the structure and function of macromolecules note sheets... · organic chemistry-the study of...

Biochemistry

The Structure and Function of

Macromolecules

NOTE TAKING SHEET ONLY

Carbon—Backbone of

Biological Molecules


Organic Chemistry-the study of

carbon compounds


Carbon Molecules

MolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene) NOTE TAKING SHEET ONLY

Carbon Molecules

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)


Carbon Skeleton Diversity

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene 2-Butene

Cyclohexane BenzeneNOTE TAKING SHEET ONLY

Hydrocarbons


Organic%20Chemistry%20notes%20PP%20.docx

Isomers

Structural isomers differ in covalent partners, as shown

in this example of two isomers of pentane.

Geometric isomers differ in arrangement about a double

bond. In these diagrams, X represents an atom or group

of atoms attached to a double-bonded carbon.

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

L isomer D isomer

Enantiomers differ in spatial arrangement around an

asymmetric carbon, resulting in molecules that are

mirror images, like left and right hands. The two

isomers are designated the L and D isomers from the

Latin for left and right (levo and dextro). Enantiomers

cannot be superimposed on each other.NOTE TAKING SHEET ONLY

Isomerism


Structural Isomers


Geometric Isomers

CisC


Enantiomers

L-Dopa

(effective against

Parkinson’s disease)

D-Dopa

(biologically

Inactive)NOTE TAKING SHEET ONLY

Enantiomers%20note.docx

Functional Groups


Functional%20Groups%20note.docx

Functional Groups


STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

.


STRUCTURE

NAME OF COMPOUNDS

EXAMPLE

Acetone, the simplest ketone

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES


STRUCTURE

NAME OF COMPOUNDS

EXAMPLE

Acetic acid, which gives vinegar

its sour taste


Acetic acid Acetate ion


STRUCTURE

NAME OF COMPOUNDS

Amine

EXAMPLE


(nonionized)

Glycine

(ionized)


STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

EXAMPLE

Ethanethiol



STRUCTURE

NAME OF COMPOUNDS

EXAMPLE

Glycerol phosphate



Biochemistry: The Molecules of Life


Biochemistry


Macromolecules - Polymers


Polymers

Short polymer Unlinked monomer

Dehydration removes a water

molecule, forming a new bond

Dehydration reaction in the synthesis of a polymer

Longer polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer


Carbohydrates


Sugars


Monosaccharides


Triose sugars

(C3H6O3)

Glyceraldehyde

Pentose sugars

(C5H10O5)

Ribose

Hexose sugars

(C5H12O6)

Glucose Galactose

Dihydroxyacetone

Ribulose

Fructose


Monosaccharides

Glucose Fructose


Monosaccharides

• In aqueous solutions, monosaccharides form rings

Linear and

ring forms

Abbreviated ring

structure


Isomers of Glucose:


33

H H HHH

H

OH OH

OHO

OH H

OHO

CH2OH

RiboseGlyceraldehyde

Triose (3-carbon sugar)

Pentoses

(5-carbon sugars)

Deoxyribose

HH

H

H

H

H

OH

OH

O

C

C

C4

5

1

3 2

4

5

1

3 2

1

3

2

CH2OH


Disaccharides

Glucose

Maltose

Fructose Sucrose

Glucose Glucose

Dehydration

reaction in the

synthesis of maltose

Dehydration

reaction in the

synthesis of sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage


Disaccharides


Polysaccharides

(a) Starch

(b) Glycogen

(c) CelluloseNOTE TAKING SHEET ONLY

Storage Polysaccharides - StarchChloroplast Starch

1 µm

Amylose

Starch: a plant polysaccharide

Amylopectin


Storage Polysaccharides - Glycogen

Mitochondria Glycogen granules

0.5 µm

Glycogen

Glycogen: an animal polysaccharideNOTE TAKING SHEET ONLY

Structural Polysaccharides

a Glucose

a and b glucose ring structures

b Glucose

Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers.NOTE TAKING SHEET ONLY

Cellulose

Cellulose

molecules

Cellulose microfibrils

in a plant cell wall

Cell walls Microfibril

Plant cells

0.5 µm

b Glucose

monomer


Chitin


Lipids


Fats

Dehydration reaction in the synthesis of a fat

Glycerol

Fatty acid

(palmitic acid)


Fatty Acids

Stearate OleateNOTE TAKING SHEET ONLY

Fats

Ester linkage

Fat molecule (triacylglycerol)NOTE TAKING SHEET ONLY

Glycerides


Saturated Fats

Saturated fat and fatty acid.

Stearic acid


Unsaturated Fats

Unsaturated fat and fatty acid.

