Study Guide for Organic Molecules

What are the characteristics of an organic molecule?

Contains carbon and is vital for life forms

What is vitalism?

A false pretense that organic molecules can only be made in organisms; a dependency on something in order to live

Can organic molecules be synthetic? If so, provide an example.

yes, Tefzel is an organic molecule that's synthetic. it's largely composed of hydrogen and carbon atoms

What properties of carbon make it important in organic chemistry

it is able to form 4 stable covalent bonds with other atoms, its tetravalency (4 valence electrons) allow for this. It's electronegativity also allows for electrons to be shared very evenly, promoting strong bonds between molecules.

What types of covalent bonds can carbon form?

Single, Double, and Triple bonds

What types of molecules can carbon bind to?

A wide variety of other atoms. Most notably hydrogen, oxygen, nitrogen, sulfur, and other carbon atoms.

What types of structures can carbon containing molecules form?

Linear, branched, or ring-like

What types of functional group can carbon bind to?

A large sum of functional groups. Especially Hydroxyl (-OH), Carbonyl (C=O), Amine (NH2), and Carboxyl (-COOH) groups

What are polymers?

Multiple monomers chained together

What is the basic subunit of a polymer called?

monomer

By what type of reaction are subunits in a polymer join

dehydration synthesis

What type of reaction is used to degrade a polymer into individual subunits?

Hydrolysis

What are the 4 major classes of biologically important organic molecules

Carbohydrates, Lipids, Proteins, and Nucleic Acids

What atoms are found in carbohydrates? In what ratio are these atoms found?

Carbon, Hydrogen, and Oxygen in a 1:2:1 ration

What are the simplest form of carbohydrates?

Monosaccharides

What are reducing sugars? What makes a sugar a reducing sugar? Be able to identify aldehyde and ketone functional groups

A reducing sugar are carbohydrates that have a free carbonyl group that can allow for another glycosidic bond

In what forms can monosaccharides exist?

Can exist in linear chains or ring like structures

What properties of glucose make it biologically important

Very water soluble and it is a highly reduced molecule which makes it a good source of energy

What are functions associated with carbohydrates?

The ability for organisms to use it as energy storage and providing structure

What is a disaccharide? How are disaccharides formed? What is the name of the covalent bond used to join monosaccharides?

A polymer of two monosaccharides joined through a glycosidic bond via dehydration synthesis. It's a reducing sugar if it has a free carbonyl group

What are oligosaccharides? Polysaccharides?

Polymers consisting of several subunits linked through a glycosidic bond

Glucose polymers (Starch, Glycogen, Cellulose)

Starch: Plants excess glucose storage, Glycogen: How animals store excess glucose, Cellulose: used in plant cell wall structure

Peptidoglycan

Found in bacteria cell walls

Chitin

Found in bugs exoskeletons

Glycosaminoglycans

Lubricant in animal joints

What are lipids composed of? List examples

Composed of Carbon, Hydrogen, and some Oxygen. Triglycerides, Waxes, Phospholipids, and Steroids

What properties are shared by lipids?

Non-polar molecules (many Carbon-Carbon, Carbon-Hydrogen bonds) highly variable in structure

Why are lipids hydrophobic?

Long chains of hydrocarbons

What functions are associated with lipids?

Membranes, Energy Storage, Cell Signaling

What are "Fatty Acids" composed of?

Hydrocarbon chains, with a carbonyl group on one end

What is the difference between a saturated and an unsaturated fatty acid?

Saturated fatty acids lack double bonds between carbons

What is the difference between a monounsaturated and a polyunsaturated fatty acid?

Monounsaturated only consist of one double bond between carbons, whereas Polyunsaturated fatty acids have several.

What are triglycerides composed of?

3-fatty acids and a glycol

What type of covalent bond is used to link fatty acids to glycerol in triglycerides?

Ester Bond

Explain how the fatty acids found in a triglyceride affect the physical properties of the triglyceride (solid vs liquid)

Saturated fatty acids can be closely compacted together making triglycerides more solid at room temp

Compare and contrast phospholipids and triglycerides

Phospholipids=2 fatty acids; Triglycerides=3 fatty acids. Phospholipids are amphipathic and Triglycerides are hydrophobic. Both are lipids

Are phospholipids classified as polar, non-polar, or amphipathic molecules?

Amphipathic, has a hydrophilic head and a hydrophobic tail

Why do phospholipids spontaneously organize into bilayers when placed in water?

To form a stable, energy efficient structure. This function is vital for cell membranes and organelles.

Why are steroids, many hormones, some vitamins and waxes considered lipids?

Non-polar molecules made of carbon, hydrogen (hydro-carbon) and a little oxygen

What structural feature is shared by molecules classified as steroids?

4 Ring structure

What structural feature is shared by waxes? Why do you think waxes are solid at room temperature?

A long chain of non-polar liquid. Solid at room temperature because they have a relatively straight structure that can be tightly packed.

What are the subunits in proteins?

Amino Acids.

What is the name of the covalent bond found in proteins?

