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Biochemistry

the study of the molecules that compose living organisms
–carbohydrates, fats, proteins, and nucleic acids

1

element

simplest form of matter to have unique chemical properties

2

trace elements

vital role in physiology despite only minute quantities in the body

3

minerals

inorganic elements extracted from the soil by plants and passed up the food chain

4

minerals in the body

mostly calcium and phosphorus
also chlorine, magnesium, potassium, sodium and sulfur

5

Major elements in the body

6

98.5% of the body
oxygen
carbon
hydrogen
nitrogen
calcium
phosphorus

6

oxygen

65%
O

7

carbon

18%
C

8

hydrogen

10%
H

9

nitrogen

3%
N

10

calcium

1.5%
Ca

11

phosphorus

1%
P

12

Lesser Elements in the body

6

.8 %
sulfur
potassium
sodium
chlorine
magnesium
iron

13

sulfur

S

14

potassium

K

15

sodium

Na

16

chlorine

Cl

17

magnesium

Mg

18

iron

Fe

19

Atomic Theory


Name

John Dalton,

20

planetary model of atomic structure

Name

Neils Bohr,

21

nucleus

center of an atom
composed of protons and neutrons

22

protons

single positive charge

23

atomic Number

number of protons in the nucleus

24

neutrons

have no charge

25

atomic mass

approximately equal to the total number of protons and neutrons

26

number of neutrons determined by

subtracting the atomic number from the atomic mass

27

electrons

single negative charge
one or more concentric clouds around the nucleus

28

valence electrons

electrons in the outermost shell
determine the chemical bonding properties of the atom

29

number of electrons per shell

first - 2
all others - max of 8

30

isotopes

–same chemical behavior, differ in physical behavior
–breakdown (decay) to more stable isotope by giving off radiation
same valance electrons

31

Atomic weight

of an element accounts for the fact that an element is a mixture of isotopes

32

radioisotopes

–unstable isotopes that give off radiation
–every element has at least one radioisotope

33

Marie Curie

first woman to receive Nobel prize and Ph.D.
coined term radioactivity

34

radioactivity

radioisotopes decay to stable isotopes releasing radiation

35

ionizing radiation

high energy radiation ejects electrons from atoms
converts atoms into ions

36

physical half-life

time required for 50% of the atoms to decay to a more stable state

37

biological half-life

time required for half of it to disappear from the body

38

ions

charged particles with unequal numbers of protons and electrons

39

anion

gains electrons and acquires a negative charge

40

cation

loses electrons and acquires a positive charge

41

electrolytes

Salts that ionize in water and form solutions capable of conducting an electric current.

42

electrolyte balance

one of the most important considerations in patient care

43

electrolyte importance

chemical reactivity
osmotic effects (influence water movement)
electrical effects on nerve and muscle tissue

44

free radicals

chemical particles with an odd number of electrons
lack complete outer shell
produced by normal metabolic reactions, radiation, chemicals
causes tissue damage

45

antioxidant

a chemical that neutralizes free radicals

46

molecules

chemical particles composed of 2 or more atoms united by a chemical bond

47

compounds

molecules composed of 2 or more elements

48

molecular formula

identifies constituent elements and shows how many of each are present

49

isomers

molecules with identical molecular formulae but different arrangement of atoms

50

molecular weight

sum of atomic weight of its atoms

51

chemical bonds

forces that hold molecules together
ionic
covalent
hydrogen
Van der Waals forces

52

ionic bond

is the attraction of a cation to an anion
weak attraction
inside molecule

53

covalent bond

form by the sharing pairs of electrons
inside molecule

54

types of covalent bonds

single
double
nonpolar covalent
polar covalent

55

single

sharing a single pair of electrons

56

double

sharing a double pair of electrons

57

nonpolar covalent

shared electrons spend approximately equal time around each nucleus
strongest of all bonds

58

polar covalent

shared electrons spend more time orbiting one nucleus than they do the other

59

hydrogen bond

weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another
between molecules

60

Van der Waals forces

weak, brief attractions between neutral atoms
between molecules
important in protein folding

61

mixture

consists of substances physically blended, but not chemically combined
Most mixtures in our bodies consist of chemicals dissolved or suspended in water

62

water properties

5

polar covalent bonds and V-shaped molecule give it a particular set of properties
solvency
cohesion
adhesion
chemical reactivity
thermal stability

