Unit 2: The Chemistry of Life

isotopes

atoms of the same element with the same number of protons but different numbers of neutrons (and therefore different atomic masses) (ex. 1 H is protium, 2 H is deuterium, and 3 H is tritium)

"form follows function" - functional groups

changing the functional group of a molecule alters its chemical properties: -methane vs. methanol; methane (CH4) is a nonpolar gas, methanol (CH3OH) is a polar liquid and an alcohol due to it containing a hydroxyl functional group -basic structure of male and female steroid hormones is identical; they have an identical carbon skeleton, but different functional groups means interactions with different targets in the body leading to different sexual characteristics (testosterone has a carbonyl whereas estrogen has a hydroxyl bound to a carbon) -RNA contains ribose, characterized by the presence of the 2' hydroxyl group on the pentose ring; this makes RNA less stable than DNA because it is more susceptible to hydrolysis

steroids function

chemical messengers (ex. cholesterol, sex hormones)

functional groups

functional groups are parts of organic molecules involved in chemical reactions; they give the organic molecules distinctive properties; changing the functional groups of a molecule alters its chemical properties

examples of dehydration synthesis - disaccharides

glucose + fructose --> sucrose glucose + galactose --> lactose, glucose + glucose --> maltose

phospholipids structure

glycerol + 2 fatty acids + PO4 (phosphate group in place of one fatty acid chain): -PO4 negatively charged due to electronegative oxygens; phosphate group leads to a hydrophilic head -fatty acid tails are non-polar and hydrophobic -dual "personality" forms a phospholipid bilayer in water

hydroxyl

organic compounds with OH = alcohols -names typically end in ol (ex. ethanol)

pH scale

pH is a measure of how acidic or basic a solution is: -7 is neutral pH -greater than 7 is basic pH (increasing [OH-]) -less than 7 is acidic pH (increasing [H+])

polar covalent bonds

-ex. H2O (water) -have unequal distribution of charge throughout molecule -pair of electrons shared unequally by two atoms -in water, oxygen has a stronger attraction for the electrons than hydrogen; it has higher electronegativity *note: all organic functional groups that we've learned about are polar

unsaturated fats

-C=C double bonds in the fatty acids (at least one carbon to carbon double bond) -plant & fish fats -vegetable oils -liquid at room temperature -the kinks made by double bonded carbons in the fatty acid chains prevent the molecules from tightly packing together

activation energy and enzymes

-Most chemical reactions require an initial input of energy, activation energy, to begin/activate -enzymes catalyze reactions by lowering the activation energy required for the chemical process, allowing them to occur

tests for lipids

-Sudan III or Oil Red O stain is added; mix in triglycerides -turns red if fats are present (lipids test + for Sudan III or Oil Red O Stain) -"Paper Bag" test -a drop of the substance is placed on a piece of brown paper bag, a positive test (if lipids) is an oily, translucent spot forming on the paper bag

ATP (adenosine triphosphate)

-a high energy nucleotide made from a ribose sugar, an adenine molecule (nitrogenous base, and three phosphate groups -drives many biochemical reactions (ex. muscle contraction, chemical synthesis; used to drive nearly all cellular activities) -often referred to as "cellular currency"; provides energy in increments useful for tasks involved with cellular function with little "lost" energy

special properties of carbon

-all of life is built on carbon -cells composition is 72% H2O, 25% carbon compounds (macromolecules), and 3% salts (containing Na, Cl, K... ) -carbon atoms are versatile building blocks 1. can form 4 stable covalent bonds (it needs four bonds to be stable and has four valence electrons) 2. can bind to itself to form long, stable, chains (carbon readily bonds with itself) 3. can form rings (ex. glucose and many other carbohydrates) 4. can form single, double, or triple bonds with itself or other atoms (ex. triple C to C bond in alkynes, double C to O bond in the carbonyl functional group)

saturated fats

-all the HC tail's carbons have two hydrogens bonded to them -no C=C (carbon double bonds) - only single bonds between carbons -long, straight chain -most animal fats are saturated (stored in adipose tissue of humans) -solid at room temp. (ex. butter, lard, shortening) -contributes to cardiovascular disease due to plaque depositing in arteries

