Unit 2: Pre-test –Avg = 5 (out of 23) –Range = unknown Termites –Follow Paper Mate ink –Acts as a pheromone Test corrections – due tomorrow I will scream

• Unit 2: Pre-test – Avg = 5 (out of 23)– Range = unknown

• Termites– Follow Paper Mate ink– Acts as a pheromone

• Test corrections – due tomorrow

• I will scream sometime during class today.

The Structure and Function of Macromolecules

Chapter 5Chapter 5

1. What are the 4 major macromolecules?– Carbohydrates– Proteins– Lipids– Nucleic acids

2. How are they all similar?– All large polymers made of smaller monomers– All formed the same way

Chapter 5 The Structure and Function of MacromoleculesChapter 5 The Structure and Function of Macromolecules

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

(b) Hydrolysis in the breaking down of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Figure 5.2 The synthesis and breakdown of polymers

1. What are the 4 major macromolecules?

2. How are they all similar?

3. What are carbohydrates & what are they made of?– Sugars– Made of monosaccharides

• CH20

• Sugars end in -ose

• Nutrient for cells (1° glucose)

• Carbon skeleton is used for other organic molecules


Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

os

es

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Ke

tos

es

FructoseFigure 5.3

Figure 5.3 Examples of monosaccharides

Figure 5.4 Linear & ring forms of glucose

H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

HOH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4



3. What are carbohydrates & what are they made of?

4. How are monomers added to carbs?


Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

(a)

H

HO

H

HOH H

OH

O H

OH

CH2OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

CH2OH

H

HO

OHH

CH2OH

HOH H

O H

OHH

CH2OH

HOH H

O H

OHO

1 41– 4

glycosidiclinkage

Glucose Glucose Maltose

OH

H





5. What are polysaccharides used for?– Energy storage

• Starch – plants

• Glycogen – animals

– Structural support• Cellulose

• Chitin


Chapter 5 The Structure and Function of MacromoleculesChapter 5 The Structure and Function of MacromoleculesMitochondria Giycogen granulesChloroplast Starch

Amylose Amylopectin

1 m

0.5 m

(a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide

Glycogen

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4OH

CH2OH

O

OH

OH

HO

41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO4

O1

OH

O

OH OHO

CH2OH

O

OH

O OH

O

OH

OH

(a) a and glucose ring structures

(b) Starch: 1– 4 linkage of a glucose monomers

1

a glucose glucose

CH2OH CH2OH

1 4 41 1

(c) Cellulose: 1– 4 linkage of glucose monomers

6. Why do we poop corn?


Cellulosemolecules

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

O

OOH

OCH2OH

O

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOH

OOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

O

O

OH CH2OH

OH

Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Figure 5.8 Cellulose

(a) The structure of the chitin monomer.

O

CH2OH

OHH

H OH

H

NH

C

CH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH






5. What are polysaccharides used for?


7. What are some common lipids?– Fats– Phospholipids– Steroids – Oils– Waxes








7. What are some common lipids?

8. How are fats made?


(b) Fat molecule (triacylglycerol)

H

H O HC

C

C

H

H OH

OH

H

HH H

HH

HH

H

HHH

H

HH

H

HH

HH

HH

H

HH

HH

H

HH

H

HC

CCC

CC

CC

CC

CC

CC

CC

Glycerol

Fatty acid(palmitic acid)

H

H

H

H

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HHHH

HHH

HH

HH

H

H

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH H

HH

HH

HH

HH

HH

HH

H

HH

HH

HH

HH

HH

HHH

HH

HO

O

O

O

O

OC

C

C C CC

CC

CC

CC

CC

CC

CC

C

C

CC

CCCC

CC

CC

CC

CC

CC

C CC

CC

CC

CC

CC

CC

CC

O

O

(a) Dehydration reaction in the synthesis of a fat

Ester linkage

Figure 5.11 The synthesis and structure of a fat, or triacylglycerol







7. What are some common lipids?

8. How are fats made?

9. What is the difference between a saturated & unsaturated fat?


(a) Saturated fat and fatty acid

Stearic acid

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12 Examples of saturated and unsaturated fats and fatty acids

Staple test corrections to test & place in box

Saturated vs Unsaturated Fats- No double bonds (C-C) - Double bonds (C=C)- Carbons are saturated - Carbons not saturated- Solid at RT - Oil at RT- Animal fats - Plant or fish fats- Butter - Vegetable oil- Bacon grease - Olive oil

What are trans fats?- Formed by hydrogenation- C=C without the “kink”

Saturated vs Unsaturated Fats- No double bonds (C-C) - Double bonds (C=C)- Carbons are saturated - Carbons not saturated- Solid at RT - Oil at RT- Animal fats - Plant or fish fats- Butter - Vegetable oil- Bacon grease - Olive oil

What are the functions of fats?- Energy storage (2X carbs)- Cushion- Insulation

Hy

dro

ph

ilic

he

ad

CH2N(CH3)3

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Choline

Phosphate

Glycerol

(a) Structural formula(b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hy

dro

ph

ob

ic t

ail

s

Hydrophilichead

Hydrophobictails

+

–

Figure 5.13 The structure of a phospholipid

Amphipathic – moleculesboth polar & non-polar

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15 Cholesterol, a steroid

10. What are the monomers of proteins?- Amino acids

11. How are all amino acids similar?


H

H

N C

R

H

C

O

OH

Aminogroup

Carboxylgroup

a carbon

S

O

O–

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 The 20 amino acids of proteins

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

OC

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–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+

NHCH2

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)

10. What are the monomers of proteins?


12. How are amino acids connected?- Dehydration (condensation) rxn- Creates a peptide bond


Carboxyl

end(C-terminus)

