5.Macromolecules

Chapter 5

Most macromolecules are polymers, built

from monomers

• A polymer is a long molecule consisting of building blocks called monomers

• Three of the four classes of life’s organic molecules are polymers:

Macromolecule Monomer Polymer

Carbohydrates Monosaccharide Polysaccharide Proteins Amino Acids Polypeptides Nucleic acids Nucleotides Nucleic acids

The Synthesis and Breakdown of Polymers

• _{Dehydration synthesis:}

Monomers join to form larger molecules

• _{Hydrolysis: Reaction that}

breaks down polymers

its Candy Time- Yahhh!!!

http://nhscience.lonestar.edu/bio l/dehydrat/dehydrat.html

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

1. Carbohydrates: Fuel and Structure

• _{Monomers: monosaccharides, or single (simple) sugars}

– Molecular formulas are usually multiples of CH₂O – _{Glucose is the most common monosaccharide}

– _{Classified by location of the carbonyl group and by number of} carbons in the carbon skeleton

Carbohydrate Monomers

Triose sugars (C3H6O3)

Glyceraldehyde A ldo se s K et o se s Pentosesugars (C₅H₁₀O₅)

Ribose

Hexose sugars (C₅H₁₂O₆)

Glucose Galactose

Dihydroxyacetone

Ribulose

• _{A disaccharide is formed when a dehydration reaction}

joins two monosaccharides

– _{This covalent bond is called a glycosidic linkage} • _{http://www.youtube.com/watch?v=UyDnnD3fMaU} Glucose Maltose Fructose Sucrose Glucose Glucose Dehydration reaction in the synthesis of maltose

Dehydration reaction in the synthesis of sucrose

Polysaccharides

• _{Polysaccharides have}

storage and structural roles

– _{structure and function are} determined by sugar

monomers and the positions of glycosidic linkages

a Glucose

a and b glucose ring structures

b Glucose

Starch: 1–4 linkage of a glucose monomers.

Storage Polysaccharides

•

Starch: a storage polysaccharide of plants

–

Consists entirely of glucose monomers

–

Plants store surplus starch as granules within

plastids

•

Glycogen: a storage polysaccharide in animals

–

Also made up of glucose

Mitochondria

Glycogen granules

0.5 µm

Structural Polysaccharides

• _{Cellulose is a major component of the tough wall of}

plant cells

• A polymer of glucose

• _{Difference from starch is based on two ring forms for}

Alpha vs Beta Glucose

• Polymers with alpha glucose are helical

• Polymers with beta glucose are straight

• H atoms on one strand can bond with OH groups on other strands

• Parallel cellulose molecules = grouped into microfibrils: strong building materials for plants

• _{Chitin, another structural polysaccharide, is found in}

the exoskeleton of arthropods and in cell walls of many fungi

Carbs recap

•

Empirical formula __________

•

Monomer: ____________

•

Polymer: _______________

– _{Some important dimers as well (like __________)} – _{_________linkages between monomers}

•

Important polysaccharides:

2. Lipids

• _{Lipids do not form polymers} • _{Lipids are hydrophobic} 

– Consist mostly of hydrocarbons

• _{The most biologically important lipids are:} 1. Fats

2. Phospholipids 3. Steroids

Fats

• _{Fats are constructed from glycerol and fatty acids}

– _{Glycerol is a three-carbon alcohol with a hydroxyl group}

attached to each carbon

– _{A fatty acid consists of a carboxyl group attached to a}

long carbon skeleton

Dehydration reaction in the synthesis of a fat

Glycerol

Fatty acid (palmitic acid)

LE 5-11b

Ester linkage

Fat molecule (triacylglycerol)

Fatty Acids

•

Fatty acids vary in length (number of carbons)

and in the number and locations of double

bonds

– _{Saturated fatty acids have the maximum number}

of hydrogen atoms possible and no double bonds

– _{Unsaturated fatty acids have one or more double}

Phospholipids

• _{In a phospholipid, two fatty acids and a phosphate}

group are attached to glycerol

– _{The two fatty acid tails are hydrophobic,}

– _{The phosphate group and its attachments form a hydrophilic} head Hydrophilic head Hydrophobic tails Fatty acids Choline Phosphate Glycerol H yd rop h o b ic t ai ls H yd ro p h il ic h ea d

Phospholipids in cell membranes

• _{When phospholipids are added to water, they}

self-assemble into a bilayer

– _{WHY? Try to draw out how it might happen..} – _{What overall shape should the bilayer take?}

• _{Phospholipids are the major component of all cell}

membranes

WATER Hydrophilic

head

Hydrophobic

Steroids

• _{Steroids: lipids characterized by a carbon skeleton}

consisting of four fused rings

3. Proteins

• _{Monomer: amino acids} • _{Polymer: polypeptides}

– _{A protein consists of one or more polypeptides}

• _{Proteins account for more than 50% of the dry mass of}

most cells

• _{Protein functions include structural support, storage,}

transport, cellular communications, movement, and defense against foreign substances

