Types of Organic compounds
Four major groups of organic compounds,
necessary for life are:
polymers
monomers
– Carbohydrates
monosacchrides
– Lipids
fatty acids
– Proteins
amino acids
– Nucleic acids
nucleotides
Carbohydrates
• Diverse group of substances formed from C, H, and O
– ratio of one carbon atom for each water molecule
(carbohydrates means “watered carbon”)
– glucose is 6 carbon atoms and 6 water molecules (H20)
• Main function is to produce energy
Diversity of Carbohydrates
• 3 sizes of carbohydrate molecules
– monosaccharides
– disaccharides
– polysaccharides
Mono saccharides
“one sugar”
•
•
•
•
Called simple sugars
Contain 3 to 7 carbon atoms
(CH2O)n
We can absorb only 3 simple sugars without
further digestion in our small intestine
– glucose found in syrup or honey
– fructose found in fruit
– galactose found in dairy products
Disaccharides (“two”)
• Formed by combining 2 monosaccharides by
dehydration synthesis (releases a water molecule)
• Name of bond= Glycosidic bond
– sucrose = glucose & fructose
Condensation Rxn & Dehydration
Synthesis
• 2 Condensation & Hydrolysis QT Mov
Disacchrides of distinction
glucose + fructose = sucrose
glucose + glucose = maltose
glucose + galactose = lactose
Polysaccharides
(“many”)
• < 100’s of monomers by dehydration synthesis
• In animals
– Glycogen: glucose polymer, found in liver & skeletal muscle,
when blood sugar level drops, liver hydrolyzes glycogen to
create and release glucose into the blood
• In plants
– Starch: used for energy storage (rice, potatoes, grains)
– Cellulose: used for structural support (Cell walls)
• In fungi
- Chitin:fungal cell walls
• In protists
- Pectin/carrageenan from algae, in food items (jam, yogurt, ice
cream) to give a creamy consistency
Polysaccharide
Lipids = fats, oils, steroids, waxes
• Formed from C, H and O
• 18-25% of body weight
• Hydrophobic
– fewer polar bonds because of fewer oxygen atoms
– insoluble in polar solvents like water
• Combines with proteins for transport in blood
– lipoproteins
Lipids: Made of C, H, O and other groups
• Three functional classes:
Storage lipid:
-Triglycerides: Common body fat.
Regulatory lipid:
- Steroids: act as hormone
- Eicosanoids: hormones
Structural lipid:
– Phospholipids: Cell membrane
– Glycolipids: Cell membrane
Triglycerides
• Neutral fats composed of a single glycerol molecule and 3
fatty acid molecules
– three-carbon glycerol molecule is the backbone
• Very concentrated form of energy
– 9 calories/gram compared to 4 for proteins & carbohydrates
– our bodies store triglycerides in fat cells if we eat extra food
Triglyceride Formation
• Triglycerides =
three fatty acids
attached by
dehydration
synthesis to one
molecule of
glycerol by an
ester bond
Figure 2.15
Saturation of Triglycerides
• Determined by the number of single or double
covalent bonds in fatty acid
• Saturated fats contain single covalent bonds and
are covered with hydrogen atoms----lard
• Unsaturated are not completely covered with
hydrogen----safflower oil, corn oil
• Polyunsaturated fats contain even less hydrogen
atoms----olive and peanut oil
Regulatory lipids: Steroids
• Formed from 4 rings of carbon atoms joined
together
• Common steroids
– sex hormones, bile salts, vitamins & cholesterol
• Cholesterol found in animal cell membranes
– starting material for synthesis of other steroids
4 ring structure of Steroid
Steroids(Wax)
Eicosanoids
• Lipid type derived from a fatty acid called
arachidonic acid
– prostaglandins = wide variety of functions
•
•
•
•
•
•
modify responses to hormones
contribute to inflammatory response
prevent stomach ulcers
dilate airways
regulate body temperature
influence formation of blood clots
– leukotrienes = allergy & inflammatory responses
Structural lipids
• Phospholipids: Glycerol+ fatty acids + phosphate
Part of cell membrane. Ex. Lecithin.
• Glycolipid: Glycerol+ fatty acid+ sugar chain.
Part of cell membrane surface.
