Biochemistry Using Organic chemistry for Life. Clicker Why are organic molecules important to...

Biochemistry

Using Organic chemistry for Life

Clicker

Why are organic molecules important to biology?

A. Living objects are constructed mostly of organic molecules.

B. Organic molecules are so varied that they are capable of many different functions.

C. Only God knows for sure and she’s not saying.

D. Look, I’m here, isn’t that good enough?

Organic molecules are LifeIf you think of all the different things an organism needs to do:A. Create energyB. Repair itself.C. GrowD. Transport materialsE. Hold its structureF. Fend off invadersG. Protect from hostile nature (heat, light, storms, electricity…)H. ReproduceI. Store blueprintsJ. Store memoriesK. Acquire sensory dataL. Process sensory data

Lots of functions require lots of molecules

Lipids

Lipids are water-insoluble components of cells including fats, fatty acids, oils, phospholipids, glycolipids, and steroids.

Your body is mostly water (aids transport, temperature control), so if every molecule in your body were water soluble, you’d melt into a salty puddle!!!

Lipids, among other uses, make up cell membranes – to keep you from collapsing into a puddle!

Fatty AcidsGuess what kind of acid?

Carboxylic acid!!!

A fatty acid is a long alkane/alkene chain with a carboxylic acid on the end!

OHC

O

CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2CH2 CH2 CH2

Myristic acid (common name)Tetradecoic acid (IUPAC name)Butterfat or coconut oil

Oleic acid (common name)

cis-octadec-9-enoic acid)

In olive oil, peanut oil

CH2CH3 CH2 CH2 CH2 CH2 CH2 CH CHCH2 CH2CH2 CH2 CH2 OHC

O

CH2 CH2 CH2

What does the “cis” mean?

It means the two H are on the same side!

CH3 CH2 CH2 CH2CH2 CH2

C C

CH2CH2 CH2CH2 CH2 CH2 OHC

O

CH2 CH2 CH2

H H

Tro, Chemistry: A Molecular Approach

7

Fatty AcidsStearic Acid – C18H36O2 a saturated fatty acid

CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 C

O

OHCH2CH2CH2CH2CH2CH3

Oleic Acid – C18H36O2 a monounsaturated fatty acid

CH2 CH2 CH CH CH2 CH2 CH2 CH2 CH2 CH2 CH2 C

O

OHCH2CH2CH2CH2CH2CH3


8

Fatty Acids

Tro, Chemistry: A Molecular Approach 9

Structure and Melting PointName

MP °C

Class

Myristic Acid 58 Sat., 14 C

Palmitic Acid 63 Sat, 16 C

Stearic Acid 71 Sat, 18 C

Oleic Acid 16 1 DB, 18 C

Linoleic Acid -5 2 DB, 18 C

Linolenic Acid -11 3 DB, 18 C

Larger fatty acid = Higher melting point

Double bonds decrease the melting point More DB = lower MP

Saturated = no DB Monounsaturated = 1 DB Polyunsaturated = many

DB

It’s all about the solubility

The alkane/alkene portion of the molecule is water insoluble. Why?

It’s non-polar. Water is polar. Remember, “like dissolves like”.

The carboxylic acid portion is water soluble. Why?

The carboxylic acid (C=0 and –OH) is polar, and so is water.

If I throw oleic acid in water…

What happens?

It forms little micelles (beads) with the hydrophobic tails all mixed together and the hydrophilic acid portion facing the water.

This is why “oil and water don’t mix”…


12

Lipid Bilayer

Fats and oils“Triglycerides”

You’ve heard the term, what does it mean? A triglyceride is actually a combination of glycerol (a triol) and 3 fatty acids. It’s actually a tri-ester!

OH

OH

OH

CHCH2 CH2

OHC

O

CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2CH2 CH2 CH2+

3

glycerolMyristic acid

O

O

O

CHCH2 CH2

CCH3 (CH2)11

C

O

CH3 (CH2)11

O

C(CH2)11CH3

O

Trimystirin

Fats and oilsThis a “saturated” fat – the hydrocarbon chain

is an alkane, no double bonds.

O

O

O

CHCH2 CH2

CCH3 (CH2)11

C

O

CH3 (CH2)11

O

C(CH2)11CH3

O

Trimystirin

Fats and oilsAn “unsaturated” fat would have double bonds.

If we did the same reaction with oleic acid.

OH

OH

OH

CHCH2 CH2+

3

glycerolOleic acid

O

O

O

CHCH2 CH2

O

Triolein

CH3 (CH2)4 CH CH(CH2)7 OHC

O

CH3 (CH2)4 CH CH(CH2)7 C

O

CH3 (CH2)4 CH CH(CH2)7 C

O

CH3(CH2)4CH CHC (CH2)7


16

Tristearin a simple triglyceride found in lard

Triglycerides

Saturated triglycerides tend to be at room temperature.

