Chapter 2.2 : Organic Chemistry Flashcards
Organic Chemistry
Study of compounds containing carbon and hydrogen
What are the four categories of organic compounds?
– carbohydrates
– lipids
– proteins
– nucleic acids
Monomers
a small identical molecules (similar
subunits) - e.g. amino acid or glucose molecule
Polymers
molecules made of a repetitive series
of identical subunits // e.g. polypeptide
Macromolecules
– polymers which continue to
“enlarge” to form very large organic molecules //
high molecular weights /// e.g. protein
Organic
molecules with carbon and hydrogen
Carbon has _ valence electrons
4
– may bind with four other atoms
– these atoms provide carbon with four more electrons to fill its
valence shell // making carbon’s valence orbit “stable”
– forms covalent bonds with hydrogen, oxygen, nitrogen, sulfur,
and other elements
Carbon atoms also bind readily with
each other
– forms branches and ring structures /// forms a carbon chain or
carbon backbones
– able to form 3D matrix (e.g. pencils & diamonds)
Carbon is the _____ that carries a variety of functional groups
backbone
Functional Groups
- small clusters of atoms
attached to carbon
backbone - determines many of the
properties of organic
molecules - E.g. = hydroxyl, methyl,
carboxyl, amino, phosphate
Dehydration synthesis
Process where monomers are joined together to form a polymer
(condensation) is how living cells form
polymers
– a hydroxyl (-OH) group is removed from one monomer, and
a hydrogen (H+) from another /// producing water as a byproduct
Hydrolysis
Splitting a polymer (lysis) by the addition of a water
molecule (hydro) // a covalent bond is broken
All digestion reactions consists of hydrolysis reactions
– a water molecule ionizes into –OH and H+
– the covalent bond linking one monomer to the other is
broken
– the –OH is added to one monomer
– the H+ is added to the other
Carbohydrates
A hydrophilic organic molecule
general formula // note: 2:1 ratio for hydrogen to oxygen
names of carbohydrates often built from:
– word root ‘sacchar-’
– the suffix ’-ose’
– both mean ‘sugar’ or ‘sweet’ // monosaccharide or glucose
Monosaccharides
Simple carbohydrates = simple sugars
glucose, galactose and fructose
glucose
is blood sugar
Disaccharides
Sugar molecule composed of 2
monosaccharides
sucrose
table sugar //
glucose + fructose
lactose
sugar in milk //
glucose + galactose
maltose
grain products //
glucose + glucose
Polysaccharides
Long chains of glucose molecules
Three important polysaccharides
(glycogen – starch - cellulose)
Glycogen
energy storage polysaccharide in animals
- made by cells of liver, muscles, brain, uterus, and vagina
- liver produces glycogen after a meal when glucose level is
high, then breaks it down between meals to maintain blood
glucose levels - muscles store glycogen for own energy needs
- uterus “sweats” glycogen to nourish embryo
Starch
energy storage polysaccharide in
plants /// only significant digestible
polysaccharide in the human diet
Cellulose
structural molecule of plant cell
walls /// this is the “fiber” in our diet our
digestive system lack enzymes to breakdown
this polymer passes out of our digestive system
as food residue
Carbohydrate Functions
- Source of energy // all digested carbohydrates converted to glucose // oxidized to make ATP
- Structural molecule when conjugated (i.e. bonded to) with lipids or proteins
– glycolipids // e.g. component of cell membrane with lipid
inserted into membrane and sugar projecting from surface of
membrane
– glycoproteins // e.g. component of cell membrane with protein
inserted into membrane and sugar projecting from surface of
membrane Carbohydrate Functions
– proteoglycans (mucopolysaccharides) // forms gel between
cells – its the “glue that binds cells and tissues together- forms gelatinous filler in umbilical cord and eye
- joint lubrication
- seen as the tough, rubbery texture of cartilage
Lipids
Hydrophobic organic molecule
– composed of carbon, hydrogen and oxygen
– with high ratio of hydrogen to oxygen
Less oxidized than carbohydrates, and therefore
has more calories/gram
Five primary human lipids
– fatty acids
– triglycerides
– phospholipids
– eicosanoids
– steroids
Fatty Acids
- Chains of 4 to 24 carbon atoms // carboxyl (acid) group on one end,
methyl group on the other and hydrogen bonded along the sides - Classified as:
– saturated – all carbon atoms saturated with hydrogen
– unsaturated - contains C=C bonds without hydrogen
– polyunsaturated – contains many C=C bonds
– essential fatty acids – obtained from diet, body can not
synthesize
Triglycerides (Neutral Fats)
- Three fatty acids covalently bonded to a three carbon alcohol (a glycerol molecule)
– each bond formed by dehydration synthesis
– once joined to glycerol /// fatty acids can no longer donate protons – it is a neutral fats
– maybe broken down by hydrolysis - Triglycerides when at room temperature
– If liquid its called an oils // often polyunsaturated fats from
plants
– If solid its called a fat // saturated fats from animals - Primary Function - energy storage, insulation and shock
absorption (adipose tissue)
Phospholipids
similar to neutral fat except
that one fatty acid replaced
by a phosphate group
* structural foundation
of cell membrane
Amphilphillic
– fatty acid “tails” are
hydrophobic // water
fear
– phosphate “head” is
hydrophilic // water
seaking
Amphiphilic
single molecule containing both a neutral and charged region
Width of a Plasma Membrane
5.5 to 7.5 nm Thick
Approximately 25 water
molecules are needed
to span the width of a
plasma membrane!
