slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
water PowerPoint Presentation
Download Presentation
water

Loading in 2 Seconds...

play fullscreen
1 / 50

water - PowerPoint PPT Presentation


  • 102 Views
  • Uploaded on

Our first “ functional group ”: hydroxyl, -OH. H. O. H. Covalent bond (strength = ~100 kcal/mole). 1. E. coli molecule #1. water. H 2 O. HOH. 105 o. Waterdeltas. Negative pole. Positive pole. 2. δ + = partial charge, not quantified Not “ + ” , a full unit charge,

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 'water' - makani


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
slide1

Our first “functional group”:

hydroxyl, -OH

H

O

H

Covalent bond

(strength = ~100

kcal/mole)

1

E. coli molecule #1

water

H2O

HOH

105o

waterdeltas
Waterdeltas

Negative pole

Positive pole

2

δ+ = partial charge, not quantified

Not “ + ” , a full unit charge,

as in the formation of ions by NaCl in solution:

NaCl  Na+ + Cl-

Water is a POLAR molecule (partial charge separation)

waterhbonds
waterHbonds

Hydrogen bond

amide3
amide3

R= any group of atoms

(the rest of the molecule)

Note: carbon atoms always make 4 bonds

R-CONH2 is an “amide”, -CONH2 is an amide group

(another functional group)

Note: Don’t think of the amide as a C=O and an –NH2; the whole thing is one functional group, the amide. It is highly polar but with no full charges

slide6

6

ethanol, an alcohol

an amide

Hydrogen bonds between 2 organic molecules

Water often out-competes this interaction (but not always)

slide7

Hydrogen bonds between 2 organic molecules

ethanol, an alcohol

an amide

They face formidable competition from water

slide8

X

Not all molecules are polar; e.g. octane, a non-polar, or apolar molecule

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3

H H H H H H H H

| | | | | | | |

H-C-C-C-C-C-C-C-C-H Note the absence of δ’s

| | | | | | | |

H H H H H H H H

slide9

Chemical Bonds

  • Bond:
  • Energy needed to break:
  • Comments:
  • Strength class-ification:
  • Covalent
  • ~100
  • kcal/mole
  • Electrons
  • shared
  • strong
slide10
1 calorie = amount of energy needed to raise the temperature of 1 gram of water (1 cc or ml. of water) one degree C

1 Calorie = dietary calorie = 1000 calories

1 kilocalorie (kcal) = 1000 calories

slide11

Chemical Bonds

  • Bond:
  • Energy needed to break:
  • Comments:
  • Strength class-ification:
  • Covalent
  • ~100
  • kcal/mole
  • Electrons
  • shared
  • strong

Hydrogen

~3

Water-water;

Organic-water;

Organic-organic(having polar functional groups)

weak

ionic bonds
Full loss or capture of an electron

Full charge separation

Full positive charge, or full negative charge (= charge of one electron)

E.g. NaCl = Na+:::Cl-Strong bond between the ions in acrystal (e.g., rock salt)

But: weak in aqueous solution

So the ionic bond of NaCl becomes weak in water

Is the bond between an Na+ ion and water ionic or an H-bond? Some characteristics of each:

a “polar interaction” or an “ion-dipole interaction”

Ionic bonds
organic ions acids and bases
BASES = amines

Gain a proton

R-NH2 + H+ R-NH3+

(net charge ≈ +1 at pH 7)

Example: ethyl amine:CH3-CH2-NH2

ACIDS= carboxylic acids

Lose a proton

O O|| ||

R-C-OH  R-C-O-+ H+

(net charge ≈ -1 at pH 7)

Example: acetic acid:

CH3-COOH

Organic IONS = acids and bases

Carboxyl group = -COOH

Amine group = -NH2

Where does the base get the proton? Are there any protons around in water at pH7?

slide14
Under the right conditions (to be seen later), two oppositely charged organic ions can form an ionic bond:

O ||

R-C-O- - - - - - +H3N-R

Weak, ~ 5 kcal/mole.

But these weak bonds are VERY important for biological molecules …….

slide15

15

The chemical structures of the functional groups used in this

course must be memorized.

See the Functional Groups handout.

This is one of very few memorizations required.

O

||

-C -- OH

“carboxyl”

Me

You

slide16

Chemical Bonds

  • Bond:
  • Energy needed to break:
  • Comments:
  • Strength class-ification:
  • Covalent
  • ~100
  • kcal/mole
  • Electrons
  • shared
  • strong

Hydrogen

~3

Water-water;

Organic-water;

Organic-organic

weak;

orientation dependent

Ionic

~5

Full charge transfer;

Can attract H-bond;

Strong in crystal

weak

van der waals bonds
Van der Waals bonds

First molecule

  • Can form between ANY two atoms that approach each other
  • “Fluctuating induced dipole”
  • Very weak (~ 1 kcal/m)
  • Effective ONLY at very close range (1A)(0.1 nm)

slide18

Chemical Bonds

  • Bond:
  • Energy needed to break:
  • Comments:
  • Strength
  • Class-
  • ification:
  • Covalent
  • ~100
  • kcal/mole
  • Electrons
  • shared
  • strong

Hydrogen

~3

Water-water;

Organic-water;

Organic-organic

weak

Ionic

~5

Full charge transfer;

Can attract H-bond;

Strong in crystal

weak

Van der Waals

~1

Fluctuating

induced

dipole;

Close range

only

weak

Why are we doing all this now?

slide19

Chemical Bonds

  • Bond:
  • Energy needed to break:
  • Comments:
  • Strength class-ification:
  • Covalent
  • ~100
  • kcal/mole
  • Electrons
  • shared
  • strong

Hydrogen

~3

Water-water;

Organic-water;

Organic-organic

weak

Ionic

~5

Full charge transfer;

Can attract H-bond;

Strong in crystal

weak

Van der Waals

~1

Fluctuating

induced

dipole;

Very close range only

weak

Hydro-phobic forces

~3

Not a bond per se;

entropy driven;

only works in water

weak

consider octane c 8 h 18 or
Consider octane, C8H18, or:

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3

Electro-negativities of C and H are ~ equal

No partial charge separation

Non-polar (apolar), cannot H-bond to water, = “hydrophobic”

Contrast: polar compounds = “hydrophilic”

slide21

Octane in water

(These numbers are made up.)

slide23
ENTROPY: related to the number of different states possible

The water molecules around the non-polar molecule have a LOWER entropy (less choices, more ordered).

