Biochemistry What does Organic Mean? Biochemistry: Packet #3 - Organic Chem

BiochemistryBiochemistry

What does Organic Mean?

Biochemistry: Packet #3 - Organic Chem

Atomic Number# of protons

(and also # of electrons)

Chemical symbol

Name of Element

Atomic MassThe weight Of carbon

atom oraverage

weight of all isotopes

6

CCarbon12.011

WhatWhat’’s so s so special about special about

Carbon??Carbon??Biochemistry: Packet #3 - Organic Chem


“Elements of Life”

Organic = carbon-based molecules

Examples: C6H12O6, CH4

Inorganic = molecules without carbon–carbon or carbon–hydrogen bonds

Examples: NaCl, NH4, H2SO4 , CO, CO2


• Carbon can form 4 covalent bonds– Leads to many different molecules

– Can form large chains or rings

• Linking of carbons can form very large molecules called Macromolecules• Each individual unit is called a monomer. When

they are linked together they are called a polymer.

• 4 macromolecules necessary for life: carbohydrates, lipids, protein, nucleic acids

Why Carbon?


Polymerization= Synthesis of organic molecules= Small subunits (MONOMERS) bond together to

form larger units (POLYMERS)


Chemical Reactions

Process that changes one set of chemicals into another set of chemicals

• Reactant + Reactant = Product + Product• Always involve changes in the chemical bonds

that join atoms in compoundsREARRANGING!


Types of Reactions• Hydrolysis

– Break apart monomers– Happens by the addition of water. – An H is added to one monomer & an OH is added to the

other monomer.

• Dehydration Synthesis (or Condensation)– Join monomers – One monomer loses a H+ and the other loses an OH-

– Water is removed– Covalent bond is formed


Hydrolysis


Dehydration Synthesis


Energy in reactions

• Bonds are the storage place of energy in molecules / compounds

– Break a bond RELEASE energy

– Make a bond REQUIRES energy


Energy in Reactions• EXERGONIC (E exiting)• Chemical reactions that release energy • Often spontaneous (occur on their own)

– But often need a “push” to get started

• ENDERGONIC (E needing)• Chemical reactions that absorb energy • Need energy input to occur

• ACTIVATION ENERGY the energy needed to get a reaction started. Enzymes (proteins) do this.

The “push”


CATABOLISM

HYDROLYSIS

EXOTHERMIC

RELEASE ENERGY

BREAK BONDS

CELL RESPIRATION

ANABOLISM

DEHYDRATION SYNTHESIS

ENDOTHERMIC

STORE ENERGY

MAKE BONDS

REDUCTION

Small Molecules

Big

Molecules METABOLISM


Condensation Reaction




So why do polymers So why do polymers (macromolecules) (macromolecules)

matter to life?matter to life?


MONOMERSMONOMERS POLYMERSPOLYMERS

Simple or Single SugarsSimple or Single Sugars Carbohydrates or Carbohydrates or

Complex SugarsComplex Sugars

Amino AcidsAmino Acids ProteinsProteins

Fatty Acids and GlycerolFatty Acids and Glycerol Fats or LipidsFats or Lipids

NucleotideNucleotide Nucleic Acids:Nucleic Acids:

RNA or DNARNA or DNA


Carbohydrates• Fxn: Primary source of Energy• Structure: Made of C, H, and O

– Ratio of C:H:O is 1:2:1

– General formula: Cn(H2O)n-1 ie. C12H22O11

• n = the # of C’s in the molecule

• Rings are usually formed as opposed to the linear structure

• Small carbs. are water soluble because of -OH groups


http://en.wikipedia.org/wiki/Image:Glucose.png

GLUCOSE: key to life

Energy is stored in the bonds between atoms.This is what our bodies break down when we eat

to obtain energy!Biochemistry: Packet #3 - Organic Chem

http://en.wikipedia.org/wiki/Image:Glucose.png

Types of Carbohydrates• Monosaccharide = Monomer

– Simple sugars: glucose, galactose, fructose– 6-C sugar molecule = “hexose”

• Disaccharides = 2 sugars linked together– Sucrose = glucose + fructose– Lactose = glucose + galactose– Maltose = glucose + glucose

• Polysaccharide = Polymer– Longterm energy storage– Plants = starch, cellulose– Animals = glycogen


ISOMERS Same molecular formula different structural formula

Glucose Fructose Galactose

What is the molecular formula for each? What are the structural differences?