Diameter of
water molecule =
0.29 nm
Eicosanoids
- 20 carbon compounds derived from a fatty acid called
arachidonic acid - hormone-like chemical signals between cells
- includes prostaglandins – produced in all tissues
– role in inflammation, blood clotting, hormone action,
labor contractions, blood vessel diameter
Steroid
a lipid with 17 of its carbon atoms in four rings
Cholesterol
the ‘parent’ steroid from which the other steroids
are synthesized
– E.g. cortisol, progesterone, estrogens, testosterone and bile
acids
– synthesized only by animals // especially liver cells // 15%
from diet, 85% internally synthesized
– important component of cell membranes
– required for proper nervous system function
– never metabolized for energy!
“Good” and “Bad” Cholesterol
‘Good’ and ‘bad’ cholesterol refers to two different
transporter “types” associated with the blood
“good” cholesterol”
HDL – high-density lipoprotein
– lower ratio of lipid to protein in its shell
– may help to prevent cardiovascular disease
“bad” cholesterol”
LDL – low-density lipoprotein
– high ratio of lipid to protein in its shell
– contributes to cardiovascular disease
Proteins
a polymer of amino acids
Greek word meaning “of first importance” // most versatile
molecules in the body /// organic molecule
Amino acid
central carbon with 3 attachments // amino group
(NH2), carboxyl group (COOH) and radical group (R group)
20 amino acids used similar “backbone” to make the proteins but unique radical (R) group
– properties of amino acid determined by -R group
– amino acids are defined as either essential or non-essential
Peptide
any molecule composed of two or more
amino acids joined by peptide bonds
Peptide bond
joins the amino group of one amino
acid to the carboxyl group of the next
– formed by dehydration synthesis
Peptides named for the number of amino acids
– dipeptides have 2
– tripeptides have 3
– oligopeptides have fewer than 10 to 15
– polypeptides have more than 15
– proteins have more than 50
Dipeptide Synthesis
Dehydration synthesis creates a peptide bond that joins amino acids // covalent
bond between carbon and nitrogen = peptide bond
Primary protein structure
protein’s sequence amino acid which is encoded in the
genes
Secondary protein structure
coiled or folded shape held together by hydrogen
bonds
– hydrogen bonds between slightly negative C=O and
slightly positive N-H groups
– most common secondary structure are:
* alpha helix – springlike shape
* beta helix – pleated, ribbonlike shape
Tertiary structure
further bending and folding of proteins into globular and
fibrous shapes
globular proteins
compact tertiary structure well
suited for proteins embedded in cell membrane and
proteins that must move about freely in body fluid
fibrous proteins
slender filaments better suited for
roles as in muscle contraction and strengthening the
skin
Quaternary structure
– associations of two or more separate polypeptide chains
– functional conformation – three dimensional shape
prosthetic group
Proteins that contain a non-amino acid moiety are called a
Hemoglobin contains four complex iron containing rings called
heme moieties
Conformation
unique three dimensional shape of
protein crucial to function
– Some proteins have ability to reversibly change their
conformation – important in:
* enzyme function
* muscle contraction
* opening and closing of cell membrane pores
Denaturation
extreme conformational change that
destroys function and protein can not revert back to its
original shape // caused by extreme heat, pH or agitation
Proteins Have Many Functions
- Structure
– keratin – tough structural protein- gives strength to hair, nails, and skin surface
– collagen – durable protein contained in deeper layers of skin,
bones, cartilage, and teeth
- gives strength to hair, nails, and skin surface
- Communication
– some hormones and other cell-to-cell signals
– receptors to which signal molecules bind
* ligand – any hormone or molecule that reversibly binds to
a protein - Membrane Transport
– channels in cell membranes that governs what passes through
– carrier proteins – transports solute particles to other side of
membrane
– turn nerve and muscle activity on and off - Catalysis
– enzymes - Recognition and Protection
– immune recognition
– antibodies
– clotting proteins - Movement
– motor proteins - molecules with the ability to change shape repeatedly - Cell adhesion
– proteins bind cells together
