Download Chapter 3 Notes – Carbon and the Molecular Diversity of Life

Chapter 3 Notes – Carbon and the Molecular Diversity of Life
Campbell Biology In Focus
Preteach Vocabulary
3.1 – Carbon Atoms
organic compound
macromolecules
valence
hydrocarbons
functional groups
adenosine triphosphate
3.2 – Polymers
polymer
monomer
enzyme
dehydration (synthesis) reaction
hydrolysis
3.3 – Carbohydrates
carbohydrate
monosaccharide
disaccharide
glycosidic linkage
polysaccharide
starch
glycogen
cellulose
chitin
3.4 – Lipids
lipids
fat
fatty acid
triacylglycerol
saturated fatty acid
unsaturated fatty acid
phospholipid
steroids
cholesterol
3.5 – Proteins
catalysts
polypeptide
protein
amino acid
peptide bond
globular
fibrous
primary structure
secondary structure
alpha helix
beta pleated sheet
tertiary structure
hydrophobic interaction
disulfide bridges
quaternary structure
sickle-cell disease
denaturation
x-ray crystallography
3.6 – Nucleic Acids
gene
nucleic acids
deoxyribonucleic acid
ribonucleic acid
polynucleotides
nucleotides
pyrimidine
purine
deoxyribose
ribose
double helix
antiparallel
Carbon Compounds & Life
- living things are made up of CHNOPS
- organic compound – compound containing carbon
- four main classes of compounds in living things:
o carbohydrates
o lipids
o proteins
o nucleic acids
- structure important to function
Concept 3.1 – Carbon atoms can form diverse molecules by bonding to four other atoms
- periodic table is Appendix B-1
- key to an atom’s chemical characteristics is its electron configuration (orbital notation)
o carbon:
o carbon behaves like it is sp3 not s2p2
o sp3 hybridization is more stable and gives carbon its4 electrons available to form 4 covalent bonds in a basic
tetrahedral shape
- you must be able to draw & understand molecular, structural, an ball-and-stick models (we’ll practice this in a lab)
- molecules are 3 dimensional; they have no left, right, top, bottom, back, front
- valence number is equal to the number of electrons involved in bonding which equals the number of covalent bonds
that can be formed (remember that covalent bonds are formed from the sharing of electrons between two
nonmetals)
H=1
O=2
N=3
C=4
(H1+) (O2-)
(N3-)
**H,O,and N all form ions in the presence of a less electronegative atom; typically, these less electronegative atoms are
metals; covalent bonds form when electronegativities are similar
-
a line representing a bond is actually representing two electrons; bonds are not physical “bars” you could grab on to
with teeny tiny hands
- study Figures 3.2 & 3.4
READ “Molecular Diversity Arising from Variation in Carbon Skeletons”
The Chemical Groups Most Important to Life
- properties of organic molecules depend on:
o 1) arrangement of its carbon skeleton
o 2) chemical groups attached to carbon skeleton
- functional groups – Figure 3.5 – MEMORIZE
o affect function because directly involved in chemical reactions
o complete table below using p. 43 & 44
Chemical Group
Structural Formula
Compound Name
Polar/Nonpolar
Other
hydroxyl
carbonyl
carboxyl
amino
sulfhydryl
phosphate
methyl
ATP: An Important Source of Energy for Cellular Processes
- adenosine triphosphate – ATP
o when ATP reacts with water, an inorganic phosphate (P i) is cleaved off and energy is released that can be
used by the cell
Complete Concept Check 3.1
Concept 3.2 – Macromolecules are polymers, built from monomers
- carbohydrates, proteins, and nucleic acids are polymers
- polymer – long molecule consisting of many similar or identical building blocks (monomers) linked by covalent bonds
The Synthesis and Breakdown of Polymers
- making and breaking polymers involves enzymes – proteins that speed up
chemical reactions
- dehydration (synthesis) reactions – reaction in which monomers are covalently
bonded together and water is formed/lost; Figure 3.6a; sometimes called
condensation reactions
- hydrolysis – process that breaks polymers down into monomers using water;
Figure 3.6b
The Diversity of Polymers
- small molecules common to all organisms are ordered into unique
macromolecules often composed of repeating subunits called monomers