A. Solid

B. Liquid

C. Gas

D. All of the above, it depends on the type.

Triglycerides

Saturated triglycerides tend to be solids at room temperature because of:

A. Van der Waal’s forces

B. Hydrogen bonding

C. Dipole-dipole interactions

D. A and B

E. B and C

Triglycerides

Unsaturated triglycerides tend to be at room temperature.

A. Solid

B. Liquid

C. Gas

D. All of the above, it depends on the type.

Triglycerides

Unsaturated triglycerides (oils) tend to be liquids at room temperature because of:

A. Van der Waal’s forces

B. Hydrogen bonding

C. Dipole-dipole interactions

D. A and B

E. B and C

Triglycerides

They are big molecules. They tend to form solids due to a combination of Van der Waal’s forces and dipole forces. BUT, unsaturated molecules can be sterically hindered so that the polar parts can’t get near the other polar parts. That leaves us with just Van der Waal’s forces and it reduces the melting point relative to saturated molecules.


22

Trioleina simple triglyceride found in olive oil

Other Lipids

Phospholipids – take a triglyceride and replace one of the fatty acids with a phosphate group.

Glycolipids – Use glucose instead of glycerol.

These are ideal for cell walls: they are strong and have a polar end and non-polar end. The polar end faces the inside (aqueous) part of the cell and the non-polar ends are internal.


24

Phospholipids Esters of glycerol Glycerol attached to 2 fatty acids and 1 phosphate

group Phospholipids have a hydrophilic head due to

phosphate group, and a hydrophobic tail from the fatty acid hydrocarbon chain

part of lipid bilayer found in animal cell membranes


25

Phosphatidyl Choline


26

Glycolipids

similar structure and properties to the phospholipids

the nonpolar part composed of a fatty acid chain and a hydrocarbon chain

the polar part is a sugar molecule e.g., glucose


27

Glucosylcerebroside(found in plasma membranes of nonneural cells)

CH

CH

CH

CH

CH

O

OH

OH

OH

O

CH2OH

CH

CH

CH2

OH CH

CH

N C

O

Steroids

Steroids are lipids with a four-ring central structure.

O

CH3

CH3

OH

Testosterone


29

Steroids

cholesterol

HO

CH3

CH3

CH3

CH3

CH3

O

CH3

CH3OH

testosterone

HO

CH3OH

estrogen-estradiol

Carbohydrates

Structurally much simpler than lipids.

Carbohydrates are polyhydroxy aldehydes or ketones.

C C C C C C

O

HH

H H H

H

H

OH OHOH OH

OH

Glucose (C6H12O6) – a monosaccharide

Carbohydrates

You can actually string together monosaccharides to make more complicated carbohydrates.

But even monosaccharides have variety!

C C C C C C

O

HH

H H H

H

H

OH OHOH OH

OH

Carbons 2, 3, 4, and 5 are all “chiral” – 4 different atoms are attached

Carbohydrates

But even monosaccharides have variety!

Mannose is an optical isomer of glucose – differing only in the relative 3D orientation of the -OH

C C C C C C

O

HH

H H H

H

H

OH OHOH OH

OH

Glucose

C C C C C C

O

HH

H H H

H

OH

OH OHOH H

OH

Mannose

Intramolecular rearrangement

Glucose can actually react with itself by addition to the carbonyl to form a 6 membered ring (5 or 6 membered rings are more stable and, therefore more likely)

C C C C C C

O

HH

H H H

H

H

OH OHOH OH

OH

O

H

H

H

HH

OH

OH

OH

OH

OH

C

C

CC

C

CH2

Intramolecular rearrangement

Equivalent representations of glucose. Similar pairs of structures exist for all sugar.

Glucose is an example of one type of sugar, called an “aldose” because of the aldehyde group in the linear structure.

C C C C C C

O

HH

H H H

H

H

OH OHOH OH

OH

O

H

H

H

HH

OH

OH

OH

OH

OH

C

C

CC

C

CH2

Fructose (C6H12O6)

Fructose is a ketose. It’s structure is similar to aldoses (like glucose) but it is a ketone in the linear representation rather than an aldehyde.

Notice: Fructose is a structural isomer of glucose!

C C C C C C

O

H2H

H H H

HOH OHOH OH

OH

Dehydration returns!

Monosaccharides can be linked together via dehydration reactions to form “glycosidic linkages”.

A glycosidic linkage is really just an ether linkage created by dehydration of 2 alcohols!


While it might seem that we can create the linkage using multiple different alcohol (-OH) sites to form the bond, there is one –OH that is more reactive than all the others!

O

H

H

H

HH

OH

OH

OH

OH

OH

C

C

CC

C

CH2

Because of the presence of the O next to it, this C-OH bond is more reactive!


The dehydration reaction that creates the “glycosidic linkage” occurs preferentially at this site!

O

H

H

H

HH

OH

OH

OH

OH

OH

C

C

CC

C

CH2O

H

H

H

H H

OH

OH

OH

OH

C

C

C C

C

CH2OH


O

H

H

H

HH

OH

OH

OH

OH

OH

C

C

CC

C

CH2O

H

H

H

H H

OH

OH

OH

OH

C

C

C C

C

CH2OH

O

H

H

H

HH

OH

OH

OH

OH

C

C

CC

C

CH2O

H

H

H

H H

OH

OH

OH

OH

C

C

C C

C

CH2 O

+ H2O

Size matters..