Chemical Nature of Phospholipids
head
tails
Lipid Behavior in Various
Environments
Nucleic acids
• Three types: DNA, RNA, ATP
• Function: Storage of genetic information
and application of genetics (Protein
synthesis), and storage of energy
Nucleic acids are chains of nucleotides
• Nucleotides are composed of a sugar, a phosphate
and a nitrogenous base
–
–
–
–
Sugar = deoxyribose (DNA) or ribose (RNA)
DNA Bases = adenine, thymine, cytosine, guanine
RNA bases = adenine, uracil, cytosine, guanine
Base Pairing: A-T, G-C or A-U. Held together by
hydrogen bonds
DNA Structure
• Huge molecules containing
C, H, O, N and phosphorus
• Each gene of our genetic
material is a piece of DNA
that controls the synthesis
of a specific protein
• A molecule of DNA is a
chain of nucleotides
• Nucleotide = nitrogenous
base (A-G-T-C) + pentose
sugar + phosphate group
DNA Fingerprinting
• Used to identify criminal, victim or a child’s
parents
– need only strand of hair, drop of semen or spot of
blood
• Certain DNA segments are repeated several
times
– unique from person to person
RNA Structure
• Differs from DNA
– single stranded
– ribose sugar not deoxyribose
sugar
– uracil nitrogenous base replaces
thymine
• Types of RNA within the cell,
each with a specific function
– messenger RNA
– ribosomal RNA
– transfer RNA
Nucleic Acids: RNA and DNA
DNA= Double
stranded
RNA= Single
stranded
Figure 2.23
Adenosine Triphosphate (ATP)
• Temporary molecular storage of energy as it is being
transferred from exergonic catabolic reactions to cellular
activities
– muscle contraction, transport of substances across cell
membranes, movement of structures within cells and movement
of organelles
• Consists of 3 phosphate
groups attached to
adenine & 5-carbon
sugar (ribose)
Formation & Usage of ATP
• Hydrolysis of ATP (removal of terminal
phosphate group by enzyme -- ATPase)
– releases energy
– leaves ADP (adenosine diphosphate)
• Synthesis of ATP
– enzyme ATP synthase catalyzes the addition of
the terminal phosphate group to ADP
– energy from 1 glucose molecule is used during
both anaerobic and aerobic respiration to create
36 to 38 molecules of ATP
Proteins
• Contain carbon, hydrogen, oxygen, and nitrogen
• Constructed from combinations of 20 amino
acids.
• Levels of structural organization
– primary, secondary and tertiary
– shape of the protein influences its ability to form bonds
•Central carbon
atom
•Amino group
(NH2)
•Carboxyl group
(COOH)
•Side chains (R
groups) vary
between amino
acids
Amino Acid structure
Figure 2.18
Formation of a peptide Bond
• Dipeptides formed from 2 amino acids joined
by a covalent bond called a peptide bond
– dehydration synthesis
• Polypeptides chains formed from 10 to 2000
amino acids.
Levels of Structural Organization
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•
•
•
Primary is unique sequence of amino acids
Secondary is alpha helix or pleated sheet folding
Tertiary is 3-dimensional shape of polypeptide chain
Quaternary is relationship of multiple polypeptide chains
The four levels of protein configuration
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•
•
•
Primary is unique sequence of amino acids
Secondary is alpha helix or pleated sheet folding
Tertiary is 3-dimensional shape of polypeptide chain
Quaternary is relationship of multiple polypeptide
chains
•
•
Protein Folding Tutorial:
Protein folding in Water
Protein Structure
Figure 2.20
Bonds of protein Structure
• Hydrogen bond forms the
secondary structure
• Disulfide bonds stabilize
the tertiary structure of
protein molecules
• Disulfide bond between 2
polypeptide chains create
quaternary structure
Protein Denaturation
• Function of a protein depends on its ability to
recognize and bind to some other molecule
• Hostile environments such as heat, acid or salts
will change a proteins 3-D shape and destroy its
ability to function
– raw egg white when cooked is vastly different
Glycoprotein and Proteoglycan
• Proteins exist in combination with sugar.
• Glycoprotein: Protein + sugar chain. Found in cell
membrane. Serve as surface proteins.
• Proteoglycan: Protein + sugar chain. Also present in
cell membrane. Can have enzymatic activity.