– immune cells to bind to cancer cells
– keeps tissues from falling apart
Enzymes
proteins that function as biological catalysts
– permit reactions to occur rapidly at normal body temperature
Substrate
substance that the enzyme acts upon
Naming Conventions
– named for substrate with -ase as the suffix (e.g. amylase =
enzyme that digests starch (note difference for amylose ///
“ose” indicates sacharide – amylose polymer of glucose)
Enzymes lower activation energy
- energy needed to get
reaction started /// enzymes facilitate molecular interaction
Enzymes are reusable
enzymes are not consumed by the
reactions
one enzyme molecule may consume
millions of substrate molecules per minute
Astonishing speed
Factors that change enzyme shape
– pH, temperature, agitation
– alters or destroys the ability of the enzyme to bind to substrate
– enzymes action have optimum pH /// salivary amylase works
best at pH 7.0 /// pepsin works best at pH 2.0
– temperature optimum for human enzymes – body temperature
(37 degrees C
Enzymes Control Metabolic Pathways
Chain of reactions // each step catalyzed by a different enzyme
Nucleotides
Organic Molecules
Three components of a nucleotide
– nitrogenous base (single or
double carbon-nitrogen ring)
– sugar (monosaccharide)
– one or more phosphate groups
ATP is the best know
nucleotide
DNA
- 100 million to 1 billion nucleotides long
- Our genes are constructed from DNA
– instructions for synthesizing all of the body’s
proteins
– transfers hereditary information from cell to
cell and generation to generation
– DNA codes for protein // either a structural
molecule or an enzyme (enzymes can make
other organic molecules)
RNA
- messenger RNA, ribosomal RNA, transfer RNA
- 70 to 10,000 nucleotides long
- carries out genetic instruction for synthesizing proteins
- assembles amino acids in the right order to produce
proteins - single strand // not double stranded like DNA
- Micro-RNA // functions as a biocatalyst
Adenosine Triphosphate (ATP)
- body’s most important energy-transfer molecule // the molecule
which provides energy for all cellular work // “molecular money” - briefly stores energy gained from exergonic reactions
- releases it within seconds for physiological work // ATP not used
to store energy - holds energy in covalent bonds
– 2nd and 3rd phosphate groups have high energy bonds //
denoted by this symbol “ ~ “
– most energy transfers to and from ATP involve adding or
removing the 3rd phosphate
Adenosine triphosphatases (ATPases)
hydrolyze the 3rd high energy phosphate bond
– separates into ADP + Pi + energy
Phosphorylation
– addition of free phosphate group to ADP molecule
– carried out by enzymes called kinases (phosphokinases)
– ATP can be formed by directly phosphorylation of ADP (substrate level phosphorylation) or by a mechanism within mitochondria called oxidation-phosphorylation which requires using an electron chain and ATP-synthetase
ATP contains
adenine, ribose and 3 phosphate groups
Overview of ATP Production
ATP consumed within 60
seconds of formation
* entire amount of ATP in
the body would support
life for less than 1 minute
if it were not continually
replenished
* cyanide halts ATP
synthesis // stops
electrons from moving
down electron transport
chain which is inside the
mitochondria
Guanosine triphosphate (GTP)
– another nucleotide involved in energy transfer
– donates phosphate group to other molecules
Cyclic adenosine monophosphate (cAMP)
– nucleotide formed by removal of both second and
third phosphate groups from ATP
– formation triggered by hormone binding to cell
surface
– cAMP becomes “second messenger” within cell
– activates metabolic effects inside cell
Cofactors
– about 2/3rds of human enzymes require a non-protein
cofactor
– inorganic partners (iron, copper, zinc, magnesium and
calcium ions)
– some bind to enzyme and induces a change in its
shape, which activates the active site
– essential to function
Coenzymes
organic cofactors derived from water-soluble vitamins
(niacin, riboflavin)
– they accept electrons from an enzyme in one metabolic
pathway and transfer them to an enzyme in another metabolic
pathway /// This is an Oxidation-Reduction Reaction
– the molecule losing the electron is “oxidized” and the molecule
gaining the electron is “reduced” (i.e. redox reaction)
– The electron carrier is reqired by the enzyme to catalyze the
reaction reaction (e.g AB —–> A + B)
– NAD to NADH or FAD to FADH are examples of electron
carriers