DESMOSOMES

OH

DESMOSOMESDESMOSOMES

OH

CH2

C

N

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SH Side chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)

(b)

Figure 5.18 Making a polypeptide chain



12. How are amino acids connected?

13. What are the 4 levels of protein structure?- 1° (Primary) – aa sequence (determined by DNA sequence)- 2° (Secondary) – based on H-bonds- 3° (Tertiary) – overall globular shape – 3D structure- 4° (Quaternary) – several 3° polypeptides (subunits)


Figure 5.20 Primary structure of a protein

• Based on amino acid sequence• Each protein has a unique sequence • Like the alphabet (letters = aa)

–

Amino acid subunits

+H3NAmino end

o

Carboxyl end

oc

Gly Pro Thr Gly

Thr

Gly

GluSeuLysCysPro

LeuMet

Val

Lys

Val

LeuAsp

Ala Val Arg GlySer

Pro

Ala

Gly

lle

SerPro Phe His Glu His

Ala

Glu

ValValPheThrAla

Asn

Asp

SerGly Pro

ArgArg

TyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSer

TyrSerThr

Thr

Ala

ValVal

ThrAsn Pro

Lys Glu

Thr

Lys

SerTyrTrpLysAlaLeu

Glu Lle Asp

O C a helix

pleated sheet

Amino acid

subunitsNCH

C

O

C N

H

C

O H

R

C N

H

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NC

O

R

C

H

NH

H

C

R

C

O H

C

R

N

H

C

OC

C

O

C

N

HH

R

C

C

O

N

HH

C

R

C

O

N

H

R

C

H C

ON

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

H

C

N H

H C R

N HO

O C N

C

RC

H

H O

CHR

N H

O C

RC

H

N H

O CH C R

N H

CC

N

R H

H

O C

H C R

N H

O C

RC

H

Figure 5.20 Secondary structure of a protein

Based on H-bonds• α-helix - β-pleated sheet• adjacent polar aa - after folding, polar aa become neighbors

and form H-bonds

Figure 5.20 Tertiary structure

CH2

OH

O

COH

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hydrogenbond

Ionic bond

Disulfide bridge

• overall globular shape – 3D structure• each protein has unique 3D shape

• recall carbon sets the 3D shape• based on 1° structure (aa sequence)• rearranged the alphabet to get new words

• Disulfide bridge • 2 cysteine amino acids• covalent bond

• van der Waals interactions• hydrophobic interactions• ionic bonds• occasional H-bonds

Figure 5.20 Quarternary structure

Polypeptidechain

Collagen

Chains

a ChainsHemoglobin

IronHeme

• more than one 3° polypeptide (subunit) needed for biological activity• not all proteins have quarternary structure• # of subunits varies by protein




13. What are the 4 levels of protein structure?

14. How much does sequence (structure) influence function?- Sickle cell anemia


Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother; eachcarries oxygen

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

a

a

10 m 10 m

a

a

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin S

Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced

Fibers of abnormalhemoglobin deform cell into sickle shape

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin Sickle-cell hemoglobin. . .. . .Val His Leu Thr Pro Glu Glu Val His Leu Thr Pro Val Glu

Figure 5.21 A single amino acid substitution in a protein causes sickle-cell disease





14. How much does sequence (structure) influence function?

15. What happens to proteins if they get too hot or experience a change in pH?


Denaturation

Renaturation

Denatured protein

Normal protein





14. How much does sequence (structure) influence function?

15. What happens to proteins if they get too hot or experience a change in pH?

16. What do proteins do?


Table 5.1 Protein function

↓

10. What are the monomers of proteins?11. How are all amino acids similar?12. How are amino acids connected?13. What are the 4 levels of protein structure?14. How much does sequence (structure) influence function?15. What happens to proteins if they get too hot or experience a change in

pH?16. What do proteins do?17. What are the different types of nucleic acids?

- DNA – deoxyribonucleic acid- RNA – ribonucleic acid

- mRNA – messenger - tRNA – transfer - rRNA – ribosomal

18. What are the monomers of nucleic acids?19. What makes up the monomers?


3’C

CHCH

Uracil (in RNA)U

5’ end

5’C

3’C

5’C

O

O

O

O

3’ end

OH

Nitrogenousbase

Nucleoside

O

O

O

O P CH2 O

5’C

3’CPhosphategroup Pentose

sugar

(b) Nucleotide

CN

NC

OH

NH2

CH

CHO

CNH

CH

HNC

O

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

N

HCNHH

C

C

C

N

NH

CNH2

AdenineA

GuanineG

Purines

OHOCH2

H

H H

OH

H

OHOH

OHOCH2

H

H H

OH

HOH H

5’

4

3’ 2’

1’

3’ 2’

1’4

5’Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)

Nitrogenous bases Pyrimidines

(c) Nucleoside components

(a) Polynucleotide, or nucleic acid

Figure5.26 Components of nucleic acids

3 end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)Old strands

Nucleotideabout to be added to a new strand

A

3 end

3 end

5 end

Newstrands

3 end

5 end

5 end

C G

C G

AT

C G

A T

A T

G C

A T

A T

T A

G

AC

C

C

G G

T

A

A

T

C

G

A

T

G

C

A

T

A

T

T

A

C

GA

T

A

T

G

C

T

AA

TT

A

C

G

A

T

T

A

C

G

T

A

C

GG

C

T

CG

5 end

Figure 5.27 DNA Double helix

Documents

Unit 2: Pre-test –Avg = 5 (out of 23) –Range = unknown Termites –Follow Paper Mate ink –Acts as a pheromone Test corrections – due tomorrow I will scream