biol 101 chp 5: the structure and function of large biological molecules

BIOL 101 General Biology I

Chapter 5

The Structure & Function of Large Biological Molecules

Rob Swatski Associate Professor of Biology

HACC – York Campus 1

2

small

molecules LARGE molecules

3

Bonds with variety of elements

Diverse sizes & shapes

Carbon-based

Many covalent

bonds

More insoluble in

water

Monomers Polymers

Properties of Organic Molecules

Macromolecules

Carbo-hydrates

Lipids Proteins Nucleic Acids

4

5

Condensation (Dehydration) Synthesis

Dehydration

Short polymer Unlinked monomer

Longer polymer

HO

HO

HO

H2O

H

H H

4 3 2 1

1 2 3

6

7

Hydrolysis

Hydrolysis

HO

HO HO

H2O

H

H

H 3 2 1

1 2 3 4

8

9

3 Major Groups of Carbohydrates

Mono-saccharides

Disaccharides Polysaccharides

10

Carbohydrate Characteristics

C-H2O

Classify by location of carbonyl (C=O)

Aldoses or Ketoses

#C atoms in skeleton

11

Carbohydrates:

General Functions

Energy Synthesis Storage

12

Monosaccharides

C6H12O6

Dihydroxyacetone

Ribulose

Fructose

Glyceraldehyde

Ribose

Glucose Galactose

Hexoses (C6H12O6)

Pentoses (C5H10O5)

Trioses (C3H6O3)

13

(a) Linear and ring forms

(b) Abbreviated ring structure 14

15

Disaccharides

Glycosidic linkage

1–2 glycosidic

linkage

16

Dehydration reaction: Sucrose synthesis

Sucrose Fructose Glucose

Maltose

1–4 glycosidic

linkage

17

Dehydration reaction: Maltose synthesis

Glucose Glucose

18

Polysaccharides

Largest carb

Polymer: 100’s of mono’s

Storage and structure

Classified by its monomer & linkages

Glycogen

19

Storage Polysaccharides

Starch

Glucose polymer

Plant plastids

Glycogen

Glucose polymer

Animal liver & muscle

Glycogen

Starch

Amylose

Chloroplast

Starch

Amylopectin

Mitochondria Glycogen granules

20

21

Structural Polysaccharides

Cellulose

Glucose polymer

Plant cell walls

Alpha () & beta () rings

beta ()

beta-Glucose monomer

Cellulose

Microfibril

Cell walls

beta-Glucose = straight chain 22

23

and Glucose Ring Structures

Glucose Glucose

Starch: 1–4 linkage of glucose monomers

(Alpha) = All same side

24

25

Cellulose: 1–4 linkage of glucose monomers

(Beta) = Both sides

26

27

Insoluble Fiber

http://www.hulu.com/watch/

10304/saturday-night-live-

colon-blow

28

Symbiosis

29

Chitin

Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

30

31

Hydrocarbons

C, H, O Hydrophobic

Nonpolar covalent

bonds No polymers

Glycerol & 1-3 fatty acids

Fats & oils

Lipids – General Characteristics

32

Lipid Structure

Fatty acid Glycerol

Dehydration synthesis of a fat

Ester linkage

Triglyceride 33

34

Triglyceride Structure

Fatty Acid Variation

Length

# and locations of

double bonds

Saturated fatty acids

Unsaturated fatty acids

35

Saturated Fats

Single covalent

bonds

Solid @ room temp

Mostly animal fats

36

37

Unaturated Fats

Cis double covalent

bond

Liquid @ room temp

Mostly plant & fish fats

38

39

Carotid artery plaque

Hydrogenation

trans fat

40

41

Adipose Tissue

Energy storage

Cushions organs

Insulation

42

Head

Polar

Hydrophilic

Glycerol & phosphate

Tails

Nonpolar

Hydrophobic

2 Fatty acids

Phospholipid Structure

Fatty acids

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tai

ls

Hyd

rop

hili

c h

ead

43

44

Phospholipid Bilayer

45

46

Cholesterol = precursor

47

Steroids

48

49

50

Proteins

C, H, O, N

Diverse shapes &

sizes

Polypeptides (polymers)

Amino acids (monomers)

51

Enzymatic Structural Storage

Transport Hormonal Receptor

Contractile & Motor

Defensive

Types of Proteins

52

Structural support

Storage

Transport Communication

Movement Immune defense

Functions of Proteins

Keratin: structural

protein

53

60 m

Collagen

Connective tissue

Structural proteins

Function: Support

Examples: Keratin is the protein of hair, horns,

feathers, and other skin appendages. Insects and

spiders use silk fibers to make their cocoons and webs,

respectively. Collagen and elastin proteins provide a

fibrous framework in animal connective tissues.

54

GABA receptor

protein 55

Signaling molecules

Receptor protein

Receptor proteins

Function: Response of cell to chemical stimuli

Example: Receptors built into the membrane of a

nerve cell detect signaling molecules released by

other nerve cells.

56

57

Actin & Myosin: contractile proteins

Muscle tissue

Actin Myosin

100 m

Contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible for the

undulations of cilia and flagella. Actin and myosin

proteins are responsible for the contraction of

muscles.

58

59

Antibodies: defensive proteins

Defensive proteins

Virus

Antibodies

Bacterium

Function: Protection against disease

Example: Antibodies inactivate and help destroy

viruses and bacteria.

60

Substrates

Active Site

Enzyme

61

Enzymatic proteins = Catalysts

Enzymatic proteins

Enzyme

Example: Digestive enzymes catalyze the hydrolysis

of bonds in food molecules.

