Biochemistry

Advanced Biology Biochemistry (the study of biology at the molecular level)

Four Classes of Biomolecules 

Carbohydrates • Monosaccharides (sugars), Polysaccharides (starches and cellulose)



Proteins • Enzymatic, structural, transport



Nucleic Acids • DNA/RNA/ATP



Lipids • Fatty acids, triglycerides, cholesterol 4.1

Monomers and Polymers 



Monomers are bonded together to form polymers Monomers form polymers by condensation reactions that remove a water molecule HO

1

3

2

H

HO

H Unlinked

Short polymer

monomer Dehydration removes a water molecule, forming a new bond HO

1

2

3

Longer polymer

H2O

4

H

4.2/4.3

Monomers and Polymers 

Polymers can disassemble by hydrolysis HO

1

2

3

4

Hydrolysis adds a water molecule, breaking a bond

HO

1

2

3

H

H

H2O

HO

H

4.3

Carbohydrates 

Monosaccharides • Are the simplest sugars • Can be used for fuel • Can be converted into other organic molecules • Can be combined into polymers

4.4

Carbohydrates 

Disaccharides • Consist of two monosaccharides • Are joined by a glycosidic linkage

4.4

Carbohydrates 

Glycosidic Linkage Formation

Be able to complete a partial diagram for examinations

4.5

Model Building n

n

n

Draw glucose on scratch paper. Build glucose. Link your glucose to that of another group. Show how water is released. Draw the molecule that results. Draw fructose. Build fructose. How is it different from glucose?

Carbohydrates 

Polysaccharides

Chloroplast

Starch

• Starch (amylose) 



Consists of glucose monomers Is the major storage form of glucose in plants 1 µm

4.4

Amylose

Amylopectin

Carbohydrates 

Polysaccharides

Mitochondria

Glycogen granules

• Glycogen 



Consists of glucose monomers Is the major storage form of glucose in animals

0.5 µm

Glycogen 4.4

Carbohydrates



Polysaccharides • Cellulose  

Is a polymer of glucose Is a structural carbohydrate in plant cell walls

Cell walls

Cellulose microfibrils in a plant cell Microfibril wall

About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall.

0.5 µm Plant cells CH2OH O OH O

4.4

OH CH2OH OH O O OH OH OH O O O O O CH OHO OH CH2OH 2 H CH2OH OH CH2OH OH O O O OH OH O OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH OH CH2OH O O O OH O OH OH OH O O O O O O CH OH OH CH2OH 2 β H

Glucose monome r

Cellulose molecules

Carbohydrates H



Cellulose •

Has different glycosidic linkages than starch

CH2OH H 4

O

H OH H H

OH

α glucose

CH2OH OH

C

H

H OH

HO

O C

HO

C

H

H

C

OH

H

C

OH

H

C

OH

H H OH

4 HO

H

O

OH

H

1 H

OH β glucose

(a) α and β glucose ring structures CH2O H O HO

1 4 O

OH

CH2OH

CH2OH

CH2OH

O

O

O

1

OH

O

4

OH

OH

1 4 O

OH

1

OH

O

OH

OH

(b) Starch: 1– 4 linkage of α glucose monomers CH2OH O HO

OH

O 1 4

OH

OH

CH2OH O

OH

O

OH

O

OH

O O CH2O CH2OH OH OH H (c) Cellulose: 1– 4 linkage of β glucose monomers

OH

4.6

Lipids • Are the one class of large biological molecules that do not consist of polymers • Share the common trait of being hydrophobic or nonpolar • Store more energy than any other biomolecule



Lipids

Fats •

Are constructed from two types of smaller molecules, a single glycerol and one or more fatty acids H H

C

O

H C

OH HO

H

C

OH

H

C

OH

C H

H C

H C

H

H

H C H

H C H

H C H

H C H

H C

H C

H

H

H C H

H C H

H C H

H C H

H C H

H C

H

H

Fatty acid (palmitic acid)

