Welcome to BI 212, Summer 2010

Lecture 1 Outline (Ch. 3, 4, 5)

I. Chemical Bonds and Shape

II. Water Molecules

III. Chemical Reactions

IV. Organic Chemistry – Carbon-based molecules

V. Macromolecules

A. Carbohydrates

B. Lipids (NOT TRUE POLYMERS)

C. Proteins

D. Nucleic Acids

VI. Lecture Concepts

Chemical properties – all about shape

• water • methane

• electronegativity: attraction of e- by atom

• non-polar = e- shared equally

• polar = e- unequal

• bonds can differ in polarity

Chemical Bonds - Covalent

• electronegativity so unequal, e- stripped

• Example: sodium chloride

Chemical Bonds - Ionic

• H atom (covalent bond), attracted to electronegative atom

• between like or unlike molecules

Chemical Bonds - Hydrogen

75% water

70-95% water

Water – chemical properties

• Cohesion – tendency of molecules to stick to each other

• Adhesion – “ ” to stick to surrounding

H2O Hg

Water – chemical properties

• Surface tension

• Capillary action

δ-

δ+δ+

- dissolve anything polar or ionic (salt, proteins)

Water – chemical properties

- poor solvent for non-polar substances (butter, cell membranes)

• hydrophilic – attracted to water

• hydrophobic – repelled by water

Water – chemical properties

• less dense when solid (ice)

• high specific heat - insulating

Water – chemical reactions

Other chemical reactions

CO2 + H2O + light C6H12O6 + O2

Carbon – history of organic compounds

• historically - compounds divided by burn/won’t burn

• early 18th century -

living – wood, fat, oil

non-living – water, rocks

living - organic

non-living - inorganic

• “vital force” – needed to make inorganic organic

Carbon – history of organic compounds

• Friedrich Wölher - 1820s

- heated ammonium cyanate

-made urea(organic compound in urine)

• 19th century - chemists – increasingly complex molecules

• Stanley Miller - 1953

- amino acids from inorganic gasses

Carbon isomers

• Isomers = same molecular formula, different shape

C4H10 C4H10

butane isobutane

• Organic compounds all contain carbon- vary atoms with which carbon bonds- vary shape/structure of molecules

Carbon isomers

Carbon – functional groups

1. Hydroxyl (-OH)

2. Carboxyl (-COOH)

4. Amino (-NH2)

5. Sulfhydryl (-SH)

-

-

3. Phosphate (-PO42-)

• functional groups – common atom combinations, reactions

6. Methyl (-CH3)

Self-Check

Which functional groups are present in the following molecule?

HO

C

O

C

C C

N

H

H

OHH

HH

Which are not present ?

1. Hydroxyl (-OH)

2. Carboxyl (-COOH)

4. Amino (-NH2)

5. Sulfhydryl (-SH)

-

-

3. Phosphate (-PO4

2-)6. Methyl (-CH3)

Macromolecules

Macromolecules = giant molecules

Four biological classes:

Synthesis –

Monomers (single units) joined into polymers (multi-unit)

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

Dehydration synthesis = remove H2O, new bond

Hydrolysis = add H2O, break bond

Macromolecules

Carbohydrates

1. Carbohydrates – sugars and sugar polymers

Carbohydrates1. Carbohydrates

• Monosaccharide – simplest sugar molecule

- multiple of CH2O

-hexose – 6 C

-Glucose

-pentose – 5

-Ribose

• In water, sugars = rings

• C @ each cornerglucose

Carbohydrates

• joined by dehydration synthesis

glycosidic bond

Carbohydrates

• Polysaccharide – 100s – 1000s of monosaccharides

Carbohydrates

Two purposes:

Storage:

- plants – starch

- animals – glycogen

Structure:

- plants – cellulose

- (animals – chitin)

Carbohydrates - storage

Animal storage - glycogen

Plant storage - starch

Carbohydrates - structure

α glucose β glucose

starch celluose

digestible (humans) indigestible (humans)

Carbohydrates

2. lipids – fats, phospholipids, steroids

• hydrophobic

• not made of monomers

i. fats – glycerol + fatty acid by dehydration – ester bond

fat molecule:

-one glycerol, 3 f.a. aka triglyceride

Lipids

• saturated fats – all C bonded to as many H as possible

• unsaturated fats – at least one C with fewer H

Lipids

ii. phospholipids – glycerol + 2 f.a. + phosphate + choline

• lipid bilayer

Lipids

iii. steroids (some) – C skeleton 4 fused rings

cholesterol

estradiol

testosterone

Lipids

cortisol

3. proteins – string of amino acids

• very diverse group of macromolecules

Proteins

1) Catalyze Chemical Reactions (e.g. amylase) 2) Structure

(e.g. keratin)

3) Energy Storage (e.g. albumin)

4) Transport (e.g. hemoglobin)

5) Hormones (e.g. insulin)

7) Movement (e.g. muscle fibers)

6) Poisons (e.g. venom)

• monomer – amino acid

• polymer – polypeptide

• joined by dehydration

• peptide bond

Proteins

Proteins – amino acids (a.a.)

