Biochemistry – PPT #2Biochemistry – PPT #2

Organic Compounds Organic Compounds – the substances of – the substances of

life…life…

CarbonCarbon Presence of C determines “organic”Presence of C determines “organic”

Carbon forms the structural Carbon forms the structural backbone of organic molecules – backbone of organic molecules – likes to SHARE electrons in covalent likes to SHARE electrons in covalent bonds…bonds…

Monomers, Polymers, and Macromolecules

• Monomers: repeating units that serve as building blocks for polymers

(there are many different monomers – depends on the organic compound!)

• Polymers: long molecule consisting of many similar or identical building blocks

linked by covalent bonds

• Macromolecules: groups of polymers

covalently bonded

Carbohydrates, Lipids, Proteins, Nucleic Acids

How do the monomers link How do the monomers link up/break back into monomers?up/break back into monomers?

Condensation reactionCondensation reaction (specifically, (specifically, dehydration synthesisdehydration synthesis): ):

two molecules covalently bond and two molecules covalently bond and lose lose a water molecule in the processa water molecule in the process

(This TAKES ENERGY TO DO!!! -- endothermic)(This TAKES ENERGY TO DO!!! -- endothermic) Hydrolysis:Hydrolysis:

polymers are disassembled to polymers are disassembled to monomers by adding a water molecule monomers by adding a water molecule backback

(THIS RELEASES ENERGY!!! -- exothermic)(THIS RELEASES ENERGY!!! -- exothermic)

(ex. Digestion of food)(ex. Digestion of food)

How can there be SO many different polymers when the number of

monomers is limited???

• ARRANGEMENT: variation in the linear sequence

(think of the number of words possible from our 26 letter alphabet…)

• Molecular logic of life is simple but elegant – and ORDERLY!!!

• Where do we get the info to put things together?

4 categories of Macromoleculesand their

Building Blocks (are in GREEN below!)

• Carbohydrates – made up of linked monosaccharides

• Lipids -- CATEGORY DOES NOT INCLUDE true POLYMERS

(grouping based on insolubility)*Triglycerides – made up of glycerol and 3

fatty acids*Phospholipids -- made up of phosphate

head and 2 fatty acid tails*Steroids – made up of ring structures

• Proteins – made up of amino acids

• Nucleic Acids – made up of nucleotides

CarbohydratesCarbohydrates

Are one type of Are one type of NutrientNutrient -- -- chemicals in foods that cells needchemicals in foods that cells need

Are the best source of Are the best source of energyenergy for for the body – quickest if are simple the body – quickest if are simple sugars…sugars…

Are made of Carbon, Hydrogen and Are made of Carbon, Hydrogen and OxygenOxygen

3 types of Carbohydrates3 types of Carbohydrates

Monosaccharides – simple sugarsMonosaccharides – simple sugars

Disaccharides – double sugarsDisaccharides – double sugars

Polysaccharides – complex sugarsPolysaccharides – complex sugars

MonosaccharidesMonosaccharides

Simple sugars: Ex. Simple sugars: Ex.

Glucose, Fructose, GalactoseGlucose, Fructose, Galactose

All have the same chemical formula All have the same chemical formula but they have different structures – but they have different structures – called called ISOMERSISOMERS because of this… because of this…

ALL are CALL are C66HH1212OO66

When diabetics test their blood, they test for the monosaccharide,glucose

Glucose, Fructose, GalactoseGlucose, Fructose, Galactose

Glucose: Glucose: *made during photosynthesis*made during photosynthesis

*main source of energy for *main source of energy for plants and animalsplants and animals

Fructose:Fructose: *found naturally in fruits*found naturally in fruits

*is the sweetest of monosacc*is the sweetest of monosacc

Galactose:Galactose: *found in milk*found in milk

*is usually in association*is usually in association with with glucose or fructoseglucose or fructose

GlucoseGlucoseCC66HH1212OO66

DisaccharidesDisaccharides

CC1212HH2222OO1111

Double sugars: sucrose, maltose, Double sugars: sucrose, maltose, lactoselactose

CC66HH1212OO66

+C+C66HH1212OO66

CC1212HH2424OO1212 – H – H220= 0= CC1212HH2222OO1111

PolysaccharidesPolysaccharides

Complex sugarsComplex sugars Are found as Are found as storage types storage types or as or as

structural types structural types

Ex. starch, glycogen, celluloseEx. starch, glycogen, cellulose

These are used for LONG TERM ENERGY These are used for LONG TERM ENERGY needs, and if don’t get used, then are needs, and if don’t get used, then are converted to lipids….converted to lipids….

