Chapter 2/3: Cell Chemistry

What is matter?

has mass and takes up space

What is an atom?

smallest particle exhibiting chemical properties of an element

How many naturally occuring elements are there?

92 that make up matter ogranized in periodic table of elements

How do the shells of atoms work?

innermost: 2

second: up to 8

What is the octet rule?

Elements lose, gain, or share electrons to obtain complete outer shells with eight electrons

What is an ion?

Atoms with a positive or a negative charge

• produced from loss or gain of one or more electrons

• significant physiological functions

What are cations?

positive charge, losing electrons

Na, K, Ca, Mg, H

What are anions?

negative charge, gaining electrons

Cl, Bicarbonate, Phosphate

What are polyatomic ions?

anions with more than one atom

What are ionic bonds?

• Cations and anions bound by electrostatic attractive forces and form salts

• giving electron

  • E.g., table salt (NaCl): Each sodium atom loses one outer shell electron to a chlorine atom.

  • Sodium and chlorine ions held together ionic bonds in lattice crystal structure (ionic compound)

What are covalently bonded molecules?

• Electrons shared between atoms of two or more different elements

• Termed molecular compounds:

  • E.g., carbon dioxide (CO2), but not molecular oxygen (O2)

What is a covalent bond?

• Atoms share electrons.

• both atoms require electrons and occurs with atoms with 4 to 7 electrons in outer shell

  • Formed commonly in human body using Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C) (CHON)

What are nonpolar covalent bonds?

Electrons shared equally between atoms

What are polar covalent bonds?

electrons unequally shared between atoms

What are intermolecular attractions and an example?

• Weak chemical attractions between molecules important for shape of complex molecules: E.g., DNA and proteins

• Hydrogen bond:

  • Forms between polar molecules. Attraction between partially positive hydrogen atom and a partially negative atom. Individually weak, collectively strong and influences how water molecules behave

What is water?

• Comprises two-thirds of the human body by weight

• Polar molecule with one oxygen atom bonded to two hydrogen atoms

  • Oxygen atom has two partial negative charges.

  • Hydrogens have single partial positive charge each.

• Can form four hydrogen bonds with adjacent molecules, which is central to water’s properties

What are the properties of water?

• cohesion

• surface tension

• adhesion

• temperature

• specific heat

• heat of vaporization

What is the cohesive property of water and an example?

Attraction between water molecules due to hydrogen bonding

• rain droplets

What is the surface tension property of water and an example?

• Inward pulling of cohesive forces at surface of water

• Causes moist sacs of air in lungs to collapse

  • Surfactant, a lipoprotein, prevents collapse

  • bellyflop on water hurts

What is the adhesive property of water and an example?

• Attraction between water molecules and a substance other than water

  • meniscus of test tube, water on side

What is the temperature property of water?

Measure of kinetic energy of atoms or molecules within a substance

What is the specific heat property of water?

• energy required to increase temperature of 1 gram of a substance by 1 degree Celsius

• Water’s value extremely high due to energy needed to break hydrogen bonds

  • Contributes to keeping body temperature constant.

What is the heat of vaporization property of water?

• Heat required for release of molecules from a liquid phase into a gaseous phase for 1 gram of a substance

• Water’s value very high due to hydrogen bonding

  • Sweating cools body by causing excess heat to dissipate as water evaporates.

What is water known as and why?

• universal solvent

  • most substances dissolve in it because of chemical properties

What substances dissolve or dissociate in water?

• Polar molecules and ions

  • Hydrophilic means “water-loving”.

• Some substances dissolve but remain intact. E.g., glucose and alcohol

• Nonelectrolytes remain intact but do not conduct current..

  • NaCl dissociates into Na+ and Cl– ions and acids and bases, such as HCl Electrolytes can conduct electrical currents.

What does the water form around the substance?

hydration shell, surrounds it

What substances don’t dissolve in water?

• Nonpolar molecules

• Hydrophobic means “water-fearing”

• Hydrophobic substances require carrier proteins to be transported within the blood.

  • E.g., fats and cholesterol are unable to dissolve within water

What is an acid?