Systems tend to change to maximize entropy (no. ofdifferent states possible to occupy).

Aggregation of the non-polar molecules with each other minimizes the number of lower entropy water molecules that are on their surface, thus maximizing the entropy of the system

slide24

Admittedly, the non-polar octane molecules lose entropy when they coalesce. That is, they are more disordered when they are separate.

  • However, this loss of entropy apparently cannot counteract the gain in entropy of the system brought about by the freeing up of water molecule from the “cage” around the non-polar molecules.
hydrophobic bonds forces
Affects NON-polar molecules that find themselves in an aqueous environment (i.e., must be in water)

They cannot H-bond with water molecules

The water molecules around the non-polar molecule are not able to constantly switch partners for H-bonding

The water molecules around the non-polar molecule are in a MORE ordered state.

Hydrophobic “forces”, not really “bonds” per se

Hydrophobic “bonds” (forces)
slide26

Water cages around methane: CH4

3 artists’ depictions

slide27
LARGE

>= ~5000 daltons

Called macromolecules

Examples:proteins, polysaccharides, DNA

SMALL

<= ~500 daltons (~ 50 atoms)

Called small molecules

Size differences are rough, there are gray areas

Examples:water, ethanol, glucose,acetamide, methane, octane

End of bonds, and water, our molecule #1Now on to the next 4999 types of molecules found in an E. coli cell:First let’s categorize: Small vs. large molecules

slide28

Propylene CH3-CH=CH2

Polypropylene, a polymer, a large molecule

slide31
A great simplification:

Large molecules are linearpolymers of

small molecules.

O-O-O-O-O-O-O-………

nomenclature for polymers

a monomer of the polymer

Nomenclature for polymers

monomer

O

O-O

dimer

trimer

O-O-O

tetramer

O-O-O-O

oligomer

O-O-O-O-O-O-O

oligomer

O-O-O-O-O-O-O-O-O-O-O

polymer

the large molecules or macromolecules of all cells can be grouped into 4 categories
polysaccharides,

lipids,

nucleic acids, and

proteins.

Many important small molecules are the monomers of these polymers.

Only about 50 of these monomers, a small number to learn about.

About another dozen important small molecules are not monomers of polymers. Mostly vitamins.

The large molecules, or macromolecules, of all cells can be grouped into 4 categories:
monomers and polymers example 1
Monomers and polymersExample 1.

Macromolecule: polysaccharide

A monomer of many polysaccharides is glucose:

Present in our minimal medium

)

.

slide35

Getting the monomers

CH3

C

Example 2:

Macromolecule: protein

Monomer: amino acids

Example at right = alanine

Looks nothing like glucose

Where does E. coli get alanine?

COOH

H2N

H

e coli makes all the monomers by biochemical transformations starting from glucose
E. coli makes all the monomers by biochemical transformations starting from glucose

glucose →A → B→C →D →E →alanine →protein

A, B, C, D, E, are “intermediates”:

i.e., intermediate chemical structures (molecules) between glucose and alanine.

very rough estimate of the total number of different small molecules in an e coli cell
50 monomers

15 non-monomer important small molecules (e.g., like vitamins)

65 total “end products”

Average pathways to monomers and important small molecules starting from glucose:= ~ 10 steps, so ~9 intermediates per pathway

65 such pathways  65 x 9 = 585 intermediates

65 end-products + 585 intermediates = 650 total types of small molecules per E. coli cell

A manageable number, and we ~know them all

Very rough estimate of the total number of different small molecules in an E. coli cell:
macromolecule class 1 polysaccharides
Monomer = sugars

Sugars = small carbohydrate molecules

Carbohydrates ~= CnH2nOn

Contain one C=O group and many –OH’s

Can contain other functional groups as well (carboxyls, amines)

Most common sugar and monomer is glucose

Macromolecule class #1:Polysaccharides
glucose straight chain depictions

C

C

Remember, always 4 bonds to carbon; Often even if not depicted

Glucose, straight chain depictions

Abbreviated

With numbering

slide41

anomeric

carbon

Fisher

view

Haworth view

Handout 2-7

Chair view

slide42

11

10

7

5

8

9

6

4

1

2

3

slide43

7

5

8

9

6

4

1

2

3

slide44

alpha-glucose

beta-glucose

slide45

anomeric

carbon

Fisher

view

Haworth view

Handout 2-7

Chair view

slide46

5

3

4

1

From Handout 2-7

slide47

Relationship between Haworth (flat ring) depiction and chair-form

Flat ring (Haworth projection) relative positions of the H and OH at each carbon, one “above” the other.

But it does not tell the positions of the groups relative to the ring plane (up, down or out). (No room “in.”)

Handout 2-8

slide49

Alpha or beta?

You try it later.

Glucose

hydroxyl

Gray = C

White = H

Red = O