elements and the periodic table

-atomic number is the number of protons in an element -atomic mass is the average mass of all naturally occurring isotopes of an element (ex. carbon's atomic mass is 12.011) -mass number is the number of protons added to the number of neutrons (in the nucleus) of an atom (ex. 14 C has a mass number of 14) -elements in the same period (row) have the same number of shells; moving from left to right, each element has a sequential addition of protons and electrons -elements in the same group/family (column) have the same number of valence electrons hence similar properties

bonding properties

-electrons determine the chemical behavior (properties) of an atom, it depends on the number of electrons in an atom's outermost shell (valence shell) -two electrons fill the innermost electron shell -eight electrons fill the next three electron shells -atoms tend to either complete or empty a partially filled valence shell -this tendency drives chemical reactions and creates bonds between atoms

protein folding and unfolding

-chaperonins are proteins that guide protein folding -keep the new protein away from cytoplasmic influences -denaturing of a protein is the unfolding of a protein -disrupts 3° (tertiary) structure -pH and high temperatures can denature a protein -unravels or denatures protein by disrupting hydrogen bonds, ionic bonds and/or disulfide bridges -some proteins (few) can return to their functional shape after denaturation, many can not

DNA (deoxyribonucleic acid)

-contains deoxyribose (5C or pentose sugar) -double-stranded (double nucleotide chain), spiraled in a double helix -used for permanent storage of genetic information

RNA (ribonucleic acid)

-contains the 5C sugar ribose (a pentose); 2' hydroxyl means susceptible to hydrolysis and unstable -single-stranded (single nucleotide chain) -uracil instead of thymine in DNA -used as temporary storage of genetic information to copy and transfer it around the cell

names of enzymes

-ending in "ase" -identifies the reactant (ex. sucrase "cuts" sucrose, lipase "cuts" lipids) -describes function (ex. oxidase catalyzes oxidation (loss of electrons during a reaction), reductase catalyzes reduction (gain of electrons during a reaction), hydrolase catalyzes hydrolysis -ending in "in" -commonly found in digestion (ex. pepsin and trypsin digest proteins)

high heat capacity and specific heat of water

-high heat capacity: water can absorb or release large amounts of energy in the form of heat while only slightly changing its temperature -high specific heat: it takes a lot of energy to raise or lower water's temperature -plays an important role in temperature regulation on earth's surface and within organisms

expansion on freezing of water

-hydrogen bonds cause water molecules to line up less efficiently in ice, molecules spread farther apart and ice floats on top of liquid water -allows lake organisms, such as fish, to survive the winter as the ice on their waters surface provides insulation

functions of carbohydrates

-immediate energy use -energy reserves/storage -raw materials -structural materials (to provide support)

cholesterol

-important cell component in animal cell membranes -helps to keep cell membranes fluid and flexible -the substance from which all other steroids form (precursor) via metabolic reactions -high levels in blood may contribute to cardiovascular disease

starch vs. cellulose

-in starch: a (alpha) glucose -in cellulose: b (beta) glucose -the monosaccharides (a and b glucose) that form these two polysaccharides are isomers starch: -easy to digest (animals contain the enzymes necessary to break down glycosidic linkages that go in one direction) cellulose: -most abundant organic compound on earth -most herbivores can digest, most carnivores and humans cannot (do not contain the enzymes necessary to break down its alternating glycosidic linkages) -that's why carnivores eat meat to get their energy and nutrients

peptide bonds

-linking NH2 (amino group) of one amino acid to COOH (carboxyl group) of another -C-N (carbon to nitrogen) bond between amino acids -amino acids are joined through dehydration synthesis

water is a good solvent

-many substances are soluble in water (water-soluble), water is called the universal solvent -water's polarity makes it a good solvent -many organic compounds and other important biochemicals are polar and therefore dissolve well in water -however, strongly polar solutes cannot dissolve strongly non-polar solutes (ex. oil and water do not mix because oil is non-polar)

chemical formulas

-molecular formulas are chemical formulas that show the number and kind of atoms in a molecule (ex. C6H12O6 - glucose) -structural formulas are chemical formulas that show how the atoms and bonds in a molecule are arranged

