Life Substances

The Biomolecules
From food webs to the life of a cell

energy

energy

energy
Metabolism
 Chemical reactions of life
 forming bonds between molecules
 dehydration synthesis
 synthesis
 anabolic reactions
 breaking bonds between molecules
 hydrolysis
 digestion
 catabolic reactions
Examples
 dehydration synthesis (synthesis)
enzyme
+

H2O

 hydrolysis (digestion)

+
enzyme

H2O
Examples
 dehydration synthesis (synthesis)

enzyme

 hydrolysis (digestion)

enzyme
 Energy & life
 Organisms require energy to live
 where does that energy come from?
 coupling exergonic reactions (releasing energy)
with endergonic reactions (needing energy)

+ + energy
digestion

synthesis

+ + energy
 CH2OH

H O
H
H
OH H
HO OH

H OH

Carbohydrates
Energy molecules
Carbohydrates
 sugar sugar sugar sugar sugar sugar sugar sugar

Carbohydrates
 Carbohydrates are composed of C, H, O
carbo - hydr - ate
General formula: CH2O
(CH2O)x C6H12O6
 Function:
 energy energy storage
 raw materials  structural

materials
 Monomer (building block): sugars
 ex: sugars, starches, cellulose
Sugars
 Most names for sugars end in -ose
 Classified by number of carbons
 6C = hexose (glucose)
 5C = pentose (ribose)

 3C = triose (glyceraldehyde) H O
CH2OH CH2OH C

H O O H H C OH
H
H
OH 6H H 5 HO 3OH
HO OH HO H H C

H OH OH H H

Glucose Ribose Glyceraldehyde

Sugar structure
5C & 6C sugars form rings in solution

Carbons are numbered

Numbered carbons
C 6'
5' C O

4' C C1'
energy stored in C-C bonds
C3' C2'
 CH2OH
Simple & complex sugars H O
H
H
 Monosaccharides HO
OH H
OH
 simple 1 monomer sugars H OH
 glucose
Glucose
 Disaccharides
 2 monomers
 sucrose

 Polysaccharides
 large polymers
 starch
 Dehydration Synthesis=
Polymerization
 Anabolic reaction
 Produces polymer
 Monomer + Monomer  Polymer + Water

2 Monomers Bond=
Remove H2O Polymer
Building sugars
 Dehydration synthesis
monosaccharides disaccharide

| | |
glucose glucose maltose
glycosidic linkage
Building sugars
 Synthesis
monosaccharides disaccharide

| | |
glucose fructose sucrose
(table sugar)
 Hydrolysis
 Catabolic reaction
 Produces monomers
 Ex) Polysaccharides monosaccharides
 Polymer + Water  Monomer + Monomer

Separate polymer into:

Add H2O 2 monomers
Polysaccharides
 Polymers of sugars
 costs little energy to build
 easily reversible = release energy

 Function:
 energy storage
 starch (plants)
 glycogen (animals)
 structure = building materials
 cellulose (plants)
 chitin (arthropods & fungi)
Linear vs. branched polysaccharides

starch
(plant)

energy
storage

glycogen
(animal)
Polysaccharide diversity
 Molecular structure determines function
in starch in cellulose

 isomers of glucose
 structure determines function…
 Digesting starch vs. cellulose

starch
easy to enzyme
digest

cellulose
hard to
digest
enzyme
Cellulose
 Most abundant organic
compound on Earth
 herbivores can digest cellulose
 most carnivores cannot digest cellulose

 that’s why they

eat meat to get
their energy &
nutrients
 cellulose = roughage
Cow
can digest cellulose well;
no need to eat other sugars

Gorilla
can’t digest cellulose well;
must add another sugar
source, like fruit to diet
Helpful bacteria
 How can cows digest cellulose?
 bacteria live in their gut & help digest
cellulose-rich (grass) meals
 Proteins
Multipurpose molecules
Proteins
Proteins
 Most structurally & functionally diverse group
 Function: involved in almost everything
 enzymes (pepsin, DNA polymerase)
 structure (keratin, collagen)
 carriers & transport (hemoglobin, aquaporin)
 cell communication
 signals (insulin & other hormones)
 receptors
 defense (antibodies)
 movement (actin & myosin)
 storage (bean seed proteins)
Proteins
 Structure H2O

 monomer = amino acids

 20 different amino acids
 polymer = polypeptide
 protein can be one or more polypeptide
chains folded & bonded together
 large & complex molecules
 complex 3-D shape

hemoglobin

Rubisco growth
hormones
Amino acids
 Structure H O
H | ||
 central carbon
—C— C—OH
—N—
 amino group
H |
 carboxyl group (acid)

