Bio Exam #1 PDF

What is life? (Chapter 1) Describe the common characteristics of living things - Made up of a common set of chemicals (proteins, lipids, carbohydrates, nucleic acids) - Cells enclosed by a plasma membrane - Molecules from environment → new biomolecules - Energy from environment → biologi...

What is life? (Chapter 1) Describe the common characteristics of living things - Made up of a common set of chemicals (proteins, lipids, carbohydrates, nucleic acids) - Cells enclosed by a plasma membrane - Molecules from environment → new biomolecules - Energy from environment → biological work (energy from light) - Universal genetic code specifies proteins - Similar fundamental set of genes that replicate - Exist in populations that evolve - Self regulate internal environment (homeostasis) Describe how we know all living things are genetically related - Life has a common ancestry - Life is made up of living organisms - Living organisms are all descended from a common origin - Life has striking similarities across gene sequences Atomic structure and bonding (Chapter 2) Correctly assign electrons to their electron shells when given the atomic number of an element - Number of protons and electrons is the same (PE) - Atomic number = number of protons and electrons (found in top left corner) - Mass number = the number with decimals - Neutrons = mass number - atomic number (protons and electrons) - First shell holds 2, second holds 8 Define isotopes and their significance - Isotopes: forms of a element with different numbers of neutrons and thus different mass numbers - Used to find the weighted average mass Correctly predict how many covalent bonds an atom will typically form to become stable (i.e., be able to apply the octet rule) - Octet rule: tendency of atoms to form stable molecules (2 or more atoms linked together) with 8 electrons in outermost shell - Covalent bonds can be shown as electrons connecting an atom Compare polar covalent bonds and nonpolar covalent bonds - Covalent bonds: atoms share one or more pairs of electrons, so that their outer shell is filled - Occur between two nonmetals - Does not have metal element (Small section to the right on periodic table + Hydrogen - Non polar covalent bond: equal sharing of electrons in the outermost shell of atoms - Atoms of the same element - Atoms with similar electronegativities - Polar covalent bonds: unequal sharing of electrons on the outermost shell of atoms - Difference in electronegativity - Water is polar Define ion, be able to recognize one when given examples, and explain how one is formed from a neutral atom - Ions: atoms or molecules that have gained or lost one or more electrons (+ or –) giving them a net electrical charge - Cations: These are ions with a positive charge, meaning they have lost one or more electrons. For example, a sodium ion (Na⁺) has lost one electron - Anions: These are ions with a negative charge, meaning they have gained one or more electrons. For example, a chloride ion (Cl⁻) has gained one electron Describe how ionic bonds are formed - Ionic bond: electrical attraction between ions bearing opposite charges - Metal + nonmetal - Weaker than covalent bonds - Most elements Explain why salt dissolves in water - The polar water is interacting with + and – ions in the salt, breaking the ionic bonds Describe how hydrogen bonds are formed. Sketch potential hydrogen bonds between a molecule and identical molecules or molecules of water - Hydrogen bonds: forms between a hydrogen atom, which is covalently bonded to a highly electronegative atom (such as nitrogen, oxygen, or fluorine), and another electronegative atom nearby - H must be covalently bonded with an F, O, N (H likes to have FON) - Weaker that ionic bonds Compare the relative strengths of covalent bonds, ionic bonds, hydrogen bonds, and van der Waals forces - Strongest to weakest: covalent, ionic, hydrogen, van der Waals forces Define hydrophilic and hydrophobic and be able to recognize molecules that fit into these categories - Hydrophilic: water ‘loving’ molecules with polar covalent bonds interact with water - Often polar - Hydrophobic: water ‘fearing’ molecules with non covalent bonds show greater attraction to one another than to water Describe hydrophobic interactions - Hydrophobic interactions: water forces hydrophobic groups together The chemistry of water (Chapter 2) List some