CELL 1010 CH 3 Dr. V Tulane University

molecule vs compound

molecule = chemical particle composed of two or more atoms united by a chemical bond (O2); compound = molecules composed of two or more elements (H20)

Functional groups

chemical groups that have not fulfilled the octet rule

functional groups exhibit the same properties in all molecules they are present in

Isomers

contain same atoms but in different bonding relationships and spatial organization, affecting chemical properties

Structural Isomers

Compounds that have same molecular formula but differ in bonding order. Synonymous with constitutional isomer. Found in alkanes. Branching.

geometric isomers

Compounds that have the same molecular formula but differ in the spatial arrangements of their atoms.
Found in alkenes and arenes (presence of double bond)
a subset of stereoisomer

cis-trans isomers

have the same covalent bonds but differ in spatial arrangements

stereoisomer

Enantiomers

mirror image of another molecule. has left and right side.
a subset of Stereoisomer

Structural Isomers vs stereoisomers

structural: different bonding
(ie. linear form of glucose, fructose)
stereo: different spatial organization
(ie. alpha & beta glucose, linear form of glucose and galactose, ring form L vs D glucose)

Isomer exception

glycine

ATP consists of

adenosine and a triphosphate tail of three phosphate groups

Adenosine =

adenine + ribose sugar

Where is C1 on the ATP molecule?

the first C is the closest one to the adenine group

4 types of macromolecules

carbohydrates - 4.3 cal/g
lipids - 9.3 cal/g
proteins -4.3 cal/g
nucleic acids

Phosphates in ATP are held together despite what forces?

electrostatic repulsion

Carbohydrates are..

the basis for synthesizing all other macromolecules. thus the first major macromolecule

Lipids are...

More efficient at storing energy

Made of HC chains which account for higher cal/g

Proteins are...

equally as efficient as carbs when storing energy

workhorses of the cell as they have multiple functions

Nucleic Acids are...

DNA, RNA -> storing info and gene expression

dehydration synthesis

A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule.

hydrolysis (hydrolytic cleavage)

Hydrolysis breaks a covalent bond by adding OH and H

When making a polysaccharide out of 20 molecules, how many water molecules do you lose?

19 water molecules are lost because n-1 (atoms - 1 = bonds)

Carbohydrates are made of which atoms?

C, O, H

Carbohydrates are usually polar or nonpolar?

polar, due to the presence of O

Monosaccharides

Simplest sugar: 3C
Most common:
5C: ribose, deoxyribose
6C: glucose

Carbohydrates usually have what structures?

Ring or linear

Threose Nucleic Acid

4C sugar thought to predate 5C sugars in DNA

Energy storage: starch vs glycogen

starch:
found in plants

glycogen:
main storage unit of CHO in animals. has significantly more branching than in starch

amylopectin vs amylose

both starches

amylopectin has more branching thus making it easier to break down than amylose

rice (amylose) is much harder to break down than potatoes (amylopectin)

Carbohydrates monomers:

Monosaccharide

The covalent bond that exists between carbohydrate monomers is

1-4 Glycosylic bond

(1st C of one glucose bonds with the 4th C of the other glucose)

Lipid monomers

triglycerides/triglycerols

Covalent bond between triglycerides (triglycerols)

Ester

Protein monomers

Amino acids

Covalent bond between amino acids

peptide bond

Nucleic acid monomers

nucleotides

Covalent bond between nucleotides

phosphodiester bond

Lipids are composed of which atoms?

H, C (hydrocarbon chains yo)

Lipids are typically polar or nonpolar?

Nonpolar due to HC chain. Insoluble in water

Saturated fat

SINGLE bonds

solid at room temp

unsaturated fats

more than 1 double bond present

liquid at room temp

High density lipoprotein (HDL)

blood fat that helps transport cholesterol out of the arteries, thereby protecting against heart disease

GOOD cholesterol

Low density lipoprotein (LDL)

blood fat that transports cholesterol to organs and tissues; excess amounts result in the accumulation of fatty deposits on artery walls

BAD cholesterol

Trans fats

has LDL

unsaturated fat

increasing heat turns cis-isomers into trans-isomers, becoming a more stable fat

cis isomer

an isomer of an alkene in which the hydrogen atoms in the double bond are on the same side

trans isomer

an isomer of an alkene in which similar groups in the double bond are on opposite sides

hydrogenation

adding H to cause double bond to become single bonds

omega 3 fatty acid

lowers BP, ensures good blood circulation, improves nerve impulses

the omega carbon is the the C FURTHEST from the functional group - ie the 3rd carbon

Phospholipid structure

Phosphate head
Glycerol connector
Two fatty acid tails

Amphipathic molecule

phosphate region - polar, hydrophilic
fatty acid chains - nonpolar

Phospholipids give the membrane...

semipermeability

because nonpolar lipid tails allow small hydrophobic molecules to pass thru

steroids

lipids characterized by a carbon skeleton consisting of four fused rings

Waxes

A type of lipid molecule consisting of one fatty acid linked to an alcohol; functions as a waterproof coating on many biological surfaces such as apples and other fruits.