 R group (side chain)

R
 variable group
 different for each amino acid
 confers unique chemical
properties to each amino acid
 like 20 different letters of an
alphabet
 can make many words (proteins)
Sulfur containing amino acids
 Form disulfide bridges
 covalent cross links betweens sulfhydryls
 stabilizes 3-D structure

H-S – S-H
Building proteins
 Peptide bonds
 covalent bond between NH2 (amine) of
one amino acid & COOH (carboxyl) of
another
 C–N bond

H2O
dehydration synthesis

peptide
bond
Building proteins
 Polypeptide chains have direction
 N-terminus = NH2 end
 C-terminus = COOH end

 repeated sequence (N-C-C) is the

polypeptide backbone
 can only grow in one direction
Protein structure & function
 Function depends on structure
 3-D structure
 twisted, folded, coiled into unique shape

pepsin

hemoglobin

collagen
Primary (1°) structure
 Order of amino acids in chain
 amino acid sequence
determined by gene (DNA)
 slight change in amino acid
sequence can affect protein’s
structure & its function
 even just one amino acid change
can make all the difference!

lysozyme: enzyme
in tears & mucus
that kills bacteria
Sickle cell anemia

I’m But I’m

hydrophilic! hydrophobic!
Secondary (2°) structure
 “Local folding”
 folding along short sections of polypeptide
 interactions between
adjacent amino acids
 H bonds
 weak bonds
between R groups
 forms sections of
3-D structure
 -helix
 -pleated sheet
Secondary (2°) structure
Tertiary (3°) structure
 “Whole molecule folding”
 interactions between distant amino acids
 hydrophobic interactions
 cytoplasm is
water-based
 nonpolar amino
acids cluster away
from water
 H bonds & ionic bonds
 disulfide bridges
 covalent bonds between
sulfurs in sulfhydryls (S–H)
 anchors 3-D shape
 Quaternary (4°) structure
 More than one polypeptide chain bonded
together
 only then does polypeptide become
functional protein
 hydrophobic interactions

collagen = skin & tendons hemoglobin

 Protein structure (review)

R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds)
3°
multiple
polypeptides
1° hydrophobic
amino acid interactions
sequence 4°
peptide bonds

determined 2°
by DNA R groups
H bonds
Protein denaturation
 Unfolding a protein
 conditions that disrupt H bonds, ionic
bonds, disulfide bridges
 temperature
 pH
 salinity
 alter 2° & 3° structure
 alter 3-D shape
 destroys functionality
 some proteins can return to their functional shape
after denaturation, many cannot
Enzymes
Metabolism
Reducing Activation energy
 Catalysts
 reducing the amount of energy to
start a reaction
uncatalyzed reaction

catalyzed reaction

NEW activation energy

reactant

product
Catalysts
 So what’s a cell got to do to reduce
activation energy?
 get help! … chemical help… ENZYMES

G
Enzymes
 Biological catalysts
 proteins (& RNA)
 facilitate chemical reactions
 increase rate of reaction without being consumed
 reduce activation energy
 don’t change free energy (G) released or required
 required for most biological reactions
 highly specific
 thousands of different enzymes in cells
 control reactions
of life
 Enzymes vocabulary
substrate
 reactant which binds to enzyme
 enzyme-substrate complex: temporary association
product
 end result of reaction
active site
 enzyme’s catalytic site; substrate fits into active site

active site
substrate products

enzyme
Properties of enzymes
 Reaction specific
 each enzyme works with a specific substrate
 chemical fit between active site & substrate
 H bonds & ionic bonds
 Not consumed in reaction
 single enzyme molecule can catalyze
thousands or more reactions per second
 enzymes unaffected by the reaction
 Affected by cellular conditions
 any condition that affects protein structure
 temperature, pH, salinity
Naming conventions
 Enzymes named for reaction they catalyze
 sucrase breaks down sucrose
 proteases break down proteins
 lipases break
down lipids
 DNA polymerase builds DNA
 adds nucleotides
to DNA strand
 pepsin breaks down
proteins (polypeptides)
Lock and Key model
 Simplistic model of
enzyme action
 substrate fits into 3-D
structure of enzyme’
active site
 H bonds between
substrate & enzyme
 like “key fits into lock”
Induced fit model
 More accurate model of enzyme action
 3-D structure of enzyme fits substrate
 substrate binding cause enzyme to