Function: Selective acceleration of chemical reactions

62

Substrate (sucrose)

Fructose

Glucose

OH

H O

H2O

63

Enzyme (sucrase)

64

Amino Acids

Amino group

- NH2

Carboxyl group

- COOH

R group

Amino group

Carboxyl group

65

Side chain

Glycine (Gly or G)

Alanine (Ala or A)

Valine (Val or V)

Leucine (Leu or L)

Isoleucine (Ile or I)

Methionine (Met or M)

Phenylalanine (Phe or F)

Tryptophan (Trp or W)

Proline (Pro or P)

Nonpolar Amino Acids (hydrophobic)

66

Serine (Ser or S)

Threonine (Thr or T)

Cysteine (Cys or C)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Glutamine (Gln or Q)

Polar Amino Acids (hydrophilic)

67

Acidic (negatively charged)

Basic (positively charged)

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Lysine (Lys or K)

Arginine (Arg or R)

Histidine (His or H)

Electrically Charged Amino Acids (hydrophilic)

68

Peptide bond

New peptide bond forming

Side chains

Back- bone

Amino end (N-terminus)

Peptide bond

Carboxyl end (C-terminus) 69

70

Functional Proteins

Ribbon model of lysozyme

Space-filling model of lysozyme

Groove Groove

71

Antibody protein Protein from flu virus

72

73

Primary

Secondary

Tertiary Quaternary

Levels of Protein Structure

Amino acid subunits

+H3N

Amino end

25

20

15

10

5

1

74

Primary Structure

Primary structure Amino acids

Amino end

Carboxyl end Primary structure of transthyretin 75

pleated sheet

helix

Secondary Structure

76

Hydrogen bond

helix

pleated sheet

strand, shown as a flat arrow pointing toward the carboxyl end

Hydrogen bond

Secondary Structure

77

78 Silk = pleated sheet

79

too freakin’ cute…

…it has eyelashes for crying out loud!

Transthyretin polypeptide

Tertiary Structure

80

Hydrogen bond

Disulfide bridge

Polypeptide backbone

Ionic bond

Hydrophobic

interactions and

van der Waals

interactions

81

Transthyretin protein

(four identical polypeptides)

Quaternary Structure

82

Collagen 83

84

Collagen

Hemoglobin

Heme

Iron

subunit

subunit

subunit

subunit

85

86

Sickle-Cell Disease

Glutamic acid Valine (mutation)

No interaction between

molecules

Normal hemoglobin 7 6 5 4 3 2 1

Glu Val His Leu Thr Pro Glu

87

Normal hemoglobin

(top view)

Sickle-cell hemoglobin

Sickle-cell hemoglobin 7 6 5 4 3 2 1

Val Val His Leu Thr Pro Glu

Exposed hydrophobic

region

88

Interaction between

molecules = crystal fiber

Primary Structure

Secondary and Tertiary Structures

Quaternary Structure

Function Red Blood Cell Shape

subunit

subunit

Exposed hydrophobic region

Molecules do not associate with one another; each carries oxygen.

Molecules crystallize into a fiber; capacity to carry oxygen is reduced.

Sickle-cell hemoglobin

Normal hemoglobin

10 m

10 m

Sic

kle

-cell h

em

og

lob

in

No

rma

l h

em

og

lob

in

1

2

3

4

5

6

7

1

2

3

4

5

6

7

89

90

Physical & Chemical Conditions Affect Protein Structure

pH changes

Salt concentration

Temperature

Denaturation

Denaturation

Renaturation

91

92

Protein Folding in the Cell

Chaperonin

The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.

Polypeptide

Correctly folded protein

Steps of Chaperonin Action:

An unfolded poly- peptide enters the cylinder from one end.

The cap comes off, and the properly folded protein is released.

3 2

1

Steps of Chaperonin Action

93

X-ray Crystall-

ography of Proteins

94

95

Nuclear Magnetic Resonance (NMR) spectroscopy

96

97 CoA Binding Site in Staphylococcus aureus

EXPERIMENT

RESULTS

X-ray source X-ray

beam

Diffracted X-rays

Crystal Digital detector X-ray diffraction pattern

RNA polymerase II

RNA

DNA

98

99

Bioinformatics

Predicts protein structure from AA sequence

100

101

C, H, O, N, P Polymer of nucleotides

DNA and RNA Molecular

biology

Regulates cell activities

Guides protein synthesis

Nucleic Acids

102

mRNA

1. Synthesis of mRNA in the

nucleus

DNA

NUCLEUS

mRNA

CYTOPLASM

2. mRNA moves into cytoplasm

via nuclear pore

Ribosome

Amino acids Polypeptide

3. Synthesis of protein

103

Nucleotides

Nitrogenous Base

Pentose Sugar

Phosphate Group

5' end

5'C

3'C

5'C

3'C

3' end

Polynucleotide (Nucleic Acid)

Nucleotide

Nucleoside

Nitrogenous base

3'C

5'C

Phosphate group Sugar

(pentose)

104

Ribose (in RNA) Deoxyribose (in DNA)

Sugars of the Nucleotide

105

Nitrogenous Bases of the Nucleotide

Purines

Guanine (G) Adenine (A)

Cytosine (C) Thymine (T, in DNA)

Uracil (U, in RNA)

Pyrimidines

106

107

108

DNA

Double helix

Antiparallel

A---T

C---G

Sugar-phosphate backbones

3' end

3' end

3' end

3' end

5' end

5' end

5' end

5' end

Base pair

Old strands

New strands

109

Sugar-phosphate backbones

Hydrogen bonds

Base pair joined by hydrogen bonding

Base pair joined by hydrogen

bonding

(b) Transfer RNA (a) DNA

5 3

5 3

110