63

solvency

ability to dissolve other chemicals
water is called the Universal Solvent
Virtually all metabolic reactions depend on the solvency of water

64

cohesion

tendency of like molecules to cling to each other
–water is very cohesive due to its hydrogen bonds
–surface film on surface of water is due to molecules being held together by a force called surface tension

65

adhesion

tendency of one substance to cling to another

66

chemical reactivity

is the ability to participate in chemical reactions
–water ionizes into H+ and OH-
–water ionizes other chemicals (acids and salts)
–water involved in hydrolysis and dehydration synthesis reactions

67

thermal stability

Water helps stabilize the internal temperature of the body
water absorbs heat without changing temperature very much
has high heat capacity
effective coolant

68

hydrophobic

do not dissolve in water

69

hydrophilic

dissolve in water
molecules must be polarized or charged

70

calorie

amount of heat required to raise 1 gram of water 1 degree Celsius

71

solution

consists of particles of matter (solute) mixed with a more abundant substance (solvent)
<1 nm, clear, particles do not settle, will pass membrane

72

colloids

mixtures of protein and water
1-100 nm, often cloudy, particles do not settle, will not pass membrane

73

suspension

blood cells in our blood plasma
>100 nm, cloudy-opaque, particles do settle, will not pass membrane

74

measures of concentration

weight per volume
percentages
molarity

75

emulsion

a suspension of one liquid in another
fat in breast milk

76

weight per volume

weight of solute in a given volume of solution

77

percentage versus molar concentrations

percentage - number of molecules unequal, weight of solute equal
molar - number of molecules equal, weight of solute unequal

78

mole

is it's molecular weight in grams

79

molarity

is the number of moles of solute per liter of solution

80

how to calculate molarity

1 - calculate molecular weight
2 - calculate number of moles - take amount given and divide by molecular weight
3- calculate molarity by dividing number of moles by volume

81

percentages

specify if percentage refers to weight or volume of solute in a given volume of solution
usually per 100 ml

82

electrolyte concentrations

miliequivalents per liter = mEq/L
1 equivalent is the amount of electrolyte that will electrically neutralize 1 mole of H+ on OH- ions

83

calculate mEq/l

multiply molar concentration times the valence of the ion

84

acid

any proton donor
hydrogen ion donor H+

85

base

a proton acceptor

86

pH

acidity is expressed in terms of pH or a measure derived from the molarity of H+

87

pH scale

Neutral is 7
Acid is below 7
base is above 7
the lower the pH value, the more hydrogen ions a solution has - more acidic

88

change in pH scale

change in one number on the pH scale represents a 10 fold change in H+ concentration

89

energy

the capacity to do work

90

pH of blood

7.35 to 7.45
Our body uses buffers to resist changes in pH

91

work

to do work means to move something

92

heat

kinetic energy of molecular motion

93

chemical energy-

potential energy stored in the bonds of molecules

94

free energy

potential energy available in a system to do useful work

95

catalysts

temporarily bond to reactants, hold in position, not used up in the reaction

96

chemical reaction

is the process by which a covalent or ionic bond is formed or broken
potential energy stored in the bonds of molecules

97

classes of chemical reactions

decomposition
synthesis
exchange

98

decomposition

large molecule breaks down into two or more smaller ones

99

synthesis

two or more small molecules combine to form a larger one

100

exchange

two molecules exchange atoms or groups of atoms

101

reversible reaction

can go in either direction under different circumstances

102

law of mass action

determines direction of the reaction
proceeds from the side of the equation with greater quantity of reactants to the side with lesser quantity

103

favorite reaction

CO2 + H2O --- H2CO3 --- HCO3- + H+
most common equation in book
carbon dioxide + water --- carbonic acid --- bicarbonate ion + hydrogen ion

