biochemistry
Download
Skip this Video
Download Presentation
Biochemistry

Loading in 2 Seconds...

play fullscreen
1 / 57

Biochemistry - PowerPoint PPT Presentation


  • 137 Views
  • Uploaded on

Biochemistry. Using Organic chemistry for Life. Clicker. Why are organic molecules important to biology? Living objects are constructed mostly of organic molecules. Organic molecules are so varied that they are capable of many different functions.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Biochemistry' - palmer-bolton


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
biochemistry

Biochemistry

Using Organic chemistry for Life

clicker
Clicker

Why are organic molecules important to biology?

  • Living objects are constructed mostly of organic molecules.
  • Organic molecules are so varied that they are capable of many different functions.
  • Only God knows for sure and she’s not saying.
  • Look, I’m here, isn’t that good enough?
organic molecules are life
Organic molecules are Life

If you think of all the different things an organism needs to do:

  • Create energy
  • Repair itself.
  • Grow
  • Transport materials
  • Hold its structure
  • Fend off invaders
  • Protect from hostile nature (heat, light, storms, electricity…)
  • Reproduce
  • Store blueprints
  • Store memories
  • Acquire sensory data
  • Process sensory data

Lots of functions require lots of molecules

lipids
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 acids

O

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

C

OH

Fatty Acids

Guess what kind of acid?

Carboxylic acid!!!

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

Myristic acid (common name)

Tetradecoic acid (IUPAC name)

Butterfat or coconut oil

slide6

O

O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH2

CH2

CH2

CH2

CH2

C

C

OH

OH

CH3

CH3

C

CH

C

CH2

CH2

CH2

CH2

CH2

CH2

H

H

Oleic acid (common name)

cis-octadec-9-enoic acid)

In olive oil, peanut oil

What does the “cis” mean?

It means the two H are on the same side!

fatty acids1
Fatty Acids

Stearic Acid – C18H36O2 a saturated fatty acid

Oleic Acid – C18H36O2 a monounsaturated fatty acid

Tro, Chemistry: A Molecular Approach

fatty acids2
Fatty Acids

Tro, Chemistry: A Molecular Approach

structure and melting point
Structure and Melting Point
  • 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

Tro, Chemistry: A Molecular Approach

it s all about the solubility
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
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”…

lipid bilayer
Lipid Bilayer

Tro, Chemistry: A Molecular Approach

fats and oils

O

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

C

OH

OH

O

OH

O

CH2

CH2

CH

CH

CH2

CH2

OH

O

O

CH3

(CH2

)11

C

CH3

(CH2

)11

C

O

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!

glycerol

Myristic acid

3

+

O

C(CH2)11CH3

Trimystirin

fats and oils1

O

O

CH2

CH

CH2

O

O

O

CH3

(CH2

)11

C

C(CH2)11CH3

CH3

(CH2

)11

C

Trimystirin

O

Fats and oils

This a “saturated” fat – the hydrocarbon chain is an alkane, no double bonds.

fats and oils2

O

O

C

C

OH

OH

O

OH

O

CH2

CH2

CH

CH

CH2

CH2

CH3

CH3

CH3

(CH2)4

(CH2)4

(CH2)4

CH

CH

CH

CH

(CH2)7

(CH2)7

OH

O

CH

CH

CH

CH

(CH2)7

Fats and oils

An “unsaturated” fat would have double bonds. If we did the same reaction with oleic acid.

Oleic acid

glycerol

3

+

O

(CH2)4

CH3

C (CH2)7

C

Triolein

O

tristearin a simple triglyceride found in lard
Tristearin a simple triglyceride found in lard

Tro, Chemistry: A Molecular Approach

triglycerides
Triglycerides

Saturated triglycerides tend to be at room temperature.

  • Solid
  • Liquid
  • Gas
  • All of the above, it depends on the type.
triglycerides1
Triglycerides

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

  • Van der Waal’s forces
  • Hydrogen bonding
  • Dipole-dipole interactions
  • A and B
  • B and C
triglycerides2
Triglycerides

Unsaturated triglycerides tend to be at room temperature.

  • Solid
  • Liquid
  • Gas
  • All of the above, it depends on the type.
triglycerides3
Triglycerides

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

  • Van der Waal’s forces
  • Hydrogen bonding
  • Dipole-dipole interactions
  • A and B
  • B and C
triglycerides4
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.

triolein a simple triglyceride found in olive oil
Trioleina simple triglyceride found in olive oil

Tro, Chemistry: A Molecular Approach

other lipids
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.

phospholipids
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

Tro, Chemistry: A Molecular Approach

phosphatidyl choline
Phosphatidyl Choline

Tro, Chemistry: A Molecular Approach

glycolipids
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

Tro, Chemistry: A Molecular Approach

glucosylcerebroside found in plasma membranes of nonneural cells
Glucosylcerebroside(found in plasma membranes of nonneural cells)

Tro, Chemistry: A Molecular Approach

steroids
Steroids

Steroids are lipids with a four-ring central structure.

