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Chemistry. Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. P.S. In Biology we talk mainly about Organic Chemistry: The chemistry of molecules containing Carbon. . Chemistry Joke of the Day a Poem….

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Chemistry

Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis

P.S. In Biology we talk mainly about Organic Chemistry: The chemistry of molecules containing Carbon.


Chemistry Joke of the Daya Poem….

Susan was in chemistry.

Susan is no more,

for what she thought was H2O

was really H2SO4.


Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization.

a. Molecules and atoms from the environment are necessary to build new molecules

.

Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

  • Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids, or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.


Living systems depend on properties of water that result from its polarity and hydrogen bonding.

  • Cohesion

  • Adhesion

  • High specific heat capacity

  • Universal solvent to support reactions

  • Heat of vaporization

  • Heat of fusion (exovs.endo)

  • Water’s thermal conductivity.


Review of Chem

Review of Chem


Essential knowledge 4.a.1: the subcomponents of biological molecules and their sequence determine the properties of that molecule.

a. Structure and function of polymers are derived from the way their monomers are assembled.

.

Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Cellulose vs. Starch. Why does one dissolve?

  • Lipids are nonpolar; however phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids.


What is the difference between Linear vs. branched polysaccharides?

slow release

starch

(plant)

What doesbranching do?

energystorage

glycogen

(animal)

Let’s go to the videotape!

fast release


Cow

can digest cellulose well; no need to eat other sugars

Gorilla

can’t digest cellulose well; must add another sugar source, like fruit to diet


How do animals break down cellulose?

  • How can herbivores digest cellulose so well?

    • Mutualism

    • BACTERIA live in their digestive systems & help digest cellulose-rich (grass) meals

Tell me aboutthe rabbits,again, George!

Coprophage

I eatWHAT!

Ruminants


a. Structure and function of polymers are derived from the way their monomers are assembled.

  • In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (A,T,C,G,U). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions.

  • In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (Hydrophobic/philic, ionic), and the interactions of these R groups determine structure and function of that region of the protein.


What are the three parts of Nucleotides?

  • nitrogen base (C-N ring)

  • pentose sugar (5C)

    • ribose in RNA

    • deoxyribose in DNA

  • phosphate(PO4)group

Nitrogen baseI’m the A,T,C,G or Upart!

Are nucleic acidscharged molecules?


H2O

Because everybody needs a Chaperonin!

How are Proteins structured?

  • monomer =amino acids

    • 20 different amino acids

  • polymer =polypeptide

    • protein can be one or more polypeptide chains folded & bonded together

    • large & complex molecules

    • complex 3-D shape

hemoglobin

RuBisCO


Sickle cell anemia

Just 1out of 146amino acids!

I’mhydrophilic!

But I’mhydrophobic!


Isomers

  • Molecules with same molecular formula but different structures (shapes)

    • different chemical properties

    • different biological functions

6 carbons

6 carbons

6 carbons


Form affects function

  • Structural differences create important functional significance

    • amino acid alanine

      • L-alanine used in proteins

      • but not D-alanine

    • medicines

      • L-version active

      • but not D-version

    • sometimes withtragic results…

stereoisomers


Form affects function

  • Thalidomide

    • prescribed to pregnant women in 50s & 60s

    • reduced morning sickness, but…

    • stereoisomer caused severe birth defects


b. Directionality influences structure and function of the polymer.

  • Nucleic acids have ends, defined by the 3’ and 5’ carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5’ to 3’)

  • Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.

The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.


Learning Objectives:

  • LO 4.1: The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties.

  • LO 4.2: The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer


A Review for You!

Chemistry of Carbon

Building Blocks of Life


Why study Carbon?

