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Calling names • ALKANES • ALKENES • ALKYNES • CYCLO• ALKYL- Cycloalkanes with Side Groups CH3 methylcyclopentane CH3 CH3 1,2-dimethylcyclopentane CH3 CH3 1,2,4-trimethylcyclohexane CH3 Bonding in ethane CH3-CH3 Bonding in ethylene CH2=CH2 Bonding in acytylene CH=CH Cis and Trans Isomers Double bond is fixed Cis/trans Isomers are possible CH3 CH3 CH = CH cis CH3 CH = CH trans CH3 isomers • Structural – chain butane methyl propane • Structural - position 2methylhexane 3methylhexane • 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 H2N—C —COOH I H 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 glycine + H3N–CH2–COO– zwitterion of glycine pH and ionization H+ + OH+ H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–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 H2N—C —COOH I H glycine CH3 I H2N—C —COOH I H alanine Types of Amino Acids Nonpolar R = H, CH3, alkyl groups, aromatic O Polar ll R = –CH2OH, –CH2SH, –CH2C–NH2, (polar groups with –O-, -SH, -N-) Polar/Acidic R = –CH2COOH, or -COOH Polar/ Basic R = –CH2CH2NH2 Classification of Amino Acids by Polarity NONPOLAR POLAR 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 gln leu ser glu lys thr asn asp cys gly his ile met phe pro 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 NH2 1 COOH NH2 2 COOH Dehydration -H2O O NH2 1 C N 2 COOH H Juang RH (2004) BCbasics H O I H2N—C —COH I H gly CH3 O I HN—C —COH I I H H ala Peptide Linkage H O CH3 O I I H2N—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 H2N- end Ser -COOH end Peptide bonds (N-terminus) name: Symbol: Or: (C-terminus) Glycyllysylphenylalanylarginylserine GlyLysPheArgSer 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 the three-letter abbreviations for the following tetrapeptide: CH CH3 SH CH2 CH O CH2 O CH2 O Focus Attention on the Side Group CH C CH O CH3 CH3 CH3 O H3N CH C N S H Alanine (Ala / A) N CH C H Leucine (Leu / L) N C H Cysteine (Cys / C) Methionine (Met / M) - 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 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, 1o – the amino acid sequence • Secondary, 2o – Local conformation of main-chain atoms (F and Y 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 1. 3. 2. Tertiary 4. Secondary Structure • The two most common regular (repetitive) 2˚ structures are: a-helix b-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 a 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 mRNA and creating the amino acid sequence of a protein is called translation. DNA template DNA Transcription T T C A G T C A G A A G U C A G U C strand Messenger RNA mRNA Codon Codon 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 10.8A • 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 a and 2 b subunits • Heme – One per subunit – Has an iron atom – Carries O2 • 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 Normal mRNA Normal protein GUG CAC CUG ACU CCU GAG GAG AAG val his leu thr pro glu glu lys 1 2 3 4 5 6 7 8 Mutation (in DNA) Mutant mRNA 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