Organic Chemistry Flashcards
Organic compounds contain
Carbon.
What type of bond do all organic compounds have?
Covalently bonded molecules
All other compounds that do not contain carbon are inorganic. Name some examples
water, salts, and many acids and bases.
All ions are considered electrolytes. What is an electrolyte?
Substances that conduct an electrical current in solution.
Why are electrolytes important?
Because they are essential for nerve impulse transmission and muscle contraction.
Maintaining proper ionic balance is our body fluids is one of the most crucial ____ roles of the kidneys.
Homeostatic.
Like salts, ___ and ___ are electrolytes. They ionize and dissociate in water and can then conduct an electrical current.
Acids, bases.
What is the definition of an acid?
An acid is a substance that releases hydrogen ions (H+) in detectable amounts. They are proton donors.
What is the definition of a base?
A base TAKES UP hydrogen ions (H+) in detectable amounts. They are proton acceptors.
Concentration of hydrogen ions in various body fluids is measured in concentration units called..?
pH units
a pH of 7 is considered..?
Neutral - neither acidic or base such as pure distilled water
Solutions with a pH below 7 are considered..?
Acidic - the hydrogen ions outnumber the hydroxyl ions.
The lower the number of a pH scale, the more ___ the solution is.
acidic
Solutions with a pH higher than 7 is considered ..?
Alkaline - hydrogen ions decrease in concentration.
When the hydrogen ion concentration increases in the pH scale, ___ ion concentration always increases.
hydroxyl
What are the organic compounds?
Carbohydrates
Lipids (fats)
Proteins
Nucleic Acids
What are the 2 exceptions the inorganic/organic rule?
Carbon dioxide and carbon monoxide contain carbon but are considered inorganic compounds.
Carbon is precisely electroneutral. What does this mean?
Electroneutral- carbon never gains or loses electrons, but always instead SHARES them.
Carbon has 4 valence shell electrons. Carbon forms 4 ____ bonds with other elements and other carbon atoms.
Covalent
Define polymer.
Polymer - chainlike molecule made of many similar or repeating units (monomers).
Polymers are joined together by ..?
Dehydration synthesis
Define dehydration synthesis.
Dehydration synthesis - Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation.
How often does the removal of water at the bond site occur?
Occurs each time a monomer is added to the growing polymer chain.
A group molecules that includes sugars and starches and represents 1-2% of cell mass.
Carbohydrates
Monosaccharides are the _____ , or the building blocks, that make up the other carbs.
Monomers
Single chain or single ring structures, simple sugars containing from 3 to 7 carbon atoms.
Monosaccharides.
What are some important monosacchs?
Pentose sugars - Ribose and deoxyriblose
Hexose sugars - Glucose (blood sugar)
How can you determine the type of monosacch?
Monosacchs are named generically according to the number of carbon atoms they contain: Pentose -5 carbon sugars, and hexose - 6 carbon sugars
What is dehydration synthesis?
When a water molecule is lost as the bond is made.
How is a disacch, or a double sugar, made?
A disacch is formed when two monosacchs are joined together by dehydration synthesis.
Are disacchs able to pass through cell membranes?
No, they are too large and must be digested down to their simple sugar units to be absorbed.
What is the process of a disacch being broken down into its simple sugar units?
Hydrolysis
Define hydrolysis
This is a decomposition process which is essentially the opposite of dehydration synthesis. A water molecule is added to each bond, breaking the bond and releasing the simple sugar units.
Name some important disacchs.
Sucrose, maltose, lactose
The process during which a water molecule is added to each bond, adding OH to one monomer and H to the other, breaking the bond and releasing the simple sugar units.
Hydrolysis (lysis = break)
What is a polysaccharide?
Polymers of simple sugars linked together by dehydration synthesis.
Since they are fairly insoluble, they are ideal storage units. Name some storage carbs.
Starch - storage carb formed by plants
Glycogen - storage carb of animal tissues stored primarily in skeletal and liver cells.
What is the major function of carbs?
Major source of cellular fuel
Structural molecules such as ribose in RNA
Most cells can only use a few types of simple sugars. Which one is the “favorite”
Glucose: the major energy fuel for forming ATP
Carbohydrates contain
C, H, O (CH20)n
Lipids contain
C, H, O but less than carbs, and sometimes Phosphorous in the more complex lipids
Lipids are ____ in water.
Insoluable
Name some of the main types of lipids
Neutral fats or triglycerides
Phospholipids
Steriods
Eicosanoids
What type of lipid is:
- Called fats when solid and oils when liquid
- Composed of 3 fatty acids bonded with a glycerol molecule
Neutral Fats/Triglycerides
What are the main functions of triglycerides?
- Energy storage
- Insulation
- Protection
What are the two building blocks of of triglycerides?