OH

CH3

CH3

O

Testosterone

steroids1
Steroids

testosterone

cholesterol

estrogen

b-estradiol

Tro, Chemistry: A Molecular Approach

carbohydrates

H

H

H

H

OH

O

H

H

C C C C C C

OH

OH

OH

OH

H

Carbohydrates

Structurally much simpler than lipids.

Carbohydrates are polyhydroxy aldehydes or ketones.

Glucose (C6H12O6) – a monosaccharide

carbohydrates1

H

H

H

H

OH

O

H

H

C C C C C C

OH

OH

OH

OH

H

Carbohydrates

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

But even monosaccharides have variety!

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

carbohydrates2

H

H

H

H

H

OH

H

H

OH

OH

O

O

H

H

H

H

C C C C C C

C C C C C C

OH

H

OH

OH

OH

OH

OH

OH

H

H

Carbohydrates

But even monosaccharides have variety!

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

Mannose

Glucose

intramolecular rearrangement

H

H

H

H

OH

O

OH

H

H

H

C C C C C C

OH

C

H

C

C

OH

OH

OH

H

OH

H

OH

H

H

C

C

OH

CH2

OH

O

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)

intramolecular rearrangement1

H

H

H

H

OH

O

OH

H

H

H

C C C C C C

OH

C

H

C

C

OH

OH

OH

H

OH

H

OH

H

H

C

C

OH

CH2

OH

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.

O

fructose c 6 h 12 o 6

H

H

H

OH

O

H

H2

OH

OH

OH

OH

H

C C C C C C

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!

dehydration returns
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!

dehydration returns1

OH

H

OH

C

H

C

C

H

OH

H

H

C

C

OH

CH2

OH

O

Dehydration returns!

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!

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

dehydration returns2

OH

OH

H

H

OH

OH

OH

C

C

H

H

C

C

C

C

H

H

OH

OH

H

H

H

H

C

C

C

C

OH

CH2

CH2

OH

OH

O

O

Dehydration returns!

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

dehydration returns3

OH

OH

H

H

OH

OH

OH

C

C

H

H

C

C

C

C

H

H

OH

OH

H

H

H

H

C

C

C

C

OH

CH2

CH2

OH

OH

O

O

Dehydration returns!

OH

OH

H

H

C

OH

OH

C

H

H

C

C

C

C

OH

H

H

OH

+ H2O

H

H

H

H

C

C

C

C

CH2

CH2

O

OH

OH

O

O

size matters
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
Clicker Question
  • I’m here
  • I’m not here
amino acids

O

C

OH

H2N

CH2

Amino Acids

Amino Acids are building blocks of proteins.

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

Glycine

amino acids1

O

C

OH

H2N

CH2

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.

Glycine

α

different substituents different amino acid

O

O

O

C

C

C

OH

OH

OH

H2N

H2N

H2N

CH

CH2

CH

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.

CH2

CH2

C = 0

OH

OH

Serine

Aspartic acid

Glycine

let s think together
Let’s think together…

bases

Amines are…

Carboxylic acids are…

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

They neutralize each other!

acids

how would that neutralization occur

O

O

O

O

C

C

C

C

O

OH

O

OH

H3 N

H2N

H3N

H2N

CH2

CH2

CH2

CH2

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.

-

Base form of Glycine

Amphoteric form of Glycine

+

+

-

Zwitterion form of Glycine

Acid form of Glycine

which one is it

O

O

O

O

C

C

C

C

O-

OH

OH

OH

H2N

H2N

H3N

H2N

CH2

CH2

CH2

CH2

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?

Base form of Glycine

Amphoteric form of Glycine

+

Zwitterion form of Glycine

Acid form of Glycine

which one is it1

O

O

O

O

C

C

C

C

O-

OH

OH

OH

H2N

H2N

H3N

H2N

CH2

CH2

CH2

CH2

Which one is it?

Could you ever have any of the other forms?

Sure! Change the pH!

Base form of Glycine

Amphoteric form of Glycine

+

Zwitterion form of Glycine

Acid form of Glycine

what happens if i mix serine and glycine

O

O

C

C

OH

OH

CH2

OH

H2N

H2 N

CH2

CH

What happens if I mix serine and glycine?

Let’s make H2O!

Glycine

Serine

dehydration not always a bad thing called condensation

O

O

O

O

O

O

C

C

C

C

C

C

OH

OH

OH

OH

OH

OH

CH2

CH2

CH2

OH

OH

OH

HNH

H2N

H2N

HNH

H2 N

H2 N

CH2

CH

CH

CH2

CH

CH2

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

+

Glycine

Serine

OR

dehydration not always a bad thing called condensation1

O

O

O

O

O

O

O

O

C

C

C

C

C

C

C

C

OH

OH

OH

OH

OH

OH

CH2

CH2

CH2

CH2

OH

OH

OH

OH

HNH

H2 N

H2 N

H2N

HNH

NH

NH

H2N

CH2

CH

CH

CH

CH2

CH2

CH2

CH

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

OR

Peptides

+ H2O

+ H2O

protein structure
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 words

11,881,376 Five letter words

141 trillion 10 letter words

structure and function
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
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 structure1
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
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
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”

ad