Che 214 lecture 02

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  • This image shows the primary structure of glycophorin A , a glycoprotein that spans the plasma membrane ("Lipid bilayer") of human red blood cells. Each RBC has some 500,000 copies of the molecule embedded in its plasma membrane. Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine (Thr) residues. One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26. Two polymorphic versions of glycophorin A, which differ only at residues 1 and 5, occur in humans. These give rise to the MN blood groups The M allele encodes Ser at position 1 (Ser-1) and Gly at position 5 (Gly-5) The N allele encodes Leu-1 and Glu-5 Genotype to Phenotype Individuals who inherit two N alleles have blood group N. Individuals who are homozygous for the M allele have blood group M. Heterozygous individuals produce both proteins and have blood group MN . Glycophorin A is the most important attachment site by which the parasite Plasmodium falciparum invades human red blood cells.
  • Black alpha carbon. Grey carbon, red oxygen, blue nitrogen
  • Che 214 lecture 02

    1. 1. CHE 214: Biochemistry Lecture Two TOPICS; •LIPIDS •PROTEINS •NUCLEIC ACIDS Lecturer: Dr. G. Kattam MaiyohFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 1
    2. 2. Lipids• Lipids include the following; – Fatty acids (Polymers of CH2 units) – Glycerol – Triglycerides – Other subunits (phosphate, choline, etc) may be attached to yield “phospholipids” • Charged phosphate groups will create a polar molecule with a hydrophobic (nonpolar) end and a hydrophillic (polar) endFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 2
    3. 3. February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 3
    4. 4. LipidsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 4
    5. 5. PhospholipidsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 5
    6. 6. February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 6
    7. 7. Phospholipid bilayer Hydrophillic heads Hydrophobic tails February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 7
    8. 8. SteroidsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 8
    9. 9. c. Proteins• Proteins serve many essential roles in the cell – Polymers of amino acids – There are 20 naturally occurring amino acids • A few modified amino acids are also used (rare) • The large number of amino acids allows huge diversity in amino acid sequence N = # of amino acids in a protein N20 = # of possible combinationsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 9
    10. 10. Protein FunctionSome examples• Structure- form structural components of the cell including: – Cytoskeleton / nuclear matrix / tissue matrix• Movement - Coordinate internal and external movement of cells, organelles, tissues, and molecules. – Muscle contraction, chromosome separation, flagella……… • Micro-tubueles, actin, myosin• Transport-regulate transport of molecules into and out of the cell / nucleus / organelles. • Channels, receptors, dynin, kinesin• Communication-serve as communication molecules between different organelles, cells, tissues, organs, organisms. – Hormones February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 10
    11. 11. Protein FunctionSome examples • Chemical Catalyst – serves to make possible all of the chemical reactions that occur within the cell. – Enzymes (thousands of different enzymes) • Defense-recognize self and non-self, able to destroy foreign entities (bacteria, viruses, tissues). – Antibodies, cellular immune factors • Regulatory-regulates cell proliferation, cell growth, gene expression, and many other aspects of cell and organism life cycle. – Checkpoint proteins, cyclins, transcription factors February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 11
    12. 12. Protein Structure• Polymers made from 20 different amino acids – All amino acids have a Common “core” • Amino end (N end) • Acid end (C end, carboxy end) – Linked by peptide bond – 20 different side chains February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 12
    13. 13. Properties of amino acids• amino acids: acidic basic hydrophobic• Amino acids all have The same basic structure• Chemical properties of the amino acids yield properties of the protein!February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 13
    14. 14. Properties of amino acidsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 14
    15. 15. Protein Structure• The 3-D shape and properties of the protein determine its function.• Shape and properties of protein determined by interactions between individual amino acid components.• Four “levels” of protein structure – Primary (Io), secondary (IIo), tertiary (IIIo), and quaternary (IVo) (sometimes).February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 15
    16. 16. Levels of Protein Structure• I0 (primary) structure – Linear order of amino acids in a protein: – 1AASXDXSLVEVHXXVFIVPPXILQAVVSIA – 31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A – 61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A – 91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S – 121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I – 151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X – 181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G – 211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X – 241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X – 271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q – 301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D – 331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L – 361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X – 391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S – 421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A – 451 X X S A X X A Single letter code for amino acids, also a three letter code. Refer to your genetic code handout.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 16
    17. 17. Levels of Protein Structure Primary Structure • Amino acids combine to form a chain • Each acid is linked by a peptide bond • Io structure by itself does not provide a lot of information.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 17
