Biochemistry

Bio 300What does Organic Mean?

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

What’s so special about

Carbon??

Biochemistry Topics

• 4 major macromolecules of life– Structure– Function

• Why are they important?• Energy and Reactions

– Hydrolysis vs. condensation/dehydration synthesis

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

“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

PolymerizationSynthesis of organic molecules

Small subunits called MONOMERS are joined to form POLYMERS

Polymers are MACROMOLECULES

Monomers Polymer

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

Nitrogenous BasesNitrogenous Bases

Phosphoric AcidPhosphoric Acid

5-Carbon Sugar5-Carbon Sugar

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 : usually 3 - 7

– Rings are usually formed as opposed to the linear structure

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

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!

Types of Carbohydrates• Monomer = Monosaccharide

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

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

• Polymer = Polysaccharide = many monosacc.s joined– 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?Why does this matter?

Polysaccharides in Plants vs. Animals

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

Glucagon

Recap…

• What is the main function of a carbohydrate?• What is the general name of the monomer for

a carbohydrate? • What is the most important, specific

monomer of carbohydrates?• What is an isomer? Give an example.• Challenge Q: Why do isomers matter?

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

& Cell membrane structure• Structure: Made of C, H, O

– No definite ratios

• 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)

Triglyceride

Glycerol

Fatty acid

Saturated

Fatty acid

Saturated

Fatty acid

Unsaturated

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

• 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

Recap

• What are 2 functions of lipids?• What atoms are in a lipid?• What is the difference between saturated and

unsaturated fat?– Which one is being banned by cities &

manufacturers for the health of the nation?

• What does amphipathic mean? What lipid fits this description?

Proteins• Fxn: control reactions (enzymes), regulate cell

processes, structure (tissues, bones, muscles), transport & help fight disease

• 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

20 Possible R groups (red)

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

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

Protein Structure• Primary structure

– Amino acids bond forming polypeptide chain

• Secondary structure– folds or twists & held by H bonds

• Tertiary Structure– More complex folding: globular (“blobby”)– Usually b/c of hydrophobicity

• Quaternary Structure– Multiple structures folded together

• This is important because the funky shapes create enzyme ‘pockets’ that are specific to a job

Causes of DenaturationChange in protein conformation/shape1. Temperature:

– Increase will cause bonds to twist too much (lose shape); decrease slows everything down

2. pH– Not enough “hydrogens” in surrounding messes

up the ionic attractions and repulsions that make structure

3. Salt Concentration- Same as pH – too many ions (+ or - ) will change the

folded shape

Recap…

• What is the monomer of a protein?• What element is in a protein that is not in a

sugar or a fat?• Describe the 4 levels of folding.• Name 3 things that can change protein shape.

– What is the name for that?

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

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

guanine)

• MONOMER: Nucleotide• POLYMER: DNA (deoxyribonucleic acid)

or RNA (ribonucleic acid)

Nucleotides:Connect with Hydrogen Bonds

Recap…

• What are the two types of nucleic acids?• What are the atoms in a nucleotide?

• We’ll study nucleic acids more in the future, when we study genetics.

So why do these macromolecules matter to life?

Studying Reactions

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!

What are two very famous biological equations?

Types of Reactions• Hydrolysis

– Break apart monomers– 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

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

• Technical note: This is truest for biological complex molecules

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

DIGESTION

EXOTHERMIC

RELEASE E

BREAK BONDS

CELL RESPIRATION

ANABOLISM

DEHYDRATION SYNTHESIS

ENDOTHERMIC

STORE E

MAKE BONDS

REDUCTION

Small Molecules

Big

Molecules METABOLISM

Condensation Reaction

Recap…

• Do Hydrolysis reactions make polymers or monomers?

• What is a condensation reaction?• What’s the difference between endergonic

and exergonic?

Are these Organic? Why/why not?

Match the Elements (Left) with Molecules (Right)

• Nitrogen• Carbon• Hydrogen• Oxygen• Phosphorus• Sulfur

a. Glucoseb. Proteinsc. Starchd. Fatse. Nucleic acidsf. All of the above