Basic Basic BiochemistryBiochemistry

Water, Carbon, and Water, Carbon, and Functional GroupsFunctional Groups

WaterWater

Abundance of Abundance of water makes Earth water makes Earth habitablehabitable

Unique propertiesUnique properties

Water MoleculesWater Molecules

Polar due to Polar due to differences in differences in electronegativityelectronegativity

Hydrogen bonds Hydrogen bonds formform

Properties of WaterProperties of Water

CohesionCohesion AdhesionAdhesion Surface tensionSurface tension

Properties of WaterProperties of Water

(What is (What is temperature?)temperature?)

High specific heatHigh specific heat Evaporative Evaporative

coolingcooling Good solventGood solvent

Interactions with WaterInteractions with Water

Hydrophilic vs. Hydrophilic vs. hydrophobichydrophobic

CarbonCarbon

Can bond to 4 Can bond to 4 other atomsother atoms

Carbon chains can Carbon chains can be long, be be long, be branched, or be branched, or be circularcircular

Hydrocarbon Hydrocarbon chainschains

Functional GroupsFunctional Groups

Most commonly Most commonly involved in involved in reactionsreactions

Types:Types: Hydroxyl, carbonyl, Hydroxyl, carbonyl,

carboxyl, amino, carboxyl, amino, sulfhydryl, and sulfhydryl, and phosphatephosphate

Chart pg. 64-65Chart pg. 64-65

ATPATP

Adenosine triphosphate used for energy Adenosine triphosphate used for energy transfertransfer

ADP + PADP + Pii ↔ ATP↔ ATP

MacromoleculesMacromolecules

ReviewReview

What are the four essential What are the four essential macromolecules in the cell?macromolecules in the cell?

What are their structures?What are their structures? What are their functions?What are their functions?

MacromoleculesMacromolecules

Can be 10,000s of atomsCan be 10,000s of atoms Polymers: linked chain of monomersPolymers: linked chain of monomers Variation in sequence is major Variation in sequence is major

differencedifference

Dehydration SynthesisDehydration Synthesis

Removal of water Removal of water to link two to link two monomersmonomers

Requires energy Requires energy and help of and help of enzymesenzymes

Hydrolysis breaks Hydrolysis breaks bonds (ex. bonds (ex. Digestion)Digestion)

CarbohydratesCarbohydrates

Sugars and their Sugars and their polymerspolymers

Mono-, di-, and Mono-, di-, and polysaccharidespolysaccharides

Monosaccharides (Monosaccharides (--oseose) can have three-) can have three-seven carbonsseven carbons

Chain or ring formsChain or ring forms

CarbohydratesCarbohydrates

Glucose (CGlucose (C66HH1212OO66) and Sucrose (C) and Sucrose (C1212HH2222OO1111) ) are most commonare most common

Polysaccharide uses: storage or structurePolysaccharide uses: storage or structure

CarbohydratesCarbohydrates

Starch = helical polymer of glucose (in Starch = helical polymer of glucose (in plants)plants)

Glycogen = more branched; stored in Glycogen = more branched; stored in liver/muscle cellsliver/muscle cells

Cellulose = most abundant organic Cellulose = most abundant organic compoundcompound

Never branched. Hydrogen bonding to nearby Never branched. Hydrogen bonding to nearby cellulose molecules. Microfibrils are structurally cellulose molecules. Microfibrils are structurally strong.strong.

Chitin = fungi structures; exoskeletonsChitin = fungi structures; exoskeletons

LipidsLipids

Fats, steroids, Fats, steroids, phospholipidsphospholipids

HydrophobicHydrophobic Fats = glycerol (3-C Fats = glycerol (3-C

alcohol) and 3 fatty alcohol) and 3 fatty acids acids (hydrocarbons)(hydrocarbons) Saturated vs. Saturated vs.

unsaturatedunsaturated Primarily energy Primarily energy

storagestorage

LipidsLipids

Phospholipids = glycerol + 2 fatty acids + Phospholipids = glycerol + 2 fatty acids + phosphatephosphate Partially hydrophilic, partially hydrophobicPartially hydrophilic, partially hydrophobic Lipid bilayer membranesLipid bilayer membranes

LipidsLipids

Steroids = four fused Steroids = four fused ringsrings Cholesterol, many Cholesterol, many

hormoneshormones

ProteinsProteins

Most structurally Most structurally complexcomplex

See chart pg. 78 for See chart pg. 78 for typestypes

Enzymes catalyze Enzymes catalyze reactionsreactions

20 different amino acids 20 different amino acids combine to create a combine to create a polypeptidepolypeptide

ProteinsProteins

Amino acids linked Amino acids linked through peptide bonds through peptide bonds in unique sequencein unique sequence

Proteins consist of Proteins consist of multiple polypeptidesmultiple polypeptides

Function relies on Function relies on proteins proteins recognizing/bonding to recognizing/bonding to other moleculesother molecules

Protein StructureProtein Structure

PRIMARY: amino PRIMARY: amino acid sequenceacid sequence

SECONDARY: SECONDARY: αα helix or helix or ββ pleated pleated sheet due to sheet due to hydrogen bonding hydrogen bonding of C-N backboneof C-N backbone