Peptide Bond

What functions are associated with proteins?

Initiate movement, protect against disease, hormones, enzymes, structural support

By what process are proteins formed?

Dehydration synthesis

How many different naturally occurring amino acids are there?

20 different naturally occurring amino acids

What is the general structure of an amino acid?

-Amino Group

-Carboxyl Group

-Side Chain

What are peptides and polypeptides?

Peptide= 2 Amino Acids bonded together, Polypeptide=3 or more Amino Acids bonded together

What is the primary structure of a protein? What is meant by the amino acid terminus and the carboxy terminus of a protein?

Linear sequence of amino acids is the primary structure. The Amino Terminus is the start of the chain and the carboxy terminus is the end. the amino group on an amino acid interacts with the other amino acids carboxyl group through dehydration synthesis

What secondary structures can be found in proteins? Can a single polypeptide have more than one secondary structure?

Alpha Helix and Beta-Pleated sheets. It's possible to have a polypeptide with both of these, alpha helix being used for stability while beta-pleated sheets being used for rigidity.

WHat is the tertiary structure of a protein?

Overall 3d shape of a polypeptide

What is the quaternary structure of a protein? Can a single polypeptide have a quaternary structure?

No, only shows multiple structures of proteins with two or more polypeptides

What is the difference between globular and filamentous proteins?

Filamentous: elongated, non-soluble, provide strength to tissues. Globular: compact, spherical, soluble, immune support , catalysis, transport

How can proteins be modified to form glycoproteins and lipoproteins?

Covalent attachment of either a carbohydrate or a lipid molecule to a protein

Where is the information for proteins stored?

In the genome which is comprised of DNA

What forces contribute to to the formation of secondary, tertiary, and quaternary structure of proteins?

Hydrogen bonds, ionic bonds,/polar interaction, hydrophobic effect, Van der waals forces, Disulfade bridges

Why is the structure of a protein important to its function?

Structure is critical for protein communication

What happens when a protein is denatured? When a protein is renatured?

Denature: disrupts function and structure. Renature: regains structure and biological activity

What is a functional domain on a protein? Be familiar with the example of a nuclear receptor discussed.

Independently folded regions that perform a function EX: estrogen, androgen

What are the subunits of acid polymers called?

Nucleotides

What covalent bonds are used to join the subunits of nucleic acid polymers? What groups participate in the formation of this covalent bond?

phosphodiester bonds; phosphate group of one nucleotide and the hydroxyl group

What are the two types of nucleic acids?

DNA and RNA

What is the function of DNA? How does DNA store genetic information?

Stores genetic information in a sequence of bases

What are the three major types of RNA discussed in class? In what process do these RNA molecules participate?

tRNA, mRNA, rRNA

What are the three basic parts of a nucleotide?

Phosphate group, nitrogenous base, and a pentose sugar (ribose or deoxyribose)

To what carbons is the base attached?

1' Carbon

To what carbon are the phosphates attached?

5' Carbon

What specific sugar is found in DNA nucleotides? What specific sugar is found in DNA?

DNA= Deoxyribose, RNA=Ribose; Ribose has an extra oxygen and both DNA/RNA are pentose sugars

What bases can be attached to DNA nucleotides? Which base is only found in DNA?

Adenine, Cytosine, Guanine, Thymine; Thymine is only found in DNA

What bases can be attached to RNA nucleotides? Which base is only found in RNA?

Adenine, Cytosine, Guanine, Uracil; Uracil is only found in RNA

What bases are classified as purines? What structural feature do purines have?

Double ringed structure of 6-Carbon; Adenine Guanine

What bases are classified as pyrimidines? What structural features do pyrimidines share?

One 6-Carbon ring; Cytosine, Thymine, Uracil

How are nucleotides joined to form nucleic acid polymers? By what general process does this occur?

Through dehydrations synthesis

What is the difference between the 5' end and the 3' end of a nucleic acid polymer? Why is this biologically significant?

5' end has a phosphate group, 3' end has a hydroxyl group. They are antiparallel to allow for linkage between nucleotides

What is the orientation of the strands in a double stranded DNA molecule? What type of bond is used to hold the two strands together? Which bases can form complementary pairs?

Hydrogen bonds pair the strands; A-T, C-G, C-U

In what form does RNA normally exist in living cells? Do RNA polymers have 5' and 3' ends? What is the orientation of the strands when a strand of RNA base pairs with a strand of DNA? What bases form complementary pairs in RNA/DNA hybrids?

RNA is typically singel stranded. RNA does have 5' to 3' ends. RNA and DNA pairs form antiparallel to each other. In a DNA/RNA hybrid: Adenine-Uracil, Thymine-Adenine, Cytosine-Guanine, Guanine-Cytosine

What is the orientation of the strands in a double stranded RNA molecule? What bases can form complementary base pairs in double stranded RNA?

Still anti-parallel; in a Double stranded RNA: Adenine-Uracil, Uracil-Adenine, Cytosine-Guanine, Guanine-Cytosine