Calling names ALKANES ALKENES ALKYNES CYCLO- ALKYL-

Cycloalkanes with Side Groups

Figure 22.12: Some selected substituted benzenes and their names

Bonding in ethane CH 3 -CH 3

Bonding in ethylene CH 2 =CH 2

Bonding in acytylene CH=CH

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

isomers Structural – chain Structural - position Structural – function Stereo - geometrical Stereo - optical butane methyl propane 2methylhexane 3methylhexane 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 Rside 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 –CH 2 –COOH H 3 N–CH 2 –COO – glycine zwitterion of glycine +

pH 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 pH neutral pH High pH ++

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 Hglycine CH 3 I H 2 N—C —COOH I Halanine

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 CH 2 NH 2

POLAR NON- POLAR TyrHis Gly AcidicNeutralBasic Asp Glu Gln Cys Asn Ser Thr Lys Arg Ala Val Ile Leu Met Phe Trp Pro Classification of Amino Acids by Polarity 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 Alanine (Ala / A) Arginine Arginine (Arg / R) Asparagine Asparagine (Asn / N) Aspartic acid Aspartic acid (Asp / D) Cysteine Cysteine (Cys / C) Glutamic acid Glutamic acid (Glu / E) Glutamine Glutamine (Gln / Q) Glycine Glycine (Gly / G) Histidine Histidine (His / H) Isoleucine Isoleucine (Ile / I) Leucine Leucine (Leu / L) Lysine Lysine (Lys / K) Methionine Methionine (Met / M) Phenylalanine Phenylalanine (Phe / F) Proline Proline (Pro / P) Serine Serine (Ser / S) Threonine Threonine (Thr / T) Tryptophan Tryptophan (Trp / W) Tyrosine Tyrosine (Tyr / Y) Valine 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 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

NH 2 COOH 1 NH2NH2 2 NH 2 C NCOOH O H 21 Amino acids are connected head to tail Formation of Peptide Bonds by Dehydration Dehydration -H 2 O 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 H O I  H 2 N—C —C — I H glyala CH 3 O I  N—C —COH I I H Dipeptide Peptide Linkage

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

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

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 3D arrangement of amino acids –Tertiary – 3D structure of a complete protein –Quaternary – 3D structure of functional protein (complex)

Types of Proteins TypeExamples Structuraltendons, cartilage, hair, nails Contractilemuscles Transporthemoglobin Storagemilk Hormonalinsulin, growth hormone Enzymecatalyzes reactions in cells Protectionimmune 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 (  and  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 Tertiary

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.

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

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

Pleated sheet

Tertiary Structure Specific overall shape of a protein Cross links between R groups of amino acids in chain IonicH-bondDisulfideHydrophobicH-bond

Figure 22.26: Permanent waving of hair

Building the Hemoglobin Protein

Figure 2 – 09 Urey/Miller Experiment

Figure 2 – 09 Urey/Miller Experiment

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. Transcription The process of transcription creates an RNA using DNA information. Translation The 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’  3’ linkage 5’ linkage Three Components of DNA Structure

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

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’ GTCATTCGG CAGTAAGCC G RNA 5’ GGUCAUUC 3’

# 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) Active Site Metal (Pink) Bridge Helix Moves DNA through Polymerase during RNA Synthesis (Green)

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’ GTCATTCGG CAGTAAGCC G RNA 5’ GGUCAUUC 3’

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 Translation DNA TTCAGTCAG template strand mRNA AAGUCAGUC Messenger RNA Protein LysineSerine Valine Polypeptide (amino acid sequence)

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

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

Sickle Cell Hemoglobin GUG CAC CUG ACU CCU GAG GAG AAG val his leu thr pro glu glu lys GUG CAC CUG ACU CCU GUG GAG AAG val his leu thr pro val glu lys 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, Acidic Valine Non-polar, Neutral

Glu 6  Val

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