change shape leading to a tighter fit

 “conformational change”
 bring chemical groups in position to catalyze
reaction
How does it work?
 Variety of mechanisms to lower
activation energy & speed up reaction
 synthesis
 active site orients substrates in correct
position for reaction
 enzyme brings substrate closer together
 digestion
 active site binds substrate & puts stress on
bonds that must be broken, making it easier
to separate molecules
Factors Affecting Enzyme Function
 Enzyme concentration
 Substrate concentration
 Temperature
 pH
 Salinity
 Activators
 Inhibitors

catalase
Compounds which help enzymes
 Activators Fe in
hemoglobin
 cofactors
 non-protein, small inorganic
compounds & ions
 Mg, K, Ca, Zn, Fe, Cu
 bound within enzyme molecule
 coenzymes
 non-protein, organic molecules
 bind temporarily or permanently to
enzyme near active site
 many vitamins Mg in
chlorophyll
 NAD (niacin; B3)
 FAD (riboflavin; B2)
 Coenzyme A
Compounds which regulate enzymes
 Inhibitors
 molecules that reduce enzyme activity
 competitive inhibition

 noncompetitive inhibition

 irreversible inhibition

 feedback inhibition
 Competitive Inhibitors
-are chemicals that resemble an enzyme’s
normal substrate and compete with it for
the active site.

Substrate
Enzyme
Competitive inhibitor

55
Noncompetitive Inhibitors
-do not enter the active site, but bind to
another part of the enzyme causing the
enzyme to change its shape, which in turn
alters the active site.

Substrate Noncompetitive
Enzyme Inhibitor
active site
altered
56
Competitive Inhibitor
 Inhibitor & substrate “compete” for active site
 penicillin
blocks enzyme bacteria use to build cell walls
 disulfiram (Antabuse)
treats chronic alcoholism
 blocks enzyme that
breaks down alcohol
 severe hangover & vomiting
5-10 minutes after drinking
Non-Competitive Inhibitor
 Inhibitor binds to site other than active site
 allosteric inhibitor binds to allosteric site
 causes enzyme to change shape
 conformational change
 active site is no longer functional binding site
 keeps enzyme inactive
 some anti-cancer drugs
inhibit enzymes involved in DNA synthesis
 stop DNA production
 stop division of more cancer cells
 cyanide poisoning
irreversible inhibitor of Cytochrome C,
an enzyme in cellular respiration
 stops production of ATP
Irreversible inhibition
 Inhibitor permanently binds to enzyme
 competitor
 permanently binds to active site
 allosteric
 permanently binds to allosteric site
 permanently changes shape of enzyme
 nerve gas, sarin, many insecticides
(malathion, parathion…)
 cholinesterase inhibitors
 doesn’t breakdown the neurotransmitter,
acetylcholine
Allosteric regulation
 Conformational changes by regulatory
molecules
 inhibitors
 keeps enzyme in inactive form
 activators
 keeps enzyme in active form

Conformational changes Allosteric regulation

Metabolic pathways

ABCDEFG







enzyme enzyme enzyme enzyme enzyme enzyme
enzyme
1 2 3 4 5 6

 Chemical reactions of life

are organized in pathways
 divide chemical reaction
into many small steps
 artifact of evolution
  efficiency
 intermediate branching points
  control = regulation
Feedback Inhibition
 Regulation & coordination of production
 product is used by next step in pathway
 final product is inhibitor of earlier step
 allosteric inhibitor of earlier enzyme
 feedback inhibition
 no unnecessary accumulation of product

ABCDEFG




X
enzyme enzyme enzyme enzyme enzyme enzyme
1 2 3 4 5 6

allosteric inhibitor of enzyme 1

 threonine
Feedback inhibition
 Example
 synthesis of amino
acid, isoleucine from
amino acid, threonine
 isoleucine becomes
the allosteric
inhibitor of the first
step in the pathway
 as product
accumulates it
collides with enzyme
more often than
substrate does
isoleucine
 Lipids
long term energy storage
concentrated energy
Lipids: Fats & Oils
Lipids
 Lipids are composed of C, H, O
 long hydrocarbon chains (H-C)
 “Family groups”
 fats
 phospholipids

 steroids

 Do not form polymers

 big molecules made of smaller subunits
 not a continuing chain
Fats
 Structure:
 glycerol (3C alcohol) + fatty acid
 fatty acid =
long HC “tail” with carboxyl (COOH) group “head”

enzyme
H2O

dehydration synthesis
Building Fats
 Triacylglycerol
 3 fatty acids linked to glycerol
 ester linkage = between OH & COOH
hydroxyl carboxyl
Dehydration synthesis

H2O

dehydration synthesis

enzyme
H2O

enzyme
H2O

enzyme
HO
Fats store energy
 Long HC chain
 polar or non-polar?
 hydrophilic or hydrophobic?