Fatty acids and glycerol
Triglycerides are called ____ when solid and ___ when in a liquid state.
fats, oils
Triglycerides are composed of __ fatty acid bonded with a ________ molecule.
3, glycerol
The ____ backbone remains the same in all triglycerides, but the ___ ___ chains vary, resulting in different kinds of fats and oils.
Glycerol, fatty acid
Nonpolar = unattracted to water. What is another name for nonpolar?
Hydrophobic
Polar = attracted to water, which is a polar molecule. What is another word for polar?
Hydrophilic
What type of saturation is considered “heart healthy”?
Unsaturated fatty acids
What determines a fatty acid’s saturation?
The number of C between atoms and number of H atoms.
Fatty acid with single covalent bonds between C atoms and a maximum number of H atoms such as solid animal fats like butter
Saturated fatty acids.
Fatty acid with one or more double bonds between C atoms and a reduced number of H atoms such as plant oils like olive oil
Unsaturated fatty acids.
Name for modified oils; unhealthy
Trans fats
Name of a specific heart healthy fatty acid
Omega-3
What type of triglyceride is a phospholipid?
Modified triglyceride
What makes phospholipids modified triglycerides?
They have glycerol + 2 fatty acids, rather than 3, and a phosphorous containing group. This technically makes them a diglyceride
The head and tail regions have different properties. What is the head and tail made of?
Head - phosphourous containing part which is polar (attracted to water)
Tail - Hydrocarbon portion which is nonpolar (hydrophobic) and interacts only with nonpolar molecules
The unique characteristics of phospholipids allows them to be used as the chief material for building ____ ____.
Cellular membranes, or cell membrane structure.
Lipid which is an interlocking 4 hydrocarbon ring structure and differ from fats and oils
Steriods
Like triglycerides, steroids are
Fat soluble and contain little oxygen
What is the most important steriod
Cholesterol
Why is cholesterol essential to human life?
- Important in cell membranes
- Vit D synthesis
- steroid hormones
- bile salts
- sex hormones
______ is the basis for all steroids formed in the body.
Cholesterol
What is the name for a lipid which are diverse and chiefly derived from a 20-carbon fatty acid (arachidic acid) found in all cell membranes?
Eicosanoids
What is the most important Eicosanoid
Prostoglandins and their relatives
Why are prostoglandins important?
They have a vital role in blood clotting, control of blood pressure, inflammation and labor contractions
What are some other fat-soluble vitamins?
Vitamins A, D, E, and K
Lipoproteins - Transport fats in the blood
What elements do Proteins contain?
C, H, O, N and sometimes S and P
Proteins are polymers, and _____ ______ (20 types) are the monomers in protein.
Amino acids
Amino acids are joined by covalent bonds called..?
Peptide bonds which then form polypeptides.
Amino acids contain ___ group and ___ group.
Amine, acid
Amino acids can act as either an ___ or ___.
Acid, base
Protein compose 10-30% of cell mass and is the basic ____ material of the body.
Structural
All amino acids are indentical except for a single group of atoms called their __ ____.
R group.
What is an R Group?
Differences in the R groups are what makes an amino acid chemically unique
Proteins are long chains of ___ ____ joined together by dehydration synthesis.
Amino acids (protein’s building blocks)
Proteins can be described in terms of 4 structural levels. What are the names of these levels.
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
What is the primary structure?
The primary structure forms the sequence of amino acids in the polypeptide chain. The R gourps may be polar or nonpolar. Resembles a strand of amino acid “beads” and is the backbone of the protein molecule.
Secondary structure?
When the chains from the primary structure forms a spiral as in the alpha helix and the beta pleated sheet, which looks like an accordion
Which of the structures of the secondary structure is most common?
The alpha helix
What type of bonds stabalize each structure of the secondary structure/
Hydrogen bonds
What is the tertiary structure?
Occurs through further H bonding between alpha helcices, beta sheets, and other portions of the polypeptide chain. Looks like a spaghetti glob.
Which structural level allows the protein to be complete once the structure level is complete?
Once the tertiary level of folding is complete, the protein is functional
What is the quaternary structure?
Occurs in a few select proteins when multiple proteins interact through H bonds and covalent disulfide bonds to form globular or filamentous proteins. Looks like a double spaghetti glob.
What are some examples of quaternary proteins?
Hemoglobin Insulin Antibodies F-actin Hair
Which structural level superimposes on the level before it?
The tertiary level superimposes onto the secondary structure. Alpha helices and/or beta sheets are folded up to form a compact globular molecule held together by intramolecular bonds.
The ultimate overall structure of any protein is very specific and is dictated by its _____ structure.
Primary.