Amino Acids

• _{Amino acids are organic molecules with carboxyl and}

amino groups

• _{Amino acids differ in their properties due to differing R}

groups

– _{Cells use 20 amino acids to make thousands of proteins}

Amino group

Carboxyl group

nationaldiagnostics .com/.../

articles_id/3

The 20 Amino Acids

Amino Acid Polymers

• _{Amino acids are linked by peptide bonds}

– _{How do you think they form??}

• _{A polypeptide is a polymer of amino acids}

– _{Polypeptides range in length from a few monomers to more} than a thousand

Protein Conformation and Function

• _{A functional protein consists}

of one or more polypeptides

• _{The sequence of amino}

acids determines a protein’s three-dimensional shape

• _{A protein’s conformation}

Four Levels of Protein Structure

• _{Primary structure : unique sequence of amino acids}

• _{Secondary structure: coils and folds in the polypeptide}

chain

• _{Tertiary structure: determined by interactions among}

various side chains (R groups)

• _{Quaternary structure : when a protein consists of}

multiple polypeptide chains

Amino acid subunits

 pleated sheet

+_H 3N

Amino end

 helix

Primary Structure

• _{The sequence of amino acids in a protein, similar to}

order of letters in a long word

Secondary Structure

• _{Results from hydrogen bonds between amino acids} • _{Typical secondary structures are the alpha helix}

(coils) and the beta pleated sheet (folds)

Amino acid subunits

 pleated sheet

Tertiary Structure

• _{Tertiary structure :}

determined by

interactions between R groups

– _{hydrogen bonds} – _{ionic bonds}

– _{hydrophobic interactions} – _{van der Waals}

interactions

– _{Strong covalent bonds} called disulfide bridges

Quaternary Structure

• _{Quaternary structure results when two or more}

polypeptide chains form one macromolecule

 Chains

 Chains Hemoglobin

Iron Heme

Collagen Polypeptide chain

Sickle-Cell Disease: A Simple Change in Primary Structure

• _{A slight change in primary structure can affect a}

protein’s conformation and ability to function

LE 5-21b Primary structure Secondary and tertiary structures

1 2 3

Normal hemoglobin Val His Leu

4 Thr 5 Pro 6 Glu Glu

7 _structurePrimary 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)        

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 region

What Determines Protein Conformation?

• _{Primary structure, physical and chemical conditions}

affect conformation

– _{Alternations in pH, salt concentration, temperature, or other} environmental factors can cause a protein to unravel

– _{Denaturation: loss of a protein’s “normal” conformation}

Denaturation

Renaturation

The Protein-Folding Problem

• _{Chaperonins are protein molecules that assist the}

proper folding of other proteins

Chaperonin

(fully assembled

)

cylinder

LE 5-23b

Polypeptide

Correctly folded protein

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

Steps of Chaperonin

Action: The cap comes_{off, and the}

properly folded protein is released. The cap attaches, causing

Protein Function: Enzymes

• _{Enzymes are a type of protein that acts as a catalyst,}

speeding up chemical reactions

– _{Enzymes lower the energy of activation}

– _{Enzymes can perform their functions repeatedly,}

– Help me get my coffee….PLEASE….

Substrate (sucrose)

Enzyme (sucrose) Fructose

Polymer Pyramid

•

Lipids

•

Carbohydrates

•

Cellulose

•

Phospholipid

•

Hydrolysis

•

Dimer

Protein quiz..kidding!

•

What is the monomer? Draw one!

•

What is the polymer? What is the name of the

bond between monomers and how does it

form?

•

What are the four levels of structure (name

and describe!)

4. Nucleic acids: store and transmit hereditary information

• _{The amino acid sequence of a polypeptide is}

programmed in DNA

• _{There are two types of nucleic acids:} – _{Deoxyribonucleic acid (DNA)}

– _{Ribonucleic acid (RNA)}

• _{DNA provides directions for its own replication}

• _{DNA directs synthesis of messenger RNA (mRNA) and,}

through mRNA, controls protein synthesis

LE 5-25

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

The Structure of Nucleic Acids

• _Monomers:

nucleotides

• _Polymers:

polynucleotides

– _{Each nucleotide}

consists of a

nitrogenous base, a pentose sugar, and a phosphate group

– _{The nitrogenous}

base and sugar (w/o the phosphate) are called a nucleoside

5¢ end

3¢ end

Nucleotides

• _{Two families of}

nitrogenous bases:

– _{Pyrimidines have a}

single

six-membered ring

– _{Purines have a}

six-membered ring fused to a five-membered ring

• In DNA, the sugar is deoxyribose

• In RNA, the sugar is ribose Nitrogenous bases Pyrimidines Purines Pentose sugars Cytosine

C Thymine (in DNA)T

Uracil (in RNA) U

Adenine A

Guanine G

Nucleotide Polymers

• _{Adjacent nucleotides are joined by covalent bonds}

between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

– how are these bonds formed?

– _{This creates a backbone of sugar-phosphate units with nitrogenous}

bases as appendages

– _{The sequence of bases along a DNA or mRNA polymer is unique for}

The DNA Double Helix

• _{A DNA molecule: two}

polynucleotides forming a double helix

– _{The two backbones run in} opposite 5´ to 3´ directions from each other, an

arrangement referred to as antiparallel

– _{The nitrogenous bases in DNA} form hydrogen bonds in a

complementary fashion: A always with T, and G always with C

Sugar-phosphate backbone 3¢ end

5¢ 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¢ end 3¢ end

Build DNA (then build RNA)!

•

Yellow = A

•

Blue = C

•

Red = G

•

Green = T (or U)