104

reaction rates

molecular motion and collisions

105

reaction rates affected by

concentration
temperature
catalysts
all three increase reaction rates

106

metabolism

all chemical reactions in the body

107

Equilibrium

exists in reversible reactions when the ratio of products to reactants is stable

108

catabolism

breaking down - energy releasing

109

anabolism

building up - energy storing

110

oxidation

any reaction in which a molecule gives up electrons and releases energy

111

oxidizing agent

takes the electrons

112

reduction

chemical reaction in which a molecule gains electrons and energy

113

reducing agent

donates electron

114

organic chemistry

study of compounds of carbon

115

4 categories of carbon compounds

–carbohydrates
–lipids
–proteins
–nucleotides and nucleic acids

116

Organic Molecules and Carbon

4 valence electrons
carbon atoms bind readily with each other
carbon backbones

117

functional groups

general

•small clusters of atoms attached to carbon backbone
•determines many of the properties of organic molecules

118

functional groups

5

hydroxyl, methyl, carboxyl, amino, phosphate

119

hydroxyl

---OH
sugars, alcohols

120

methyl

---CH2
fats, oils, steroids, amino acids

121

carboxyl

---COOH
amino acids, proteins

122

amino

---NH2
amino acids, proteins

123

phosphate

---H2PO4
nucleic acids, ATP

124

Macromolecules

very large organic molecules
proteins, DNA

125

polymers

molecules made up of a repetitive series of identical or similar subunits called monomers

126

Monomers

an identical or similar subunits

127

Polymerization

joining monomers to form a polymer
dehydration synthesis
hydrolysis

128

dehydration synthesis

dehydration synthesis (condensation) is how living cells form polymers

129

hydrolysis

opposite of dehydration synthesis
Splitting a polymer (lysis) by the addition of a water molecule (hydro)

130

dehydration synthesis

dehydration synthesis (condensation) is how living cells form polymers
Monomers covalently bond together to form a polymer with the removal of a water molecule

131

names of carbohydrates

–word root „sacchar-’
–the suffix ‟-ose’

132

monosaccharide

simplest form of carbohydrate or simple sugars
glucose, fructose and galactose
–same molecular formula -C6H12O6
•isomers

133

disaccharides

sugars composed of two monosaccharaides
sucrose, lactose and maltose

134

sucrose

glucose + fructose

135

lactose

glucose + galactose

136

maltose

glucose + glucose

137

Polysaccharides

long chains of glucose
Glycogen, Starch, Cellulose

138

glycogen

energy storage polysaccharide made in the body
only polysaccharide found in body tissue

139

starch

corresponding energy storage polysaccharide of plants

140

cellulose

structural polysaccharide that gives strength to cell walls in plants

141

Carbohydrate Functions

quickly mobilized source of energy
–all digested carbohydrates converted to glucose

142

glycolipids

external surface of cell membrane

143

lipids

hydrophobic organic molecule
–composed of carbon, hydrogen and oxygen
–with high ratio of hydrogen to oxygen

144

primary types of lipids

5

fatty acids
triglycerides
phospholipids
eicosanoids
steroids

145

Fatty Acids
Classified

–saturated
–unsaturated
-Monounsaturated
–polyunsaturated
–essential fatty acids

146

saturated

carbon atoms saturated with hydrogen

147

unsaturated

contains C=C bonds without hydrogen

148

Monounsaturated

single C=C bond

149

polyunsaturated

contains many C=C bonds

150

essential fatty acids

obtained from diet, body can not synthesize

151

triglycerides

neutral fats
molecule with three fatty acids covalently bonded to a glycerol

152

triglycerides

Primary Function

energy storage, insulation and shock absorption (adipose tissue)

153

triglycerides at room temperature

when liquid called oils
when solid called fat

154

Amphiphilic

–fatty acid “tails” are hydrophobic
–phosphate “head” is hydrophilic

155

phospholipids

similar to triglycerides but have a phosphate group in place of one of the fatty acids
structural foundation of cell membrane

156

eicosanoids

20 carbon compounds derived from arachidonic acid
includes prostaglandins

157

steroids

is a lipid with 17 of its carbon atoms arranged in four rings

158

cholesterol

parent steroid from which other steroids are synthesized
synthesized only by animals
–important component of cell membranes
–required for proper nervous system function

159

good and bad cholesterol

HDL
LDL

160

HDL

high-density lipoprotein –“good” cholesterol

161

LDL

low-density lipoprotein –“bad” cholesterol

162

protien

a polymer of amino acids

163

amino acid

central carbon with 3 attachments
–amino group (NH2), carboxyl group (COOH) and radical group (R group)

