Chapter 2 Chemistry Flashcards
Organic Molecules
-organic molecules in human body are
either solids, or in one of three types of
water-based solutions:
1. solution = uniform mixture
2. colloid = solution containing
dispersed proteins or other large
solutes e.g. milk
3. suspension = solution containing
large particles that will settle out e.g. blood
Carbohydrates
-make up ~3% of body mass
-sugars & starches
-composed of C:H:O in 1:2:1 ratio in
monomer form (carbon + water)
-mostly catabolized for energy but also
necessary for RNA & DNA, amino
acids, and nutrient reserves
-organized into 3 groups based on complexity of structure:
A. monosaccaride
B. Disaccaride
C. polysaccharide
Lipids
-make up 12-24% of body mass
-fats, oils and waxes, nonpolar
-simple lipids are composed of C, H, O but
usually O < C, more complex can have
functional groups
-function in energy storage (~2X more
energy in lipid compared to carbohydrate of equal size), cell membranes, and cellular communication
-organized into 5 classes based on structure
Lipids are organized into 5 classes based on structure
-Fatty acids
-Eicosanoids
-Glycerides
-Steroids
-Phospholipids and Glycolipids
Fatty acids
-hydrocarbon chain with carboxyl group -long hydro-
carbon chain is hydrophobic making molecule insoluble
-chain can be saturated (all single covalent bonds on the Cs) or unsaturated (one or more double covalent bonds between Cs)
-Saturated fatty acids tend to come from animal sources,
- unsaturated fatty acids from plants: “hydrogenated”
-“trans” fats have hydrogen chemically added making what had been an unsaturated fatty acid saturated
Eicosanoids
-derived from arachidonic acid (a
polyunsaturated
omega-6 fatty
acid) constructed
from essential
omega fatty acids in the diet
-function in cellular communication -two types:
a. leukotrienes: used by cells to signal injury
b. prostaglandins: used for cell-to- cell signaling to coordinate events e.g. pain and inflammation after injury
Glycerides
-glycerol (C3H8O3) + fatty acids (up
to 3)
-named for the number of fatty acids
bound to the glycerol group by a dehydration synthesis:
a. monoglyceride (mono = one)
b. digylyceride (di=two)
c. triglyceride (tri=three)
Triglycerides make up fat deposits on animals, important for:
-energy storage
-insulation
-mechanical protection (e.g. knees, eye sockets)
All excess organic calories (molecules containing C, H and O) can be converted into triglycerides for storage via dehydration synthesis reactions; will require hydrolysis reactions with oxygen to “burn” them
Steroids
-structure involves 4 carbon rings e.g. cholesterol
-important for many basic functions:
1. cell membrane formation and maintenance, cell division and osmotic stability of the cell (cholesterol)
2. regulation of sexual function (steroid based sex hormones e.g. testosterone)
3. tissue metabolism and mineral balance (steroid based metabolism hormones e.g. aldosterone)
4. processing of dietary fats (structural component of bile salts)
Phospholipids and Glycolipids
Phospholipid = diglyceride + phosphate group (PO3) +
non-lipid group
Glycolipid = diglyceride +
carbohydrate
-predominant molecules
of cell membrane
Bipolar molecule
-Hydrophilic head group (phosphate/carbohyrate +glycerol) makes solutions with water
-Hydrophobic tail group (hydrocarbon chains): avoids water “wants to be shielded from water
-If phospholipids and/or glycolipids are mixed with water, will spontaneously form a micelle
Proteins
-make up ~20% of body mass
-most abundant organic molecules in cells
-composed of C, H, O, N, sometimes S
-essential to cell structure and function:
1. support (e.g. structural proteins)
2. movement (e.g. contractile proteins in muscle)
3. transport (e.g. transport proteins in blood)
4. buffering: regulate pH of body fluids (e. coordination and control e.g. hormones)
5. defense (e.g. keratin in skin, antibodies, clotting factors)
*6. metabolic activity and regulation (e.g. enzymes necessary for all reactions)
-monomer building blocks: amino acids
Characteristics of Proteins
-formed from amino acids that are assembled into polypeptides that are folded into the proper native conformation/structure
-monomer building blocks : amino acids
Amino acid structure:
-central carbon (alpha-carbon)
-carboxyl group (COOH)
-amino group (NH2)
-H
-R group = unique side chain
20 different amino acids: vary on nature of R group
-some charged (+ or –)
-some hydrophobic
-some hydrophilic
-some make disulfide bonds
-proteins are formed from long strings of peptide bonded amino acids:
-amino group of one bound to carboxyl
group of next via dehydration
synthesis
(resulting bond = peptide bond)
-chain of peptide bonded amino acids = a polypeptide, this folds into a protein
-proteins only work if folded correctly into the proper native structure or native conformation
Levels of protein organization
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
Two basic shapes are possible for protein organization
a. globular
b. fibrous
Homeostasis necessary to avoid denaturation= loss of protein shape due to unfavorable temp, pH, salinity etc.