• dissociates in water to produce H+ and an anion

• Proton donor, increases concentration of free H+

What is the difference between a weak and strong acid?

• More dissociation of H+ with stronger

  • E.g., HCl in the stomach.

• Less dissociation of H+ with weaker

  • E.g., carbonic acid in the blood

What is a base?

• accepts H+ when added to solution: Proton acceptor, decreases concentration of free H+

What is the difference between a weak and strong base?

• More absorption of H+ with stronger

  • E.g., ammonia and bleach.

• Less absorption of H+ with weaker

  • E.g., bicarbonate in blood and in secretions released into small intestine

What is pH?

• measure of H+

• Relative amount of H+ in a solution

• Range between 0 and 14

What is the pH of water?

7

What is the relationship between pH and H?

As H+ concentration increases, pH decreases. As H+ concentration decreases, pH increases

What are mixtures?

• combining two or more substances:

• Two defining features:

  • not chemically changed

  • substances can be separated by physical means

What are the 3 types of water mixtures?

suspension, colloid, solution

What is a suspension and an example?

• material larger in size than 1 mm mixed with water.

  • E.g., blood cells within plasma or sand in water.

• Does not remain mixed unless in motion.

• Appears cloudy or opaque; scatters light

What is a colloid and an example?

• smaller particles than a suspension, but larger than those in a solution.

  • E.g., fluid in cell cytosol Remains mixed when not in motion.

• Scatters light

What is a solution and an example?

• homogeneous mixture of material smaller than 1 nanometer that dissolves in water.

• Does not scatter light;

• does not settle if solution not in motion.

  • E.g., sugar water, salt water, blood plasma

What are biological marcomolecules?

• large organic molecules synthesized by the body

• Always contain carbon, hydrogen, and oxygen

  • Some may also have nitrogen, phosphorus, or sulfur

What are hydrocarbons?

• only carbon and hydrogen atoms.

• May contain functional groups.

• Most are polar and able to hydrogen bond

What is the carbon skeleton formation?

• Bonds in straight chains, branched chains, or rings.

• Carbon present where lines meet at an angle.

• Additional atoms are hydrogen.

• Can form single, double, and triple bonds

What are polymers?

• Large molecules made of monomers

  • CHO, PRO, nucleic acids

What are monomers?

• repeating subunits bound together to form polymers through dehydration synthesis and broken apart through hydrolysis

  • CHO → sugars

  • nucleic acids → nucleotides

  • PRO → amino acids

What is dehydration synthesis?

• (condensation)

• synthesis of biomolecules.

• One subunit loses an —H, while the other subunit loses an —OH.

• New covalent bond formed and water produced

What is hydrolysis?

• breakdown of biomolecules

• Water is used

  • An —H added to one subunit and an —OH added to another subunit

What is glucose?

• Six-carbon carbohydrate.

• Most common monosaccharide.

• Primary nutrient supplying energy to cells.

• Concentration must be carefully maintained

What is glycogen?

• stored in Liver and skeletal muscle

• bind glucose monomers together (glycogenesis).

• Liver hydrolyzes glycogen into glucose as needed (glycogenolysis).

• Liver can also form glucose from noncarb sources (gluconeogenesis)

What are the types of fats?

triglycerides (saturated, unsaturated, polyunsaturated), phospholipids, steriods, cholesterol, nucleic acids, ATP

What are polysaccharides?

• three or more sugars

• Glycogen common in animals.

• Starch and cellulose found in plants.

• Plant starch is a major nutritional source of glucose for humans.

• Cellulose is a source of fiber (nondigestible).

What are triglycerides?

• long-term energy storage.

• Formed monomers of glycerol and three fatty acids.

  • Saturated, lack double bonds

  • Unsaturated, one double bond.

  • Polyunsaturated, two or more double bonds.

• Adipose tissue stores triglycerides:

• Lipogenesis—formation of triglycerides when conditions of excess nutrients exist.

• Lipolysis—breakdown of triglycerides when nutrients are needed

What are phospholipids?

• Amphipathic molecules that form chemical barriers of cell membranes.