Strand-like water-insoluble, and stable proteins which mostly have tertiary or quaternary structure (giving it a 3-D shape).
Fibrous (structural) proteins.
Fibrous (structural) proteins provide
Support and tensile strength
What are some examples of Fibrous proteins?
Elastin
Collagen (single most abundant in the body)
Certain contractile fibers
Compact, spherical, water-soluble and sensitive to environmental changes which have specific functional regions (active sites) and display tertiary or quaternary (3-D) structure.
Globular (functional) protein
What are some examples of Globular (functional) proteins?
Antibodies
Hormones
Molecular chaperones
Enzymes
Which of the globular or fibrous proteins are stable?
Fibrous. Globular are quite unstable.
What is protein denaturization?
When hydrogen bonds begin to break, when the pH drops or the temp rises above normal physiological levels, it causes the protein to unfold and lose their specific 3-D shape. Irreversible if changes are extreme such as a cooked egg. Active sites destroyed.
Globular proteins which ensure quick, accurate folding and association of other proteins, prevent incorrect folding, assist in translocation of proteins and ions across membranes, promote breakdown of damaged proteins and help trigger the immune response.
Molecular chaperones.
Molecular chaperones produces in response to stressful stimuli and are important to cell function during stress. They can also delay aging by patching up damaged proteins and refolding them.
Stress proteins.
What are enzymes?
Globular proteins that act as biological catalysts.
What is a catalyst?
Substances that regulate and accelerate the rate of biochemical reactions but are not used up or changed in those reactions.
Enzymes lower the activation energy and
increase the speed of reaction (millions of reactions per minute)
Amino acids are connected by a covalent bonds, but what is the specific name for the bond between each amino acid in a protein?
Peptide bonds
The functional enzyme consists of two parts which are both called:
Holoenzyme
What are the two parts to a holoenzyme?
apoenzyme and cofactor
What is apoenzyme?
The protein portion of the enzyme
What is the cofactor?
Cofactor is the metal ion or coenzyme which is the organic molecule that is often a vitamin. Many enzymes require cofactors to function.
Enzymes are specific and act on a specific
Substrate
Enzymes usually end in the letters
-ase
They are often named for the reaction they catalyze such as
Hydrolases, oxidases
What is the first step of the mechanism of the enzyme action?
Substrates such as an amino acid bind to the enzyme’s active site forming an enzyme-substrate complex
What is the second step of the mechanism of the enzyme action?1
Energy is absorbed, and a bond is formed, and water is released. The enzyme-Substrate complex undergoes internal rearrangements that form the product.
What is the third step of the mechanism of the enzyme action?
The enzyme releases the product after peptide bond is formed.
What is made by one or more polypeptides?
A protein
Many amino acids joined by peptide bonds form a
polypeptide
The largest molecules in the body that are composed of C, H, O, N and P.
Nucleic acids
What are the two major classes of Nucleic Acids?
Deoxyribonucleic acid
Ribonucleic acid
What are the structural units of nucleic acids?
Nucleotides
What are the 3 components that each nucleotide consists of?
A nitrogen base
A pentose sugar (ribose or deoxyribose)
and A Phosphate group
What are the 5 major varieties of nitrogen-containing bases that can contribute to nulceotide structure?
Adenine (abbreviation "A") Guanine (G) Cytosine (C) Thymine (T) Uracil (U)
DNA utilizes 4 nitrogen bases. Which are the two large, 2-ring nitrogen bases called purines?
Adenine and Guanine
Which are the three smaller single-ring nitrogen bases called pyrimidines?
Cytosine, thymine, uracil
Nucleic Acids are polymers. What is the monomer for nucleic acids?
Nucleotides
What is the base-pair rule?
Each base pairs with its complementary base: A always pairs with T, and G always pairs with C
DNA is a double-stranded helix. What sugar does DNA contain?
Deoxyribose pentose sugar
DNA contains which 4 out of the 5 nitrogen bases?
DNA contains A, G, C, T
RNA contains which of the 4 out of 5 nitrogen bases?
RNA contains the bases A, G, C, U
Which RNAs are involved in carrying out DNA’s instructions for protein synthesis?
Messenger, Ribosomal, and transfer RNA
Which is the helical and which is the single strand?
DNA is the helical shape, RNA is the single strand.
For DNA, T pairs with A
For RNA, what nitrogenous base pairs with A?
U
Nucleic acid is a form of
ATP
Nitrogen bases in DNA extend to the side of the DNA strand. The nitrogen bases of one DNA strand are hydrogen-bonded to the nitrogen bases of the _______ strand in complimentary fashion - A & T, C& G and in RNA A & U compliment each other to form a complimentary pair.
Antiparellel
The sequence of the nitrogen bases along the DNA strand define the _____ _____ of the organism.
Genetic code.