Carboxyl (-COOH)Amino (-NH2)

amino terminus (N)

carboxy terminus (C)

Structure of an amino acid

Alpha C

Amino group

Carboxyl group

“R” group – changes

Proteins

Carboxyl (-COOH)

Amino (-NH2)?

Proteins – amino acids (a.a.)

20 different a.a.

• non-polar

• polar

• charged

“R” group different

Classes:

mature proteins - processed, folded

Proteins

ii. Secondary – coiled and folded (sheet or helix)

*determined by amino-carboxyl H-bonds

N

C

Proteins

Four levels of protein structure:

i. Primary – unique sequence of a.a.

*determined by peptide bonds

Four levels of protein structure:

iii. Tertiary – regions linked

*determined by R-group H-bonds

iv. Quaternary – >1 protein

*determined by protein-protein interaction

Proteins

sickle cell normal cell

Proteins

Alterations to protein structure:

• mutations – Ex. sickle cell anemia

• environment – pH, temp, chemicalsEx. hair perm

• denatured – unfolded proteins- Sometimes reversible, usually not

Biomolecules

Self-CheckSpecific Molecule

Which Biomolecule Group?

Building blocks/ Monomers?

Joining Bond?

Biological Function?

CELLULOSE

FAT

STARCH

STEROID -----

GLYCOGEN

PHOSPHO-LIPID

PROTEIN

DNA

RNA

Which term includes all others in the list?

a. Monosaccharide

b. Glycogen

c. Starch

d. Carbohydrate

e. Polysaccharide

Which of the following is NOT a protein?

a. Hemoglobin

b. Cholesterol

c. A keratin molecule

d. An enzyme

e. Insulin

Self-Check

Relationship of DNA to RNA, Proteins

DNA

RNA

Proteins

Relationship of DNA to RNA, Proteins

DNA – macromolecule; 4. Nucleic Acids

• Two types:

i. DNA – deoxyribonucleic acid

ii. RNA – ribonucleic acid

· RNA – copy of gene, directions for protein synthesis

· DNA – nucleus, contains genes

Nucleic acids

• Monomer – nucleotide • Polymer – nucleic acid

• Ends different,

5’ end –

PO42- on C#5

3’ end –

OH group on C#3

Nucleic acid - structure

a. pentose sugarb. nitrogenous base

c. phosphate group

Nucleic acids

OH

• Monomers - dehydration

• Bond formed – phosphodiester bond

Nucleic acid - formation

H

Nitrogenous bases:

- two types – pyrimidines & purines

- cytosine (C)

- thymine (T)

- uracil (U)

UU- adenine (A)

- guanine (G)

Pentose sugars:

- deoxyribose & ribose

DNA

RNA

(DNA) (RNA)

Nucleic acid - components

* *

*

*

*

*

*

*

* *

• “backbone” - PO4 and sugars

• nitrogenous bases - on sugar

• polymer = nucleic acid strand

DNA – two strands

RNA – one strand

Nucleic acid - comparisons

5’

3’5’

3’

• DNA - antiparallel

Nucleic acids

• double helix

• Hydrogen bonds

– base to paired base

• Covalent bonds

- sugars to phosphates

- bases to sugars

Self-Check

DNA RNA

• double stranded • single strand

• •

• •

• •

• •

• •

• •

# strands

Sugar name

Bases used

Function

Backbone

H-bonds?

Covalent bond locations?

Nucleic acid – Comparisons

Lecture 1 Concepts- Discuss properties of water and explain using its structure

- Define the term ‘organic’ according to biochemistry

- Name the six functional groups and draw each one

- Recognize and explain dehydration synthesis and hydrolysis

- Compare and contrast glycogen, starch, and cellulose

- Explain how fats/oils, phospholipids, & steroids are different

- List and recognize the four levels of protein structure – explain what determines each level

- Draw a generalized amino acid (example p.78) & explain how protein primary structure is determined

- Draw a generalized nucleotide – this makes up what molecule(s)?- Discuss how the two ends of a DNA strand are different and what is

meant by ‘antiparallel’

- List four types of macromolecules, including monomer, polymer, examples, bond type

- Write out a list of new terminology and provide descriptions