If 2 sugar molecules can form a glycosidic linkage, then the most reactive site is used. BUT, there’s no reason why you can’t use the less preferred sites.

Carbohydrates are “polysaccharides” formed by multiple glycosidic linkages between sugar molecules.

Clicker Question

A. I’m here

B. I’m not here

Amino Acids

Amino Acids are building blocks of proteins.

Amino Acids are exactly what the name suggests: amines AND carboxylic acids

CH2H2N OHC

O

Glycine

α - Amino Acids

Glycine is the simplest of the α - amino acids. The α refers to the carbon immediately next to the carbonyl group. To be an α - amino acid, the amine must be bonded to this carbon.

CH2H2N OHC

O

Glycine

α

Different substituents, different α - amino acid

If the α – carbon has different substituents (besides the 2 H’s of glycine) it is a different amino acid.

CH2H2N OHC

O

Glycine

CHH2N OHC

O

OH

CH2

Serine

CHH2N OHC

O

OH

CH2

C = 0

Aspartic acid

Let’s think together…

Amines are…

Carboxylic acids are…

What happens when you mix an acid and a base together?

They neutralize each other!

bases

acids

How would that neutralization occur?

The –COOH is an acid, the –NH2 is a base. Any –COOH can donate a proton to any –NH2. Some amino acids are stronger acids/bases than others based on the side group, but they are all acids/bases.

CH2H2N OC

O

Base form of Glycine

CH2H2N OHC

O

CH2H3N OHC

O

CH2H3 N OC

O

Amphoteric form of Glycine

Acid form of Glycine

+

Zwitterion form of Glycine

+

-

-

Which one is it?

If you had a beaker full of glycine in distilled water at 25 C and 1 atm of pressure, which one would be the dominant form?

CH2H2N O-C

O


CH2H2N OHC

O

CH2H3N OHC

O

CH2H2N OHC

O



+


Which one is it?

Could you ever have any of the other forms?

Sure! Change the pH!

CH2H2N O-C

O


CH2H2N OHC

O

CH2H3N OHC

O

CH2H2N OHC

O



+


What happens if I mix serine and glycine?

Let’s make H2O!

CH2H2N OHC

O

Serine Glycine

CHH2 N OHC

O

OH

CH2

Dehydration…not always a bad thing! [Called “condensation”]

CH2H2N OHC

O

Serine

Glycine

CHH2 N OHC

O

OH

CH2

+

CH2HNH OHC

O

CHH2 N OHC

O

OH

CH2

CH2H2N OHC

O

CHHNH OHC

O

OH

CH2

OR

Dehydration…not always a bad thing! [Called “condensation”]

CH2HNH OHC

O

CHH2 N OHC

O

OH

CH2

CH2H2N OHC

O

CHHNH OHC

O

OH

CH2OR

+ H2O

CH2 NH OHC

O

CHH2 N C

O

OH

CH2

CH2H2N C

O

CH NH OHC

O

OH

CH2

+ H2O

Peptides

Protein structure

One way to look at protein “information” is in the sequence of the amino acids.

Consider the alphabet, with 26 letters.

If you had 26 amino acids, how many 3 letter words could you write?

17,576 (26x26x26)456,976 Four letter words11,881,376 Five letter words141 trillion 10 letter words

Structure and Function

Unlike words, proteins are 3-D objects. The function of a given protein is determined by its “sequence”=which amino acid follows which amino acid called the “primary structure”, but it is also determined by the secondary, tertiary, and even quarternary structure.

Secondary structure

Once the amino acids are in a sequence, it is possible for them to form “superstructures” by hydrogen bonding with each other across chains.

Secondary structure is a multi-amino acid structure.

Secondary structure

An alpha helix (α-helix) is a right-handed (clockwise) spiral in which each peptide is in the trans conformation. The amine group of each peptide bond runs upward and parallel to the axis fo the helix; the carbonyl points downward.

A β-pleated sheet consists of neighboring chains that are anti-parallel to each other. Each peptide bond is trans and planar. The amine and carbonyl point toward each other.

Tertiary structure

Once the amino acid sequences are arranged into secondary “superstructures”, these secondary structures can be arranged differently relative to each other. A kind of “super-superstructure”.

This tertiary structure is usually constructed largely by disulfide bonds between cysteine amino acid groups.

Quarternary structures

Some proteins are made up of multiple polypeptide subunits (different chains of amino acids). Each subunit has its own primary, secondary, and tertiary structure.

The subunits are arranged relative to each other in “quarternary super-super-superstructures”

Biochemistry Using Organic chemistry for Life. Clicker Why are organic molecules important to...

Documents

Transcript of Biochemistry Using Organic chemistry for Life. Clicker Why are organic molecules important to...