sugars

-most names for sugars end in -ose (ex. glucose, fructose, cellulose -classified by number of carbons -6C = hexose (ex. glucose), 5C = pentose (ex. ribose), and 3C = triose (ex. glyceraldehyde) -5C and 6C sugars form rings "carbons at the corners" -energy stored in C-C (carbon to carbon) bonds

nucleotides

-nitrogenous base (carbon-nitrogen ring); the four nitrogenous bases in DNA are Adenine (A), Thymine (T), Guanine (G), and Cytosine (C) -pentose (5C) sugar -ribose in RNA and deoxyribose in DNA -phosphate (PO4) group

pH in living things

-pH of cells must be kept around 7 (neutral) -pH affects the shape of molecules, and the shape of the molecules affects their function, therefore pH affects cellular function -pH is controlled by buffers -buffers act as a reservoir of H+ (hydrogen ions); they donate H+ when [H+] falls below buffering range, and absorb H+ when [H+] rises above buffering range

phospholipids and the cell membrane

-phospholipid bilayer (double layer) forms when phospholipids surrounded by aqueous solution -hydrophilic heads on outside -heads in contact w/ aqueous solution outside of the cell (surrounding environment) and with aqueous solutions inside of the cell -hydrophobic tails on inside of the membrane -form the membrane's core

levels of structure in proteins

-primary (1°) is the order of amino acids in chain -amino acid sequence determined by gene, DNA -secondary (2°) structure is local folding -folding along short sections of polypeptides -determined by interactions of H bonds between R groups (sidechains) of adjacent amino acids; forms either alpha (α) helices or beta (β) pleated sheets -tertiary (3°) is whole molecule folding -determined by hydrophobic and van der Waals interactions between R groups (sidechains) -hydrophobic interactions are clustering of hydrophobic groups away from water -anchored by disulfide bridges (HS-SH), also hydrogen and ionic bonds in tertiary structure -quaternary (4°) structure is more than one polypeptide chain joined together -only in quaternary structure is there a functional protein -folding of polypeptide chains is determined by hydrophobic interactions

protein structure and function

-protein's function depends on their structure -they are large, complex, 3D molecules -twisted, folded, and coiled into a unique shape for each protein

atomic structure

-protons are positively charged (+) particles found in the nucleus of an atom -neutrons are particles with a neutral (no/0) charge found in the nucleus -electrons are negatively charged (-) particles that orbit outside the nucleus, ordinarily equivalent in number to protons in the nucleus; their attraction to protons is what holds the electrons and protons of an atom together -the nucleus of an atom is tiny, 10^-13 cm. -Protons and neutrons have approx. the same mass of one atomic mass unit (amu), electrons have near 0 mass -Protons, neutrons, and electrons together are known as subatomic particles

3 characteristics of enzymes

-reaction specific -enzymes must physically fit a specific substrate to function properly (the place where a substrate fits in an enzyme is called the enzyme's active site) -reusable -sensitive -structurally changed (denatured) due to extreme conditions (ex. pH, temperature) and therefore lose their function ("form follows function")

functions of proteins

-regulate cell processes (cellular maintenance, growth, and cell signaling/communication) (ex. enzymes - pepsin, polymerase and hormones - insulin) -structure (proteins are the basic structural molecule for all the tissues in an organism) (ex. keratin, collagen) -transport substances (ex. channel proteins embedded in the cell membrane) -help fight disease (ex. antibodies) -contractile (responsible for movement in the body) (ex. actin and myosin regulate muscle movement)

enzymes-substrate complex

-substrates are reactants which bind to enzymes, forming an enzyme-substrate complex (a temporary association) -products are the end results of a reaction

amino acids

-the monomers of proteins structure of amino acids: -central carbon -hydrogen -amino group (basic) -carboxyl group (acidic) -R group (sidechain or "rest of the molecule"); variable group -determines the unique chemical properties of the amino acid (ex. cysteine forms disulfide bridges; its sidechain has -SH (sulfhydryl) group)

covalent bonds

-very strong and stable bonds singular (ex. H2 - hydrogen gas and H2O - water): -two atoms share a pair of electrons -both atoms hold onto the electrons multiple (ex. CH4 - methane): -two or more atoms share several pairs of electrons -double bond - 2 pairs of electrons -triple bond - 3 pairs of electrons

high heat of vaporization of water

-water has a relatively high boiling point of 100 degrees C (212 degrees F) -organisms rely on water's high heat of vaporization to remove body heat

amino (functional group)

