Download Amino Acids

Organic Chemistry
What is it?
define
Why do we care?
Major groups of organic molecules...
Refer to chapter 3 in text.
Carbon:
the defining atom of organic chemistry.
Mader defines as C and H, but that is debated.
← Four electrons available for
covalent bonding
(valence electrons).
-Forms chains, branches, rings. →
- Can carry a wide variety of “add-ons”.
Carbon molecules in living things that are NOT organic…
carbonates: CO3-2…
hydrocarbonates: HCO3- …
oxides of carbon: CO, CO2…
so, pretty simple things,
but methane (CH4) IS organic,
produced by the anaerobic
decomposition of living things.
Vitalism: early idea that “organics”
only come from living things,
but urea is a non-example.
(There are many others).
Mostly we will focus on the carbon-based macromolecules
of which you are made
http://web.mnstate.edu/provost/Provost/
Do you recognize what the
“functional” groups are?
Macromolecules
… BIG molecules
Polymer:
Macromolecule formed
by stringing together
smaller monomers.
Dehydration synthesis:
→
aka condensation (←IB)
a water molecule is
removed to form a bond
between monomers.
Hydrolysis:
→
a water molecule is
inserted,
breaking (lysing) a bond.
(What are the 4 kinds of organic molecules?)
Types of organic molecules; 1 of 4
Carbohydrates
One to many sugars: mono-, di-, polysaccharides.
Uses: energy, structure, components of other molecules.
Examples of monosaccharides:
Note especially:
-general formula (CnH2nOn)
-the ending “-ose”
denotes a sugar
-used for energy,
or as subunits of other molecules,
glucose: the currency of
cellular energy exchange.
ribose: part of nucleic acids.
galactose: subunit of lactose,
“brain sugar”.
fructose: found in fruit, part of (and
twice as sweet as) sucrose.
http://getyournotes.blogspot.com/2011/01/glucose.html
http://gt.inkblue.net/biokeemia/Biokeemia%20I/Kontroll/ribose.jpg
Can you see the differences
between these?
You should be able to draw these.
Note:
- dehydration reaction
- called a glycosidic bond
- used for short-term energy
storage
-maltose made by
amylase from
starch
(glu + glu)
- sucrose is table
sugar, can’t further
polymerize
(glu + fruc)
-lactose is in milk
In mammals,
adult lactose intolerance is
normal.
(glu + gal)
Carbohydrates (cont.)
Disaccharides
Carbohydrates (cont.)
Polysaccharides
Note:
- these ones are for
longer-term energy storage;
starch
amylose: unbranched
amylopectin: branched
Degrading enzymes act
from loose ends,
therefore….
in plants
glycogen (more branched)
in animals
Link to visualization software: http://jmol.sourceforge.net/ .
Carbohydrates (cont.)
Polysaccharides (cont.)
Note:
-cellulose is a structural
carbohydrate (in plants)
- The difference between
digestible (to us) starch and
indigestible cellulose is…
(can you see it?)
[Only certain bacteria make
the enzymes to digest
cellulose. Generally,
any animal living
off grass or wood has these
specific bacteria in their
guts to break the cellulose
into digestible disaccharides.]
triglycerides
Glycerol backbone with 3 fatty
acid add-ons, so
aka
Note:
- another dehydration!
- called an ester linkage
- C, H,… very little O.
- non-polar, hydrophobic
- This is NOT a polymer.
←methyl
group
Uses: long-term energy storage
(twice the energy/g as carbs.),
thermal insulation,
structural, hormonal,
waterproofing …
←hydocarbon
chain
Lipids
←acid group
Types of organic molecules; 2 of 4
Lipids (cont.)
Saturated fatty acids (draw) are solid at lower temperatures,
and may contribute more to blocked blood vessels than
Unsaturated fats, which have double bonds.
Oleic acid is a cis unsaturated
fatty acid that comprises
55-80% of olive oil.
Eleidic acid is a trans
unsaturated fatty acid found
in partially hydrogenated
vegetable oils.
(Trans is rare in nature,
and seems to contribute to
heart disease.)
Stearic acid is a saturated fatty acid
found in animal fats and is the
intended product of hydrogenation.
http://en.wikipedia.org/wiki/Trans_fat
Lipids (cont.)
Phospholipids
- Instead of the third
fatty acid, these have
a phosphate group,
which is hydrophilic
← Things can be added to the
phosphate group. The choline
here makes this ‘lecithin’.
As the “heads” stay in contact with water,
and the “tails” stay away,
small droplets
and bilayers
spontaneously form.
Cells and organelles
are surrounded by these
phospholipid bilayers.
Lipids (cont.)
Cholesterol
is a lipid that doesn’t fit
the structural model.
-It is hydrophobic.
-It is required for
membrane flexibility
(though too much in the
diet precipitates out).
-It can be converted
into any of many
steroid hormones.→
(There are hydrophobic,
so can enter cells
and act directly on
gene expression.)
student.britannica.com/eb/art-62250
LDL… HDL…?
Lipoproteins transport lipids in blood
(recall that lipids are… non-soluble in water).
Low density lipoproteins also regulate cholesterol synthesis
and transport into the blood,
so lots of them may indicate a cholesterol problem,
so these complexes are called “bad cholesterol”.