POLYSACCHARIDESStructural Materials & Energy Storage

1. Plant Cell walls: Cellulose (not digestable)2. Plant tissue: Starch (yummy!)3. Arthropod Exoskeleton: Chitin4. Cell Walls of Fungi: Chitin5. Cell Walls of Bacteria: Peptidoglycan6. Animals: Glycogen (liver & muscles)

InsulinGlycogen Glucose

GlucagonBiochemistry: Packet #3 - Organic Chem


LIPIDS Fats, Oils, Waxes• Fxn: Long-term energy storage

& cell membrane structure

• Structure: Made of C, H, O– No definite ratios but very high amount of H’s

• Nonpolar – not soluble in water; hydrophobic– Examples: triglycerides - saturated & unsaturated

fats, phospholipids, sterols (steroids &cholesterol, hormones and vitamins


Lipid Properties• MONOMER: 1 glycerol and 1-3 fatty acids

• POLYMER: Lipid• Properties of lipid depends on fatty acids

– (saturated vs. unsaturated)


GLYCEROLGLYCEROL


Saturated vs. Unsaturated • All single bonds connect C• Solid at room temp• Ex: butter, lard• “Straight, stackable”

• Contain double bonds• Liquid at room temp• Ex: olive oil, corn oil• Typically plant-based



What are trans-fats?

• “Trans” double bonds are not naturally found in biological systems

• When unsat. fats are “hydrogenated” to become sat. fat (easier to store, ship,use), the H’s can rearrange and ‘straighten out’ the molecule

• Trans fat is bad b/c it is not recognized by our body’s enzymes


• Component of cell membrane

• Two fatty acids + glycerol + phosphate group

• Amphipathic– Polar head: hydrophilic

• Phosphate group attached to glycerol

– Non-Polar Tail: Hydrophobic• Two fatty acid chains attached

to glycerol


http://bioweb.wku.edu/courses/BIOL115/Wyatt/Biochem/Lipid/P_lipid2.htm

• Required to build and maintain cell membranes

• Regulates membrane fluidity• May act as an antioxidant• Aids in the manufacture of bile• Important for the metabolism of fat-

soluble vitamins (A, D, E, & K)• Synthesis in hormones: cortisol,

aldosterone & sex hormones• HDL good, LDL bad


Proteins• Structure: contain N, C, H, O

– Have an amino group (-NH2) – Have a carboxyl group (-COOH)– Have an “R” group (“other”)

• there are 20 different R groups• Three major groups: Polar, Ionic, and Nonpolar


The “R” group is in a white box


Proteins• MONOMER: amino acid• POLYMER: Polypeptide or Protein

– 2 amino acids are joined by a peptide bond– 4 levels of protein structure


Proteins

• Functions: – Control cellular reactions (enzymes)– Regulate cell processes– Structure (tissues, bones, muscles)– Transport – Help fight disease


Protein Structure• Primary structure

– Amino acids bond forming polypeptide chain

• Secondary structure– Chain folds or twists into specific configuration– Stabilized by H bonds (ex: α helices, β pleats)

• Tertiary Structure– More complex folding: globular or spherical– Usually b/c of hydrophobicity

• Quaternary Structure– Multiple structures folded together



Causes of Denaturation (changing shape)

What can cause a change in protein conformation/shape1. Temperature:

– Increase or decrease will possibly cause bonds to be disrupted.

2. pH– Disrupt the pattern of ionic attractions and

repulsions that contribute to tertiary structure. 3. Salt Concentration

– Disrupt the pattern of ionic attractions and repulsions

4. Solvents (liquids that dissolve)Biochemistry: Packet #3 - Organic Chem

Nucleic Acids• Fxn: Store or transmit genetic information• Structure: contains H, O, N, C, P• MONOMER: Nucleotide

– Nucleotide made of three parts:• 5-carbon sugar (ribose or deoxyribose)• Phosphate• Nitrogen base (adenine, thymine, uracil, cytosine,

guanine)

• POLYMER: DNA (deoxyribonucleic acid) or RNA (ribonucleic acid)


Nucleotide Organization


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Biochemistry What does Organic Mean? Biochemistry: Packet #3 - Organic Chem