of the properties that water has due to its hydrogen bonds - High heat of vaporization: sweating uses evaporation of water to cool the body - Surface tension: water molecules stick to one another and help prevent certain creatures from sinking - Cohesion: water’s cohesive strength helps it to flow from the roots to the leaves in a tree Explain why ice floats and why this is beneficial to aquatic organisms - Hydrogen bonds → ice floats - Density differences between ice and water due to H-bonding (help aquatic organisms) Describe what the pH scale measures, including how it changes when the concentration of H+ ions changes - pH scale: measures how acidic or basic a solution is - When the concentration of H⁺ ions increases, the solution becomes more acidic - Low pH = a strong acid - High pH = strong base Building organic molecules (Chapter 3.1) List the four types of macromolecules found in cells and the monomers or building blocks from which they are constructed Monomers: smaller molecules/building blocks Polymers: larger molecules/composed of monomers - Monomer: Amino acids (20 different types) → Polymer: Proteins - Monomer: Monosaccharides → Polymer: Carbohydrates - Monomer: Nucleotides (4 different types) → Polymer: Nucleic acids (DNA & RNA) - Monomer: Lipid monomers (fatty acid & glycerol) → Polymer: Lipids Be familiar with the important functional group categories and their properties (e.g., how do they interact with water?) Functional groups: groups of atoms that give biological molecules their chemical properties (polar, acidic, basic, charged) - Polar groups: hydroxyl group (-OH), carbonyl group (C=O), amino group (-NH₂), carboxyl group (-COOH), phosphate group (-PO₄³⁻) - Acidic groups: carboxyl group (-COOH), phenol group (-OH attached to an aromatic ring), sulfhydryl group (-SH), phosphate group (-PO₄³⁻), sulfonic acid group (-SO₃H) - Donate a proton (H+) - Basic groups: amino group (-NH₂) - Accept protons (H+) - Functional group: (-SH) - Disulfide bridge Define and recognize structural, cis and trans, and optical isomers - Isomers: molecules with the same chemical formula, but their atoms are arranged differently - Structural isomers: differ in how their atoms are joined together - cis and trans Isomers: differ in the atom orientation around a double bond (cis = same, trans = different) - Optical isomers occur when a carbon atom has four different atoms or groups of atoms attached to it (mirror image) Describe condensation (dehydration) reactions - Condensation (Dehydration) Reactions: formation of covalent bonds between monomers via release of water - Water is removed in condensation - A covalent bond forms between monomers Describe the events that occur during a hydrolysis reaction - Polymers are broken down into monomers in hydrolysis reactions (hydro = “water”; lysis = “break”) - Water is added in hydrolysis - A covalent bond between monomers is broken List the important functions of proteins, carbohydrates, and lipids - Proteins: enzymes, structural support, transport, regulation, storage - Carbohydrates: - Source of stored energy - Transport stored energy - Carbon skeletons for new molecules - Extracellular assemblies that provide structure - Lipids: - Fats and oils store energy (more than carbohydrates) - Phospholipids: structural role in cell membranes - Carotenoids and chlorophylls capture light energy in plants - Steroids and modified fatty acids: hormones and vitamins - Animal fat: thermal insulation - Lipid coating around nerves provides electrical insulation - Oil and wax on skin, fur, and feathers repel water Proteins (Chapter 3.2) Be able to identify an amino acid and point out its amino, carboxyl, and R groups, as well as its α (alpha) carbon - Amino group - Carboxyl group - R group - Alpha carbon Be able to describe the properties of amino acids based on their R groups (charged + or –, polar, nonpolar, etc.) - Hydrophilic (10) - Ionized (5): + = basic, – = acidic - Acidic (2) - Basic (3) - Polar (5) - Hydrophobic; nonpolar (7): likely to cluster on the interior of a protein - Special cases (3): cysteine, glycine, proline Explain/recognize how a peptide bond is formed by a condensation reaction - The covalent bonds connecting amino acids are called peptide bonds (–N–C–C–) Identify the peptide bonds, N terminus, and C terminus of a polypeptide - N terminus: the amino group of the FIRST amino acid in a