1

Calling names

• ALKANES

• ALKENES

• ALKYNES

• CYCLO-

• ALKYL-

Cycloalkanes with Side GroupsCH3

CH3

CH3

CH3

CH3

CH3

methylcyclopentane

1,2-dimethylcyclopentane

1,2,4-trimethylcyclohexane

Figure 22.12: Some selected substituted benzenes and their names

Bonding in ethane

CH3-CH3

Bonding in ethylene

CH2=CH2

Bonding in acytyleneCH=CH

2

Cis and Trans Isomers

Double bond is fixedCis/trans Isomers are possible

CH3 CH3 CH3

CH = CH CH = CH

cis trans CH3

isomers

• Structural – chain

• Structural - position

• Structural – function

• Stereo - geometrical

• Stereo - optical

butanemethyl propane

2methylhexane3methylhexane

cistrans

alkan-OL

alkan-AL

alkan-ONE

Amino Acids and Proteins

Types of ProteinsAmino Acids

The Peptide Bond

Amino Acids

• Building blocks of proteins• Carboxylic acid group• Amino group• Side group R gives unique characteristics

R side chainI

H2N—C —COOHIH

Amino Acids as Acids and Bases

• Ionization of the –NH2 and the –COOH group

• Zwitterion has both a + and – charge• Zwitterion is neutral overall

NH2–CH2–COOH H3N–CH2–COO–

glycine zwitterion of glycine

+

3

pH and ionization

H+ OH-

H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–

Positive ion zwitterion Negative ionLow pH neutral pH High pH

+ +

Most Amino Acids Have

Non-Superimposable Mirror ImagesWhat is the exception?

D vs L Alanine

Examples of Amino Acids

HI

H2N—C —COOHIH glycine

CH3I

H2N—C —COOHIH alanine

Types of Amino Acids

Nonpolar R = H, CH3, alkyl groups, aromaticO

Polar llR = –CH2OH, –CH2SH, –CH2C–NH2,

(polar groups with –O-, -SH, -N-)Polar/Acidic

R = –CH2COOH, or -COOHPolar/ Basic

R = –CH2CH2NH2

POLA

RN

ON

-P

OLA

R

Tyr His

Gly

Acidic Neutral Basic

Asp

Glu GlnCys

Asn Ser

Thr Lys

Arg

AlaVal

IleLeu Met

Phe TrpPro

Classification of Amino Acids by Polarity

Polar or non-polar, it is the bases of the amino acid properties.

Juang RH (2003) Biochemistry

4

Nonpolar R groups

ISOPROPYL

Polar R groups.

Polar R groups 20 “standard” amino acids used by cells in protein biosynthesis

Alanine(Ala / A)

Arginine(Arg / R)

Asparagine(Asn / N)

Aspartic acid(Asp / D)

Cysteine(Cys / C)

Glutamic acid(Glu / E)

Glutamine(Gln / Q)

Glycine(Gly / G)

Histidine(His / H)

Isoleucine(Ile / I)

Leucine(Leu / L)

Lysine(Lys / K)

Methionine(Met / M)

Phenylalanine(Phe / F)

Proline(Pro / P)

Serine(Ser / S)

Threonine(Thr / T)

Tryptophan(Trp / W)

Tyrosine(Tyr / Y)

Valine(Val / V)

This information will be available on information sheets provided with the final exam,

If needed

ala arg asn asp cys

gln glu gly his ile

leu lys met phe pro

ser thr trp tyr val20 “Standard” Amino Acids

Essential Amino Acids

• 10 amino acids not synthesized by the body

• arg, his, ile, leu, lys, met, phe, thr, trp, val

• Must obtain from the diet• All in dairy products • 1 or more missing in grains

and vegetables

5

NH2 COOH1 NH2 COOH2

NH2 C N COOHO

H21

Amino acids are connected head to tail

Formation of Peptide Bonds by Dehydration

Dehydration-H2O

Juang RH (2004) BCbasics

H OI ||

H2N—C —COHIH

gly

CH3 OI ||

HN—C —COHI IH H

ala

H OI ||

H2N—C —C —IH

glyala

CH3 OI ||

N—C —COHI IH H

Dipeptide

Peptide Linkage

Peptides• Amino acids linked by amide (peptide)

bonds

Gly Lys Phe Arg Ser

name: GlycyllysylphenylalanylarginylserineSymbol: GlyLysPheArgSerOr: GKFRS

H2N- end -COOH endPeptide bonds

(N-terminus) (C-terminus)