terpenes

long-chain lipids that are components of many biologically important pigments

responsible for bright pink pigments in flamingoes

Examples of lipids

Steroids: 4C rings
Waxes: one long fatty acid chain

Fatty acid

A long carbon chain carboxylic acid. vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat.

hydrolyzable lipids

waxes, triacylglycerols, phospholipids

nonhydrolyzable lipids

steroids, fat-soluble vitamins,

proteins consist of

C, H, N, O, and trace amounts of S

2 characteristics important to preserving life

the colligative properties of water

the existence of strong and short C=C bonds

2 definitions of proteins

workhorse of the cell (transport, hormones, enzymes)

relating genes as tools of gene expression

Amino acids are classified by their

functional group (R-group)

There are how many amino acids?

20

Protein polymer

polypeptides linked by peptide bond

Structure of amino acid without presence of H2O

central carbon, carboxyl group to the right (COOH), amine group to the left (NH2), hydrogen above and R group below

Structure of amino acid with the presence of H2O

central carbon, carboxyl group to the right (COO-), amine group to the left (NH3+), hydrogen above, R group below

Exception to isomerism

Glycine

has no D or L form because it has 2 hydrogens attached to the central C atom making it unable to form an enantiomer

The D form glucose

OH on right

L form glucose

OH on left

All protein translation begins with

methionine

(the amino acid that corresponds to the codon of AUG)

two types of amino acids

nonessential: made in the body (12 aa)
essential: consumed from external sources (8 aa)

peptide bonds are created by

dehydration synthesis/condensation reaction (water is lost to form a larger molecule)

Name of protein is related to...

the function of a protein

proteins must...to become active

fold and twist

where are the charges placed in a polypeptide chain?

the + charge on the left (amine group, NH3+)

the - charge on the right (carboxyl group, COO-)

myoglobin has what structure?

has 153 aa that form 1 polypeptide chain

primary, secondary, tertiary

hemoglobin has what structure?

has 2 alpha globins and 2 beta globin. have a total of 574 amino acids and 4 polypeptide chains

primary, secondary, tertiary, quaternary (bc 4 polypeptide chains)

primary structure

first level of protein structure

sequence of amino acids

never found in existence by itself but IS THE MOST IMPORTANT STRUCTURE

what is primary structure responsible for?

the sequence of amino acids determines structure and function of proteins thus making it the most important structure

sickle cell anemia

example of the importance of primary structure

mutation in the primary structure of beta globin (change of one nucleotide from GLU to VAL) affects hemoglobin. Ultimately resulting in sickle rather than spherical shape of red blood cells

Secondary Structure

held together by only H-bonds (intermolecular H-bonds between distant amine/carboxyl groups pushes amino acids outwards, forming alpha helical structure)

Motif

part of secondary structure

shape that isn't helical or pleated sheet

specific shape that is important to function

ie. enzyme active site specificity

The strength of a protein is determined by which structure?

secondary structure

components of secondary structure

alpha helices, beta pleated sheets, and motifs (super secondary structures)

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

components of tertiary structure

H-bonds and ionic polar bonds
hydrophobic exclusion
van der waals forces
disulfide bridges

hydrophobic exclusion

repulsion when interacting with water - nonpolar

disulfide bridges

the ONLY covalent bonds that extend from amino acids that contain sulfur

stabilize tertiary structure and quaternary structure

Do all polypeptides exhibit tertiary structure?

Yes

Do all proteins exhibit tertiary structure?

No. Some proteins do not have tertiary structure (disordered proteins)

A protein or polypeptide has 3D structure, what does this imply?

the protein or polypeptide has tertiary structure

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

tertiary polypeptide is not yet functional, what must it do to become a functional protein?

combine with another polypeptide(s), attain quarternary structure to become functional

Domains of proteins

quarternary proteins contain several domains

domains contain their own motifs

each domain is involved in distinct biological function. proteins that share domain share same function

Active sites

shape and chemical composition only allows binding of certain molecules

this shape and composition comes from amino acids

While proteins may have different functions and shapes, what is one thing they have in common?

Domains/motifs. Proteins MUST bind to DNA as as genetic tool. To bind to DNA, they all req the same active site/domain/motif

Denaturation

protein unfolding, destruction of structure

any protein can undergo denaturation, regardless of structure (both myoglobin and hemoglobin can denature)

results in metabolic disease

protein dissociation

only affects proteins with multiple polypeptides/quaternary structure

(myoglobin cannot undergo protein dissociation but hemoglobin can)

Is it more energy efficient to have forces of attraction or covalent bonds in between proteins?

Forces of attraction exist between proteins (enzyme-substrate rxns)

no disulfide bridges (covalent bond) during protein-protein interactions (disulfide bridges req more permanent situations and are more difficult to break)

Is it more energy efficient to have forces of attraction or covalent bonds in between polypeptides?

Covalent peptide bonds exist in between polypeptides, thus are more energy efficient

nucleic acids contain which elements?

C, N, O, P, H