Transcript Biochemistry PPT Nts

BIOLOGICAL MOLECULES
Ch. 3, 6.4 + 6.5
Ch. 3 Biological Molecules
3-1: Why is Carbon So Important in Biological Molecules?
3-2: How are Organic Molecules
Synthesized?
3-3: What are Carbohydrates?
3-4: What are Lipids?
3-5: What are Proteins?
3.6: What are Nucleotides and Nucleic Acids?
6.4: How Do Enzymes Promote Biochemical Reactions
6.5: How are enzymes regulated?
Chemical Compounds
Organic
- carbon backbone bonded to
H atoms (CH4)
- can be very complex
- more organic cmpds than
inorganic
- common in all living
organisms
Inorganic
- lack carbon (H2O /
NaCl) or hydrogen
atoms (CO2)
- less complex
- less diverse
3.1: Why is Carbon So Important ..?
 unique bonding properties of carbon are key to the complexity of
organic molecules
1. versatile  4 valence electrons
(room for 8)
can form up to 4 bonds with other atoms
or itself
capable of making single, double, and
triple bonds
hydrogen
carbon
nitrogen
oxygen
2. can assume complex shapes (branched chains, rings, sheets, and
helices)
3. can attach to functional groups which will determine
characteristics and reactivity of molecule
 functional groups – less stable & more likely
to reacte with others
sulfhydryl
carboxyl
phosphate
amine
3.2: How Are Organic Molecules Synthesized?
 Macromolecules are large polymers
Ex.carbohydrates
lipids,
proteins
nucleotides/nucleic acids
1. Biomolecules are joined through
Dehydration synthesis or condensation reactions JOINS monomers together
 H & OH are REMOVED to form 1 H2O molecule
https://www.youtube.com/watch?v=QltPTqEhSaQ – explains monomers & polymers as well - good
2. Biomolecules are broken down through
b) Hydrolysis breaks apart polymers into monomers
 1 H2O molecule is forced between the monomers
https://www.youtube.com/watch?v=QltPTqEhSaQ – 4:15 starts hydrolysis
3.3: What Are Carbohydrates?
http://www.tv411.org/science/tv411-whats-cooking/carbohydrates-science-lesson - online activity for Intro to
Carbs (chemistry & digestion)
A. Carbohydrate Basics
 C, H and O atoms in the ratio of 1:2:1
 most small carbs are water soluble (hydrophilic = water
loving) due to OH functional group (i.e sugar cube in
H20)
 provide and store energy for cells (i.e cellular respiration)
 structural support (plants, insects, bacterial cell walls)
Sugar dissolving in water
hydrogen
bond
water
hydroxyl
group
B. Specific types of Carbohydrates
1.
Monosaccharides: C6H12O6 (CH2O)n n = 3-7C
 1 simple sugar (1:2:1 ratio of C,H,O)
 most end in “ose” and named by # of Carbons
Examples
a) glucose/hexose (6-C)-most common in organisms
b) fructose - fruit sugar (corn syrup, honey)
c) galactose - milk sugar found in lactose
d) ribose/pentose (5-C) or deoxyribose
(RNA)
and
(DNA)
Numbered carbons
C 6'
These will become
important!