 Function:
 energy storage
 concentrated
 all H-C!
 2x carbohydrates
 cushion organs
 insulates body

 think whale blubber!

Saturated fats
 All C bonded to H
 No C=C double bonds
 long, straight chain
 most animal fats

 solid at room temp.

 contributes to
cardiovascular disease
(atherosclerosis)
= plaque deposits
Unsaturated fats
 C=C double bonds in
the fatty acids
 plant & fish fats
 vegetable oils

 liquid at room temperature

 the kinks made by double

bonded C prevent the
molecules from packing
tightly together
Saturated vs. unsaturated
saturated unsaturated
Phospholipids
 Structure:
 glycerol + 2 fatty acids + PO4
 PO4 = negatively charged
Phospholipids
 Hydrophobic or hydrophilic?
 fatty acid tails = hydrophobic
 PO4 head = hydrophillic

 split “personality” “attracted to water”

interaction with H2O

is complex & very “repelled by water”
important!
Phospholipids in water
 Hydrophilic heads “attracted” to H2O
 Hydrophobic tails “hide” from H2O
 can self-assemble into “bubbles”
 bubble = “micelle”
 can also form a phospholipid bilayer
 early evolutionary stage of cell?
water

bilayer

water
Why is this important?
 Phospholipids create a barrier in water
 they make cell membranes!
Steroids
 Structure:
 4 fused C rings + ??
 different steroids created by attaching different
functional groups to rings
 different structure creates different function
 examples: cholesterol, sex hormones

cholesterol
Cholesterol
 Important cell component
 animal cell membranes
 precursor of all other steroids

 including vertebrate sex hormones

 high levels in blood may contribute to
cardiovascular disease
Cholesterol
Important component of cell membrane

helps keep
cell membranes
fluid & flexible
From Cholesterol  Sex Hormones
 What a big difference a few atoms can make!
Nucleic Acids
Information storage
Nucleic acids

2006-207
 Nucleic Acids
 Function:
 genetic material
 stores information
 genes
 blueprint for building proteins
 DNA  RNA  proteins
DNA  transfers information
 blueprint for new cells
 blueprint for next generation

proteins
 T
G A
T C
C A
A G
G
A
T
C
Nucleic Acids
 Examples:
 RNA (ribonucleic acid)
 single helix
 DNA (deoxyribonucleic acid)
 double helix
 Structure:
 monomers = nucleotides

DNA RNA
Nucleotides
 3 parts
 nitrogen base (C-N ring) Nitrogen base
I’m the
 pentose sugar (5C) A,T,C,G or U
part!
 ribose in RNA
 deoxyribose in DNA
 phosphate (PO4) group
Types of nucleotides Purine = AG
Pure silver!
 2 types of nucleotides
 different nitrogen bases
 purines

 double ring N base

 adenine (A)
 guanine (G)
 pyrimidines
 single ring N base
 cytosine (C)
 thymine (T)
 uracil (U)
Nucleic polymer
 Backbone
 sugar to PO4 bond
 phosphodiester bond

 new base added to sugar of

previous base
 polymer grows in one direction
 N bases hang off the
sugar-phosphate backbone
Pairing of nucleotides
 Nucleotides bond between
DNA strands
 H bonds
 purine :: pyrimidine

 A :: T

 2 H bonds
 G :: C
 3 H bonds
DNA molecule
 Double helix
 H bonds between bases
join the 2 strands
 A :: T
 C :: G
Rosalind Franklin (1920-1958)
Biomolecule
Review
Carbohydrates
 Structure / monomer
 monosaccharide
 Function
 energy
 raw materials

 energy storage glycosidic bond

 structural compounds

 Examples
 glucose, starch, cellulose, glycogen
Lipids
 Structure / building block
 glycerol, fatty acid, cholesterol, H-C chains
 Function
 energy storage
 membranes

 hormones

 Examples ester bond (in a fat)

 fat, phospholipids, steroids
Proteins
 Structure / monomer
 amino acids
 levels of structure

 Function
 enzymes  defense
 transport  structure peptide bond
 signals  receptors

 Examples
 digestive enzymes, membrane
channels, insulin hormone, actin
Nucleic acids
 Structure / monomer
 nucleotide
 Function
 information storage
& transfer
 Examples
 DNA, RNA

phosphodiester bond