joined by glycosidic linkages.

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Lactose

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glucose+galactose, present in milk

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Sucrose

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glucose+fructose, transport sugar used by plants, harvested by humans for food

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Maltose

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glucose+glucose, present in germinating seeds

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Polysaccharides

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Hundreds or thousands of monosaccharides in straight or branched chains.

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Cellulose

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Structural material made of glucose, what cell walls are made of

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Chitin

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Structural material in arthropod exoskeletons

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Starch

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Plant energy storage

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Glycogen

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Energy storage in muscles and liver

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Four Important Polysaccharides

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Glycogen, chitin, cellulose, starch

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Glycosidic Linkage

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Monosaccharides joined by glycosidic linkage

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Cellulose/Starch differences based on glycosidic linkage

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Alpha glucose particles, OH group on bottom of ring
Beta glucose particles, OH group on top of ring
Starch is made of only alpha glucose particles (all on one side)(cis)
Cellulose alternating alpha and beta glucose particles (trans)

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Dehydration/Condensation

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Removes water molecule forming a new bond, creating polymers by joining monomers together

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Hydrolysis/Cleavage

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One molecule splits into two molecules with the addition of water

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Functional Groups of Carbohydrates

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aldehyde, ketone, one or more hydroxyl

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Monomers, polymers of Carbohydrates

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monosaccharides and polysaccharides

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Functional Groups of Lipids

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Hydrocarbon chain with hydroxyl group at one end

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Monomers/polymers of Lipids

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Fatty acids and glycerols

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Two different monomers required for a Triglyceride

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Steric acid x2, oleic acid x1, and glycerol

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Energy associated with hydrocarbons

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Lipids=rich source of energy, much more than carbohydrates

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Fats

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Saturated fatty acids, solid at room temperature. Have no double bonds in their fatty acid tails

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Oils

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Unsaturated fatty acids, liquid at room temperature due to one or more double bonds in between the carbons in the fatty acids causing kinks in the tails

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Phospholipids Structure and Function

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Two fatty acids, a glycerol, and a phosphate. Main component of membranes arranged in bilayers.
Hydrophilic head=glycerol
Hydrophobic tail=phosphate and fatty acid tail

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Sterols

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Back bone of four carbon rings and no fatty acid tails

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Derivatives of sterol

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Cholesterol, found in animal cells.
Sterol can be modified to form sex hormones (estrogen and testosterone) as well as vitamin D

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Primary Function of Nucleotides

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Chemical messengers, energy carriers (ATP), electron transport

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Functional groups of Nucleotides

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Phosphate group, five carbon sugar, nitrogen containing base

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Functions of parts of nucleotides

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Five carbon sugar and phosphate group provide the backbone of the DNA double helix while the nitrogen containing bases code for amino acids

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Importance of ATP to living organisms?

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An energy carrier

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Function NADP+, NAD+, and FAD+ to oxidation/reduction reactions

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Serve as electron transporters

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DNA>RNA>Protein

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RNA copies the DNA and transports it outside the nucleus to a ribosome which creates a protein

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Types of proteins

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Structural, Storage, Transport, Hormonal, Receptor, Contractile, Defensive, Enzymes

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Structural Proteins

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Provide support. Structures such as collagen and elastin are fibrous framework for animal connective tissue. Keratin is protein of hair and horns and other skin appendages

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Storage Proteins

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Storage of amino acids. Ovalbumin protein in egg whites used as amino acid source. Plants have storage proteins in their seeds

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Transport Proteins

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Transport substances. Hemoglobin is iron containing protein transports oxygen. Other proteins transport molecules across membranes

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Hormonal Proteins

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Coordination of an organism's activities. Insulin, created by pancreas, regulates concentration of sugar in the blood

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Receptor Proteins

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Response of a cell to chemical stimuli. Receptors built into the membrane of nerve cells that detect chemical signals released by other nerve cells

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Contractile Proteins

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Movement. Actin and myosin are responsible for movement of muscles. Other proteins are responsible for movement of organelles, these are cilia and flagella.

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Defensive Proteins

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Protect against disease. Antibodies combat bacteria and viruses

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Enzymes

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Acceleration of chemical reactions. Digestive enzymes catalyze the hydrolysis of polymers in food

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Five Major classes of enzyme function

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Dehydration/condensation reactions, hydrolysis and cleavage reactions (2 most important), functional group transfer, electron transfer, rearrangement (internal bonds are rearranged to convert one type of molecule to another)

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Amino Acid Structure

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Amino acid= An amine group, and alpha carbon, and R group, a Hydrogen, and a carboxyl group

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Why "amino" and "acid"

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amino because of the amine group, acid due to the carboxyl group

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General classes of amino acids based on presence/absence of functional groups

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Nonpolar (non polar side chains (R groups) dont like to interact with polars), electrically charged (Both acidic and basic), polar (OH groups, carbonyl, polar add ons)

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Peptide Bond

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Dehydration to combine acids. Peptides are a result o ribosome action, RRNA synthesized from N terminus (amino end) to the C terminus (carboxyl end)

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Primary Structure

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Ordered sequences of amino acids linked by peptide bonds to form polypeptide chains

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Secondary Structure

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Bending and hydrogen bonding of polypeptide back bone to form repeating patterns

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Alpha helices

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secondary structure that occurs when the polypeptide chain forms a helical coil alpha keratin found in hair

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Beta Sheets

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Sheet like array of polypeptide chains (flat layers of protein) beta keratin found in nails

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Tertiary Structure

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Folding due to bonding among R groups along polypeptide chain. Bonds such as hydrogen bond, covalent bond, ionic bond, and hydrophilic interactions

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Quaternary Structure (Hemoglobin)

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When two or more polypeptide chains combine. Hemoglobin is an example of four interacting polypeptide chains that form a globular protein that coordinate the position of a heme.