READ p. 45
Complete Concept Check 3.2
Concept 3.3 – Carbohydrates serve as fuel and building materials
- carbohydrates – sugars and polymers of sugars
o monosaccharides – simple sugars; monomers of complex carbohydrates
o disaccharides – double sugars
o polysaccharides – macromolecules; polymers of sugars joined by dehydration reactions
Sugars
- monosaccharides – have molecular formulas that are a multiple of CH2O
o ex) glucose – C6H12O6
 has a carbonyl and multiple hydroxyl groups
 one of several hexoses
 name ends in –ose like most sugars
 only linear when in crystalline form
 ring structure when in aqueous solution Figure 3.8
 along with other small sugars, serves as a major nutrient for cells
 ex) cellular respiration, synthesis of amino acids
 if not used, stored
1:2:1 ratio C:H:O
-
disaccharides – one storage form of glucose (or other small sugar)
 joined by glycosidic linkage – covalent bond formed by a dehydration reaction; Figure 3.9
 ex) sucrose – composed of glucose and fructose
 called transport sugars – allow molecules to be moved from place to place in an organism
without being used up in a metabolic pathway
 also lactose & maltose
Polysaccharides
- polysaccharides – macromolecules composed of hundreds to thousands of monosaccharides joined by glycosidic
linkages
o storage
 starch – plant storage form of carbohydrate
 Figure 3.10
 broken down by hydrolysis
 digestible by most animals
 1-4 linkage
 amylose –unbranched form of starch
o amylopectin – more complex starch with 1-6 linkages at the branching points
 glycogen – animal storage form of carbohydrate
 extensively branched
 stored mainly in liver and muscle cells
 also hydrolyzed when glucose is needed by the organism for energy
o short-term only – depleted in about a day if no eating
o structural
 cellulose – structural polysaccharide in plant cell walls
 most abundant organic cpd on earth
  1-4 linkages
 Figure 3.11
 distinct differences in 3D shape resulting from beta linkages makes cellulose undigestible
 never branches; straight molecule
 straight molecules group together into microfibrils
 Why is cellulose “fiber” in the animal (human) diet?
 organisms that can digest cellulose include a few prokaryotes and protists and some fungi
o prokaryotes/protists – live in the digestive tracts of herbivores
o fungi – break down cellulose in a decomposition process of plants
3.4 – Lipids are a diverse group of hydrophobic molecules
- lipids – grouped together because they mix poorly if at all with water
- they’re nonpolar
- hydrophobic due to the hydrocarbon regions
- vary in form and function
- include fats, phospholipids, steroids, and pigments
Fats
- fats – constructed from 2 kinds of smaller molecules glycerol and fatty acids
o glycerol – alcohol – 3 carbons, each with a hydroxyl group
o fatty acid – 16-18 carbon chain with carboxyl at the end of the chain
o Figure 3.12
o triglycerides – 3 fatty acids linked to one glycerol
 saturated – holds all the hydrogen it possibly can because it contains no double or triple bonds
 straight chains allow the molecules to pack tightly together
 usually solids at room temperature
 mostly come from animals
 unsaturated – is not holding all the hydrogen it possibly can because it contains at least one double
or triple bond
 the chains bend or kink at the double/triple bonds
 generally liquids at room temperature
 mostly come from plants or fish
o primary function is energy storage
o Figure 3.13
Phospholipids
- phospholipids – essential for cells because they are major constituents of cell membranes
o Figure 3.14
o glycerol with a phosphate and 2 fatty acid chains
o creates a polar/hydrophilic end of the molecule
o nonpolar/hydrophobic end of the molecule
o self-assemble into double layer called “lipid bilayer”
Steroids
- steroids – lipids characterized by a carbon skeleton consisting of four fused rings
o Figure 3.15
o distinguished by the chemical groups attached to the rings
o cholesterol – crucial in animals
 component of cell membranes
 precursor from which other steroids are synthesized
 estrogen
 testosterone