Storage PolysaccharidesStorage Polysaccharides Glycogen:Glycogen: *found in animals*found in animals

*stored in liver and in *stored in liver and in muscle cells (ex. meat)muscle cells (ex. meat)

*glycogen bank is *glycogen bank is depleted within 24 hours depleted within 24 hours – needs replenishing– needs replenishing

Starch:Starch: *found in plants*found in plants

*stored in roots and stems *stored in roots and stems Ex. potatoEx. potato

Structural PolysaccharidesStructural Polysaccharides

Cellulose:Cellulose: **major component major component of of plant cell wallsplant cell walls

*most abundant organic *most abundant organic compound on compound on

EarthEarth

*polymer of glucose*polymer of glucose

Structural Polysaccharides (con’t)Structural Polysaccharides (con’t)Chitin:Chitin: makes up the exoskeleton of makes up the exoskeleton of

insectsinsects

Mono, Di, or Polysaccharide?Mono, Di, or Polysaccharide?

Chemical Identification of Carbohydrates

• Benedict’s Test: Identifies the presence of a MONOSACCHARIDE by changing from blue to orange in the presence of heat

• Iodine Test : Identifies the presence of a POLYSACCHARIDE by changing from yellow to purple/black

When compare the first two and get NO reaction:• Process of Elimination: If there is no reaction

with either the Benedict’s or Iodine Tests, then a DISACCHARIDE is present.

LipidsLipids

Are used for Are used for energy storage energy storage andand insulation in the body insulation in the bodyInsolubleInsoluble (does not break down) in water, (does not break down) in water, SolubleSoluble (breaks down) in organic solvents (breaks down) in organic solventsWaterproofWaterproof (hydrophobic) (hydrophobic)Are a component of the cell membrane – phospholipid bilayerAre a component of the cell membrane – phospholipid bilayer

Are made of Carbon, Hydrogen, and OxygenAre made of Carbon, Hydrogen, and OxygenIncludes waxes and certain pigments, tooIncludes waxes and certain pigments, too

Lipid Structure -- TriglyceridesLipid Structure -- Triglycerides Lipid molecules that are made Lipid molecules that are made

up of 3 fatty acids and 1 up of 3 fatty acids and 1 glycerolglycerol

Types of TriglyceridesTypes of TriglyceridesSaturated fats vs. unsaturated fats

•Saturated:

•single bonds only

•Ex: butter, steak (usually animal fats)

•solid at room temp

•Unsaturated

•double/triple bonds•olive oil,corn oil (usually plant fats)

•liquid at room temp

Examples of saturated and unsaturated fats and fatty acids 

An important cellular lipid• The outer

membrane of all cells is made of a…

• phosphoLIPID BILAYER

Another lipid -- SteroidsAnother lipid -- Steroids

Cholesterol Cholesterol – found in cell – found in cell membranes of animalsmembranes of animals

is an originator from which other is an originator from which other steroids may be synthesized steroids may be synthesized

if is found in high levels in the blood, if is found in high levels in the blood, contributes to atherosclerosiscontributes to atherosclerosis

Many hormones are steroids – sex Many hormones are steroids – sex hormoneshormones

Cholesterol in cell membrane

Chemical ID of Lipids

• Translucence Test – lipids leave a semi-transparent spot on brown paper

• Solubility Test – Lipids are insoluble in water, but soluble in an organic solvent such as alcohol or lighter fluid

----------------we will only do the first two!---------------

• Sudan III Test – Lipids will stain red in the presence of Sudan III

ProteinsProteins Proteins control the rate of Proteins control the rate of

reactions and regulate cell reactions and regulate cell processes. processes.

(Ex. enzymes are proteins)(Ex. enzymes are proteins)

Proteins are used to form bones Proteins are used to form bones and musclesand muscles

Proteins transport substances Proteins transport substances into or out of cells or help to fight into or out of cells or help to fight diseasedisease

Building blocks for Proteins: Building blocks for Proteins:

amino acidsamino acids

General structure of amino acid

• All differ in the R-group • The physical and chemical properties of the R-group

determine the characteristics of the amino acid.

COOHNH2

H

RR

Nonpolar, Polar, and Electrically Charged

Amino Acids join…

• Carboxyl group of one is adjacent to amino group of another, dehydration synthesis occurs, forms a covalent bond –

PEPTIDE BOND• When repeated over and over, get a

polypeptide• On one end is an N-terminus (amino end);

On other is a C-terminus (carboxyl end)

Figure 5.16 Making a polypeptide chain

Protein StructureProtein Structure

There are four levels of structure in a proteinThere are four levels of structure in a protein primary structure of proteinprimary structure of protein

*chain of amino acids*chain of amino acids Secondary structureSecondary structure

*alpha helix and beta pleated sheet*alpha helix and beta pleated sheet Tertiary structureTertiary structure

*interactions between groups*interactions between groups Quaternary structureQuaternary structure

*groups of polypeptides bond*groups of polypeptides bond

Figure 5.24 Review: the four levels of protein structure

Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein

Figure 5.23 The quaternary structure of proteins

What determines Protein configuration…

• Polypeptide chain of given amino acid sequence can spontaneously arrange into

3-D shape• Configuration also depends on physical and

chemical conditions of protein’s environment

(if pH, salt [ ], temp, etc. are altered, protein may unravel and normal shape –

denaturation

Figure 5.25 Denaturation and renaturation of a protein

Collagen denaturation….

