AP Biology: Organic Chemistry and Macromolecules

Organic Chemistry

the study of cpds with covalently bonded carbon

Organic Compounds

compounds that contain carbon and hydrogen

What forms the skeletons of many molecules

carbon chains; can differ in length, branching, double bond position, and presence of rings

hydrocarbons

organic molecules consisting of only carbon and hydrogen

functional groups

chemical groups attaches to the carbon skeleton that participate in chemical reactions

Macromolecules

large molecules made of smaller subunits

what makes carbon such a versatile element?

its ability to form four covalent bons

how do functional groups affect the structure and behavior of organic molecules

functional groups affect the way that a molecule is shaped and their polarity. an organic molecule being polar (hydrophillic) or nonpolar (hydrophobic) directly affects the chemical reactivity and behavior of the molecule

what is the difference between hydrocarbons and other organic molecules?

hydrocarbons contain ONLY carbon and hydrogen, but organic molecules can contain other elements

dehydration reaction

covalently bonds two monomers with loss of H2O

hydrolysis

breaks the covalent bonds in a polymer by adding H2O

polymers

chain-like macromolecules made of similar or identical repeating units that are covalently bonded together

monomers

the repeating units that make up polymers

differentiate between and hydrolysis and a dehydration reaction

dehydration reactions create covalent bonds with the loss of H2O while hydrolysis breaks covalent bonds with the addition of H2O

carbohydrates

includes sugars and polymers of sugars; contains a carbonyl group and many hydroxyl groups (C, H, O in a 1:2:1)

monosaccharides

simple sugars. they are molecular formulas with multiples of the unit CH2O. most common is glucose— used as nutrients, fuel for cells, and in cellular respiration. can serve as building blocks for amino acids or as monomers for di and polysaccharides

disaccharides

two monosaccharides joined together by covalent bondsmost common is sucrose from glucose and fructose

polysaccharides

polymer with many sugars joined via dehydration reaction

starch

storage polysaccharide; plants store STARCH (polymer of glucose monomers): allows plants to store excess glucose

Glycogen

Animals store GLYCOGEN (polymer of glucose): stored in liver and muscle cells

Cellulose

structural polysaccharides: (plants) tough substance that forms plant cell walls

Chitin

structural polysaccharides: (animals) forms exoskeletons of arthropods

glycosidic linkage

a type of covalent bond that joins a carbohydrate (sugar) molecule to another carbohydrate

what are polysaccharides? what are their monomers?

polysaccharides are polymers with many sugars joined via dehydration reaction. their monomers are monosaccharides

what important roles do polysaccharide play in animals? in plants?

polysaccharides are used for storage and structure in both plants and animals. In animals, glycogen is stored in liver and muscle cells, and Chitin is used to form the skeleton of arthropods. In plants, starch is stored to allow plants to store excess glucose, and cellulose is used to form cell walls

lipids

class of molecules that do not include true polymers; generally small in size and are NONPOLAR- hydrophobic

types of lipids

fats, phospholipids, steroids, and cholesterol

fats

a type of lipid that provides energy storage, supports cell functions, and provides insulation to keep mammals warm; composed of glycerol and fatty acids

glycerol

classified as an alcohol (hydroxyl)

fatty acids

long carbon chains (carboxyl group at one end)

how do fatty acids and glycerol join?

via ester linkage: bond between a hydroxyl and carboxyl group

saturated fatty acid

single bonds between carbons in the carbon chain= more hydrogen (think: saturated with hydrogen)

unsaturated fatty acid

contains one or more double bonds— causing the fatty tails to form kinks (bends); the more double bonds, the more liquid at room temp.

phospholipid

type of lipid that is a major component of cell membranes; two fatty acids attached to a glycerol and a phosphate. hydrophobic heads, hydrophilic tails

steroids

hormones that support psychological functions like growth and development, energy metabolism, and homeostasis; have four fused rings and groups attached determine the type

Cholesterol

provides structural stability to animal cell membranes

where can phospholipids be found in the cell and what is their function?

they can be found in the cell membrane and their function is to regulate what enters and leaves the cell (phospholipid bilayer)

how does saturation affect fatty acid structure/ function

saturation affects the number of double bonds, whether the fatty acid is solid or liquid at room temperature, and the amount of kinks the fatty acid has

nucleic acids

polymers made up of nucleotide monomers— function is to store, transmit, and express hereditary information; two forms: deoxyribonucleic acid and ribonucleic acid

nucleotides

monomers of nucleic acids; contains a nitrogenous base, five carbon sugar, and a phosphate group

components of nucleic acids

nucleotides → polynucleotides → nucleic acides

two types of nitrogenous bases

pyrimidine and purine

pyrimidine

nitrogenous base one ring with 6 atoms; Cytosine, Uracil, Thymine

purines

nitrogenous base one ring with 6 atoms bonded to one ring with 5 atoms (two rings); Adenine and Guanine

