The Molecules of Cells… dun dun dahhhhh – ch 3

Organic chem -

Carbon – most versatile building block – why?

Tetravalence –

Where does the C in your body come from?

Valences of common atoms in orgs

What is the bonding capacity of H?What is the bonding capacity of O?What is the bonding capacity of N?What is the bonding capacity of C?

Which of these would be improperly bonded?

Variation in C skeletons contributes to diversity of organic molecules

Straight, branched, closed rings, some have double bonds, triple

Isomers• molecules w/ same molecular formula (same

number and kinds of atoms) but diff atom arrangements (which atoms are attached to which and how)

Classes of isomers: structural, geometric, enantiomers

Geometric isomers = share same covalent partnerships, but differ in their spatial arrangements.• Result from fact that double bonds will not allow the atoms they join to rotate freely about the axis of the bonds.• Subtle differences affects biological activity.

 

• Enantiomers = mirror images of each other.• Can occur when 4 diff atoms or groups of atoms are

bonded to the same carbon (asymmetric carbon).• 2 diff spatial arrangements of the four groups around

the asymmetric carbon. These arrangements are mirror images.

• Usually one form is biologically active and its mirror image is not.

How many asymmetric carbons are present?

Functional Groups• contribute to molecular

diversity of life• frequently bonded to

carbon skeleton of organic molecules.

• Have specific chemical and physical properties.

• Are the regions of organic molecules which are commonly chemically reactive.

• Behave consistently from one organic molecule to another.

• Depending upon their number and arrangement, determine unique chemical properties of organic molecules in which they occur.

Hydroxyl

- OH• polar group• Conveys water solubility • Organic compounds with hydroxyl groups are called

alcohols.

Carbonyl Group-C=O• polar group• Conveys water solubility.• found in sugars.• at the end of skeleton called aldehyde.• at the middle of skeleton called ketone  

Carboxyl Group• polar group • Conveys water solubility • Since it donates protons, has acidic properties. • Compounds w/ this group are called carboxylic acids.

Amino Group

• polar group • Conveys water solubility• Acts as weak base. The unshared pair of electrons on

the nitrogen can accept a proton, giving it a +1 charge.• Organic compounds w/ this group are called amines.

Sulfhydryl Group• Help stabilize the structure of proteins. • Organic compounds with this functional group are

called thiols.

What other functional groups do you see in this molecule?

Could this molecule have an enantiomer isomer? How do you know?

Phosphate Group• Loss of two protons leaves phosphate group w/ a -

charge.• Has acid properties since it loses protons.• Polar group • Conveys water solubility• Important in cellular energy storage & transfer

Methyl Group

• Non polar• Conveys hydrophobic properties

Macromolecules, baby!

CarbsLipidsProteinsNucleic acids

Some basics

Polymer – long molecule consisting of many similar or identical building blocks linked by covalent bonds

Monomer -

How do the bonds b/t monomers form?Condensation rx or dehydration synthesis – removal of

water from monomersFacilitated by enzymes – speed up the rx

How do the bonds b/t monomers break?

Hydrolysis – bonds broken by addition of water Hydro = waterLysis = breakEx: digestionEnzymes facilitate

Diversity of macromolecules

26 letters make many words40-50 monomers make many macromoleculesKey is in arrangement of monomers

Tac Act Cat

Carbohydrates • Function – fuel & building mat.• Sugars & their polymers• simplest are monosaccharides or simple sugars.• Disaccharides (double sugars) consist of 2 monosaccharides

joined by condensation reaction.• Polysaccharides - polymers of many monosaccharides.

monosaccharides• some multiple of the unit CH2O.• Ex: glucose = C6H12O6.• Funcitonal groups: carbonyl group (>C=O) and multiple hydroxyl

groups (—OH).• names end in -ose.•

Diversity of monosaccharides• classified by # of carbon atoms in skeleton (3-7)• Some are enantiomers of each other - spatial

arrangement of their parts around asymmetric C atoms.

Structural isomers enantiomers

Monosaccharides cont…• most form rings in aqueous solutions.• major nutrients for cellular work.

Disaccharides• glycosidic linkage to form a disaccharide via

dehydration.• Maltose - joining 2 glucose• Sucros- joining glucose & fructose. • Lactose - joining glucose & galactose.