• Phospholipid structure similar to a triglyceride.

• one end of the glycerol has a polar phosphate group.

  • Glycerol, phosphate, and organic groups are polar → Form hydrophilic head.

  • Fatty acid group is nonpolar → Form hydrophobic tails

What are steriods?

• hydrocarbons arranged in multi-ringed structure.

• Four carbon rings;

  • three have 6 carbon atoms,

  • one has 5 carbon atoms.

  • Differ in side chains extending from their rings.

What is cholesterol?

• Component of animal plasma membranes.

• Precursor to other steroid synthesis:

  • Steroid hormones (e.g., testosterone and estrogen) and Bile salts

What are nucleic acids?

• Store and transfer genetic information

  • Deoxyribonucleic acid (DNA)

  • Ribonucleic acid (RNA).

  • Both are polymers composed of nucleotide monomers.

  • Monomers are linked covalently through phosphodiester bonds

What are the 3 components of nucleic acids?

1. Sugar: Five-carbon pentose

2. Phosphate group: Attached at carbon 5 of sugar

3. Nitrogenous base: Attached to same sugar at carbon one. Single-ring or double-ring structure

What is ATP?

• Nucleotide

  • nitrogenous base adenine, a ribose sugar, and three phosphate groups

• Central molecule in transfer of chemical energy within cell

• Covalent bonds between last two phosphate groups are unique and energy rich.

• Release energy when broken Important nucleotide-containing

What is the function of proteins?

• Serve as catalysts (enzymes) in metabolic reactions,

• Act in defense,

• Aid in transport,

• Contribute to structural support,

• Cause movement,

• Perform regulation

What is the general structure of protein?

• One or more strands of amino acid monomers

• 20 different amino acids found in living organisms

• Each has an amine and a carboxyl functional group. Both covalently linked to same carbon atom

• Carbon also covalently bonded to a hydrogen and different side chain structures

• R groups, which distinguish different amino acids from one another

What is the conformation of protein?

• three-dimensional shape of the protein.

• Crucial for protein function.

• Involve levels of organization beyond primary structure.

• Arrangements dependent upon intramolecular attractions between amino acids.

• Obtained through folding with help of specialized proteins, chaperones

What is the primary structure of protien?

linear sequence of amino acids

What is the secondary structure of protein?

• Patterns that may repeat several times and confer unique characteristics. Two types:

  • Alpha helix—spiral coil gives elasticity to fibrous proteins (e.g., skin and hair).

  • Beta sheet— planar pleat arrangement gives flexibility to globular proteins (e.g., enzymes).

What is the tertiary struture of proteins?

• (a “scribble”): Three-dimensional shape of polypeptide chain.

• Two categories L Globular proteins fold into compact shape.

• Fibrous proteins are extended linear molecules

What is the quaternary structure of proteins?

• Present in proteins with two or more polypeptide chains.

  • E.g., hemoglobin with its four polypeptide chains

What is the denaturation of proteins?

• Conformational change to a protein.

• Disturbs protein activity.

  • Usually irreversible.

• May occur due to increased temperature or in response to changes in pH

What 3 criteria are chemical reactions based on?

1. Changes in chemical structure

2. Changes in chemical energy

3. Whether the reaction is irreversible or reversible

What are the classification for changes in chemical structure?

• Decomposition reactions

• Synthesis reactions

• Exchange reactions

What is a decomposition reaction?

• Initial large molecule broken down into smaller structures

  • AB → A + B

    • For example, hydrolysis reaction of sucrose into glucose and fructose

• All decomposition reactions in the body are referred to as catabolism or catabolic reactions

What is a synthesis reaction?

• Two or more structures combined to form a larger structure

  • A + B → AB

    • For example, dehydration synthesis reaction forming a dipeptide

• Anabolism (anabolic reactions) is the collective term for all synthesis reactions in the body

What is an exchange reaction?

• Groups exchanged between two chemical structures

  • Has both decomposition and synthesis components

  • Most prevalent in human body AB + C → A + BC

• For example, production of ATP in muscle tissue