Loss of native conformation/structure= denatured, protein no longer functional
Enzymes
-most abundant proteins in body
-biological catalysts, catalytic proteins used for all metabolism ( chemistry) of living cells
-speed up reactions by lowering activation energy
-are not used up or changed by the reaction
Characteristics of enzymes (3 things)
- Specificity
- Saturation limits
- regulation
Specificity
each enzyme has a unique 3D shape that creates a pocket called the active site
saturation limits
there is a maximum rate of reaction, adding more substrate will increase the reaction rate until saturation, at saturation the active site is always full and reaction can go no faster to produce product
regulation
cofactors or other regulators can turn enzymes on or off: this provides short term control over reaction rates
cofactor: ion or molecule that binds to enzyme to activate it usually a metal ion e.g Mg2+
coenzyme: non-protein organic molecule that acts as cofactor e.g vitamin
Conjugated proteins
=protein bound to other organic molecule
-Glycoprotein
-Proteoglycan
Nucleic Acids
-less that 1% of body mass
-composed of C,H,O,N and P
-function to store and process info at the molecular level
-2 types: deoxyribonucleic acid (DNA) for information storage
ribonucleic acid (RNA) for protein synthesis
-composed of nucleotides
each has 3 parts:
-pentose sugar (ribose or deoxyribose)
-phosphate group
-nitrogen containing base
Nitrogenous base
Purines:
(double ring)
Adenine (A)
Guanine (G)
Pyrimidines:
(single ring)
Cytosine (C)
Thymine (T)
Uracil (U)
nucleotides are linked together by
dehydration synthesis
RNA
-single stranded linear molecule
-backbone= ribose and phosphate
-bases= A,U,G,C (no T)
DNA
-double helix: 2 strands intertwined
-backbone = alternating deoxyribose sugar and phosphate
-held together by H-bonds between complementary bases
-base pairing A to T (two H-bonds) G to C (three H-bonds)
no U in DNA
DNA contains genes
-gene = specific order of bases on a
strand of DNA that encodes RNA which
usually encodes a protein
-the order of the nucleotides in the DNA
gene (A,T,G,C) is the information; it is copied into an
mRNA form
(A,U,G,C) so the information can be used by the cell to assemble the primary structure of a protein (the order and number of amino acids)
High energy molecules
-used by cells to store chemical bond energy from food molecules in easy to use form
-involves phosphorylation: bonding of
phosphate group to organic molecule
-phosphate groups are negatively
charged, multiple bonded in series creates unstable bonds that are easy to break and release energy from; energy then used by the cell to do work
-most common high energy molecules is
ATP: adenosine triphosphate adenine + ribose 3 phosphate groups
-hydrolysis of bond to the 3rd phosphate releases energy for use by cell
Primary structure
unique sequence of amino acids dictated by the DNA; linear order of amino acids peptide bonded together (~300-3000, depending on the specific protein)
Secondary structure
local twisting and folding of polypeptide due to H- bonds between neighboring amino & carboxyl groups, creates a-helices and b-pleated sheets (many of both can occur simultaneously)
Tertiary Structure
global folding due to chemical interactions between R-groups (H-bonds, ionic bonds, disulfide links,
hydrophobic interactions, etc.)
Quaternary Structure
aggregation of 2 or more tertiary-folded polypeptide chains (for multi-subunit proteins)
Globular
compact, rounded, typically soluble e.g. enzymes and transport proteins
Fibrous
sheets or strands, non-soluble e.g. structural proteins
Glycoprotein
small carbohydrate attached to large protein e.g. mucus
Proteoglycan
large polysaccharide linked by polypeptides e.g. the “glue: in connective tissue
dehydration synthesis
sugar of one to phosphate of next creating a linear “backbone” with the bases hanging off the side
3 types of RNA
- mRNA
- rRNA
3.tRNA
mRNA
(messenger) template for a protein, order of amino acids (the primary structure of a protein)
rRNA
(ribosomal) forms ribosomes: organelle for protein synthesis
tRNA
(transfer) carrier to bring amino acids to the ribosome
monosacharride
simple sugar, 3-6
carbons e.g. glucose C6H12O6
(most important human fuel)
Disacharride
2 covalently bonded
monosaccharides e.g. sucrose
(glucose + fructose)
Polysaccaride
3 or more
covalently bonded monosaccharides,
large ones are insoluble e.g.
glycogen, “animal starch” is the
storage form of glucose produced by skeletal muscle and liver cells
micelle
micelle = sphere formed with hydrophilic heads oriented out toward water and hydrophobic tails pointed in away from water (basic principle of how soap functions to remove greasy dirt)