164

peptide

any molecule composed of two or more amino acids joined by peptide bonds

165

peptide bond created by

Dehydration synthesis

166

Peptides named for the number of amino acids

dipeptides have 2 amino acids but only 1 peptide bond

167

peptide bond

joins the amino group of one amino acid to the carboxyl group of the next

168

primary structure

protein's sequence amino acid which is encoded in the genes

169

secondary structure

coiled or folded shape held in place by hydrogen bonds

170

tertiary structures

formed by further bending and folding into various shapes

171

quaternary structure

association of 2 or more polypeptide chains with each other

172

conformation

unique three dimensional shape of protein crucial to function

173

Denaturation

extreme conformational change that destroys function
•extreme heat or pH

174

Conjugated Proteins

Proteins that contain a non-amino acid moiety called a prosthetic group
•Hemoglobin contains four complex iron containing rings called a heme moieties

175

protein functions

7

structure
communications
membrane transport
catalysis
recognition and protection
movement
cell adhesion

176

structure

keratin and collagen

177

communications

some hormones and other cell-to-cell signals are proteins

178

membrane transport

some proteins for channels in cell membranes others act as carriers

179

catalysis

most metabolic pathways controlled by enzymes that function as catalysts

180

recognition and protection

glycoproteins in immune recognition and response

181

cell adhesion

bind cells to each other

182

movement

motor proteins -proteins with their ability to change shape repeatedly are the basis for all movement

183

enzymes

proteins that function as biological catalysts
–permit reactions to occur rapidly at normal body temperature

184

substrate

the substance an enzyme acts upon

185

Enzymes Naming Convention

–named for substrate with -ase as the suffix
•amylase enzyme digests starch (amylose)

186

activation energy

energy needed to get a reaction started

187

active site

pocket on the enzyme surface

188

Enzyme Structure and Action

Substrate approaches active site on enzyme molecule
•Substrate binds to active site forming enzyme-substrate complex
Enzyme breaks covalent bonds between monomers in substrate

189

enzyme-substrate complex

substrate binds to an enzyme

190

reaction products

result of an enzymatic reaction

191

enzyme-substrate specificity

allows only one specific substrate to bind at an active site
highly specific fit –‟lock and key‟

192

Enzymatic Action

•Reusability of enzymes
–enzymes are not consumed by the reactions
•Astonishing speed
–one enzyme molecule can consume millions of substrate molecules per minute

193

cofactor

–about 2/3rds of human enzymes require a nonprotein cofactor

194

Coenzymes

organic cofactors derived from water-soluble vitamins (niacin, riboflavin)

195

Factors that change enzyme shape

–pH and temperature
–enzymes vary in optimum pH
–temperature optimum for human enzymes –body temperature (37 degrees C)

196

metabolic pathways

a chain of reactions with each usually catalyzed by a different enzyme

197

nucleotides

organic compounds with 3 components:
nitrogenous base
a monosaccharide
one or more phosphate groups

198

adenosine triphosphate
ATP

best know nucleotide
–adenine (nitrogenous base)
–ribose (sugar)
–phosphate groups (3)

199

Adenosine Triphosphate (ATP)

•body's most important energy-transfer molecule
•briefly stores energy gained from exergonic reactions
•releases it within seconds for physiological work
•holds energy in covalent bonds
–2nd and 3rd phosphate groups have high energy bonds ~

200

Cyclic adenosine monophosphate (cAMP)

cAMP becomes “second messenger” within cell

201

nucleotides

components

3 components of nucleotides
–nitrogenous base (single or double carbon-nitrogen ring)
–sugar(monosaccharide)
–one or more phosphate groups

202

adenosine triphosphate
ATP
components

best know nucleotide
–adenine (nitrogenous base)
–ribose (sugar)
–phosphate groups (3)

203

deoxyribonucleic acid

DNA
constitutes genes
•instructions for synthesizing all of the body's proteins
•transfers hereditary information from cell to cell and generation to generation

204

ribonucleic acid

RNA
3 types
–messenger RNA, ribosomal RNA, transfer RNA
–carries out genetic instruction for synthesizing proteins
–assembles amino acids in the right order to produce proteins

205

a-

not

206

aero-

oxygen

207

amphi-

both

208

caloro-

heat

209

collo-

glue

210

hydro-

water

211

-mer

part

212

mono-

one

213

oligo-

few

214

-philic

loving