polypeptide - C terminus: carboxyl group of the LAST amino acid in a polypeptide Explain why a protein’s shape is crucial to its function Peptide Bond = the covalent bonds connecting amino acids (-N-C-C-) are peptides bonds - A peptide bond is formed by a condensation reaction when carboxyl group of one amino acids reacts with amino acid group of another amino acid Describe what is meant by primary, secondary, tertiary, and quaternary structures, and identify the types of attractive forces that are important in each case - Primary: sequence of amino acids in a polypeptide chain, most stable - Secondary: polypeptide chains may form α (alpha) helix and β pleated sheet, nothing but hydrogen bonds - Tertiary: (folding) determined by interactions of R-groups via: aggregation of hydrophobic side chains, disulfide bridges, van der Waals forces, hydrogen bonds, ionic bonds (salt bridges) - Quaternary: determined by interactions of a protein’s subunits (hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces), subunits are individual polypeptides, not all proteins have quaternary structure Describe and identify an α (alpha) helix and a β (beta) pleated sheet. - α (alpha) helix: Every N–H hydrogen bonded to C=O of the amino acid located 3–4 residues earlier in sequence - Right-handed coil - β (beta) pleated sheet: N–H hydrogen bonded to C=O of an amino acid in an adjacent chain Describe disulfide bridges/bonds and the amino acid involved in these covalent reactions. Disulfide Bridge = Covalent bond between sulfur and 2 cysteine amino acids Identify environmental factors that affect protein structure (and thus their function). - Temperature increases - pH - High concentrations of polar or nonpolar substances - Structure changes often reversible, but not always Recognize noncovalent interactions (e.g., hydrogen bonds) between proteins. - Van Der Waals and Hydrophobic Carbohydrates (Chapter 3.3) Describe the general structure of carbohydrates - Large group of molecules with similar atomic compositions but differ in size, chemical properties, and biological functions - Typical formula: Cm(H2O1)n - Monomers can exist as straight chains or ring forms (they’re rings when in water) Be able to recognize a monosaccharide - Monosaccharides — simple sugars (ends with ose) - Vary in number of carbons - Often structural isomers Recognize glucose in its ring form (and α vs. β configuration) α vs. β Glycosidic Bonds - α bond on opposite side of –CH2OH group (HOH) - β bond on same side as –CH2OH group (OHH) Recognize glycosidic bonds (formed by a condensation reaction) and explain the significance of an α-glycosidic bond vs. a β-glycosidic bond (e.g., as in maltose vs. cellobiose) Define oligosaccharides and describe important functions they serve - Contain 3–20 monosaccharides, sometimes with additional functional groups - Often covalently bonded to cell-surface proteins (glycoproteins) or lipids (glycolipids) as recognition signals - Human blood groups are determined by oligosaccharides on red blood cells - Ex: plants, lactose Define polysaccharides and give examples - Up to thousands of monosaccharides connected by glycosidic bonds - Can be branched - Ex: starch, cellulose — potatoes Recognize the structures and know the properties and functions of starch, glycogen, and cellulose Starch: - H2O soluble - Major energy storage in plants α-1,4 and α-1,6 glycosidic bonds Glycogen: - H2O insoluble - Major energy storage in animals (stored in liver & muscle) α-1,4 and α-1,6 glycosidic bonds Cellulose: - Very compacted, parallel strands; H2O insoluble - Most abundant organic molecule on Earth! structural component in plants β-1,4 glycosidic bonds Lipids (Chapter 3.4) Explain why lipids are hydrophobic and why they are not hydrophilic - Made up of nonpolar hydrocarbon chains, lack charge, nothing to stick to, does not interact favorably with water - Fats don't mix with water (salad dressing separates) Explain how triglycerides are constructed from glycerol and fatty acids via three condensation reactions that form three ester linkages/bonds - Fats and oils = triglycerides - 3 condensation reactions → 3 ester linkages - Ester linkage: covalent bond between carboxyl group of fatty acid and a hydroxyl group of glycerol - Structure: - 1 Glycerol: has 3 –OH groups  - 3 Fatty acids: nonpolar hydrocarbon chains with a polar carboxyl group at end Describe what makes a