  • All of life is built on carbon

  • Cells

    • ~72% H2O

    • ~25% carbon compounds

      • carbohydrates

      • lipids

      • proteins

      • nucleic acids

    • ~3% salts

      • Na, Cl, K…


Chemistry of Life

  • Organic chemistry is the study of carboncompounds

  • C atoms are versatile building blocks

    • bonding properties

    • 4 stable covalent bonds

H

C

H

H

H


Complex molecules assembled like TinkerToys


Hydrocarbons

  • Combinations of C & H

    • non-polar

      • not soluble in H2O

      • hydrophobic

    • stable

    • very little attraction between molecules

      • a gas at room temperature

methane(simplest HC)


Hydrocarbons can grow


Isomers

  • Molecules with same molecular formula but different structures (shapes)

    • different chemical properties

    • different biological functions

6 carbons

6 carbons

6 carbons


Form affects function

  • Structural differences create important functional significance

    • amino acid alanine

      • L-alanine used in proteins

      • but not D-alanine

    • medicines

      • L-version active

      • but not D-version

    • sometimes withtragic results…

stereoisomers


Form affects function

  • Thalidomide

    • prescribed to pregnant women in 50s & 60s

    • reduced morning sickness, but…

    • stereoisomer caused severe birth defects


Diversity of molecules

  • Substitute other atoms or groups around the carbon

    • ethane vs. ethanol

      • H replaced by an hydroxyl group (–OH)

      • nonpolar vs. polar

      • gas vs. liquid

      • biological effects!

ethanol (C2H5OH)

ethane (C2H6)


Functional groups

  • Parts of organic molecules that are involved in chemical reactions

    • give organic molecules distinctive properties

      hydroxylamino

      carbonylsulfhydryl

      carboxylphosphate

  • Affect reactivity

    • makes hydrocarbonshydrophilic

    • increase solubility in water


Viva la difference!

  • Basic structure of male & female hormones is identical

    • identical carbon skeleton

    • attachment of different functional groups

    • interact with different targets in the body

      • different effects


Hydroxyl

  • –OH

    • organic compounds with OH = alcohols

    • names typically end in -ol

      • ethanol


Carbonyl

  • C=O

    • O double bonded to C

      • if C=O at end molecule = aldehyde

      • if C=O in middle of molecule = ketone


Carboxyl

  • –COOH

    • C double bonded to O & single bonded to OH group

      • compounds with COOH = acids

        • fatty acids

        • amino acids


Amino

  • -NH2

    • N attached to 2 H

      • compounds with NH2 = amines

        • amino acids

      • NH2 acts as base

        • ammonia picks up H+ from solution


Sulfhydryl

  • –SH

    • S bonded to H

      • compounds with SH = thiols

      • SH groups stabilize the structure of proteins


Phosphate

  • –PO4

    • P bound to 4 O

      • connects to C through an O

      • lots of O = lots of negative charge

        • highly reactive

      • transfers energy between organic molecules

        • ATP, GTP, etc.


Macromolecules

Building Blocksof Life


Macromolecules

  • Smaller organic molecules join together to form larger molecules

    • macromolecules

  • 4 major classes of macromolecules:

    • carbohydrates

    • lipids

    • proteins

    • nucleic acids

    • And a minor one: ATP


H2O

HO

H

HO

H

HO

H

Polymers

  • Long molecules built by linking repeating building blocks in a chain

    • monomers

      • building blocks

      • repeated small units

    • covalent bonds

Dehydration Synthesis http://sciencestage.com/v/621/chemistry-experiment-science-dehydration-sugar.html


H2O

HO

H

HO

H

enzyme

HO

H

How to build a polymer

You gotta be open to“bonding!

  • Synthesis

    • joins monomers by “taking” H2O out

      • one monomer donates OH–

      • other monomer donates H+

      • together these form H2O

    • requires energy & enzymes

Dehydration synthesis

Condensationreaction


H2O

HO

H

enzyme

H

HO

H

HO

How to break down a polymer

Breaking upis hard to do!

  • Digestion

    • use H2O to breakdown polymers

      • reverse of dehydration synthesis

      • cleave off one monomer at a time

      • H2O is split into H+ and OH–

        • H+ & OH– attach to ends

    • requires enzymes

    • releases energy

Hydrolysis

Digestion


Any Questions??


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