 synthesized in the liver or comes from diet
 high levels contribute to atherosclerosis, including saturated fats
Complete Concept Check 3.4
Concept 3.5 – Proteins include a diversity of structures, resulting in a wide range of functions
-
protein function is diverse – Figure 3.16
Type of Protein
Enzymatic proteins
Storage proteins
Hormonal proteins
Contractile and motor proteins
Defensive proteins
Transport proteins
Receptor proteins
Structural proteins
Function
Example
-
catalysis is one of the most important functions, carried out by enzymes – molecules that speed up reactions without
being consumed by the reaction
most structurally sophisticated molecules known
made of polymers of amino acids called polypeptides
defined as a biologically functional molecule that consists of one or more polypeptides folded and coiled into a
specific three-dimensional structure
Amino Acids
- 20 different molecules that make up polypeptide chains
- organic; contains amino group and carboxyl group
- PRACTICE DRAWING and LABELING the general structure of an amino acid (p. 52)
- STUDY Figure 3.17 – you are not trying to memorize it, but rather see the patterns and
generalities among the groups of amino acids
o
o
o
o
o
o
What criteria do nonpolar amino acids have in common?
How do they behave in water?
What criteria do polar amino acids have in common?
How do they behave in water?
What is the difference between the acid and basic amino acids besides their charge?
How do they behave in water?
Polypeptides
- formed by dehydration synthesis reactions between adjacent amino acids
- covalent bond formed between the carboxyl of one amino acid and the
amine group of another
- Figure 3.18
- each polypeptide has an N-terminus and a C-terminus
- chemical nature of the polypeptide is determined by the side chains
Protein Structure and Function
- to be a functional protein, a polypeptide chain must be folded into the
exact 3-D structure needed
- proteins can be globular or fibrous
- Figure 3.20 shows the specificity of the structure of an antibody which
allows it to function as needed
- receptor proteins also have specific structures which allow them to
function in the body
Four Levels of Proteins Structure
- Figure 3.21 illustrates and explains the 4 levels of protein structure
- primary structure – chain of amino acids held together by peptide bonds
between neighboring amino acids
- secondary structure – coils and folds of sections of the chain held in place by hydrogen bonds
o alpha helix – coil
o beta pleated sheet – fold
- tertiary structure – overall 3-D shape of the protein resulting from interactions between side chains (R groups)
o hydrophobic interaction – nonpolar side chains fold in, away from the watery environment – stabilized by van
der Waals
o dipole-dipole – forces of attraction between polar side chains
o hydrogen bonds
o ionic bonds
o disulfide bridges (S-S bond)
- quaternary structure – association of two or more polypeptides present in some proteins
Tertiary Structure
Sickle-Cell Disease: A Change in Primary Structure
- Figure 3.22
- sickle-cell disease – inherited blood disorder resulting from the substitution of one amino acid for the normal one at a
specific site on the polypeptide for hemoglobin
What Determines Protein Structure?
- sequence of the amino acids is key to the resulting 3-D functional protein
- environment is also critical – deviations from the normal conditions of the cell can result in disruptions of the bonds
and intermolecular forces holding the protein into its normal state and resulting in it becoming nonfunctional – called
denaturation – READ p. 58-9
o pH
o salt concentration
o temperature
Protein Folding in the Cell
- complicated process with several intermediate steps
- currently an area of research and software development
- misfolding associated with disease, including Alzheimer’s, Parkinson’s, mad cow, and senile dementia
- scientists use X-ray crystallography, NMR, and bioinformatics to determine the structures
Figure 3.24 Inquiry: What can the 3-D shape of the enzyme RNA polymerase II tell us about its function?
