Human Physiology: Chapter 2

atom

the smallest unit of an element. It has:

a. A nucleus with positively charged protons and uncharged neutrons

b. Orbiting electrons with negative charges

c. An atomic mass equal to the number of protons plus the number of neutrons

d. An atomic number equal to the number of protons

electron orbitals

a. Orbitals (or shells) are energy levels that surround the nucleus of an atom.

b. Electrons fill the shells, starting with the one closest to the nucleus.

The first shell holds 2 electrons.

Each shell thereafter holds 8 electrons. (Nonbiological elements fill distant shells that hold more than 8.)

c. Atoms are most stable when the outer shell is filled. Electrons in unfilled outer shells participate in bonding; they are called valence electrons.

chemical bonds

a. Chemical bonds are formed when electrons in atoms interact.

b. The number of bonds an atom can form is determined by the number of valence electrons.

Hydrogen has one electron; it needs one more to fill the inner shell so that it can form one bond.

Carbon has 6 electrons; 2 fill the inner shell and 4 are valence electrons. It needs 4 more electrons, so that it can form 4 bonds.

covalent bonds

a. Valence electrons are shared because energy levels overlap.

Electrons are shared equally form a nonpolar covalent bond; example - 2 hydrogen atoms

Electrons that are not shared equally form a polar covalent bond; they have positive and negative ends; example – between oxygen and hydrogen in water

b. Water

Polar molecule

Good solvent (substances dissolve in it)

Can form strong hydrogen bonds

Polar molecules (covalent bonds) may dissolve in water and are called hydrophilic

Nonpolar molecules do not dissolve in water and are called hydrophobic

ionic bond

a. In an ionic bond, one atom gives electrons to another so that both have filled valence shells.

The electron donor becomes positively charged; the ion is called a cation.

The electron receiver becomes negatively charged; the ion is called an anion.

b. Cations and anions attract each other to form ionic compounds.

c. Most ionic compounds dissociate (come apart with no reaction) when dissolved in water.

The negative side of water is attracted to the cation, and the positive side of water is attracted to the anion.

This is a strong attraction that pulls the ions apart

Water molecules then surround the ions to form hydration spheres

These free ions are critical to many physiological processes

hydrogen bond

a. Weak bond formed between two polar molecules based on opposite charges attracting (not based on electron sharing)

b. Forms between electropositive H atoms and electronegative O or N atoms

c. Forms between water molecules; responsible for surface tension and capillarity

d. Forms between amino acids on a protein to produce the 3D structure of the protein

e. Holds the two strands of the DNA molecule together

acids, bases, and pH

• Some water molecules ionize to form free hydrogen ions or protons (H+) and hydroxide ions (OH−).

• When this happens, there are the same number of H+ ions as OH− ions in solution, so the solution is neutral.

• A neutral solution is said to have a pH of 7 (which means 10−7 molar concentration H+).

• When a solution has more H+ ions than OH− ions, this is called an acid, and its pH is below 7; often called a proton donor

• When a solution has more OH− ions than H+ ions, this is called a base, and its pH is above 7.

(Such solutions are also called alkaline.); often called a proton acceptor

pH scale

a. Runs from 0 to 14, with 0 the strongest acid and 14 the strongest base.

b. pH is calculated by

c. Pure water has a H+ concentration of 10−7, so the pH is 7. A pH 6 solution actually has 10 times the number of H+ ions.

buffers

a. Buffers stabilize pH in a solution.

b. Has 2 components – a weak acid and a weak base (buffer pair)

For Chapter 2, you only need to know what is written on the pages of this outline.

c. In blood, two molecules stabilize pH: bicarbonate ion (HCO3−) and carbonic acid (H2CO3).