Polysaccharides - storage• Function in storage & structural roles.• 100s – 1000s of monosaccharides joined• Starch - plant storage polysac composed entirely of glucose

monomers.• Plants store surplus glucose as starch granules within plastids,

including chloroplasts & withdraw as needed for E or C.• Glycogen – animal storage polysac. Store 1 day supply in liver

& muscles

Polysaccharides - structural• Cellulose – plant structural polysac - major component of cell walls

– most abundant organic compound on Earth.– Like starch, cellulose is polymer of glucose. However, the glycosidic

linkages in these two polymers differ.– Digestion... Symbiotic orgs

• Chitin – animal structural polysac - found in the exoskeletons of arthropods– also provides structural support for cell walls of fungi.

Lipids• Consist mostly of hydrocarbon• Little – no affinity for H2O (water insoluble)• Not polymers• 3 families

– Fats– Phospholipids– Steroids

Fats• Glycerol & & fatty acid• Dehydration synthesis• Linkage – ester• Vary in length & the # & location of double bonds• Functions:

– E storage– Cushions organs– Insulates body

2 main types of fats1. Saturated – saturated w/ H; no double bonds

– Animal fats– Solid @ room temp… why?– Contribute to arteriosclerosis

Yum!

2 main types of fats2. Unsaturated – not saturated w/ H; has double bonds

Creates kink in shape @ double bondLiquid @ room tempPlants & fishPeanut butter? Why solid?

Phospholipids• 1 glycerol• 2 fatty acids• 1 phosphate group

Phospholipids

• Amphipathic• Major component of cell membranes• Structure determines function

Steroids

• C skeleton consisting of 4 interconnected rings.• Vary based on functional groups• Cholesterol – imp. In membranes of animal cells

– Most other steroids made from it

Proteins!• large • funcitons:

– Structure (silk)– Storage (casein)– Movement (actin &

myosin)– Defense (antibodies)– Regulation of metabolism

(enzymes)– Transport (hemoglobin)– Communication

(hormones)– receptor proteins

basics• Monomer –

amino acids (20 diff)– Vary based on

R groups– Structure of aa– Linkage –

peptide bond– Backbone– Aka

polypeptide

Condensation reaction or dehydration synthesis

Conformation = 3 D shape of a protein molecule

Shape determines functionDNA codes for the type of aa & what order they’re

bonded in So…

DNA codes for which proteins you make & which proteins you make determines your physical characteristics

Proteins are so complex that we

describe their structure on 4

levels

1. Primary structure• the seq of aa• Det by DNA• Sanger, insulin

Notice primary structure & backbone

Proteins are so complex that we

describe their structure on 4 levels

2) Secondary structure• Pattern of folds &

coils that result from the H-bonding at regular intervals along the polypeptide backbone.

• 2 types: alpha helix & pleated sheet

Proteins are so complex that we

describe their structure on 4 levels

3) Tertiary structure• Irregular contortions

that result from bonding b/t R groups of the aa

• Types of bonds that can occur b/t R groups:– H-bonds, disulfide

bridges, ionic, hydrophobic interactions

Proteins are so complex that we

describe their structure on 4

levels

4) Quaternary structure

• Only those composed of 2 or more polypeptide chains

• Overall structure that results from the aggregation of polypeptide chains

Emergent property?

Specific function of a protein arises from the architecture of the molecule

Denaturation?• Loss of conformation of a protein• Causes? High temps, change in salt concentration,

change in pH

Review of levels

•Deoxyribonucleic acid (DNA) & RNA•Double helix•Watson and Crick—1953•Made of smaller molecules called nucleotides bonded together

Nucleic Acids

Relationship between DNA & chromosomes?

Chromosomes are made of DNA!

Monomers are nucleotides

5 Different ones • Deoxyribose: sugar molecule• Phospahte group: a phosphorus atom surrounded by oxygen• Nitrogen containing base: molecule containing nitrogen

adenine (A)guanine (G)cytosine (C)thymine (T)

Dehydration synthesis & then H-bonds b/t N bases

Complementary Base Pairing

• Cytosine - Guanine• Adenine - Thymine• Connected by H-bonds• Allows DNA to make exact

copies of itself

DNA REPLICATION

http://www.lewport.wnyric.org/jwanamaker/animations/DNA%20Replication%20-%20long%20.html

Complementary Base Pairs

• TTACGGCAT base pair would be????

DNA & RNA

DNA & RNA Compared

DNA RNA

Sugar deoxyribose ribose

Strands double single

Bases A,G,C,T A,G,C,U

(uracil)

Notice the difference between

the 2 sugars?

Sugar in DNA

Sugar in RNA

How is DNA the code for life?• Gene – portion of DNA that codes for the making

of polypeptide (protein) • What makes you unique is all the particular

proteins you make.