What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

6

Tripeptides possible from one each of leucine, glycine, and alanine

Leu-Gly-AlaLeu-Ala-GlyAla-Leu-GlyAla-Gly-LeuGly-Ala-LeuGly-Leu-Ala

Tripeptide containing glycine, cysteine, and alanine

Source: Photo Researchers, Inc.

Write the three-letter abbreviations for the following tetrapeptide:

H 3 N C HC H 3

CO

NH

C H CO

NH

C H CO

NH

C H C O -OC H

C H C H 3

C H 3

C H 2

S HC H 2

C H 2

SC H 3

Alanine(Ala / A)

Leucine(Leu / L)

Cysteine(Cys / C)

Methionine(Met / M)

Focus Attention on the Side Group

Proteins

• Proteins are sequences of amino acid residues– Amino acid: carbon atom (C), amino group

(NH3),carboxyl group (COOH), variable sidechain (20 different types)

– Amino acids are linked with the peptide bond

• Protein structure:– Primary – sequence of amino acids– Secondary – local 3D arrangement of amino acids– Tertiary – 3D structure of a complete protein– Quaternary – 3D structure of functional protein

(complex)

Types of Proteins

Type Examples• Structural tendons, cartilage, hair, nails• Contractile muscles• Transport hemoglobin• Storage milk• Hormonal insulin, growth hormone• Enzyme catalyzes reactions in cells• Protection immune response

Proteins Vary Tremendously in Size

• Insulin - A-chain of 21 residues, B-chain of 30 residues -total mol. wt. of 5,733

• Glutamine synthetase - 12 subunits of 468 residues each - total mol. wt. of 600,000

• Connectin proteins - alpha - MW 2.8 million!• beta connectin - MW of 2.1 million, with a

length of 1000 nm -it can stretch to 3000 nm!

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Four Levels of Protein Structure

• Primary, 1o

– the amino acid sequence• Secondary, 2o

– Local conformation of main-chain atoms (Φand Ψ angles)

• Tertiary, 3o

– 3-D arrangement of all the atoms in space (main-chain and side-chain)

• Quaternary, 4o

– 3-D arrangement of subunit chains

HIERARCHY OF PROTEIN STRUCTURE

Tertiary

1. 2.

3. 4.

Secondary Structure

• The two most common regular (repetitive) 2˚ structures are:α-helixβ-sheet

• Both use hydrogen bonding between N-H & C=O of peptide group as primary stabilizing force.

Nter

Cter

Helices (1)

Hydrogen bonds: O (i) <-> N (i+4)

The β-strand

Extended chain is flat “Real β-strand is twisted”

N-H---O-CHydrogen bonds

8

Pleated sheetTertiary Structure

• Specific overall shape of a protein• Cross links between R groups of amino acids in

chain

Ionic H-bond Disulfide Hydrophobic H-bond

Figure 22.26: Permanent waving of hairBuilding the Hemoglobin Protein

Figure 2 – 09

Urey/Miller Experiment

Figure 2 – 09

Urey/Miller Experiment

9

Cytoplasm

Nucleus

DNA

DNA is the genetic material within the nucleus.

Central Dogma

RNA

Protein

Replication

The process of replication creates new copies of DNA.

TranscriptionThe process of transcription creates an RNA using DNA information.

TranslationThe process of translation creates a protein using RNA information.