N bonded to 2Hs: -compounds with NH2 = amines (ex. amino acids) -NH2 acts as a base

water in life

-water is the most abundant molecule in living things -all life occurs in water, whether it be inside or outside the cell water has special traits that make it important to life: -water's ability to dissolve biologically significant compounds, from organic salts to large organic molecules, makes it a vital "universal solvent" in organisms and cells -water is an essential part of most metabolic processes -anabolic reactions: water removed from small molecules to make larger ones (ex. dehydration synthesis forms maltose from two glucose subunits) -catabolic reactions: water is used to break bonds in larger molecules to make smaller molecules (ex. hydrolysis on sucrose breaks it apart into its two subunits, glucose and fructose)

fats/oils (triglycerides) structure

1 glycerol (3 carbon alcohol) and 3 fatty acid chains: -fatty acids are long hydrocarbon tails w/ carboxyl groups at their heads -ester linkage between OH (hydroxyl in glycerol) and COOH (carboxyl in fatty acid chains); ester linkage forms when glycerol and fatty acid chains are joined by dehydration synthesis -fats/oils (triglycerides) are non-polar and hydrophobic

steroids structure

4 fused carbon rings -different steroids created by attaching different functional groups to rings

carbonyl

O double bonded to C: -if carbonyl at end of molecule (C=O and H), then aldehyde -if carbonyl in middle of molecule (C=O), then ketone

"form follows function" - proteins

A slight change in the amino acid sequence of proteins can affect its primary (1°) structure and disrupt its function. One amino acid shift can make a difference. For example, sickle cell hemoglobin has valine for its 6th codon instead of glutamic acid due to a single (A to T) nucleotide substitution in DNA forming modified hemoglobin, which leads to sickle cell anemia.

testing for proteins

Biuret is added (mixed in to) substance -turns purple if proteins are present (proteins test + for Biuret reagent)

carboxyl

C double bonded to O and single bonded to OH (hydroxyl group) -compounds containing COOH = acids (ex. fatty acids, amino acids)

biologically important elements

Carbon (6), Hydrogen (1), Nitrogen (7), Oxygen (8), Phosphorus (15), Sulfur (16); CHNOPS

elements in carbohydrates

Carbon (carbo-), Hydrogen (-hydr-), Oxygen (-ate) -these elements are in a ratio of 1 (C): 2 (H): 1(O) in monosaccharides, and 2 (H): 1 (O) in all carbohydrates -aldoses are sugars with aldehyde functional groups, and ketoses are sugars with ketone functional groups

elements in nucleic acids

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus (ex. RNA - ribonucleic acid and DNA - deoxyribonucleic acid)

elements in lipids

Carbon, Hydrogen, and Oxygen, and Phosphorus in phospholipids: -long, hydrocarbon chains -lipids have a much greater ratio of H:O than carbs -large, nonpolar molecules -many more C & H atoms than O atoms -electrons are shared equally among the atoms, no + and - ends; lipids are nonpolar and thus are not water-soluble *lipids do not really have monomers, and do not form polymers; they are just molecules made of smaller subunits and are not made of repeating monomers

ionization of water

H+ splits off from H2O, leaving OH- -if [H+] = [OH-], water is neutral -if [H+] > [OH-], water is acidic -if [H+] < [OH-], water is basic

sulfhydrl

S bonded to S: -compounds w/ SH = thiols -SH groups stabilize the structure of proteins (anchored by disulfide bridges in their tertiary structure)

phosphate (functional group)

P double bound to 4 Os: -bonds to C through an O -lots of O = lots of electronegativity (highly reactive) -transfers energy between organic molecules (ex. ATP, GTP)

"form follows function" - nucleic acids

RNA contains ribose, characterized by the presence of the 2' hydroxyl group on the pentose ring, this makes RNA less stable than DNA because it is more susceptible to hydrolysis

"form follows function" - lipids

Saturated fats are solid at room temperature because they contain no double bonds and are long straight chains, this leads to their molecules being closely packed together, which is why they are solid at room temperature. Unsaturated fats have carbon double bonds in their fatty acid hydrocarbon chains, creating kinks in them and preventing them from tightly packing together; this decreases their density in comparison to saturated fats and leads to them liquid at room temperature. Phospholipids have a phosphate group in place of one fatty acid chain. The phosphate functional group is negatively charged due to electronegative oxygens, and is polar leading to a hydrophilic head. Fatty acid tails are non-polar and hydrophobic. The different characteristics in these two molecules leads phospholipids to have a dual "personality" when surrounded by an aqueous solution; the hydrophilic heads are in contact with aqueous solutions outside and inside of the cell, and the hydrophobic tails are on the inside and form the core of the cell membrane.

