organic macromolecules packet #5 -...

Organic Macromolecules Packet #5

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Entry Checkpoint #1KWHLAQTopic :-Organic Macromolecules

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Introduction

• Organic Chemistry• The chemistry of carbon

• Why carbon?• Backbone of all life

• Any object on earth that contains carbon is considered as being organic

• Not to be confused with organic foods

• Has the ability to make four chemical bonds

• Remember, carbon has four valence electrons

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Four Organic CompoundsCompounds of Life

• There are four groups of organic macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

• They exist in the form of monomers or polymers.

• Polymers are two/more monomers joined together.

• Via polymerization

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Four Organic CompoundsCompounds of Life

• There are four groups of organic compounds

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

• They exist in the form of monomers or polymers.

• Polymers are two/more monomers joined together.

• Via polymerization

Organic Macromolecules

Carbohydrates Lipids Proteins Nucleic Acids

Organic Molecules

Monomers Polymers

Exist in two forms

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Exit Checkpoint #1KWHLAQ…Organic Macromolecules

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Exit Checkpoint #1BLevels & Student Derived Questions

LEARNING GOALSSTUDENT EVIDENCE

{Student developed Questions}

4In addition to level 3, the student will be able to:

3The student will be able to:


1With help, the student has a partial understanding of some of the simpler details and processes.

Organic Compounds/Macromolecules

Carbohydrates

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Entry Checkpoint #2KWHLAQTopic :-Carbohydrates

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CarbohydratesIntroduction

• Mainly used for energy

• Other names for carbohydrates

• Sugars

• Saccharide

• Starches

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Types of Carbohydrates

• Monosaccharides

• Monomer

• Simple sugar

• Glucose

• Fructose

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• Monosaccharides

• Can be placed into groups based on the number of carbon atoms in the sugar orthe presence of an organic molecule within the sugar’s structure.

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• Glyceraldehyde (a)

• Dihydroxyacetone (k)

Triose

• Ribose (a)

• Deoxyribose (a)

• Ribulose (k)

Pentose

• Glucose (a)

• Galactose (a)

• Fructose (k)

Hexose

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• Di-saccharides

• Polymer

• Combination of two monosaccharides via polymerization (dehydration synthesis chemical reaction).

• Sucrose

• Glucose & Fructose joined together

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• Polysaccharide

• Polymer

• Combines many monosaccharides together (polymerization…dehydration synthesis chemical reaction)

• Cellulose

• Several thousand glucose molecules joined together.

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Polysaccharides

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Exit Checkpoint #2KWHLAQ…Carbohydrates

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Organic Macromolecules Lipids

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Entry Checkpoint #3KWHLAQTopic :-Lipids

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Lipids Structure

• Commonly called fat is formed through polymerization (dehydration synthesis)

• Composed of two parts

• Glycerol

• Fatty acids

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Lipids

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Saturated vs. Unsaturated Fat

• Saturated

• The fatty acids only single bonds

• Unsaturated

• The fatty acids have one or more multiple bonds

• Better for your health because the ”kinks” prevent the fat molecules from packing closely together.

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PhospholipidsSpecial Class of Lipids

• Found at the surface of cells

• Four main components

• Glycerol

• Fatty acids

• PO4

{Phosphate/Phosphate Group}

• Organic molecule

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Phospholipids II

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Exit Checkpoint #3KWHLAQ…Lipids

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Organic Macromolecules

Nucleic Acids

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Entry Checkpoint #4KWHLAQTopic :-Nucleic Acids

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Nucleic Acids I

• Makes up genes and chromosomes

• Nucleic Acids are composed of multiple nucleotides joined together.

• Hence, a nucleic acid is a polynucleotide.

• Examples

• DNA

• Deoxyribonucleic Acid

• RNA

• Ribonucleic Acid

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Nucleic Acids—Nucleotides

• Nucleotide {Monomer}

• Three main components

• Sugar

• Deoxyribose

• DNA ONLY

• Ribose

• RNA ONLY

• Phosphate group

• Nitrogenous base

• Adenine; Guanine; Cytosine; Thymine; Uracil

• Uracil is only found in the Nucleic Acid RNA

• Thymine is only found in the Nucleic Acid DNA

Nucleic Acids

DNA

Sugar Deoxyribose

Phosphate

Nitrogenous Bases

Purines

Adenine

Guanine

Pyrimidines

Thymine

Cytosine

RNA

Sugar Ribose

Phosphate

Nitrogenous Bases

Purines

Adenine

Guanine

Pyrimidines

Cytosine

Uracil

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Components of Nucleotides

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DNA Nucleotides & DNA Strands

• Nucleotides are linked together by covalent phosphodiester bonds

• Each phosphate attaches to the 5’ end (carbon #5) of one deoxyribose and to the 3’ end (carbon #3)

of the neighboring deoxyribose

• Makes up the sugar-phosphate backbone

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DNA Strands

• Each DNA strand, that is composed of multiple nucleotides, has a head and a tail.