Protein StructureProtein Structure TERTIARY: TERTIARY:

interactions between interactions between ‘R’ groups (ionic, ‘R’ groups (ionic, hydrogen bonds, hydrogen bonds, hydrophilic/phobic)hydrophilic/phobic)

QUATERNARY: QUATERNARY: multiple polypeptide multiple polypeptide chains overlappingchains overlapping

Denaturing…Denaturing…

Nucleic AcidsNucleic Acids

DNA/RNADNA/RNA Direct protein Direct protein

synthesissynthesis Nucleotides Nucleotides

polynucleotidespolynucleotides Pyrimidines (T, U, Pyrimidines (T, U,

G) vs. purines (C, G) vs. purines (C, A)A)

Nucleic AcidsNucleic Acids

Antiparallel Antiparallel double helixdouble helix

5’: phosphate5’: phosphate 3’: C-OH3’: C-OH Replication, Replication,

transcription, transcription, translationtranslation

Phosphodiester BondPhosphodiester Bond

OverviewOverview

Higher levels of Higher levels of organization result organization result in new, more in new, more complex properties.complex properties.

The structure of The structure of each each macromolecule macromolecule relates specifically relates specifically to its function.to its function.

Self-Quiz, Self-Quiz, Chapter 5Chapter 5

MacromoleculesMacromolecules

11

Which term Which term includes all others includes all others in the list?in the list?

1.1. MonosaccharideMonosaccharide

2.2. DisaccharideDisaccharide

3.3. StarchStarch

4.4. CarbohydrateCarbohydrate

5.5. PolysaccharidePolysaccharide

22

Which of the Which of the following following statements statements concerning concerning unsaturatedunsaturated fats is true?fats is true?

1.1. They are more common in They are more common in animals than plants.animals than plants.

2.2. They have double bonds I They have double bonds I the carbon chains of their the carbon chains of their fatty acidsfatty acids

3.3. They generally solidify at They generally solidify at room temperature.room temperature.

4.4. They contain more They contain more hydrogen than saturated hydrogen than saturated fats having the same fats having the same number of carbon atoms.number of carbon atoms.

5.5. They have fewer fatty acid They have fewer fatty acid molecules per fat molecules per fat molecule.molecule.

33

The structural The structural level of a protein level of a protein least affected by a least affected by a disruption in disruption in hydrogen bonding hydrogen bonding is theis the

1.1. Primary level.Primary level.

2.2. Secondary level.Secondary level.

3.3. Tertiary level.Tertiary level.

4.4. Quaternary level.Quaternary level.

5.5. All structural All structural levels are equally levels are equally affected.affected.

44

Which of the Which of the following pairs following pairs of base of base sequences sequences could form a could form a short stretch short stretch of a normal of a normal helix DNA?helix DNA?

1.1. 5’-purine-pyrimidine-5’-purine-pyrimidine-purine-pyrimidine-3’ with purine-pyrimidine-3’ with 5’-purine-pyrimidine-5’-purine-pyrimidine-purine-pyrimidine-5’purine-pyrimidine-5’

2.2. 5’-A-G-C-T-3’ with 5’-T-C-5’-A-G-C-T-3’ with 5’-T-C-G-A-3’G-A-3’

3.3. 5’-G-C-G-C-3’ with 5’-T-A-5’-G-C-G-C-3’ with 5’-T-A-T-A-3’T-A-3’

4.4. 5’-A-T-G-C-3’ with 5’-G-C-5’-A-T-G-C-3’ with 5’-G-C-A-T-3’A-T-3’

5.5. 1, 2, and 4 are all 1, 2, and 4 are all correct.correct.

55 Enzymes that Enzymes that

break down DNA break down DNA catalyze the catalyze the hydrolysis of the hydrolysis of the covalent bonds covalent bonds that join that join nucleotides nucleotides together. What together. What would happen to would happen to DNA molecules DNA molecules treated with these treated with these enzymes?enzymes?

1.1. The two strands of DNA The two strands of DNA would separate.would separate.

2.2. The phosphodiester bonds The phosphodiester bonds between deoxyribose sugars between deoxyribose sugars would be broken.would be broken.

3.3. The purines would be The purines would be separated from the separated from the deoxyribose sugars.deoxyribose sugars.

4.4. The pyrimidines would be The pyrimidines would be separated from the separated from the deoxyribose sugar.deoxyribose sugar.

5.5. All bases would be All bases would be separated from the separated from the deoxyribose sugars.deoxyribose sugars.

66

Which of the Which of the following is not a following is not a protein?protein?

1.1. HemoglobinHemoglobin

2.2. CholesterolCholesterol

3.3. An antibodyAn antibody

4.4. An enzymeAn enzyme

5.5. insulininsulin

77

Which of the Which of the following following statements statements about the 5’ about the 5’ end of a end of a polynucleotide polynucleotide strand is strand is correct?correct?

1.1. The 5’ end had a The 5’ end had a hydroxyl group.hydroxyl group.

2.2. The 5’ end has a The 5’ end has a phosphate group.phosphate group.

3.3. The 5’ end is identical The 5’ end is identical to the 3’ end.to the 3’ end.

4.4. The 5’ end is The 5’ end is antiparallel to the 3’ antiparallel to the 3’ end.end.

5.5. The 5’ end is in the fifth The 5’ end is in the fifth position on one of the position on one of the nitrogenous bases.nitrogenous bases.