5'C
4'
O
C
C
1'
energy stored in C-C bonds
harvested in cellular respiration
C 3'
C 2'
 Isomers –molecules w/ same number of atoms but different
arrangement (same chemical formula with a different
structural formula)
C6H12O6
2. Disaccharide: C12H22 O11
 2 monosaccharides joined via dehydration synthesis
 general formula is used for short-term energy storage
Examples:
1) sucrose (table sugar) = glucose + fructose
2) maltose (malt sugar)= glucose + glucose
3) lactose (milk sugar) = galactose + glucose
Formation of a Disaccharide
Glucose
(monomer)
Fructose
(monomer)
Sucrose + water
(disaccharide)
dehydration
synthesis
H2O
+
3. Polysaccharides
 chains of monosaccharides (no set formula)
 costs little to build; easily reversible = release energy
Examples:
1) starch: plant energy-storage
2) glycogen: animal energy-storage
3) cellulose: most imp. structural polysaccharide (cell walls of
plants)
4) chitin: armour of crabs, spiders, fungi
Polysaccharide diversity
• Molecular structure determines function
in starch
in cellulose
isomers of glucose
 structure determines function…

Starch vs. Cellulose
starch
easy to
digest
enzyme
cellulose
hard to
digest
enzyme
only bacteria can digest
Cellulose = undigestible roughage
• most abundant organic cmpd on Earth
• herbivores have evolved a mechanism
to digest cellulose
• most carnivores have
not and that’s why
they eat meat to get
their energy & nutrients
Cows digest cellulose well; no need to eat other sugars
Gorillas can’t digest cellulose well; must add another sugar
source, like fruit to diet
helpful BACTERIA
live in an herbivores
digestive systems &
help digest celluloserich (grass) meals
Breakdown of Disachharides & Polysaccharides
Via Hydrolysis
Polymer + H2O  Monomer + Monomer
Polysaccharide + H2O  Disaccharides or Monosaccharides
Disaccharide + H2O  2 Monosaccharides
Starch + H2O  Glucose + Glucose + Glucose + Glucose
hydrolysis
Ch. 3.4
A. Lipid Basics
 high ratio of H to C atoms
 contain large chains of non-polar hydrocarbons
(hydrophobic/H2O insoluble)
 long term energy storage (btwn C-H bonds)
 structural component; building blocks
https://www.youtube.com/watch?v=ulIjtl4FPDQ – Lipid structure and function (12 min)
B. Specific types of Lipids
1. Triglycerides (oils and fats):
* only contain C, H, & O
* made up of 3 monomers called fatty acids (long chains of C & H
with a carboxyl group – COOH on 1 end) attached to a glycerol (3C
backbone)
* uses primarily as energy-storage molecules
* contain 2X as many calories/gram than Carbs & Proteins
Formation of Fats via Dehydration Synthesis
Triglyceride
3
H2O
https://www.youtube.com/watch?v=eESpP5okA1I (@ 4 min energy
and formation of)
all single bonds
btwn C-atoms
- animal fats
(solids; red meat;
whole milk
at least 1 double bond
btwn C-atoms
- plant oils (liquids; fish
nuts)
1 double bond
more than 1
double bond
Good Fats vs. Bad Fats?
Fats (solid)
Oils (liquid)
(butter/lard)
corn/canola oil
-produced by animals -found in seeds of plants
- saturated FA
- unsaturated FA
- lots of H
- less H
Hydrogenation & Trans Fats?
 commercial process where some double bonds in
unsaturated FA are broken and hydrogens are added to the
carbons
- converts liquid oils to
solid fats (trans fat)
http://healthland.time.com/2013/11/07/7-foods-that-wont-bethe-same-if-trans-fats-are-banned/ - explains trans fats and
shows examples of fods that contain them
2. Wax
* chemically similar to fats (1 fatty acid)
but have a long alcohol chain
* humans & most animals lack appropriate
enzymes to break them down
* highly saturated (solid @ room temp.)
* structural component &
waterproofing function
3. Phospholipids
* chemically similar to oils (1 glycerol, 2 fatty acids) but have a
phosphate group
* crucial structural component of cell membranes
Phosphate
Glycerol
Fatty acids
3. Steroids
 don’t resemble fats; have 4 carbon rings
 cholesterol – most common steroid
 precursor to Vit D, testosteronel, estrogen
 structural component in animal cell membranes
 2% of human brain (insulate/nerve cells)
 too much of the wrong form = bad news
3.5: What Are Proteins?
A. Protein Basics
 consist of C, H, O, N
 chains of amino acids bonded by peptide
bonds via dehydration synthesis
 act as enzymes to promote rxns
 structural component (keratin)forms hair,
nails, scales & feathers (silk protiens)  webs
cocoons
 nutritional (albumin in eggs & casein in milk)
 hemoglobin protein transports oxygen
 movement (actin & myosin are contractile
proteins in muscle)
 some are hormones (insulin & GH)
 some are antibodies that fight infection
 few are toxins (snake venom)
Amino Acids: Monomers of Proteins
1.
2.
3.
4.
5.
Amino group
R group (side chain)
Single H
Carboxylic acid group
Central Carbon
can make
disulfide bonds
Amino Acids join via Dehydration Synthesis to make peptides or proteins.
OH + H
a.a + a.a  (di)peptide + H20
H2O
H2O
H2O
a.a. + a.a + a.a. + a.a. + etc  polypeptide +
3 H20
Levels of Protein Organization
 interactions btwn the R groups of A.A. cause twists, folds, and
interconnections that give proteins 3-D structure
Primary Structure
Secondary
Structure
Tertiary Structure
Quaternary
Structure
https://www.youtube.com/watch?v=qBRFIMcxZNM
– organization and function
1. Primary Structure – sequence of amino acids
depends on 1) kind, 2) number and 3) arrangement of amino
acids
2. Seconday Structure – simple repeating units
a) alpha helix
or
b) beta sheets
 maintained by H-bonds btwn polar portion of A.A.