Enzymes
• Enzymes are protein molecules that act as catalysts by
lowering Activation Energy
• Enzyme = apoenzyme + cofactor
– Apoenzymes are the protein portion
– Cofactors are nonprotein portion
• may be metal ion (iron, zinc, magnesium or calcium)
• may be organic molecule derived from a vitamin
• Enzymes usually end in suffix -ase and are named for the
types of chemical reactions they catalyze
• How Enzymes Work
• Enzyme Tutorial
• Enzyme Catalysis
Enzyme Functions
• Bonds made or broken when atoms, ions or
molecules collide
• Enzymes speed up reactions by properly
orienting colliding molecules
• 1000 known enzymes speed up metabolic
reactions to 10 billion times that in beaker
• Composed of protein portion (apoenzyme) &
nonprotein portion (cofactor)
– cofactors can be metal ions or vitamins
Enzyme Functionality
• Highly specific
– acts on only one substrate
• active site versus induced fit
– speed up only one reaction
• Very efficient
– speed up reaction up to 10
billion times faster
• Under nuclear control
• Co-factors first bind to the
enzyme = enzyme
activated
Enzyme Structure Interactions
Enzyme Substrate Complex
• Lock and Key: shape and
active site of enz is only
compatible w/ substrate,
forming substrate enzyme
complex
• -enz
reused but are
eventually
decomposed=constant
synthesis
• -usually end in "ase" and
take name of substrate
Factors Affecting Enzyme Action
•
Temperature:
-40oC, denaturation
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•
•
Enzyme Saturation
Concentration of substrate
pH
-pepsin ( gastric protease) pH 2
-trypsin (pancreatic protease) pH 8
Saturation
Cofactors
Cofactors can aid how enzyme works. If they are organic, then
they are “coenzymes” these are enzyme activators
Allosteric Cofactors
inhibitors
activators
Pharmacological Enzyme Inhibitors
Allosteric Regulation
Biochemical Pathway
• Competitive vs Noncompetitive Inhibitors
In this animation, the enzyme is olive, the substrate is green, the
competitive inhibitor is red and the products A & B are yellow and blue.
The enzyme has binding site into which either the substrate or the
competitive inhibitor may fit. The substrate binds to the enzyme and is
then converted to the two products, A & B. The competitive inhibitor
binds to active site and prevents the substrate from binding, preventing
the enzyme catalyzed reaction from occuring. Sometimes the products of
an enzymatic reaction can also be competitive inhibitors of the reaction.
Which product, A or B, would most likely be a competitive inhibitor?
The enzyme is gray, the substrate is green, the non-competitive inhibitor
is red and the products are yellow (A) and blue (B). The enzyme has
two binding sites, one for the substrate (the active site) and the other
for the non-competitive inhibitor (the regulatory site). When the noncompetitive inhibitor is not bound to the regulatory site, the enzyme
can bind substrate at the active site and catalyze the production of
product. However, when the non-competitive inhibitor binds to the
enzyme at the regulatory site, the shape of the active site changes so
that it can no longer bind its substrate or catalyze the production of
product. The enzyme will remain inhibited until the non-competitive
inhibitor leaves the regulatory site. Allosteric Activation
• The enzyme is olive, the substrate is green, the allosteric activator is
red and the products of the enzymatic reaction are yellow (A) and blue
(B). The enzyme has two binding sites, one for the substrate (the
active site) and the other for the allosteric activator (the regulatory
site). When the allosteric activator is not bound to the regulatory site,
the active site of the enzyme is not able to bind substrate and catalyze
the production of product. However, when the allosteric activator
binds to the enzyme at the regulatory site, the shape of the active site
changes so that it can bind its substrate and catalyze the production of
products A and B. The enzyme will remain activated until the
allosteric activator leaves the regulatory site.
Negative Feedback/ Feedback Inhibition
When the product is in
abundance, it binds competitively
with its enzyme's active site; as
the product is used up, inhibition
is reduced and more product can
be produced. In this way the
concentration of the product is
always controlled within a certain
range.
•Operons in gene regulation
•Temperature regulation in animals
•Plants response to water limitations
Positive Feedback
• Amplification occurs when the stimulus is further
activated, which in turn initiates an additional
response that produces system change
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Lactation in mammals
Onset of labor in childbirth
Ripening of fruit
Blood clotting
Estrogen & Progesterone in Female System
Resources
• http://www.biology.lsu.edu/introbio/tutorial/spotted/BioStud
io/2ORGANICMOLE/1OrMo.html
• Animations: bio.winona.edu/berg/ANIMTNS/cinhban.htm
• Microbiology:
http://student.ccbcmd.edu/courses/bio141/lecguide/unit6/
• BioTopics Contents:
http://www.biotopics.co.uk/conten.html
• What is an Enzyme:
http://www.northland.cc.mn.us/biology/biology1111/animati
ons/enzyme.swf