09-15-15 Lecture 3 Bio

carbon is the most important atom in all organic molecules

the definition of an organic molecule is that it has carbon in it (with some exceptions)

carbon is a very stable atom - due to its outer shell having only 4 electrons

wants to complete its outer shell to satisfy the octet rule

thus will to share electrons

its nature is not to give away full or steal electrons - that would not be the optimal way to gain a total of 8 electrons in its out shell

thus covalent sharing bonds are formed - unlike ionic bonds are not easy to break, carbon WANTS to keep those other 4 electrons shared

since it forms stable bonds - makes sense that it would be used to form stable structures within an organism's body, needs structure

also maximizes the number of bonds can be made (4 bonds versus just one, two etc.)

one circle in the middle - number of + protons

one ring around - 2 e-

second ring around - 4 e-

overlapping rings of another atom - draw a circle to designate each electron shared between the two overlapping rings

1)carbon backbone

string of carbons

2) functional groups

attached to the carbon backbone

provides molecule its characteristics

1)OH - hydroxyl/alcohol group

found in alcohol, sugars

2)PO4 - phosphate group, positively charged, when it bonds creates high energy bonds

3) NH3 amine groups found in amino acids

4) COOH - carboxyl group

(a carbonyl C=O and a hydroxyl group attached)

organic compounds are made of monomers - repeating units that link => create POLYMERS

1) carbohydrates

2) lipids

3) proteins

4) nucleic acids

C,O and H

1C, 2H, 1O

O-H is a polar covalent bond

C-H is a non polar covalent bond

C-O is a polar covalent bond

because O has higher electronegativity that C and H

thus carbohydrates are POLAR MOLECULES, are HYDROPHILLIC

in the bonds electrons are not shared evenly

monosaccharide

simple sugar

two lines meeting = a carbon atom

a line with a blank space = hydrogen atom

glucose atoms are arranged in a certain order and orientation

when other molecules have their atoms arranged in different ways but have the same molecular formula = isomers of each other

fracture, galactose

all have the molecular formula of C6H12O6

same functional groups

taste sweet

are also simple sugars

glucose + glucose = maltose

glucose + fructose = sucrose

glucose + galactose = lactose

polysaccharide

long chains of monosaccharides bonded together via dehydration synthesis

one longer chain of multiple glucose molecules

acts as an energy storage molecule for plants, animals can eat this and get energy from it as well

another polysaccharide made by plants

BRANCHED chains of glucose

cannot be digested by animals

also known as fiber, indigestible

animal energy storage molecule

stored in liver

if you have high glucose intake and its not going to be used immediately, they link together within the animal

multibranched polysaccharide of glucose

a structural carbohydrate that make up insect shells

monomer is N-Acetylglucosamine

which is a derivative of glucose

is NOT digestable

C,O and H

but do not occur in the same ratios as carbs

have more C-H bonds

C-H bonds are predominant in lipids

C-H share electrons evenly, thus nonpolar

nonpolar molecules do not mix well interact with polar molecules, are hydrophobic

1) triglyceride

2) phospholipids

3) steroids

consists of a glycerol molecules and three fatty acid chains

the polymer of a lipid

large molecule is not complex

has a carboxyl group at one end of a carbon backbone, rest of the carbons bind to hydrogen

called HYDROCARBON TAIL

the carboxyl end of the fatty acid chain interacts with the hydroxyl group on the glycerol

1) saturated

all carbons have max number of hydrogens bonded

saturated with hydrogens (2 per carbon)

thus at room temp, they line up perfectly, solidly, bad for you

2) unsaturated

not fully saturated with hydrogens

because carbons double bonded to each other

kinks

thus at room temp, will not stack perfectly

will instead be fluid at room temp, oils

are triglycerides but with phosphate groups attached to one of the hydroxyl groups of the glyecerol

last OH does not add a FA but a phosphate group

PO4-

negatively charged polyatomic ion

they create a MICEL - circle with hydrophilic parts facing the water, hydrophobic tail parts facing inwards

cannot fully dissolve in water

detergents have hydrophilic heads and hydrophobic tails, form micels when in water