Silk
Keratin (hair)
Hemoglobin subunits
(blood)
H-bonds
3. Tertiary Structure - 2o structure folds on itself forming Hbonds w/ H2O & disulfide bridges w/ cysteine A.A.
 include enzymes and antibodies
 disruption of 2o and 3o bonds = denatured proteins (loss of
function)
4. Quaternary Structure – when multiple proteins are linked
together
 hemoglobin - 4 protein chains of 150 amino acids
 some enzymes
Protein Function Related to Structure
 sickle-cell anemia – mutation in hemoglobin
 egg frying – denaturation in albumin
 perms – denaturation of keratin in hair
 bacteria and viruses killed by denaturing their proteins
http://on.aol.com/video/learn-about-protein-denaturation-83227098 review protein organization and protein denaturation
3.6: What Are Nucleotides and Nucleic Acids?
A. Nucleotide basics
 1 nucleotide consists of
1) a 5-C sugar (either deoxyribose or ribose)
2) a phosphate group
3) 1 of 5 different nitrogen –containing bases





adenine
guanine
cytosine
thymine
uracil
B. Specific Types of Nucleotides and Nucleic Acids
 ATP (adenosine tri-phosphate), FAD &
NAD+
• all energy-carrier molecules
 chains of nucleotides form polymers or
nucleic acids
1) DNA – deoxyribonucleic acid
• deoxyribose sugar & A, T, G, C
2) RNA – ribonucleic acid
• Ribose sugar & A, U, G, C
ATP as an Energy Carrier
 ATP – adenosine triphosphate
 ribose nucleotide
 3 phosphate groups
 stores energy in bonds btwn phosphate groups
 energy released when last phosphate bond is broken
 available energy is then used to drive other rxns
(i.e. linking amino acids)
How is ATP made and broken down?
1. ADP + Energy + Phosphate  ATP
(stores energy) dehydration synthesis
2. ATP  ADP + Phosphate + Energy
(releases energy)
hydrolysis
Making and Breaking Down Macromolecules
Polymer or
Monomer
Macromolecule
(Building Blocks)
______________________________________
Carbohydrates
monosaccharides
_____________________________________
Lipids(triglycerides)
fatty acids + glycerol
______________________________________
Proteins or Polypeptides
amino acids
______________________________________
Nucleic Acids
nucleotides
_______________________________________
<-------- Dehydration Synthesis
Hydrolysis -------------
http://www.youtube.com/watch?v=H8WJ2KENlK0 – Crash Course Bio Molecules Review(14min)
How Do Enzymes Promote Biochemical Reactions
(Ch. 6.4)
 activation energy determines the speed at which a chemical
reaction occurs
https://www.youtube.com/watch?v=VbIaK6PLrRM – explains activation energy
* some rxns occur too slowly b/c they have a high activation energy
 enzymes (proteins) are biological catalysts, which help speed up
the rate of reactions (by lowering activation energy) without
themselves being used up or permanently altered
https://www.youtube.com/watch?v=1e9EvrThk1Y –
how a catalytic converter works
https://www.youtube.com/watch?v=hNl5WYSM5DE
Elephant Toothpaste
.
 not advantageous to
speed up dozens of rxns
at once; so it is a
selective process
 structure of enzyme determines its function (just like proteins);
that structure allows them to catalyze specific reactions
Induced-fit model
 shape and charges of the active site (a.a.) determines what
molecules can enter (amylase can digest starch but not cellulose)
https://www.youtube.com/watch?v=lfuOQZJ_MIM (firefly)
 each catalyzes only a few types of reactions (most only catalyze 1)
 https://www.youtube.com/watch?v=tI69AVRW0DU (cartoon enzymes in human digestion)
 https://www.youtube.com/watch?v=r1ryDVgx0zw (how enzymes work)
Reactant
(1 disaccharide)
EnzymeSubstrate
Complex
Products
(2
monosaccharides)
 Cells regulate metabolic pathways by controlling the _____
produced.
