Chemistry of Life - saddleback.edu€¦ · © 2012 Pearson Education, Inc. All Matter Consists of...
Transcript of Chemistry of Life - saddleback.edu€¦ · © 2012 Pearson Education, Inc. All Matter Consists of...
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Chemistry of
Life
Biology 20
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Biological OrderBiological Order
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All Matter Consists of Elements
• Chemistry is the study of matter• Matter is
» Anything that has mass and occupies space
» Composed of elements
• Elements
• Cannot be broken down to a simpler form
• Periodic table of elements: lists all known elements
• Compound• 2 or more elements
• Fixed ratio
• Water (H2O), NaCl
Na+ + Cl- = NaClCompound formation
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© 2012 Pearson Education, Inc. Figure 2.2
Groupnumber
Atomicnumber
Element symbol
Atomic mass
Nonmetals
Metals
Transition elements
Lanthanides
Actinides
Metals Nonmetals
Periodic Table
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Elements in the body
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Trace Elements
• Required in small
quantities• Iron (Fe)
• Iodine (I)
• Boron (B)
• Zinc (Zn)
• Copper (Cu)
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Fortified Foods
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Deficiencies
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Which of the following elements do you need
in small quantities to help bind oxygen?
A. Carbon
B. Oxygen
C. Sodium
D. Iron
E. Lead
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Atoms smallest functional unit of elements
• Charges: (+) proton
(-) electron
(0) neutron
• Mass in Daltons:
protons 1
neutrons 1
electrons 1/1000
Electron cloud
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© 2012 Pearson Education, Inc. Figure 2.3
Electron
Proton
Shell
Neutron
Nucleus
a) Hydrogen1 proton
b) Oxygen8 protons8 neutrons8 electrons
in 2 shells
c) Sodium11 protons11 neutrons11 electrons
in 3 shells
Structure of
Atoms
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ATOMS Atomic & Mass Number
• Atomic number
# protons
• Atomic mass or mass number
# of protons + # neutrons
• Neutral atom• # protons = # electrons
6 C12
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Electron Orbital
• Arranged in shells
• Chemical property outmost shell
• Full electron shell 8
– Exception: 1st shell 2
HYDROGEN (H)
Atomic number = 1CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8Phosphorus (P)
Atomic number = 15
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Unfilled Electron Orbital
• Gain, lose or share electrons
• How many electrons do each of the
following need to have a full orbital?
HYDROGEN (H)
Atomic number = 1CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8Phosphorus (P)
Atomic number = 15
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Electron Configurations
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Isotopes
• Different # of neutrons
• Same # of protons & electron
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Radioactive Isotopes
• Dangerous unstable• Emits energy radiation
• Usefulness:• Imaging (PET scan)
• Metabolic tracers
• Dating fossils
• Power supply pacemakers
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Isotopes2.1 From Atoms to Molecules
Figure 2.3 Medical uses for
low-level radiation.
a.
larynx
thyroid gland
trachea
missing
portion
of organ
2.3a: © Biomed Commun./Custom Medical Stock Photo; 2.3b(patient): © National Institutes of Health; 2.3b(scan):
© Mazzlota et al./Science Source
b.
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What is the atomic mass of helium?
A. 1
B. 2
C. 3
D. 4
E. none
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How many electrons does He (Helium)
have?A. 1
B. 2
C. 3
D. 4
E. none
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Chemical Bonds
• Between elements
Covalent bonds
Ionic bonds
• Between molecules
Hydrogen bonds
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Covalent Bond Types
• Sharing of electrons
• Non-polar covalent• Equal sharing
• Polar covalent• Unequal sharing
• Animation – covalent bond
Figure 2.5
Writtenformula
Structural representation
Structuralformulawithcovalentbond
Hydrogen
(H2)
Oxygen
(O2)
Water(H2O)
Two single
covalent bonds
Single covalent bond
Double covalent bond
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Ionic Bond
• Electron transfer
• Ion: atom with a charge (+ or - charge)
• Cation: + charge
• Anion: - charge• Animation
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Electrolytes
• Free ions in solution
• Physiologically
important ones:
• Examples:
Na+, K+, Ca2+, Mg2+,
Cl−, HPO42−, HCO3
−
Hydration room
LA Times article –
Paula Newby Frazer
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Hydrogen Bond
• Occurs BETWEEN molecules
• Opposite charges
• Importance:
– Water & its unique properties
– DNA structure
– Temporary communication• Animation – water structure
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Figure 2.7
Molecule
Oxygen (O)
Hydrogen (H)
Water Ice
Hydrogen Bond between H2O
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Water
• 75% of Earth’s surface
• 70-95% of living organisms
• Polar molecule – why?
