BIO - Organic molecules

What are the characteristics of an organic molecule?

carbon-based, covalently bonded, structurally diverse

What is Vitalism

it says organic molecules can only be synthesized by living organisms

Can Organic molecules be synthetic? If so, provide an example

Yes, Tefzel (used to create domes and cover wires)

Properties of Carbon that make it important

Backbone, because of its four val el-, versatile, stable but reactive

What types of Covalent bonds can carbon form?

single, double, and triple: due to its 4 val el-

What type of molecules can carbon bind to

can bind to a wide variety due to the 4 val el-

what types of structures can carbon containing molecules form

Linear, Branched, or rig like

What types of functional groups can carbon bond to

A variety

What are polymers

long molecules with individual subunits linked together

what is the basic subunit of a polymer

a Monomer: simple molecule that can later form chains

by what type of reaction are subunits in a polymer joined

Hydrolysis, as by taking a water molecule out allows them to bind

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

hydrolysis

what are the four major classes of biologically important organic molecules

Carbohydrates, Lipids, Proteins, and Nucleic acids

what atoms are found in carbohydrates? in what ratio

H, C, O. in a 1:2:1 ratio

What is the simplest form of carbphydrates

Monosaccarides

what are reducing sugars? what makes it a reducing sugar?

monosaccharides is a reducing sugar as it has free aldehyde and ketone groups. it makes them reduce because those free groups allow for oxidation to happen

Aldehyde vs Ketone

( O=C-H) and (>C=O)

in what forms can a monosaccharide exist?

Chains, cyclic forms

what properties of glucose make it biologically important

Store energy, very soluble

what functions are associated with carbohydrates

Structural, store energy

What is a disaccharide, how are they formed? what is the covalent bond used to join monosaccharides

Disaccharides are polymers made of 2 monosaccharides bonded covalently together by glycosidic bonds.

what are oligosaccharides? polysaccharides?

Oligosaccharides: polymers with short chains

Polysaccharides: polymers with long chains

Some polysaccharides:

Glucose: starch, Peptidoglycan: Bacterial cell walls, Chitin: insect exo skeleton, Glycosaminoglycans: lubricant

What are lipids composed of? examples of lipids?

Carbon, Hydrogen, and a little bit of Oxygen

Fats, Oils, Waxes, Triglycerides, phospholipids, steroids, hormones, vitamins

what properties are shared by lipids

C-C and C-H bonds

why are lipids hydrophobic

because they are nonpolar

what functions are associated with lipids

Membranes, energy storage, cell signaling

what are fatty acids composed of

Long hydrocarbon chains with a carbon group at one end

what is the difference between a saturated and unsaturated fatty acid

Saturated fatty acids: zig-zag structure, have all single covalent bonds

Unsaturated fatty acids: zigzag with a bend, 1 or more double bonds in hydrocarbon chain

what is the diff between a monosaturated and polysaturated fatty acid

Monosaturated fatty acids: one double bond along hydrocarbon

Polysaturated fatty acids: 2 or more double bonds on a hydrocarbon

what are triglycerides composed of

composed of 3 fatty acids that are attracted to a molecule of glycerol

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

ester bonds: dehydration of glycerol

explain how fatty acids found in triglycerides affect the physical properties of the triglycerides (Solid vs Oil)

Solid: saturated fatty acids, denser molecule

Oil: unsaturated fatty acids, less dense molecule

compare and contrast phospholipids and triglycerides

Phospholipids: 2 fatty acids + 1 Phospholipid, amphipathic, membrane

Triglycerides: 3 fatty acids, nonpolar, energy storage

are phospholipids classified as polar, non-polar, amphipathic? explain

Ampipathic: Phosphate is polar and fatty acid is nonpolar

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

because of its polar and nonpolar states, the nonpolar regions being hydrophobic go inward and the polar outward, creating the bilayer

Why are steriods, horomones, some vitamins, and waxes considered lipids

they are considered lipids due to them being hydrophobic, nonpolar

what structural feature is shared by molecules classified as steriods

their 4-ring structure determines if their a steriod

what structural feature is shared by waxes? why do you think waxes are solid at room temp

their ester bonds: long fatty acids and long alcohols

they are solid at room temp because of their highly saturated fatty acids

what are the subunits is protien

Amino acids

what is the name of the covalant bond found in protien

peptide bonds

what functions are associated with protiens

Immunity

enzymes

cellular structure

transport proteins

By what process are protiens formed?