Oleic acid

cis double bondcauses bending


Fat Sources


Phospholipids

Structural formula Space-filling model Phospholipid symbol

Hydrophilic

head

Hydrophobictails

Fatty acids

Choline

Phosphate

Glycerol


Micelle

Phospholipid bilayerWater

Water

Water Lipid head (hydrophilic)

Lipid tail (hydrophobic)

Phospholipids


Phospholipids

WATERHydrophilic

head

Hydrophobic

tailsWATER


Steroids


Proteins


Amino Acids

Amino

group

Carboxyl

group

a carbon


O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

Amino Acids


O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

O

C

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electrically

charged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NH

CH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)

Tyrosine

(Tyr)Asparagine

(Asn)

Glutamine

(Gln)

Acidic Basic

Aspartic acid

(Asp)

Glutamic acid

(Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acids


Amino Acids and Peptide Bonds


Protein Conformation and Function

A ribbon model

Groove

Groove

A space-filling modelNOTE TAKING SHEET ONLY

Four Levels of Protein Structure

Amino acidsubunits

b pleated sheet

a helix


Primary Structure

Amino acidsubunits

Carboxyl end

Amino end


Secondary Structure

Amino acid

subunits

b pleated sheet

a helix


Tertiary Structure

Hydrophobic

interactions and

van der Waals

interactions

Polypeptide

backbone

Disulfide bridge

Ionic bond

Hydrogen

bond


Quaternary Structure

b Chains

a ChainsHemoglobin

Iron

Heme

CollagenPolypeptide chain

Polypeptidechain


Levels of Protein Structure


http://www.youtube.com/watch?v=lijQ3a8yUYQ

72

Interactions that Contribute to a Protein’s Shape

727272NOTE TAKING SHEET ONLY

73NOTE TAKING SHEET ONLY

Sickle-Cell Disease: A Simple Change in

Primary Structure

Red blood

cell shapeNormal cells are

full of individual

hemoglobin

molecules, each

carrying oxygen.

10 µm 10 µm

Red blood

cell shape

Fibers of abnormal

hemoglobin deform

cell into sickle

shape.


Sickle Cell Anemia

Primary

structure

Secondary

and tertiary

structures

1 2 3

Normal hemoglobin

Val His Leu

4

Thr

5

Pro

6

Glu Glu

7Primary

structure

Secondary

and tertiary

structures

1 2 3

Sickle-cell hemoglobin

Val His Leu

4

Thr

5

Pro

6

Val Glu

7

Quaternary

structure

Normal

hemoglobin

(top view)

a

b

b

b

b

a

a

a

Function Molecules do

not associate

with one

another; each

carries oxygen.

Quaternary

structure

Sickle-cell

hemoglobin

Function Molecules

interact with

one another to

crystallize into

a fiber; capacity

to carry oxygen

is greatly reduced.

Exposed

hydrophobic

regionb subunit b subunit


Conformation

Denaturation

Renaturation

Denatured proteinNormal protein


Nucleic Acids


The Roles of Nucleic Acids


NUCLEUS

DNA

CYTOPLASM

mRNA

mRNA

Ribosome

Amino

acids

Synthesis of

mRNA in the nucleus

Movement of

mRNA into cytoplasm

via nuclear pore

Synthesis

of protein

PolypeptideNOTE TAKING SHEET ONLY

The Structure of Nucleic Acids


5 end

3 end

Nucleoside

Nitrogenous

base

Phosphate

group

Nucleotide

Polynucleotide, or

nucleic acid

Pentose

sugar


Phosphate group

Sugar

Nitrogenous base

N

N

O

4’

5’

1’

3’ 2’

28

7 6

39 4

5

P CH2

O

–O

O–

OH R

OH in RNA

H in DNA

O

N

NH2

N1


Nucleotide MonomersNitrogenous bases

Pyrimidines

Purines

Pentose sugars

Cytosine

C

Thymine (in DNA)

T

Uracil (in RNA)

U

Adenine

A

Guanine

G

Deoxyribose (in DNA)

Nucleoside components

Ribose (in RNA)


Nitrogenous bases

Adenine

Guanine

CC

NN

N

C

H

N

C

CH

O

H

Cytosine (both DNA and RNA)

Thymine (DNA only)

Uracil (RNA only)

HCC

NC

H

N

C

NH2

N

N

CHOCC

NC

H

N

CH

H

OCC

NC

H

N

C

O

HH3C

H

OCC

NC

H

N

C

O

HH

H

P U R I N E S

P Y R I M I D I N E S

NH2

NH2


Nucleotide Polymers


The DNA Double Helix

Sugar-phosphate

backbone

3 end5 end

Base pair (joined by

hydrogen bonding)

Old strands

Nucleotide

about to be

added to a

new strand

5 end

New strands

3 end

5 end3 end

5 end


ATP


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