Calling names ALKANES ALKENES ALKYNES

Calling names • ALKANES • ALKENES • ALKYNES • CYCLO • ALKYL-

Cycloalkanes with Side Groups

Bonding in ethane CH 3 -CH 3

Bonding in ethylene CH 2=CH 2

Bonding in acytylene CH=CH

Cis and Trans Isomers ¾Double bond is fixed ¾Cis/trans Isomers are possible CH 3 CH = CH cis CH 3 CH = CH trans CH 3

isomers • Structural – chain butane methyl propane • Structural - position 2 methylhexane 3 methylhexane • Structural – function • Stereo - geometrical • Stereo - optical cis trans

alkan-OL alkan-AL alkan-ONE

Amino Acids and Proteins Types of Proteins Amino Acids The Peptide Bond

Amino Acids • • Building blocks of proteins Carboxylic acid group Amino group Side group R gives unique characteristics R side chain I H 2 N—C —COOH I H

Amino Acids as Acids and Bases • Ionization of the –NH 2 and the –COOH group • Zwitterion has both a + and – charge • Zwitterion is neutral overall + NH 2–COOH H 3 N–CH 2–COO– glycine zwitterion of glycine

p. H and ionization H+ + OH- + H 3 N–CH 2–COOH H 3 N–CH 2–COO– H 2 N–CH 2–COO– Positive ion zwitterion Negative ion Low p. H neutral p. H High p. H

Most Amino Acids Have Non-Superimposable Mirror Images What is the exception?

D vs L Alanine

Examples of Amino Acids H I H 2 N—C —COOH I H glycine CH 3 I H 2 N—C —COOH I H alanine

Types of Amino Acids Nonpolar R = H, CH 3, alkyl groups, aromatic O Polar ll R = –CH 2 OH, –CH 2 SH, –CH 2 C–NH 2, (polar groups with –O-, -SH, -N-) Polar/Acidic R = –CH 2 COOH, or -COOH Polar/ Basic R = –CH 2 NH 2

Classification of Amino Acids by Polarity NONPOLAR Acidic Neutral Basic Asp Asn Ser Arg Cys Tyr His Gln Thr Lys Glu Gly Ala Ile Phe Trp Val Leu Met Pro Polar or non-polar, it is the bases of the amino acid properties. Juang RH (2003) Biochemistry

Nonpolar R groups ISOPROPYL

Polar R groups.

Polar R groups

20 “standard” amino acids used by cells in protein biosynthesis Alanine (Ala / A) Glutamic acid (Glu / E) Leucine (Leu / L) Serine (Ser / S) Arginine (Arg / R) Glutamine (Gln / Q) Aspartic acid (Asp / D) Glycine (Gly / G) Lysine Methionine (Lys / K) (Met / M) Threonine (Thr / T) Asparagine (Asn / N) Histidine (His / H) Phenylalanine (Phe / F) Cysteine (Cys / C) Isoleucine (Ile / I) Proline (Pro / P) Tryptophan Tyrosine Valine (Trp / W) (Tyr / Y) (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 val 20 “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

Formation of Peptide Bonds by Dehydration Amino acids are connected head to tail NH 2 1 COOH NH 2 2 COOH Dehydration -H 2 O O NH 2 1 C N H 2 COOH Juang RH (2004) BCbasics

H O I H 2 N—C —COH I H gly CH 3 O I HN—C —COH I I H H ala Peptide Linkage H O CH 3 O I H 2 N—C —C —N—C —COH I I I H H H glyala Dipeptide

Peptides • Amino acids linked by amide (peptide) bonds Gly Lys Phe Arg Ser H 2 N- end (N-terminus) -COOH end Peptide bonds (C-terminus) name: Glycyllysylphenylalanylarginylserine Symbol: Gly. Lys. Phe. Arg. Ser Or: GKFRS

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

Tripeptides possible from one each of leucine, glycine, and alanine Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Gly-Leu-Ala

Tripeptide containing glycine, cysteine, and alanine Source: Photo Researchers, Inc.