• 3 forms (solid/liquid/gas)
• 5 unique properties
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Properties of Water
1) Cohesiveness
• Cohesion: sticks to H2O
• Adhesion: ability to cling
• Surface Tension: ability to
stretch or break liquid’s surface
• Importance:
– Water transport from roots to
leaves
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Properties of Water1) Cohesiveness
• Drawback:
– Premature babies Neonatal respiratory distress syndrome
(NRDS)
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Properties of Water
2) High Specific Heat– How much heat must be
absorbed or lost to raise 1 g of water 1oC?
– Heat?
– Temperature?
• Significance:– Stabilizes environment
– Prevents drastic changes in temperature
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Fig. 3-5
San Diego 72°
40 miles
Pacific Ocean
70s (°F)
80s
90s
100s
Santa Barbara 73°
Los Angeles(Airport) 75°
Burbank
90°
San Bernardino
100°
Riverside 96°
Santa Ana
84°Palm Springs
106°
Moderates/stabilizes environment
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Properties of Water
3) Heat of Vaporization
– Amt of heat absorbed to
go from liquid to a gas
• Significance
– Evaporative Cooling
• High humidity & hot days
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Properties of Water
4) Density of Water
• Solid water (ice)
– Crystal structure is
spacious
– Fewer molecules/equal
vol.
– Less dense floats
• Significance
– Insulation for aquatic
organisms
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H2O molecule
Liquid water
Ice
Figure 2.13
Properties of Water
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Figure 2.8
Ionsin solution
Moleculesof water
Salt crystal
5)Versatile Solvent• Ionic or polar
• Significance• Chemical reactions
• Digestion
Properties of Water
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Water as a Solvent
• Solvent
• Solute:
• Solution:
• Aqueous
solution:
• Substance that does the
dissolving
• Substance being dissolved
• A mixture of 2 or more
substance
• Water is the solvent
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Versatile solvent uses
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Dissociation of Water
H2O H+ + OH-
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Figure 2.8
Ionsin solution
Moleculesof water
Salt crystal
5)Versatile Solvent• Ionic or polar
• Significance• Chemical reactions
• Digestion
Properties of Water
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Which of the following is the solute?
A.
B.
C.
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Which of the following is the solution?
A.
B.
C.
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pH scale
• pH = - log [H+]
• pH = 7 neutral
• pH > 7 basic/alkaline
• pH < 7 acidic
• Inverse relationship
– Increase [H+] decrease pH
– Decrease [H+] increase pH
• pH: 6 – 8/9
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High H+ concentration
Low H+ concentration
HCl—hydrochloric acid (0.0)
Stomach acid (1.6–1.8) Lemon juice (2.0)
Cola, beer, wine,
orange juice (3.0)
Tomato juice (4.0)
Coffee (5.0)
Rain (5.7)
Urine (4.6–8.0)
Saliva (6.7–7.0) Pure water (7.0)
Blood, tears (7.35–7.45)
Pancreatic juice (7.5–8.0)
Seawater (7.8) Bile (7.8–8.6)
Baking soda (8.1)
Phosphate-based
detergents (9.0)
Soap (10.0)
Household ammonia (11.5)
Household bleach (12.5)
NaOH—sodium hydroxide (14.0)
Milk (6.6)
Figure 2.14
H+ concentration
(moles per liter)pH
value
Strong
Base
Strong
Acid
pH scale
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pH Scale
1. pH values of acidic solutions
2. pH values of basic (alkaline) solutions
3. point at which H+ equal OH-
4. progressing from a weak to strong acid
5. progressing from a weak to a strong base
6. results of adding more hydrogen to a solution
a b
c d
0 7 14
(e) (f) (g)
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Acids & Bases
• Acids• Donate H+
• Lowers pH
• Bases• Accepts H+
• Raises pH
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Buffers
• Minimizes changes in pH
• Accept H+ when in
excess
• Donate H+, when
depleted
• Carbonic Acid/
Bicarbonate• H2CO3 carbonic acid
• HCO3- bicarbonate
• Blood pH = 7.4 + 0.05
• If pH falls below 7.35
• If pH rises above 7.45
CO2 + H2O H2CO3 HCO3- + H+
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Figure 42.32a
Body tissue
Capillary
wall
Interstitial
fluid
Plasma
within capillary
CO2 transport
from tissuesCO2 produced
CO2
H2O
H2CO3 HbRedbloodcell Carbonic
acid
Hemoglobin (Hb)
picks up
CO2 and H+.