DNA Double Helix-Held Together with

H-Bonds

Base Pairs Double Helix

base: thymine(pyrimidine)

sugar: 2’-deoxyribose

monophosphate

no 2’-hydroxyl

(5’ to 3’)

5’

3’

base:adenine(purine)

1’2’

4’

α

3’ linkage

5’ linkage

Three Components of DNA Structure Pyrimidines used in Base Pairs, DNA

6-membered rings only

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Purines used in Base Pairs, DNA

Fused 5 and 6 member rings

DNA Base Pairing

A-T pairing

2 H-Bonds

G-C pairing

3 H-bonds

A-T and G-C Base Pairs Hold the DNA helices together

A-T and G-C Base Pairs Hold the DNA helices together

A-T and G-C Base Pairs Hold the DNA helices together

A-T and G-C Base Pairs Hold the DNA helices together

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A-T and G-C Base Pairs Hold the DNA helices together

A-T and G-C Base Pairs Hold the DNA helices together

Hydrogen-Bonding’s Role in DNA Structure Transcription• The new RNA molecule is formed by incorporating • nucleotides that are complementary to the

template strand.

DNA coding strand

DNA template strand

DNA

5’

3’

5’

3’

G T C A T T C G G

C A G T A A G C C

G

RNA

5’

GG U C A U U C

3’

# of strands

kind of sugar

bases used

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RNA Polymerase is the Enzyme that Catalyzes Transcription of DNA Information to RNA

DNA (Blue)

Newly Synthesized RNA (Red)

Active Site Metal (Pink)

Bridge Helix Moves DNA through Polymerase during RNA Synthesis (Green)

• The “words” of the DNA “language” are triplets of bases called codons– 3 bases or nucleotides make one

codon– Each codon specifies an amino acid– The codons in a gene specify the amino

acid sequence of a polypeptide

Genetic information written in codons is translated into amino acid sequences

• Virtually all organisms share the same genetic code

• All organisms use the same 20 aa

• Each codon specifies a particular aa

The genetic code is the Rosetta stone of life

Figure 10.8A

• Tryptophan and Methionine have only 1 codon each

• All the rest have more than one

• AUG has a dual function

• 3 stop codons that code for termination of protein synthesis

• Redundancy in the code but no ambiguity

Figure 10.8A

Translation• The process of reading the RNA sequence of an

mRNA and creating the amino acid sequence of a protein is called translation.

Transcription

Codon Codon Codon

Translation

DNA

T T C A G T C A G

DNAtemplatestrand

mRNA

A A G U C A G U C MessengerRNA

Protein Lysine Serine ValinePolypeptide(amino acidsequence)

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Structure of the Heme GroupPorphyrin Ligand

Heme Group Found Bonded to Proteins

Hemoglobin• Multi-subunit protein (tetramer)

– 2 α and 2 β subunits• Heme

– One per subunit– Has an iron atom– Carries O2

• In red blood cells

Sickle Cell AnemiaGenetic Disease

Heterozygous individuals – carriersHomozygous individuals – diseased

HemoglobinFound in red blood cellsCarries oxygen to tissues

SCA Results from Defective HemoglobinHemoglobins stick togetherRed blood cells damaged

Complications from low oxygen supply to tissuesPain, organ damage, strokes, increased infections, etc.

Incidence highest among Africans and IndiansHeterozygotes protected from Malaria

Sickle Cell Hemoglobin

GUG CAC CUG ACU CCU GAG GAG AAGval his leu thr pro glu glu lys1 2 3 4 5 6 7 8

GUG CAC CUG ACU CCU GUG GAG AAGval his leu thr pro val glu lys1 2 3 4 5 6 7 8

Mutation (in DNA)

Normal mRNA

Normal protein

Mutant mRNA

Mutant protein

Glutamate (glu), a negatively charged amino acid, is replaced by valine (val), which has no charge.

Structures of Amino Acids

Glutamic Acid

Polar, AcidicValine

Non-polar, Neutral

14

Glu 6 → Val

A single amino acid substitution in a protein causes sickle-cell disease