H

Glycerol

Dehydration reaction in the synthesis of a fat

Ester linkage O

H H

C

O

C

H C H

O H

C

O

C

H C H

O H

C H

O

C

H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

Fat molecule (triacylglycerol)

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C H H C H H C H

H C

H

H H C

H

H H C H

H

4.7

Lipids 

Saturated fatty acids • •

Have the maximum number of hydrogen atoms possible Have no double bonds

Stearic acid

Saturated fatty acid

4.8

Lipids 

Unsaturated fatty acids •

Have one or more double bonds

Unsaturated fatty acid

Oleic acid

cis double bond causes bending

4.8

Lipids 

Phospholipids • •

Have only two fatty acids Have a phosphate group instead of a third fatty acid

Lipids 

Phospholipid structure

Hydrophobic tails

Hydrophilic head

•

Consists of a hydrophilic “head” and hydrophobic “tails” +N(CH )

CH2

3 3

CH2 O O

P

O–

Choline Phosphate

O CH2

CH

O

O

C

O C

CH2

Glycerol

O

Phospholipid symbol

Fatty acids

Hydrophilic head Hydrophobic tails

Structural formula

Space-filling model

Lipids 

Phospholipid structure •

Results in a bilayer arrangement found in cell membranes WATER Hydrophilic Head Groups

Hydrophobic Tails

Hydrophilic Head Groups

WATER

Lipids 

Steroids • Are lipids characterized by a carbon skeleton consisting of four fused rings CH3

H3C

CH3

CH3

CH3

HO

Cholesterol •Is found in cell membranes •Is a precursor for some hormones

Lipids - ??? 

Name three common food products and describe how their state of matter (solid or liquid) relates to their lipid structure.

4.9

Proteins 

Proteins 





Have many structures and roles inside the cell 20 amino acids leads to great variability Types • • • •

Structural - collagen Enzymatic – DNA polymerase Transport - hemoglobin Receptor – insulin receptor

Proteins 

Amino Acid – Polypeptide – Protein • Amino acids are the monomers • Polypeptides are the polymers • Proteins consist of one or more polypeptides

4.10

Proteins 

Amino Acids • 20 types • Differ in their “R” groups

4.12

Proteins Peptide bond formation

OH

SH

CH2

CH2

H H

N



Peptide bond CH2

H C

C

H

O

N

H C

C

H

O

OH

H

N

C

C

H

O

OH

H2O

OH

CH2 H

H H

4.11

N

Side chains

SH Peptide CH2 bond CH2

OH

C

C

H

O

Amino end (N-terminus)

N

H C

C

H

O

N

C

C

H

O

Carboxyl end (C-terminus)

OH

Backbone

Proteins 

Non-polar amino acids

4.13

Proteins



4.13

Polar amino acids

Proteins

Beta sheets

Alpha helix



Determining conformation

Groove

• Primary structure • Secondary structure

ribbon model

• Tertiary structure • Quaternary structure Groove

4.14

space-filling model

Four Levels of Protein Structure Gly Pro Thr Gly

Amino acid subunits

Thr

H3N Amino end +

Gly

Leu

Seu Pro Cys Lys

Glu

Met Val



Primary structure

Lys Val Leu

Asp

Ala Val Arg Gly

Ser Pro Ala

• Is the unique sequence of amino acids in a polypeptide

Glu Lle Asp

Thr Lys Ser

Lys Trp Tyr Leu Ala

Gly lle Ser

Pro Phe His Glu His Ala Glu

Ala Thr Phe Val

Asn Asp Ser

Gly Pro

Arg

Arg

Val

Tyr

Thr

lle Ala Ala Leu Leu

Thr

Ser Tyr

Ser

Tyr Pro

Ser

Thr

o o– Carboxyl end Ala

Val

Val

4.14

Thr

Asn Pro

Lys Glu

c

Four Levels of Protein Structure 

Secondary structure •

Is the folding or coiling of the polypeptide into a repeating configuration Includes the α helix and the β pleated sheet