a) type of enzymes
b) quantity of enzymes
c) activity levels of enzymes
 as substrate/enzyme levels increase, the rxn
rate increases until active sites of all enzymes
are being continuously occupied by a new
substrate
 Genes that code for enzymes can turn on or off (i.e. marathon
runners after high-carb pre-competition meals)
 Some enzymes only synthesized at specific stages in organisms life
(65% of ppl produce less lactase as they age)
 inactive forms of enzymes only become activated when needed
(i.e. protein digesting enzymes pepsin & trypsin)
Competitive or Noncompetitive Inhibition Enzyme Control
 Enzymes need to be inhibited at times to prevent
1) substrates from being used up
2) producing too much product
 Competitive inhibition: a substance, other than the enzyme’s
normal substrate, binds to active size of enzyme & competes with
the actual substrate for active site)
- structural similarities
Ex. 1: nerve gases & insecticides (blocks active site of
acetylcholinesterase; excess acetylcholine overstimulates
muscles causing paralysis) https://www.youtube.com/watch?v=-gIqZ8IxctE (poisoned grasshopper)
Ex. 2: antibiotic penicillin  inhibits synthesis of bacteria cell walls
Ex. 3: aspirin & ibuprofen (advil) inhibits synthesis of molecules that
contribute to swelling, pain, fever.
 Noncompetitive inhibition: molecule binds to a site on enzyme
different from active site; distorts active site; enzyme less able to
catalyze rxn

Ex 1: Potassium Cynaide (blocks an enzyme that uses
oxygen to produce ATP – deadly)
https://www.youtube.com/watch?v=PILzvT3spCQ (short comparison)
 Allosteric regulation: noncompetitive inhibition where enzymes
switch easily between 2 different shapes that either activate or
inhibit the enzyme (i.e. ADP)
https://www.youtube.com/watch?v=d5fDEUhjo-M – allosteric
Regulation
https://www.youtube.com/watch?v=DHZtOKyMPRY – feedback
inhibition
 Feedback inhibition: form of
allosteric regulation; causes metabolic
pathways to stop producing its end
product when its concentration reaches
reaches an optimal level (thermostat)
intermediates
enzyme 1
threonine
(initial
reactant)
enzyme 2
enzyme 3
enzyme 4
enzyme 5
As levels of isoleucine rise,
isoleucine binds to the regulatory
site on enzyme 1, inhibiting it
enzyme 1
isoleucine
isoleucine
(end product)
Factors that Affect Enzymes
 enzymes have a narrow range of conditions (pH, temp., salt) in
which they function optimally (H-bonds btwn polar a.a.)
 human cellular enzymes work best around pH 7.4; human
digestive enzymes work best around pH 2
 enzymes become denatured
in unfavorable conditions and lose
3-D structure required to function
properly
fast
fast
rate
of
reaction
For pepsin, maximum
activity occurs at
about pH 2
For trypsin, maximum
activity occurs at
about pH 8
For most cellular
enzymes, maximum
activity occurs
at about pH 7.4
For most human enzymes
maximum activity occurs
at about 98.6F (37C)
rate
of
reaction
slow
Effect of pH on enzyme activity
slow
32
0
68
104
20
40
temperature
140 (F)
60 (C)
Effect of temperature on enzyme activity
Enzymes in our Digestive System
 food travels through many organs of the digestive system & broken
down into usable nutrients
1. mouth: 1 minute
 mechanical digestion via teeth
 chemical digestion via enzyme AMYLASE
2. esophagus: 2-3 seconds
 tube that leads to the stomach via peristalsis
3. stomach: 2-4 hours
mechanical digestion via muscle churning
chemical digestion via enzyme PEPSIN
4. small intestine: 3-5 hours
 bile (liver/gall bladder) & LIPASE chemically breaks down fat
 enzymes MALTASE, SUCRASE & LACTASE break down carbs
 nutrients are absorbed
5. large intestine: 10 hrs – days
 absorbs H2O and eliminates wastes
amylase
Lipase
Maltase
Sucrase
Lactase
pepsin
Study
 Ch. 3, 6.4 & 6.5 Key Vocab Terms
 Read summary of key concepts Ch. 3 and 6.4 and 6.5
 Be able to answer the Learning Outcomes in Ch. 3 LO
1-7 and Ch. 6.4 and 6.5 LO 5-7.
 Be able to answer all the Check Your Learning
questions and check answers for all sections
 Complete Thinking through the Concepts and Applying
the Concepts for all sections.
 Go to the Study Area on MasteringBiology for
practice, animations, quizzes, activities, etc.