H+HCO3
Bicarbonate+
HCO3
To lungs
CO2
CO2
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Figure 42.32b
HCO3
CO2 transport
to lungs
H2CO3
H2O
H++
Hb
Hemoglobinreleases
CO2 and H+.
CO2
Alveolar space in lung
To lungs
HCO3
CO2
CO2
CO2
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Because of a sudden hormonal imbalance,
a patient’s blood pH was tested and was
7.5. What does this pH value mean?
A. This is more acidic than normal blood
B. It represents a weak alkaline fluid
C. This is caused by a release of large
amounts of H+ into the system
D. H2CO3 HCO3- + H+ is pushed to the left
E. This is probably caused by excess CO2 in
the blood
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The Organic Molecules of Living Organisms
• Carbon, the building
block of living things• Comprises 18% of the body
by weight
• Forms four covalent bonds
• Can form single or double
bonds
• Can build micro- or
macromolecules
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Organic chemistry carbon
• Atomic # 6
• 4 valance electrons
• Bonds with: C, H, O, N
The Organic Molecules of Living Organisms
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2_Page35
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Hydrocarbons
• Consists of C & H only
• Energy stores
• Found:
– Petroleum
– Fatty acids
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Functional Groups
Functional groups song
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Functional Groups
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Large Biological Molecule Terms
• 4 classes of bio. molecules– Carbohydrates (sugars)
– Proteins
– Nucleic acids
– Lipids
• Monomers (subunits): single-part– Building blocks for macromolecules
• Polymers: many-parts– Composed of many monomers
– Covalently bonded
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© 2012 Pearson Education, Inc. Figure 2.13
Sugars
Hyd
roly
sis
De
hyd
rati
on
syn
the
sis
Carbohydrate
Energy Energy
Dehydration
Synthesis
• Remove H2O
• Form bonds
• Polymer
formation
• Anabolic
Hydrolysis
• Add H2O
• Break bonds
• Catabolic
• “Digestion”
animation
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Figure 2.15
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Dehydration reactions (synthesis) are used in
forming which of the following compounds?
A. Fats
B. Proteins
C. Polysaccharides
D. Nucleic acids such as DNA
E. All of these
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Carbohydrates: Used for Energy and Structural
Support
• General formula: Cn(H20)n
• Monosaccharides: “simple” sugars• Glucose
• Fructose
• Galactose
• Ribose
• Deoxyribose
Ribose Deoxyribose
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Carbohydrates
• Disaccharides• Dehydration synthesis
• Examples:
» Maltose
» Lactose
» Sucrose
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© 2012 Pearson Education, Inc. Figure 2.14b
Glucose(a monosaccharide)
Fructose (a monosaccharide)
Sucrose (a disaccharide)
b) Two 6-carbon monosaccharides (glucose and fructose) arejoined together by dehydration synthesis, forming sucrose.
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Figure 2.17
Polysaccharides: thousands of
monosaccharides joined in
chains and branches
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Polysaccharides Store Energy
• Polysaccharides: thousands of
monosaccharides joined in chains and
branches
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Storage Polysaccharides
• Starch– Plant storage form
– Roots & tubers
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Figure 2.15
Glucose Glucose
Dehydrationsynthesis
a) Glycogen is formed bydehydration synthesis fromglucose subunits.
b) A representation of the highly branched nature of glycogen.
Glycogen granules
c) A portion of an animal cell showing granules of stored glycogen
(blue). The large pink structures are mitochondria.
Storage Polysaccharides
Glycogen
– More branched
– Animal storage form
– Liver & skeletal muscles
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Structural Polysaccharides
• Cellulose
– Most abundant polysacc.
– Plant structural support
– Different bond arrangement
• Chitin
– Exoskeleton of arthropods
– Cell wall of fungi
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Lactose, found in milk, is formed by joining
glucose and galactose. How would you
classify this lactose molecule?