HCO3− + H+ ↔ H2CO3

Bicarbonate neutralizes excess acid

Carbonic acid neutralizes excess base

d. If blood falls below pH 7.35, the condition is called acidosis.

e. If blood rises above pH 7.45, the condition is called alkalosis.

f. The action of the bicarbonate/carbonic acid buffer system as well as the lungs and kidneys work together to prevent acidosis or alkalosis.

organic molecules

Contain Carbon and Hydrogen

a. Because carbon must form 4 bonds to satisfy the valence shell, it can form chains and rings of carbons while still bonding with other atoms.

b. Two carbons can share 1 or 2 pairs of electrons. If 2 pairs are shared, it is a double bond and can bond with 2 additional atoms. If 1 pair of electrons are shared, it can bond with 3 additional atoms

Hydrocarbon Structures

a. Carbons are not shown but are understood to be at the corners of the molecule. Some show double bonds.

b. Carbon chains and rings form backbones for more reactive groups of atoms called functional groups.

c. Functional groups allow organic compounds to be classified into groups which provides unique chemical properties

Stereoisomers

a. Molecules that have exactly the same atoms arranged in exactly the same sequence, but still differ in the spatial organization of their functional groups.

This characteristic is critical to function. A given enzyme may interact with one stereoisomer but not with another.

The sugars glucose, galactose, and fructose are stereoisomers.

b. Types of Stereoisomers, Continued

Cis-trans isomers – geometric isomers

Enantiomers (optical isomers) – mirror images; rotate right (D) or left (L)

hydrocarbon structures

a. Carbons are not shown but are understood to be at the corners of the molecule. Some show double bonds.

b. Carbon chains and rings form backbones for more reactive groups of atoms called functional groups.

c. Functional groups allow organic compounds to be classified into groups which provides unique chemical properties

stereoisomers

a. Molecules that have exactly the same atoms arranged in exactly the same sequence, but still differ in the spatial organization of their functional groups.

This characteristic is critical to function. A given enzyme may interact with one stereoisomer but not with another.

The sugars glucose, galactose, and fructose are stereoisomers.

b. Types of Stereoisomers, Continued

Cis-trans isomers – geometric isomers

Enantiomers (optical isomers) – mirror images; rotate right (D) or left (L)

carbohydrates

Characteristics

a. Organic molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.

b. Serve as a major source of energy in the body

c. Includes sugars and starches

d. -ose suffix of name denotes sugars

classification of carbohydrates

a. Monosaccharide: simple sugar, one carbon ring

Examples: glucose, fructose, galactose

Formula is C6H12O6 – structural isomers

b. Disaccharide: two monosaccharides joined by a covalent bond; examples: sucrose, maltose, lactose

c. Polysaccharides

Polysaccharide: several monosaccharides (generally glucose) joined together

For Chapter 2, you only need to know what is written on the pages of this outline.

Starch – plant storage of sugar; composed of thousands of glucose molecules

Glycogen – sugar storage in an animal cell; similar to starch but more highly branched

Cellulose – makes up cell walls of plants; cellulose is not digestible by humans.

Chitin – forms exoskeleton of arthropods; similar to cellulose but with amine groups in the glucose subunits.

dehydration synthesis and hydrolysis

a. Covalent bonds that hold monosaccharides together are formed via dehydration synthesis where a hydrogen atom is removed from one molecule, and a hydroxyl group is removed from another to form water.

b. Hydrolysis breaks bonds between monosaccharides; add water and split the molecule

c. These processes are also used to build/break fats, proteins, and nucleic acids

lipids

Characteristics

a. Lipids consist of nonpolar hydrocarbon chains and rings that makes them hydrophobic (insoluble in water).

b. There are several categories of lipids

triglycerides

Include fats (solids) and oils (liquids)

b. Composed of one molecule of glycerol and three molecules of fatty acids

Glycerol is a 3-carbon alcohol

Fatty acid – long, nonpolar hydrocarbon chain with a carbonyl (COOH) at one end

a) If every carbon on the fatty acid chain shares a single pair of electrons, the fatty acid is saturated.

b) If there are double bonds between carbons, the fatty acid is unsaturated.

c) Also called neutral fats when stored in adipose tissue.

d) Trans fats – artificially produced straight-chained fatty acids made from vegetable oils.

e) Cis – trans fats

f). Ketone bodies

Hydrolysis of triglycerides forms free fatty acids in the blood. These can be used for energy or converted into ketone bodies by the liver.

a) Strict low-carbohydrate diets and uncontrolled diabetes can result in elevated ketone levels, called ketosis.

b) Ketone levels high enough to lower pH can cause ketoacidosis, which can lead to coma and death.

c) A sign of ketoacidosis is “acetone” breath

phospholipids

a. Lipids with a phosphate group, which makes them part polar and part nonpolar - amphipathic

b. Major component of cell membranes as a double layer, with hydrophilic phosphates pointing outward on each side and hydrophobic fatty acids and glycerol pointing inward.

c. As micelles, phospholipids can act as surfactants. The polar nature of the molecule decreases the surface tension of water.