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Quaternary Structure (Sickle-Cell Anemia)

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Sickle cell anemia occurs because of single point mutation in hemoglobin gene. One amino acid that is altered, caused massive change in secondary and tertiary structure thus resulting in rope like sticks in the cells instead of globs

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Quaternary Structure (Collagen)

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A complex fibrous protein. Collagen helps hold cells together, to each other. Bonding in collagen highly sensitive to UV rays. The ropes that hold the cells together fall apart, creating wrinkles.

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Denaturation/Renaturation

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High temperatures and pH may cause a protein to lose its normal 3D shape (A cooked egg, cooking meat, etc.) Normal functioning is lost and can be irreversible. Proteins are easier to digest if cooked and denatured

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Fluid Mosaic Model

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The plasma membrane is a fluid mosaic. The membrane is a fluid structure and a mosaic of proteins are embedded in its structure

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The Fluidity of Membranes

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Phospholipids can move within the fluid membrane bilayer. Lateral movement common, transverse movement very rare. Temperature decrease=fluidity decrease. Unsaturated tails=resistance to solidification

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Effect of Cholesterol on Animal cell membranes

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Stabilizes the fluidity of membranes. At higher temps restrains movement of phospholipids, at lower temps prevents tight packing of phospholipids

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Integral and Peripheral Proteins

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Integral proteins penetrate hydrophilic core
peripheral proteins bond to the surface of the membrane. THE ALPHA HELIX TURNS R GROUP IN, ALLOWING HYDROPHOBIC TENDENCIES SO PROTEIN CAN SPAN HYDROPHILIC REGION OF MEMBRANE

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Passive Diffusion

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Solids and solutions diffused across membranes moving down the concentration gradient

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Active Diffusion

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Pumped against the gradient, (uses ATP to do so)

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Enzymes (membrane proteins)

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Anchored in membrane, found with mitochondria/chloroplasts, responsible for transferring energy, like in an oxidation reduction reaction of mitochondrial respiration

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Signal transduction

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Relays information from external signal molecule to the inside of the cell. Signal molecule=ligand. If ligand binds, causes protein to change its shape, transducting signal through membrane

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cell-cell recognition

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Glygoprotein serves as an identification tag that can be read by membrane proteins on another cell.

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Intercellular Joining of cells

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Gap and tight junctions. Various types of junctions in which cells bind together very strongly in cases such as the lining of your stomach

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Attachment to the cytoskeleton

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Proteins that attach to the extracellular matrix to stabilize cell shape and proximity to neighboring cells. Binds material on the inside of the cell to material on the outside of the cell

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Selective Permeability based on phospholipid structure

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O2 can diffuse all by itself, small and nonpolar. Water is attracted to hydrophilic heads and repelled by hydrophobic tails. methane (CH4) diffuses by itself, wich is why it can poison easily. C2H12O6 can not diffuse by itself because it is big and has polarity. Na+ and Cl- have charges so they are repelled by the hydrophobic region in the membrane. H2o gets across membrane with aqua purins. Regulate flow of water across membranes

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Passive Transport (diffusion)

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Diffusion of substances across membrane without the use of energy. Diffuse until equal numbers on both sides. Diffusion=tendency for molecules to spread out evenly in available space. Occurs down a concentration gradient across a permeable membrane

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Osmosis

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Diffusion of water across a selectively permeable membrane. Occurs from areas of high water concentration (low solute) to areas of low water concentration (high solute)

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Tonicity

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The ability of a solution to gain or lose water. Isotonic=no net movement of water in or outside the cell.(normal animal cell, flaccid plant cell) Solute the same inside and outside the cell. Hypertonic=Solute is greater than inside the cell, net movement of water outside the cell (shriveled animal cell, plasmolyzed plant cell) Hypotonic=Solute is lower than inside the cell, net movement of water into cell (lysed animal cell, happy turgid plant cell)

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Turgor in Plant cells

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Plant cells in hypotonic solution swell and push out against their cell walls creating pressure against each other because they are overfilled with water, this creates turgor pressure. If plants are isotonic solution the pressure will be lost and the plant will wilt. Plants die in hypertonic solution as the water flows out of their cells.

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Facilitated Diffusion

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Passive diffusion of solute. Protein provides path for it to move along concentration gradient. Channel proteins provide corridors for specific molecules

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Active Transport

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Use of energy to move solvents, requires ATP. Moves solutes against their concentration gradients. Allows cells to maintain solute concentrations that differ from their surroundings.

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Effect on Gradients

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Ion pumps maintain a membrane potential across a membrane. Membrane potential=quantitative difference in charge across a membrane(voltage). Created by differences in distribution of positive and negative ions. Ions move across gradient in response to the electro chemical gradient.

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Sodium Potassium pump

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A form of active transport that can bind 3 ions, moving against concentration gradient.

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Electrogenic pump

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Transport proteins generate voltage across membrane. Proton pump=major electrogenic pump in plants, fungi, and bacteria. The sodium potassium pump=main electrogenic pump in animals

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Cotransport

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Active transport of solute indirectly drives transport of another solute. Plants use gradient of hydrogen ions generated by protein pumps to transport substances into cells. (Piggy backs on energy of other molecules moving)