•

β pleated sheet

O H H O H H O H H R R R C C N C C N C C N C C N N N N N C C C C C C C C C R R R R H O H H O H H OH H O H

O

R

Amino acid subunits

O C C

R

O C N H C O H C R H C R N H O C O C N H C H R N

O

H

C

R

H N

H

H

O C

N H C H C R H C R N H O C O C N H C H R

C

R O

R O

C H H C H N HC N H C N H C N C H H C O C O R R

O C H H NH C N C H C O R

R H C N HC N H O C

H

α helix

4.16

Four Levels of Protein Structure 

Tertiary structure • •

Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups CH2 CH 2

Hydrogen bond HO

O H O

H3C

Hydrophobic and van der Waals interactions

CH

CH3 H3C CH3 CH

C CH2

Polypeptide backbone

CH2 S S CH2

O

Disulfide bridge

CH2 NH O C CH2 Ionic bond + 3

4.17

Four Levels of Protein Structure 

Quaternary structure •

•

Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Hemoglobin contains four subunits – two alpha and two beta chains of amino acids

β Chains

Iron

α Chains

Hemoglobin

Heme

Protein Folding 

Chaperonins •

Are protein molecules that assist in the proper folding of other proteins Chaperonin (fully assembled)

Primary polypeptide sequence

Cap

Correctly folded protein

Hollow cylinder

Steps of Chaperonin Action:

4.18

1 An unfolded poly- 2 The cap attaches, causing

3 The cap comes

the cylinder to change shape in off, and the properly peptide enters the folded protein is cylinder from one end. such a way that it creates a hydrophilic environment for the released. folding of the polypeptide.

4.19

Proteins 

Denaturation • Is when a protein unravels and loses its native conformation • Caused by unfavorable: temperatures, pH, salt concentration, and other chemicals Denaturation

Normal protein

Renaturation

Denatured protein

Nucleic Acids 

Nucleic acids

(DNA/RNA)

• Store and transmit hereditary information 

Genes • Are the units of inheritance • Code for the amino acid sequence of polypeptides • Are made of nucleic acids

Nucleic Acids (DNA/RNA) 

Consists of monomers called nucleotides made of • • •

Phosphate group Nitrogenous base Ribose sugar

Nucleoside

Nitrogenous base O −

O

P

O

O− Phosphate group

5’ CH2

O

4’

1’ 3’ 2’ Ribose sugar

Nucleotide 4.20/4.21

Nucleic Acids (DNA/RNA) Nitrogenous bases

Pyrimidines Prymidines

N



Nitrogenous Bases

C O

NH2

O

C

C

HN

CH CH

N

C N

C

C

CH3

CH CH

HN C

CH

H

Thymine (in DNA) T

Uracil (in (inRNA) RNA) Uracil UU

H

O

Purines NH2 N

C C

H

Adenine A

O

C N

HC N

CH CH

N H

O

Cytosine C

O

CH N

N

C

C

HC N H

NH C

N

Guanine G

NH2

Nucleic Acids (DNA/RNA) 

Pentose Sugars • Ribose • Deoxyribose Pentose sugars 5

”

HOCH2 H

4’ H

OH

O H

1’ H

3’ 2’ H OH

Deoxyribose (in DNA)

4.21

5” HOCH2 H

4’

OH

O H

1’ H

H 3’ 2’ OH OH

Ribose RNA) Ribose (in (in RNA)

Nucleotide Polymers (DNA/RNA) 

Nucleotide polymers •

Are made up of nucleotides linked by the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

5’ end 5’C

O

3’C

Phosphate

O

O

5’C

Sugar

O

3’C

4.20

OH

3’ end

Nucleic Acid Chain

Adenosine Triphosphate (ATP) 

A nucleic acid • One nucleoside + 3 phosphates

4.22

Adenosine Triphosphate (ATP) 

ATP stores energy • Energy is released from ATP when the terminal phosphate bond is broken

P

P

P

triphosphate (ATP) Cells Adenosine use this energy to perform cellular HO functions Energy 2

P

4.24

i

+

P

P

Adenosine diphosphate (ADP)