    18. 18. • 20 (secondary) structure – Based on local interactions between amino acids • Common repeating structures found in proteins. – Two types: alpha-helix and beta-pleated sheet. • In an alpha-helix the polypeptide main chain makes up the central structure, and the side chains extend out and away from the helix. • The CO group of one amino acid (n) is hydrogen bonded to the NH group of the amino acid four residues away (n +4). • From amino acid sequence - Can predict regions of secondary structure February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 18
    19. 19. Ribbon Diagram α-helical regionsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 19
    20. 20. Beta sheet• Two types; – Parallel – anti-parallelFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 20
    21. 21. Beta Sheet ribbon diagram parallel antiparallelFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 21
    22. 22. Protein Structure• 30 (tertiary structure) – Complete 3-D structure of protein (single polypeptide) hexokinase Chymotrypsin with inhibitorFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 22
    23. 23. Protein Structure• 40 (quaternary) structure – Not all proteins have 40 structure – Only if they are made of multiple polypeptide chainsFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 23
    24. 24. d. Nucleic Acids• DNA – deoxyribonucleic acid – Polymer of deoxyribonucleotide triphosphate (dNTP) – 4 types of dNTP (ATP, CTP, TTP, GTP) – All made of a base + sugar + triphosphate• RNA – ribonucleic acid – Polymer of ribonucleotide triphosphates (NTP) – 4 types of NTP (ATP, CTP, UTP, GTP) – All made of a base + sugar + triphosphate• So what’s the difference? – The sugar (ribose vs. deoxyribose) and one base (UTP vs. TTP)February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 24
    25. 25. February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 25
    26. 26. Function • Nucleic Acids – Information Storage • DNA / mRNA – Information transfer / Recognition • rRNA / tRNA / snRNA – Regulatory • microRNA ?February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 26
    27. 27. DNA •Information for all proteins stored in DNA in the form of chromosomes or plasmids. •Chromosomes (both circular and linear) consist of two strands of DNA wrapped together in a left handed helix (imagine screwing inwards) •The strands of the helix are held together by hydrogen bonds between the individual bases. •The “outside” of the helix consists of sugar and phosphate groups, giving the DNA molecule a negative charge.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 27
    28. 28. February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 28
    29. 29. Complimentary Base Pairs A-T Base pairing G-C Base PairingFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 29
    30. 30. DNA Structure• The DNA helix is “anti-parallel” – Each strand of the helix has a 5’ (5 prime) end and a 3’ (3 prime) end.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 30
    31. 31. DNA Structure 3’ end 5 ‘ end Strand 2 Strand 1 (Crick strand) (Watson strand) 5’end 3 ‘ endFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 31
    32. 32. DNA Structure 1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag 61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg 121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg 181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc 241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg 301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct 361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt 421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata Because of the base pairing rules, if we know one strand we also know what the other strand is. Convention is to right from 5’ to 3’ with 5’ on the left.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 32
    33. 33. Chromosomes and Plasmids • Chromosomes are composed of DNA and proteins. – Proteins (histone & histone like proteins) serve a structural role to compact the chromosome. – Chromosomes can be circular, or linear. • Both types contain an antiparallel double helix! – Genes are regions within a chromosome. • Like words within a sentence.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 33
    34. 34. RNA• Almost all single stranded (exception is RNAi).• In some RNA molecules (tRNA) many of the bases are modified (e.g. psudouridine).• Has capacity for enzymatic function -ribozymes• One school of thought holds that early organisms were based on RNA instead of DNA (RNA world).February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 34
    35. 35. RNA • Several different “types” which reflect different functions – mRNA (messenger RNA) – tRNA (transfer RNA) – rRNA (ribosomal RNA) – snRNA (small nuclear RNA) – RNAi (RNA interference)February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 35
    36. 36. RNA function • mRNA – transfers information from DNA to ribosome (site where proteins are made) • tRNA – “decodes” genetic code in mRNA, inserts correct A.A. in response to genetic code. • rRNA-structural component of ribosome • snRNA-involved in processing of mRNA • RNAi-double stranded RNA, may be component of antiviral defense mechanism.February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 36
    37. 37. RNA A - hairpin loop B- internal loop C- bulge loop D- multibranched loop E- stem F- pseudoknot Complex secondary structures can form in linear moleculeFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 37
    38. 38. mRNA• Produced by RNA polymerase as product of transcription – Provides a copy of gene sequence for use in translation (protein synthesis). – Transcriptional regulation is major regulatory point – Processing of RNA transcripts occurs in eukaryotes • Splicing, capping, poly A addition – In prokaryotes coupled transcription and translation can occurFebruary 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 38

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