fatty acid saturated or unsaturated - Saturated fatty acids - No double bonds - The carbons are “saturated” with hydrogens - Single bonds - Unsaturated fatty acids - One or more double bonds in carbon chain - Double bonds cause kinks in the chain - Monounsaturated = one double bond - Polyunsaturated = more than one double bond - Two bonds between two carbons make an unsaturated fatty acid Recognize the structure of a cis unsaturated fatty acid vs. trans unsaturated fatty acid and be able to explain why they are an oil vs. a fat - Fats are solid at room temperature - Oils are liquid at room temperature - cis unsaturated fatty acid: straight - trans unsaturated fatty acid: angled Describe phospholipids and how they arrange themselves to form a membrane - Phospholipids: type of lipid molecule that have a hydrophilic ("water-loving") head containing a phosphate group, and two hydrophobic ("water-fearing") tails derived from fatty acids - They form a bilayer that excludes water from the core. Define amphipathic and how it relates to phospholipids - Amphipathic: has both hydrophilic and hydrophobic parts - Phospholipids are a class of amphipathic molecules Recognize the structure and know the functions of carotenoids, steroids, and waxes - Carotenoids: - Light-absorbing pigments in photosynthesizing organisms - β-carotene is broken down to form Vitamin A - Steroids: - Have multiple ring structures - Vitamins - Hormones - Waxes: - Saturated fatty acid and a long-chain alcohol joined by an ester linkage - Very nonpolar → impermeable to water Nucleic Acids (Chapter 4.1) List and identify the three components to a nucleotide - Base - Sugar - Phosphate Describe and recognize ribose and deoxyribose - Sugar is ribose - Has a hydroxyl group attached to 2’ C (DNA has a hydrogen) Define and recognize pyrimidines vs. purines, and know which bases are in each category - Pyrimidines: Cytosine, Uracil, Thymine (CUT the pyramid) - Purines: Adenine, Guanine (Pure as Gold) Describe how two nucleotides are linked together by a phosphodiester bond - Base attached to 1’ carbon of sugar - Phosphate connected to sugar at 5’ carbon Describe how the secondary structure of nucleic acids is determined by hydrogen bonds between nitrogenous bases - Secondary structure - Bases bind via hydrogen bonds - Complementary and antiparallel - 5’ to 3’ Be able to give the complementary base pair sequence (in DNA and RNA) when given a strand of DNA - A and T (U replaces T in RNA) - G and C - A sample of DNA is made up of 28% adenine. How much of that sample is guanine?: 22% Recognize and describe DNA and RNA structure: similarities and differences - RNA: - Single stranded - Has a hydroxyl group (OH) attached to 2’ C - Uracil present - DNA - Double stranded - Has a hydrogen (H) attached to 2’ C - Thymine present Describe the important functions of nucleic acids - Primary purpose is information storage and transmission Describe the flow of information from nucleic acid to protein - DNA carries information and is expressed through RNA Cell Theory and Prokaryotic Cells (Chapter 5.1–5.2) Describe cell theory and its implications for studying life - Cells are the fundamental units of life - Cell theory is a unifying biological principle: - Cells are the fundamental units of life - All living organisms are composed of cells - All cells come from preexisting cells - Your cells can be traced back to the original cell! - Origin of life = origin of first cell Explain the importance of surface area-to-volume ratio in cells - As an object increases in volume, surface area increases at a lower rate - Why is this important? - Volume determines the amount of chemical activity a cell can perform - Surface area determines the amount of resources than can enter and amount of waste that can exit the cell Compare characteristics of prokaryotic cells and eukaryotic cells Label in a diagram and describe the structure and function of the prokaryotic structures discussed in class: flagella, pili, and general structure of the cell wall - Domains = Archaea and Bacteria - Small size and simple structure, but huge numbers and tremendous diversity - Individuals are single cells, but they often form chains or clusters - Flagella: - Composed of flagellin - Spin like propellers to move cell - Pili - Hair-like structures projecting from cell surface - Help bacteria adhere to other cells - (Singular = pilus)