Write three-letter abbreviations for the following tetrapeptide: Focus Attention on the Side Group Alanine (Ala / A) Leucine (Leu / L) Cysteine (Cys / C) Methionine (Met / M)

Proteins • Proteins are sequences of amino acid residues – Amino acid: carbon atom (C), amino group (NH 3), 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 3 D arrangement of amino acids Tertiary – 3 D structure of a complete protein Quaternary – 3 D structure of functional protein (complex)

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

Four Levels of Protein Structure • Primary, 1 o – the amino acid sequence • Secondary, 2 o – Local conformation of main-chain atoms (F and Y angles) • Tertiary, 3 o – 3 -D arrangement of all the atoms in space (main-chain and side-chain) • Quaternary, 4 o – 3 -D arrangement of subunit chains

HIERARCHY OF PROTEIN STRUCTURE 1. 3. 2. Tertiary 4.

Secondary Structure • The two most common regular (repetitive) 2˚ structures are: § -helix § -sheet • Both use hydrogen bonding between N-H & C=O of peptide group as primary stabilizing force.

Helices (1) Cter Nter Hydrogen bonds: O (i) <-> N (i+4)

The b-strand N-H---O-C Hydrogen bonds Extended chain is flat “Real b-strand is twisted”

Pleated sheet

Tertiary 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 hair

Building the Hemoglobin Protein

Urey/Miller Experiment Figure 2 – 09

Urey/Miller Experiment Figure 2 – 09

Central Dogma DNA is the genetic material within the nucleus. Replication The process of replication creates new copies of DNA. The process of transcription creates an RNA using DNA information. DNA Transcription RNA Nucleus The process of translation creates a protein using RNA information. Translation Protein Cytoplasm

DNA Double Helix-Held Together with H-Bonds

Base Pairs Double Helix

Three Components of DNA Structure base: thymine (pyrimidine) monophosphate sugar: 2’-deoxyribose 5’ 4’ 3’ (5’ to 3’) 1’ 2’ 3’ linkage base: adenine (purine) 5’ linkage no 2’-hydroxyl

Pyrimidines used in Base Pairs, DNA 6 -membered rings only

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

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

Transcription • The new RNA molecule is formed by incorporating • nucleotides that are complementary to the template strand. DNA coding strand 5’ 3’ DNA G T C A T T C G G 3’ G U C A U U C G G 3’ C A G T A A G C C 5’ DNA template strand 5’ RNA

# of strands kind of sugar bases used

RNA Polymerase is the Enzyme that Catalyzes Transcription of DNA Information to RNA DNA (Blue) Newly Synthesized RNA (Red) Bridge Helix Moves DNA through Polymerase during RNA Synthesis (Green) Active Site Metal (Pink)

Transcription • The new RNA molecule is formed by incorporating • nucleotides that are complementary to the template strand. DNA coding strand 5’ 3’ DNA G T C A T T C G G 3’ G U C A U U C G G 3’ C A G T A A G C C 5’ DNA template strand 5’ RNA

Translation • The process of reading the RNA sequence of an m. RNA and creating the amino acid sequence of a protein is called translation. DNA T Transcription T C A G A A G U C DNA template strand Messenger RNA m. RNA Codon Translation Protein Lysine Serine Valine Polypeptide (amino acid sequence)

Genetic information written in codons is translated into amino acid sequences • 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

The genetic code is the Rosetta stone of life • Virtually all organisms share the same genetic code • All organisms use the same 20 aa • Each codon specifies a particular aa Figure 10. 8 A

• 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. 8 A

Structure of the Heme Group Porphyrin Ligand

Heme Group Found Bonded to Proteins

Hemoglobin • Multi-subunit protein (tetramer) – 2 and 2 subunits • Heme – One per subunit – Has an iron atom – Carries O 2 • In red blood cells

Sickle Cell Anemia Genetic Disease l Heterozygous individuals – carriers l Homozygous individuals – diseased Hemoglobin l Found in red blood cells l Carries oxygen to tissues SCA Results from Defective Hemoglobin l Hemoglobins stick together l Red blood cells damaged Complications from low oxygen supply to tissues l Pain, organ damage, strokes, increased infections, etc. Incidence highest among Africans and Indians l Heterozygotes protected from Malaria

Sickle Cell Hemoglobin Normal m. RNA Normal protein GUG CAC CUG ACU CCU GAG AAG val his leu thr pro glu lys 1 2 3 4 5 6 7 8 Mutation (in DNA) Mutant m. RNA Mutant protein GUG CAC CUG ACU CCU GUG GAG AAG val his leu thr pro val glu lys 1 2 3 4 5 6 7 8 Glutamate (glu), a negatively charged amino acid, is replaced by valine (val), which has no charge.

Structures of Amino Acids Glutamic Acid Valine Polar, Acidic Non-polar, Neutral

Glu 6 Val

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