• Head = 5’ end

• Phosphate group

• Tail = 3’ end

• Hydroxyl group

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DNA Molecule

• Each DNA molecule consists of two DNA strands (polynucleotide chains) that associate as a double helix

• The two strands/chains run antiparallel

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Base-Pairing Rules for DNAChargaff Rules

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• The two DNA strands are joined together at the nitrogenous bases.

• Holding the bases together, and allowing the formation of the double helix, are hydrogen bonds.

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Base-Pairing Rules for DNAChargaff Rules II

• Adenine forms two hydrogen bonds with thymine

• Guanine forms three hydrogen bonds with cytosine

• These pairings are known as Chargaff ’s rules

• A always pairs with T

• G always pairs with C

• Complementary base pairing

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Chargaff Rules III

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Exit Checkpoint #4KWHLAQ…Nucleic Acids

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Organic Macromolecules Proteins

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Entry Checkpoint #5KWHLAQTopic :-Proteins

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Proteins

• Functions

• Provide support

• Used for storage

• Transports other substances

• Composed of polypeptide chains

• A sequence of amino acids (building blocks)

• Amino acids are joined together via polymerization (dehydration synthesis chemical reaction)

• Proteins can become “active”

• Enzymes

• Regulate metabolism

Proteins

Support Storage Transport

Amino Acids

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Introduction

• Over 300 amino acids have been described in nature

• However, only 20 common as constituents of mammalian proteins

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Structure

• Carboxyl group

• At a pH of 7.4, group is dissociated forming a negatively charged carboxylate ion

• Amino group

• At a pH of 7.4, group is protonated forming a positively charged ion

• Distinctive side chain

• “R-group”

• Linked to the α-carbon atom

• Nature of the side chain determines the role an amino acid plays in a protein

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Types of Side chains

• Non-polar

• Polar Charged Acidic

• Polar Uncharged

• Polar Charged Basic

Amino Acids

Non-PolarPolar

Uncharged

Polar Charged Acidic

(Negative)

Polar Charged Basic (Positive)

Side Chains

Proteins

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Introduction

• The 20 common amino acids found in proteins are linked together by peptide bonds.

• The sequence contains information necessary to generate a protein molecule with a unique 3D shape

• Proteins have four organizational levels

• Primary

• Secondary

• Tertiary

• Quaternary

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Structures of Proteins

• Primary Structure• Long chain of amino acids

• Secondary Structure• Polypeptide chain folded into or helixes.

• Tertiary Structure• Occurs when the helix folds on into itself

• Quaternary Structure• Combination of a number of polypeptide chains

along with associated non protein groups

• * Specific order of amino acids, that make up the primary structure (polypeptide chain) determine the overall shape of the protein.*

• *The type of amino acids, making up the polypeptide chain, AND THE INTERACTIONS AMONG THEM, determine the shape of the protein.*

Protein Structure

Primary Secondary

Alpha Helix

Beta pleated sheet

Tertiary Quaternary

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Remember…PolymerizationHow Proteins are Produced

• Proteins are composed of amino acids linked together.

• The amino acids are joined together via a condensation reaction in order to form a peptide bond {Type of Covalent Bond}.

• Α-carboxyl group of one amino acid binds to the α-amino group of another

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Primary Structures III

Students should know the name of, and

how to identify, the ends of polypeptide

chain.

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Sequencing of Primary Structures

• Determined by using Edman’s reagent

• Cleavage into smaller fragments

• DNA sequencing

Sequencing Primary

Structures

Edman’sReagent

CleavageDNA

sequencing

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Secondary Structures

• There are two forms of secondary structures.

• α-Helix

• β-pleated sheet

• Occurs when the polypeptide backbone, chain, does not assume a random 3D structure

• Generally forms regular arrangements of amino acids that are located near to each other in the linear sequence.

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Alpha vs. Beta

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TertiaryStructure

Globular proteins

Primary structure determines its tertiary structure

Hydrophobic side chains buried in interior

Hydrophilic groups found on the surface of molecule

Stabilized by

Disulfide bonds

Hydrophobic interactions

Hydrogen bonds

Ionic interactions

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Tertiary Structure

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Quaternary Structure

• Consist of two or more polypeptide chains that may be structurally identical or totally unrelated

• Two subunits

• Dimeric

• Three subunits

• Trimeric

• Several subunits

• Multimeric


Dimeric

Two subunits

Trimeric

Three subunits

Multimeric

Several subunits

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Interactions Within & Between Tertiary & Quaternary Structures

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Exit Checkpoint #5KWHLAQ…Proteins

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