Surfactant keeps lungs from collapsing

steroid

a. A steroid is structurally very different from a triglyceride but is nonpolar, so considered a lipid

b. 3 six-carbon rings + 1 five-carbon ring + functional groups

c. Cholesterol is a steroid used (1) as a precursor to steroid hormones, such as testosterone, estrogen, and corticosteroids, and (2) to make molecules such as vitamin D and bile salts

prostaglandins

a. Type of fatty acid with a cyclic hydrocarbon group

b. Serve as regulatory molecules between cells in the same organ

c. Help regulate blood vessel diameter, ovulation, uterine contractions, inflammatory reactions, blood clotting, and many other functions.

proteins

A. Characteristics of Protein

• Composed of an amino acid chain

• An amino acid has an amino group, a carboxyl group, and a functional (R) group.

• There are 20 different amino acids that can be combined in an endless number of ways.

• The functional group is what differentiates the 20 amino acids.

• Amino acids can be polar or nonpolar, so they attract or repel each other to form kinks and folds in the protein.

making a protein

When amino acids are joined, a H is stripped from the amino end and a OH is stripped from the carboxyl end in dehydration synthesis. This is called a peptide bond.

When amino acids are added together to form a chain, it is the primary structure of a protein

protein structure

a) A chain of amino acids is called a polypeptide chain.

i. The chain varies in length from 3 to 4,500 amino acids.

ii. The chain is called the primary structure of the protein.

iii. The sequence of amino acids in a chain is determined by

DNA.

iv. Weak hydrogen bonds may form between neighboring

amino acids.

v. This may form an alpha helix or a beta pleated sheet.

vi. This is called the secondary structure of the protein.

b) Attraction to amino acids further away produces bends and folds, creating a specific 3D shape.

i. This is the tertiary structure of the protein.

ii. This structure dictates function.

iii. Since weak bonds hold tertiary structure together, a protein is easily denatured (unfolded) by changes in pH or temperature.

iv. Some tertiary structures are made more stable by disulfide bonds (S-S) between cysteines. Some functional proteins are composed of multiple polypeptide chains covalently bonded together.

• This is called the quaternary structure of the protein.

• Examples are the hemoglobin (4 polypeptides) in blood and the hormone insulin (2 polypeptides).

conjugated proteins

Sometimes proteins are combined with other molecules to become functional

a. Glycoprotein = Protein + Carbohydrate

Examples: some hormones, in cell membranes

b. Lipoprotein = Protein + Lipid

Example: in cell membranes, carrier molecules in blood

protein functions

Structural: collagen fibers in connective tissues; keratin in skin

Enzymes: assist every chemical process in the body

Antibodies: part of the immune system

Receptors: receive communication from other cells for regulation of cell activity

Carriers: across cell membranes or in blood

nucleotides

Building blocks for nucleic acids

Composed of a five-carbon sugar, a phosphate group, and a nitrogenous base

Nitrogenous bases fall into two categories:

a. Pyrimidine: a single carbon ring + nitrogen

Cytosine, thymine, uracil

b. Purine: 2 carbon rings + nitrogen

Guanine, adenine

Pentose sugars are deoxyribose or ribose

Deoxyribonucleic Acid (DNA)

The sugar in this molecule is called deoxyribose and can bind to one of four nitrogenous bases:

a. Guanine (G)

b. Thymine (T)

c. Cytosine (C)

d. Adenine (A)

Deoxyribose bonds with a phosphate group (via dehydration synthesis) to form a long chain, which serves as the backbone of the molecule.

DNA structure

Each nitrogenous base can form a hydrogen bond with another to result in a double-stranded molecule.

a. Cytosine can only bind with guanine.

b. Thymine can only bind with adenine.

c. This is the Law of Complementary base pairs

The two chains of DNA are twisted, forming a double helix.

DNA is the basis of the genetic code – the sequence of bases codes for amino acids to make a protein

ribonucleic acid (RNA)

Similar to DNA except:

a. Has ribose sugar instead of deoxyribose

b. Is single-stranded instead of double-stranded

c. Has uracil instead of thymine