A. A monosaccharide
B. A polysaccharide
C. A disaccharide
D. A pentose sugar
E. Tasty?
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Proteins
• Monomers: amino acids
• 20 different amino acids
– Amine & carboxyl grps
• Peptide bond
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© 2012 Pearson Education, Inc. Figure 2.20
Amino
acids
Isoleucine (Ile) Alanine (Ala) Valine (Val)
Polypeptide
Dehydration synthesis for polymer formation
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Figure 2.19
Amino acids with nonpolar R groups
Alanine (Ala)
Isoleucine (Ile)
Leucine (Leu)
Methionine (Met)
Phenylalanine (Phe)
Proline (Pro)
Tryptophan (Trp)
Valine (Val)
Amino acids with negatively charged R groups
Aspartic acid (Asp)
Glutamic acid (Glu)
Amino acids with uncharged polar R groups
Asparagine (Asn)
Cysteine (Cys)
Glutamine (Gln)
Glycine (Gly)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
Amino acids with positively charged R groups
Arginine (Arg)
Histidine (His)
Lysine (Lys)
20 Amino Acids
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4 Levels of Protein Structure
Figure 2.21
Primary structure
(sequence ofamino acids)
Secondarystructure
(orientation inspace of chainsof amino acids)
Alpha helix Beta sheet Random coil
Alpha helix
Beta sheet
Random
coil
Hydrogen
bonds
Tertiary
structure
(three-dimensional
shape)
Quaternarystructure
(number of polypeptidechains and their
association)
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Figure 2.19
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4 Levels of Protein Structure
• Primary level
– Amino acids linked w/ peptide
bonds (polypeptide)
– Linear sequence
– Errors in DNA sequence
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4 Levels of Protein Structure
• Secondary level
– Results from H-bonds
– Alpha helix
– Beta-pleated sheets
Figure 2.21bHydrogenbonds
Secondarystructure
(orientation in
space of chains
of amino acids)
Alpha helix Beta sheet Random coil
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4 Levels of Protein Structure
• Tertiary level
– 3-dimenstional shape
– Globular or fibrous
shape
Figure 2.21c Alpha helix
Beta sheet
Random
coil
Tertiarystructure
(three-dimensional
shape)
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4 Levels of Protein Structure
• Quaternary level
– 2 or more polypeptide chains
aggregated together
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Denaturation
• Bond disruption• Inactive protein
• Causes:
» Excessive heat
» Wrong pH
» Wrong ionic concentrations
» Organic solvents
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Figure 2.21
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8 Protein Functions
1. Structural protein
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8 Protein Functions
2. Storage protein
albumin
cotyledon
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8 Protein Functions
3.Transport protein
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8 Protein Functions
4. Hormonal protein
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8 Protein Functions
5. Receptor protein
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8 Protein Functions
6. Contractile protein
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8 Protein Functions
7. Defense proteins (antibodies)
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8 Protein Functions
8. Enzymatic proteins
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8 Protein Functions
1. Structural
2. Storage
3. Transport
4. Hormonal
5. Receptor
6. Contractile
7. Defense
8. Enzymatic
1. Connective tissue (tendons,
ligaments)
2. Albumin, casein
3. Hemoglobin, ion channels, etc
4. Insulin
5. Detects other signals (stimuli)
6. Movement
7. Immune system (antibodies)
8. Increase chemical reactions
(Digestion, cellular respiration)
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Which of the following is NOT a protein?
A. Hemoglobin
B. Cholesterol
C. An antibody
D. An enzyme
E. insulin
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Nucleic Acids Store Genetic Information
• Nucleotides: building blocks of nucleic
acids
• Each nucleotide contains
– 5 carbon sugar
• DNA nucleotides: deoxyribose
• RNA nucleotides: ribose
– Nitrogenous base
– Phosphate group
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Figure 2.22
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© 2012 Pearson Education, Inc. Figure 2.23
Adenine (A)
Phosphate
Deoxyribose
Thymine (T)Cytosine (C) Guanine (G)
5 Nitrogenous Bases
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Nucleic Acids Store Genetic Information
• Two main types:• DNA: deoxyribonucleic acid
• RNA: ribonucleic acid
• Functions• Store genetic information
• Provide information used in making proteins
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Base pair
Phosphate
Sugar
Nucleotide
Figure 2.24
Nucleic Acids Store Genetic Information
• Structure of DNA (deoxyribonucleic acid)• Double–stranded (dbl helix)
• Nucleotides contain
– Deoxyribose (sugar)
– Nitrogenous bases» Adenine
» Guanine
» Cytosine
» Thymine
• Pairing
» Adenine - Thymine
» Guanine - Cytosine
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Nucleic Acids Store Genetic Information
• Structure of RNA (ribonucleic acid)• Single–stranded
• Nucleotides contain
– Ribose
– Nitrogenous bases
» Adenine
» Guanine
» Cytosine
» Uracil
Figure 2.25
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DNA RNA Protein
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ATP Carries Energy
Figure 2.26a
Triphosphate
Adenosine
Ribose
Adenine (A)
a) The structure of ATP.