"form follows function" - carbohydrates

Starch is easy to digest because animals contain the enzymes necessary to break down glycosidic linkages that go in one direction, but cellulose is hard to digest because most carnivores and humans do not contain the enzymes necessary to break down its alternating glycosidic linkages.

glycosidic bond/linkage

a covalent bond formed between two monosaccharides by dehydration synthesis

solution

a homogenous mixture composed of two or more substances; in a solution, one substance is dissolved in another substance, forming a mixture that has the same proportion of substances throughout

adhesion of water

adhesion is the bonding of a water molecule to another substance (intermolecular forces) (ex. water molecules bonding to glass in graduated cylinder): -capillary action is the ability of a liquid to flow against gravity in a narrow space (ex. water flows up straw in a glass of water; water created hydrogen bonds with surface of straw causing it to adhere to surface) -capillary action is important in moving water upwards through small spaces (ex. movement of water between soil particles, from roots to leaves in a plant, and through blood vessels in animals)

metabolism and energy transfer

chemical reactions (rxns) of life: -metabolism is the sum of all chemical changes taking place continuously in a cell or an organism -anabolic reactions are "building up" reactions; they are endergonic (require the input of energy) (ex. dehydration synthesis) -catabolic reactions are "breaking down" reactions (ex. hydrolysis)

cohesion of water

cohesion is the tendency of water molecules to stick together: -hydrogen bonds between molecules lead to its "stickiness" -surface tension occurs in a body of water because hydrogen bonds constantly pull molecules in many directions, but on the surface only they are pulled side to side and down (no H bonds pulling them upwards on the surface); ex. Basilisk lizard can walk on water

hydrocarbons

combinations of carbon and hydrogen (ex. CH4 - methane): -non-polar, not water-soluble, and hydrophobic -stable -very little attraction between molecules, a gas at room temperature

organic compounds

compounds containing carbon and almost always hydrogen; exceptions: CO2 (carbon dioxide) and CO (carbon monoxide)

inorganic compounds

compounds not formed in living things or from the remains of living things, they do not contain carbon; (ex. H2O - water)

square brackets - [ ] - are chemical shorthand for

concentration of an element or compound

dehydration synthesis

dehydration synthesis is for building large molecules, it joins monomers by taking H2O out; one monomer donates OH- and another monomer donates H+ (together these combine to form H2O - water); requires enzymes and uses energy

elements in proteins

elements: Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur

fats/oils (triglycerides) function

energy storage (2x more than carbs)

function of enzymes

enzymes are catalysts for biochemical reaction (they control metabolic reactions in organisms); catalysts speed up the rate of biochemical reactions in a cell (help w/ cellular functioning)

three types of lipids

fats/oils, phospholipids, and steroids

properties of water

good solvent, cohesion and adhesion, high heat capacity and high specific heat, high heat of vaporization, expansion on freezing

hydrogen bonds

hydrogen bonds are weak molecular attractions that are many many times between molecules: -ex. H2O (water) -polarity of water creates molecular attractions -H+ atom in one H2O attracted to O- in other -occurs often when an OH (hydroxyl) functional group exists in a large molecule (ex. cellulose) -holds together the two nucleotide chains of a DNA molecule; A to T (Adenine to Thymine) has two hydrogen bonds, G to C (Guanine to Cytosine) has three hydrogen bonds

hydrolysis

hydrolysis (digestion) is for breaking down large molecules, it uses H2O to breakdown polymers (the reverse of dehydration synthesis), cleaving off one monomer at a time; H2O is split into H+ (a hydrogen ion) and OH- (a hydroxide ion), they attach to the ends of the monomers; requires enzymes and releases energy