Fire burnAcid burn

Chemical Tests for Protein ID

• For a liquid:

Biuret Reagent Test:solutions containing a protein will

turn lavender/purple when combined with blue Biuret Reagent

• For a solid:

Xanthoproteic Test:solids (that are light in color) will turn

yellow when exposed to nitric acid

Chemical Reactions and Chemical Reactions and EnzymesEnzymes

Chemical ReactionChemical Reaction- a process that changes one - a process that changes one set of chemicals into anotherset of chemicals into another– Involves breaking bonds and forming new onesInvolves breaking bonds and forming new ones

Photosynthesis: COPhotosynthesis: CO2 2 + H+ H22O O C C66HH1212OO6 6 + O+ O22

Energy is usually absorbed or released in a Energy is usually absorbed or released in a reactionreaction

Reactants Products

Chemical Reactions and Chemical Reactions and EnzymesEnzymes

Activation energyActivation energy-- energy needed to get a energy needed to get a reaction startedreaction started

CatalystCatalyst – A substance – A substance that speeds up the rate of a that speeds up the rate of a chemical reactionchemical reaction

EnzymesEnzymes are proteins that are proteins that act as act as biologicalbiological catalystscatalysts (speed up (speed up a reaction)a reaction)

Chemical Reactions and Chemical Reactions and EnzymesEnzymes

Enzymes speed up a reaction by lowering the Enzymes speed up a reaction by lowering the activation energy of a reactionactivation energy of a reaction

Enzymes act as a site of a reaction and are not Enzymes act as a site of a reaction and are not used upused up

Called theInduced Fit model of activity – shape of enzyme changes slightly to “fit” the proper substrate, builds or breaks bonds

• How Enzymes Work

Remember:

• What happens if the environment changes?

If the pH, salt concentration, or temp are too

much for the enzyme, it will denature or start to fall apart – can’t function any longer!

Fig. 8-19

(a) Normal binding (c) Noncompetitive inhibition(b) Competitive inhibition

Noncompetitive inhibitor

Active siteCompetitive inhibitor

Substrate

Enzyme

What would happen if another molecule blocked the active site?

If the substrate can’t get to the active site, then the the enzyme can’t do its job!!!

Nucleic AcidsNucleic Acids

Store and transmit hereditary or Store and transmit hereditary or genetic informationgenetic information– (RNA and DNA)(RNA and DNA)– RNA- ribonucleic acidRNA- ribonucleic acid– DNA- deoxyribonucleic acidDNA- deoxyribonucleic acid

DNA has a double helix structureDNA has a double helix structure

DNA

Nucleic Acid StructureNucleic Acid Structure

Nucleic Acids are Nucleic Acids are made up of made up of nucleotidesnucleotides bonded bonded together together (phosphodiester bond)(phosphodiester bond)

NucleotidesNucleotides consist consist of 3 partsof 3 parts– 5-carbon sugar5-carbon sugar– A phosphate groupA phosphate group– And a nitrogenous baseAnd a nitrogenous base

(the bases are A,T,C,G)(the bases are A,T,C,G)

Nucleic AcidsNucleic Acids Exist as 2 types : DNA and RNAExist as 2 types : DNA and RNA

*DNA -- *DNA -- *double stranded (entire code)*double stranded (entire code)*sugar is deoxyribose*sugar is deoxyribose*never leaves nucleus*never leaves nucleus*bases are A,T,C,G*bases are A,T,C,G*involved in replication and *involved in replication and protein synthesisprotein synthesis

*RNA --*RNA -- *single stranded (partial code)*single stranded (partial code)*sugar is ribose*sugar is ribose*mobile – nucleus and *mobile – nucleus and

cytoplasmcytoplasm*bases are A,U,C,G*bases are A,U,C,G*involved in Protein Synthesis*involved in Protein Synthesis

Replication of DNAReplication of DNA

Making an EXACT copy of the original Making an EXACT copy of the original DNA to put in a new cell… happens DNA to put in a new cell… happens ONLY in the nucleusONLY in the nucleus

Protein Synthesis –Protein Synthesis –

Using the DNA code to put together amino Using the DNA code to put together amino acids to make proteins; needs info from acids to make proteins; needs info from DNA in nucleus, and uses RNA to assemble DNA in nucleus, and uses RNA to assemble in the cytoplasmin the cytoplasm

Organic Macromolecules

include

that consist of

which contain

that consist of that consist of that consist of

which contain which contain which contain

Organic Macromolecules

include

that consist of

which contain

that consist of that consist of that consist of

which contain which contain which contain

Carbohydrates Lipids Proteins Nucleic Acids

MonosaccharidesSEVERAL POLYMERS Amino Acids Nucleotides

C,H,O

(~1:2:1)

C,H,O

(but MUCH less O)

C,H,O,N C,H,O,N,P