• Structure and function of adenosine
triphosphate (ATP)• Nucleotide – adenosine triphosphate
• Universal energy source
• Break the bonds releases energy
• High energy bond
• ATP → ADP + P + energy
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Figure 2.26b
Hydrolysis of ATP
produces useful energy
for the cell
AdenosineAdenosine
Energy for ATP synthesis
comes from food or body
stores of glycogen or fat
b) The breakdown and synthesis of ATP.
The breakdown (hydrolysis) of ATP yields
energy for the cell. The reaction is reversible,
meaning that ATP may be resynthesized
using energy from other sources.
ATP Cycle
• Where does the energy
Come from for ATP?
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Nucleic Acid Function
• DNA: instructions for making proteins via RNA• Information storage
• Information transfer
• RNA: instructions for making proteins • Protein synthesis DNA → RNA → Proteins
• Proteins: direct most of life’s processes
• Transfer of chemical energy
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RNA differs from DNA because:
A. RNA contains Uracil and DNA does not
B. RNA is more stable and broken down by
enzymes less easily than DNA
C. RNA has the 6 carbon sugar
D. RNA is double stranded
E. RNA is a much larger molecule than DNA
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Lipids: Insoluble in Water
• Three important classes of lipids
– Triglycerides: energy storage molecules
– Phospholipids: cell membrane structure
– Steroids: hormones, communication
– Waxes: waterproofing, decrease water loss
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Triglycerides
• Includes fats and oils
• Composed of glycerol and three fatty acids
– Fatty acids
• Saturated (in fats)
• Unsaturated (in oils)
• Stored in adipose tissue
• Energy storage molecules
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Figure 2.24
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© 2012 Pearson Education, Inc. Figure 2.16
Glycerol
Saturatedfatty acid
a) Triglycerides (neutral fats) aresynthesized from glycerol andthree fatty acids by dehydrationsynthesis.
b) Triglycerides with saturated fatty acids have straight tails, allowing them to pack closely together.
c) Triglycerides with unsaturated fatty acids have kinked tails, preventing them from packing closely together.
Triglycerides
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© 2012 Pearson Education, Inc. Figure 2.16a
Glycerol
Saturatedfatty acid
a) Triglycerides (neutral fats) aresynthesized from glycerol andthree fatty acids by dehydrationsynthesis.
Triglycerides
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© 2012 Pearson Education, Inc. Figure 2.16b
b) Triglycerides with saturated fatty acids have straight tails, allowing them to pack closely together.
Saturated Fats
• Max. # of H to C ratio
• No DBL bonds btn C’s
• Solid @ room temp
• Most animal fats
• Lard, butter, grease
Triglycerides
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Figure 2.16c
c) Triglycerides with unsaturated fatty acids have kinked tails, preventing them from packing closely together.
• Unsaturated Fats• 1 or more DBL bonds btn C’s
• Tails kinked (C=C)
• Liquid @ room temp
• Most plant fats
• Corn, olive, peanut oils
Triglycerides
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Fats
• Saturated
– Max. # of H to C ratio
– No DBL bonds btn C’s
– Solid @ room temp
– Most animal fats
Lard, butter, grease
• Unsaturated
– 1 or more DBL bonds btn
C’s
– Tails kinked (C=C)
– Liquid @ room temp
– Most plant fats
Corn, olive, peanut oils
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Phosphate
Glycerol
Fatty acid
Membrane structure
Polar head
Nonpolar tail
Figure 2.17
Phospholipids
Hydrophilic head
Hydrophobic tails
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Steroids
a) Cholesterol:
A normal component ofthe cell membrane.
b) Estrogen (estradiol):
Female sex hormonesynthesized from cholesterol.
c) Testosterone:
Male sex hormone
synthesized from cholesterol.
Figure 2.18
• Structure
– Composed of four carbon rings
• Examples:• Cholesterol
• Hormones
– Estrogen
– Progesterone
– Testosterone
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Sex hormones
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Lipid Functions
• Energy storage
• Insulation
• Cushioning organs
• Prevents water loss
• Chemical messengers
• Membranes
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Lipids that are liquid at room temperature:
A. Are fats
B. Contain more hydrogen atoms than lipids that are
solid at room temperature
C. If polyunsaturated, contain several double bonds in
their fatty acid chains
D. Lack glycerol
E. Are not stored in cells as triglycerides
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Table 2.4