Five Carbon Sugar

a sugar bonded to the base. in DNA, sugar is deoxyribose, in RNA sugar is ribose that differ in structure and function; ribose has an -OH group where deoxyribose has an H group

phosphate group

added to the 5’ carbon of the sugar (which is attached to the base) to form a nucleotide

nucleoside

portion without the phosphate group

polynucleotide

phosphate groups link adjacent nucleotides via phosphodiester linkage; diretionality is 5’ to 3’

gene

a section of DNA that codes for a protein; dictates AA sequence, primary structure of a protein, and 3d structure of a protein

antiparallel

refers to opposite directional orientation

DNA

consists of two polynucleotides that form a double helix; strands are antiparallel and help together by hydrogen bonds between bases (C to G, A to T)

RNA

single stranded polynucleotide at varies in shape due to base pairing (A to U, C to G)

what forms the “backbone” of DNA

the phosphates and five carbon sugar (deoxyribose) form the backbone of DNA

what does it mean that DNA is antiparallel?

It means that the two strands have opposite directional orientation, one strand is 3’ to 5’ while the other is 5’ to 3’.

why are DNA strand antiparallel?

The strands are antiparallel because if they were parallel, the nitrogenous bases wouldn’t be able to form bonds in the middle of the strands.

Identify the three components of a nucleotide

1. nitrogenous base

2. five carbon sugar

3. phosphate group

what is the monomer of a nucleic acid called if it is lacking a phosphate group?

the monomer is called a nucleoside

list the possible nitrogenous bases that can be found in nucleotides

Adenine, Cytosine, Guanine, Thymine, Uracil

Compare and Contrast DNA and RNA

Similarities: Adenine, Cytosine and Guanine, consists of polynucleotides, have five carbon sugars, are polynucleotides, sugar-phosphate backbone, genetic info, phosphodiester linkages

differences: sugar (deoxyribose vs ribose), number of strands, Uracil vs Thymine, DNA is antiparallel

where can DNA be found in a cell? RNA?

DNA is mainly found in the nucleus while RNA is mainly found in the cytoplasm but is made in the nucleus

What functional group defines the 5’ end?

the phosphate group

What functional group defines the 3’ end?

the hydroxyl group

how many bonds connect adenine and thymine? How does this differ from cytosine and guanine?

two hydrogen bonds connect Adenine and Thymine, which is one less bond than Cytosine and Guanine, which has 3 hydrogen bonds

protein

molecule consisting of poly peptides (polymers of amino acids) folded into a 3D shape; C, H, O, N, S

Shape

determines function

amino acids

molecules that have an amino group and a carboxyl group; monomers of proteins

variable side chain

R, can be categorized as polar, nonpolar, or charged/ionic. Side chains interact, which determine the shape and function of the protein

polypeptides

many AA linked by peptide bonds; each polypeptide has a unique sequence of AAs and directionality one end is a free amino group (N-terminus) and one end is free carboxyl group (C-terminus)

what happens when a polypeptide twists and folds because of R group interactions?

it forms a protein

functions of proteins

Antibody: helps protect body from disease

Enzymes; carry out chem reactions or assist in creating new molecules

Messenger: transmit signals (i.e hormones)

Structural: provide structure and support

Transport/Storage: bind to and carry small atoms and molecules through body

primary level of protein structure

linear chain of AAs; determined via genes and dictate secondary and tertiary forms

secondary level of protein structure

coils and fold due to hydrogen bonding within the polypeptide backbone.

• β pleated sheet- hydrogen bonds between polypeptide chains lying side by side

• α-helix- hydrogen bonding between every 4th AA

tertiary level of protein structure

3D folding due to interactions between the side chains of the AAs; reinforced by hydrophobic interactions, hydrogen bonds, ionic interactions, and DISULFIDE bridges of side chains

• the covalent bond formed between sulfur atoms and two cysteine monomers

quaternary level of protein structure

association of two or more polypeptides (found in only some protein)

what determines the primary structure of a protein?

the sequence of amino acids

How does the primary structure of a protein affect the other structural levels?

the specific chain of amino acids in the primary structure directly affects the shape of the protein in every other level

Would the function of a protein chance if the amino acid sequence changed? Why or why not?

Yes, the function of the protein would change, because the AA sequence determines shape which determines function

What interactions occur in the secondary structure? Tertiary structure? Quaternary structure?

In the second structure, there is hydrogen bonding within the poly peptide backbone. In the tertiary structure, there are interactions between the side chains of the AAs which are reinforced by hydrophobic interactions, ionic interactions, hydrogen bonding, and disulfide bridges of the side chains. In the quaternary structure, there are associations between the polypeptides

True or false? A change in a protein’s structure will change the protein’s function.

True, change in shape will create change in function.

How many monomers of proteins are there?

There are 20 different amino acids

How do the R groups of amino acids contribute to protein structure?

The R groups, or unique side chains, can be classified as polar, nonpolar, or charged/ ionic. Side chains interact, determine shape (which way the protein folds), and determine functions of proteins.