- READ and think about the What If
Complete Concept Check 3.5
Concept 3.6 – Nucleic acids store, transmit, and help express hereditary information
- gene – discrete unit of inheritance that programs the primary structure (amino acid sequence) of the protein
- nucleic acid – polymer made of monomers called nucleotides
The Roles of Nucleic Acids
- two types
o DNA – deoxyribonucleic acid
 provides directions for its own replication
 directs RNA synthesis from its genes
 inherited from each parent as chromosomes, each
consisting of one long strand of DNA
 the cell’s software
o RNA – ribonucleic acid
 controls protein synthesis (Figure 3.25)
 messenger RNA (mRNA) – directs the production
of protein molecules at the ribosome
The Components of Nucleic Acids
- Figure 3.26
- macromolecules existing as polymers called polynucleotides
- monomers are called nucleotides
o nitrogenous base
nucleoside
o 5-carbon sugar (pentose)
o one or more phosphate groups
- nitrogenous bases
o purines – 2 rings, adenine & guanine
o pyrimidines – 1 ring, cytosine, thymine (DNA only), and uracil (RNA only)
o attached to the 1’ carbon
- pentose
o deoxyribose in DNA
o ribose in RNA
o carbons numbered with “prime” (‘)
- phosphate
o attached to the 5’ carbon
Nucleotide Polymers
- joined by phosphodiester linkage (type of covalent bond), creating a sugar-phosphate backbone
- each end is different
o 5’ carbon with phosphate
o 3’ carbon with hydroxyl
o nucleotides are joined 5’ to 3’
The Structures of DNA and RNA Molecules
- double helix – DNA structure of two strands winding around each other
- antiparallel – the two DNA strands run in opposite directions, one has the 5’ end where
the other has the 3’ end
o Figure 3.27
- hydrogen bonds – hold the two strands together by IM forces between the complementary
bases
o A=T (in DNA) or A=U (in RNA)
o C=G
- bonding between DNA and RNA is also complementary, resulting in the information in
the genes of the DNA being carried in the RNA outside of the nucleus
o also important in the codon/anticodon base-pairing between mRNA and tRNA
DNA and Proteins as Tape Measures of Evolution
- important concept in understanding biological evolutionary theory
- organisms that are closely related share DNA sequences and therefore amino acid sequences, resulting in similar
traits
Complete Concept Check 3.6
Review the Summary of Key Concepts
Complete Test your Understanding
Scientific Skills Exercise: Analyzing Polypeptide Sequence Data
Are Rhesus Monkeys or Gibbons More Closely Related to Humans?
As discussed in Concept 3.6, DNA and polypeptide sequences from closely related species are more similar to each other
than are sequences from more distantly related species. In this exercise, you will look at amino acid sequence data for
the  polypeptide chain of hemoglobin, often called -globin. You will then interpret the data to hypothesize whether the
monkey or the gibbon is more closely related to humans.
How Such Experiments are Done
Researchers can isolate the polypeptide of interest from an organism and then determine the amino acid sequence. More
frequently, the DNA of the relevant gene is sequenced, and the amino acid sequence of the polypeptide is deduced from
the DNA sequence of its gene.
Data from the Experiments
In the data below, the letters give the sequence of the 146 amino acids in -globin from humans, rhesus monkeys, and
gibbons. Because a complete sequence would not fit on one line here, the sequences are broken into three segments.
Note that the sequences for the three different species are aligned so that you can compare them easily. For example,
you can see that for all three species, the first amino acid is V (valine; see Figure 3.17) and the 146 th amino acid is H
(histidine).
Interpret the Data
1. Scan along the monkey and gibbon sequences letter by letter circling any amino acids that do not match the
human sequence. (a) How many amino acids differ between the monkey and the human sequences. _________
(b) Between the gibbon and the human? _________
2. For each nonhuman species, what percent of its amino acids are identical to the human sequence of -globin?
______________
3. Based on these data alone, state a hypothesis for which of these two species is more closely related to humans.
What is your reasoning? ______________________________________________________________________
____________________________________________________________________________________________
____________________________________________________________________________________________
4. What other evidence could you use to support your hypothesis? _______________________________________
____________________________________________________________________________________________
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