ionic bonds

ionic bonds are formed when one or more electrons are transferred from one atom to another (ex. NaCl - sodium chloride) -ions are charged particles; there are two types, anions and cations

types of chemical bonds

ionic, covalent, hydrogen (covalent is strongest, then ionic, then hydrogen)

anions

ions that have gained extra electron(s) and have a negative (-) charge

cations

ions that have lost extra electron(s) and have a positive (+) charge

polysaccharides

large polymers made of "many sugars" (ex. starch): -provide cells w/ intermediate and long term energy (reserves) -energy storage: starch in plants, glycogen in animals -structural support -structure: cellulose in plants (adds rigidity to cell wall), chitin in fungi (primary cell wall component and structural support), arthropods/insects/crustaceans (exoskeletons)

organic macromolecules

macromolecules are large, organic (carbon-containing) molecules in living cells: -built by linking (with covalent bonds) repeating building blocks, or monomers, to form a chain, or polymer -the four major classes of macromolecules are carbohydrates, lipids, proteins, and nucleic acids

modern atomic theory

matter is anything that takes up space and has mass; all matter is made up of elements -elements are pure substances that consist entirely of one type of atom -atoms are the smallest units of matter that can enter chemical reactions

isomers

molecules with the same molecular formula but different structures (shapes/different structural arrangement of their atoms): -different chemical properties and biological functions (ex. galactose and fructose are both structural isomers of glucose; the three share the same chemical formula C6H12O6) -enantiomers are mirror image isomers

nucleic acids structure

monomers are nucleotides of amino acids

testing for carbohydrates

monosaccharides: -Benedict's reagent is added and solution is heated -turns orange if glucose is present (glucose tests + for Benedict's Reagent) polysaccharides: -iodine is added -turns brown to blackish/purple (polysaccharides test + for Lugol's reagent, iodine) disaccharides: -test negative for both Benedict's Reagent and Lugol's Reagent (iodine)

monosaccharides

simple one monomer sugars (ex. glucose, fructose, galactose): -the monomer of carbohydrates -provides cells with immediate energy

nucleic acids function

store and transmit hereditary information -store and transmit instructions for every protein needed by a living thing (many organisms use DNA to permanently store the instructions and RNA to copy and transfer the info. around the cell)

phospholipids function

structural component of membranes (ex. the phospholipid bilayer of the cell membrane)

"form follows function" - isomers

structural differences create important functional significance: -amino acid alanine; L-alanine used in proteins but not D-alanine -medicines; L-version active but not D-version (ex. L-Dopa may treat Parkinson's disease but not D-Dopa) -thalidomide exists as two enantiomers -R-thalidomide prescribed as an antidepressant, S-thalidomide linked to severe birth defects

acids

substances that dissociate in water and release hydrogen ions (H+); a substance is acidic if its pH is less than 7

bases

substances that take up hydrogen ions (H+) or release hydroxide ions (OH-); a substance is basic of its pH is greater than 7

nucleic polymer backbone

sugar to PO4 (phosphate group) bond, known as phosphodiester bond: -new base added to the sugar of previous base -polymer (nucleotide chain) grows in one direction -nitrogenous bases are connected with hydrogen (H) bonds -A to T - Adenine to Thymine - (uracil replaces thymine in RNA) have two hydrogen (H) bonds -G to C - Guanine to Cytosine - have three hydrogen (H) bonds

solubility

the ability of a solute to dissolve in a particular substance

solute

the dissolved substance in a solution

CHNOPS

the most common elements of life: -Carbon, Hydrogen, Nitrogen, and Oxygen make up ~95% of your body weight -Carbon can form single, double, or triple bonds with other elements and bond to other carbons -Hydrogen only has one electron and can only form single bonds; it needs one bond to be stable -Oxygen is the most abundant element in life (65%) and can form two bonds total; it can form a double bond to one element (ex. O=O) or a single bond with two other elements (ex. H-O-H) -Many molecules of these elements join resulting in biomolecules or polymers (mono mer means one unit or molecule, poly mer means many units or molecules) -Phosphorus, Sulfur, Potassium, and Calcium required in trace amounts

organic chemistry

the study of carbon (organic) compounds

solvent

the substance which dissolves the solute

disaccharides

two monomer sugars (ex. sucrose, maltose, lactose) -provide cells w/ intermediate energy