thus fats other nonpolar molecules will go into the micel to cling to the phobic areas of the micel, while heads are able to cling to water, so will wash away and bring the nonpolar molecules with it

they break up fat, lipids in water, act as emulsifiers

bile

produced in the liver, stored in the gallbladder

bile is made of phospholipids, its hydrophobic tails surround the fat, breaking it apart into smaller globs of fat

able to surround the fat with water, since their heads are hydrophillic

when you eat very greasy foods

they go into an aqueous environment within the stomach

to break up the fats, for enzymes to get to them

1) phospholipid bilayer

2) micel

phospholipid bilayers are made of two layers of phospholipids

the two sets of tails will face each other

while the heads will face towards the water

the membrane of a cell

the phospholipid bilayer will the curve around to form a sac the cell

so that the cytoplasm can be aqueous, the outside of the cell is obviously aqueous

and the middle of the bilayer is hydrophobic, nonpolar

hydrophobic, thus will try to avoid water at all costs

will naturally form together, the hydrophobic regions try to reach each other

DIFFICULT TO FALL APART IN WATER

unlike glucose or some other molecule - if something were made of glucose could fall apart in water, not adverse to water, no hydrophobic side to counteract wants to avoid the water

large hydrophobic ring structures

act as chemical messengers in the body

proteins

are many many many different types of proteins

because have all different functions they need to fulfill

C,H,O and N

NITROGEN

carboxyl group on one end, middle carbon, H, R group, and amine group on the other end

thus when amine and carboxyl group bind together, creates a...sort of carbon backbone

R group is the variable group = thus why diversity of amino acids

due to the variability of the R groups which determine the type of amino acid

there are 20 amino acids

can be +/- charged

small as hydrogen or large ring groups

hydrophilic or hydrophobic

via dehydration synthesis between the carboxyl group and the amine group

the OH of the carboxyl group leaves and the H on the amine leaves -> water leaves

C=O and NH are directly linked together

creating PEPTIDE BOND which is found only in proteins

important in detecting peptide bonds

amino acid won't have peptide bonds between them unless of course they somehow were made into proteins

proteins are peptides linked together

hundreds of amino acids

polymers made of amino acids

1)primary

2) secondary structure

3) tertiary structure

4) quaternary structure

the amino acid sequence of a protein

simplest organization of a protein

* order of this linkage, types of amino acids involved, are very important* because will affect later structure

the beta sheets and alpha helices formed from the amino acid chains

amino acids interact with each other to from these preliminary 3D structures

water interacts with the backbone to fold it into secondary structures

the protein folding into its overall 3D shape due to hydrogen bonding/hydrophilic/hydrophobic/charged IONIC INTERACTIONS between the R groups within the protein

the water outside is hydrophilic, some R groups are hydrophobic to the outside, this encourages folding

alpha helix - phone cord structure

beta sheet - stair case structure

formed via hydrogen bonding between the surrounding water molecules and the carbon-nitrogen backbone

as well as hydrogen bonding between the carboxyl group and amine group on the backbone

1)hydrophobic interactions (hydrophobic R groups hiding from outside water)

2)hydrogen bonding (polar R groups hydrogen bond to each other or to the outside water)

3) disulfide bonds (S atoms on the R groups covalently bonding to each other)

4)IONIC INTERACTION - some R groups have +/- charges

more than one peptide subunits joining together -> create an overall functional protein -> quaternary structure

peptide subunits would have their secondary and tertiary structures formed

because there are so many types

due to all the R groups, interactions, layers of structures

thus a huge variety of functions they can do

enzymes, structure,

accomplish everything in your body

look at primary sequence

can determine how they interact with each other in water or under certain conditions

-> predict what their overall structures are

find new uses for them, where the fit in biologically, what other proteins do they interact with

C,O,H, N and P

all atoms we use in biology

nucleotides

bind together to make nucleic acids - polymers

1) ribose/deoxyribose sugar (5 carbon sugar)

2) phosphate group

3) nitrogenenous base/nucleobase

with the sugar at the middle, bonded to phosphate group on one side, nitrogenous base on the other side

ribonucleic acid

deoxyribonucleic acid