proteins are processed by amino acid subunits binded together by peptide bonds

How many naturally occuring amino acids are there

20

what is the general structure of an amino acid? be able to recognize an amino acid

the generally structure of an amino acid contains one or more polypeptide chains

What are peptide and polypeptides

Peptides: short polymer amino acids

Polypeptides: long polymer amino acids

What is the primary structure of a protein? what is meant by the amino terminus and the carboxy terminus of a protein? What functional groups on an amino acid are involved in the formation of a peptide bond?

Primary structure of a protein: linear sequence of amino acids

Amino terminus: the amino end of polypeptide

Carboxy Terminus: carboxyl end of a polypeptide

functional groups: Carboxly and amino groups

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

Secondary structures: sequence of amino acids forming hydrogen bonds, causing the region to fold/spiral: Alpha helix/Beta pleated

More than one secondary struct?: yes

what is a tertiary structure of a protien?

2nd structures and random coiled regions folding into 3-D shape

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

Quaternary Structure: 2+ polypeptides can bind to each other to form functional protein

more than one Quanternary struct?: no

What is the difference between a globular and a filamentous protein?

Globular: Spherical, soluble, functional

Filamentous: elongated, insoluble, structural

How can proteins be modified to form glycoproteins and lipoproteins

Glycoproteins: Protein binding to carbohydrate

Lipoproteins: Protein binding to lipid

Where is the information for making proteins stored?

Genes

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

Hydrogen bonds:

Ionic Bonds:

Hydrophobic Effect:

Van Derwall’s disulfide:

why is the structure of a protein important to its function

for it to allow functions to happen around the body

what happens when a protein is denatured? when a protein is renatured?

denatured: loss of biological activity

renatured: regaining biologial activity

what is a functional domain on a protein? be familiar with the example of a nuclear receptor discussed in class

functional domain on a protein: independently folded regions on a protein that prefers a characteristic function

What are subunits of nucleic acid polymers called?

Nucleotide

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

Covalent bonds used: Phosphodiester bonds

Groups that participate: Phosphate group, 3’ hydroxyl

what are the two types of nucleic acid?

Deoxyribonucleic acid

Ribonucleic acid

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

Function: String genetic info

How it is stored: in a sequence of its nitrogen bases (A T G C)

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

Three major types of RNA: mRNA, RibosomalRNA, IRNA.

Process of the three major types: Protein synthesis

What are the three basic parts of a nucleotide? to what carbon is the base attached? to what carbon are the phosphates attached?

3 basic parts: Phosphate, Nitrogen base, sugar

The base is attached to the 1st Carbon

The Phosphates are attached to the 5’ Carbon

What specific sugar is found in DNA nucleotides? what specific sugar is found in RNA nucleotides? how are these sugars similar and how are they different

Sugar in DNA: Deoxyribose; no Oxygen, H on 2nd Carbon

Sugar in RNA: Ribose; Hydroxyl group on 2nd Carbon

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

Bases attached to DNA: ATCG

only found in DNA: T (Thymine)

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

Bases attached to RNA: AUCG

Only found in RNA: U (Uracil)

What bases are classified as purines? what structural feature do purines share?

Purine bases: Adenine, guanine

Structural feature: double ring structure

What bases are classified as pyrimidines? what structural feature do pyrimdines share?

Pyrimidines bases: Uracil, Cytosine, Thymine

Structural features: Single ring

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

Nucleotides joined to form nucleic acid polymers by: Phosphodiester bonds which come from Dehydration reactions.

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

Biological significance: allows for direction/structure

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?

5’ to the 3’ and 3’ to the 5’

held by hydrogen bonding

A and T, G and C form complementary pairs

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 complimentary pairs RNA/DNA hybrids?

normally exist: 2 ring structure

they have 5’ and 3’ ends

the orientation of RNA pairing with DNA is A=U

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

Orientation: double strand RNA molecule, same as DNA

bases that form complementary base pairs: C=G, A=U