High-density lipoproteins tend to transport cholesterol
back into the liver for storage,
so tend to be called “good cholesterol”.
It’s all the same cholesterol….
wax
such as for a plant leaf cuticle,
or the cells in a bee hive,
lanolin in wool,
paraffin from petroleum,
or in your ear.
Hey! What kind of a reaction does that involve?
http://en.wikipedia.org/wiki/File:Cetyl_palmitate.png
Types of organic molecules; 3 of 4
Nucleic Acids
Polymers of 4
Uses: Information transformation
from cell generation to generation (DNA)
and from genome to protein (RNA)
(Some RNA also works as a catalyst/enzyme)
We will have more detail later, when we study
DNA replication
(making sure that all cells get the same information),
Transcription
(DNA sequence directing RNA sequence), and
Translation
(RNA directing amino acid sequence
in proteins).
(What do you recall about nucleic acid structure?)
Nucleic Acids (cont.) Note:
- nucleotides have three parts
- letters correspond to the nitrogenous base
- differences between DNA and RNA
ribose→
Nucleic Acids (cont.)
Note:
-complementary base pairing
-held together by hydrogen bonds,
-to form the double helix
-chains run in opposite directions…
-Phosphodiester linkage is another
dehydration reaction!↓
original.britannica.com/eb/art-106485/The-hum...
We will get into a lot more detail
when we do genetics.
www.web-books.com/MoBio/Free/Ch3A5.htm
Types of organic molecules; 4 of 4
Proteins
Polymer of amino acids (20)
Uses: many …
structural
amino acid storage
transport
hormones (some)
receptors
sensors
movement
defense
enzymes
chaperonins
web silk, collagen in cartilage, keratin in nails….
ovalbumin in eggs, casein in milk…
hemoglobin in blood, membrane proteins…
insulin to control blood glucose…
on cell membranes, so they can sense chemicals..
e.g. rhodopsin in retina senses light…
actin and myosin in muscles…
antibodies of the immune system…
facilitate chem. reactions, like peptidase, rubisco…
protein chambers to sequester other proteins
during folding….
IB wants you to know four functions, with named examples,
and strangely exclude membrane proteins from this directive…
(We will encounter many of these throughout the year…)
the Amino Acids
Note
-common core structure:
carbon atom
“amine” (nitrogen) group
“acid” (here a carboxyl
group)
variable “R” group
(R=“radical”)
generalized amino acid
(draw)
Peptide bond
This is another
dehydration reaction.
(Can you identify the
amino acids illustrated?)
Proteins:
Their complex structure
contributes to their
functioning.
primary structure:
sequence of amino acids.
secondary structure:
H bonds, mostly between
repeating cores, form α helices
and β pleated sheets.
tertiary structure: R group interactions.
Note the bond types involved.
Amino acids with
non-polar R groups
will hide inside, and
hydrophilic ones
outside… if the
protein is soluble.
Integral membrane
proteins will tend to
be the other way around...
and maybe a channel lined
with polar amino acids.
Why?
Polarity also affects active
site specificity.
quaternary structure: multiple molecules;
maybe a (non-protein) prosthetic group
to make a conjugated protein, like
glycoprotein, lipoprotein, cytochrome…
Globular proteins have less 2o structure,
but lots of 3o structure,
and often 4o structure.
This provides the active site specificity
to enzymes,
and makes them more susceptible
to denaturation.
←sperm whale
myoglobin
catalase →
www.phschool.com/.../labbench/lab2/active.html
a fibrous protein has 2o structure,
little or no 3o structure,
and often 4o structure.
Only made in animals
This makes a strong, usually insoluble strand.
↓tropocollagen in tendons (α)
spider silk (β) →
Chaperonin proteins
form something like a
dressing room
for newly polymerized proteins
to acquire 2o, 3o and 4o structure
in the absence of
environmental
interference.
(May be more about re-folding/
editing/correcting....)
http://en.wikipedia.org/wiki/Chaperonin
Identify the following:
What are the major categories
of organic molecules?
What are the uses of each type?
Give named examples.
What are the monomers for each group?
How many different ones are there?
How many can you name?
Names ways in which the various groups
are interconnected…
How is each type manufactured?
What kind of bond?
What 3 dimensional structure
does each assume?
Branching increases H bonds in starches,
so which makes a better adhesive?
organic chemistry
carbohydrate
lipid
nucleic acid
protein
valence electron
monosaccharide
glycerol
nucleotide
amino acid
vitalism
glucose
triglyceride
phosphate group
peptide bond
macromolecule
ribose
ester linkage
ribose
primary structure
polymer
galactose
saturated fatty acid
nitrogenous base
secondary structure
monomer
fructose
unsaturated fatty acid
complementary base pairing
α helix
dehydration synthesis
glycosidic bond
phospholipid
double helix
β pleated sheet
condensation
disaccharide
phosphate group
phosphodiester linkage
tertiary structure
hydrolysis
maltose
phospholipid bilayer
quaternary structure
sucrose
cholesterol
prosthetic group
lactose
steroid hormone
conjugated protein
polysaccharide
lipoprotein
fibrous protein
starch
wax
globular protein
amylose
denaturation
amylopectin
chaperonin
glycogen
cellulose