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Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: [email protected] Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;Office Hours: MTW 8:00 - 10:00 am; ThF 9:00 - 10:00 am 1:00 - 2:00 pm.
December 19, 2014: Test 1 (Chapters 12-13)January 26 , 2015: Test 2 (Chapters 14-16)February 13, 2015: Test 3 (Chapters 17-19)March 2, 2015: Test 4 (Chapters 20-22March 3 , 2015: Make Up Exam: Chapters 12-22)
Bring Scantron Sheet 882-E
Chemistry 121(001) Winter 2015
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CHEM 121 Winter 2015
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Chapter 20 and GHW#10 Questions
Proteins and Peptides
CHEM 121 Winter 2015
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ProteinsNaturally occurring bioorganic polyamide polymers containing a sequence of various combinations of 20 amino acids. Amino acids contain the elements carbon, hydrogen, oxygen, and nitrogen and few also contain sulfurAmino acids: Polyfunctional bioorganic compunds
R = 20 different alkyl, alcohols, amines , acids and heterocyclic aminesZwitterion form
Abbreviationsglycine Gly Galanine Ala Avaline Val Vleucine Leu Lisoleucine Ile Imethionine Met Mphenylalanine Phe Ftryptophan Trp WProline Pro PCHEM 121 Winter 2015
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amino acid three letter code
single letter code
glycine Gly Galanine Ala Avaline Val V
leucine Leu Lisoleucine Ile I
methionine Met Mphenylalanine Phe F
tryptophan Trp Wproline Pro P
Abbreviations
serine Ser Sthreonine Thr Tcysteine Cys Ctyrosine Tyr Y
asparagine Asn Nglutamine Gln Q
aspartic acid Asp Dglutamic acid Glu E
lysine Lys Karginine Arg Rhistidine His H
Electrically Charged (negative)
Electrically Charged (positive)
Non Polar Neutral
Non Polar
CHEM 121 Winter 2015
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1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).
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1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).
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Protein Function• Enzymes - catalyze biological reactions (alcohol dehydrogenase,
glucokinase) • Hormones - signals between cells (insulin, growth hormone) • Storage Proteins- store nutrients (ferritin storing iron in the
liver)• Transport Proteins - transport nutrients through the body
(hemoglobin transport of oxygen) • Structural Proteins- form structure of cells ( keratin, elastin,
collagen) • Protective Proteins- have specific protective function
(antibodies bind to foreign proteins)
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2) Draw the optical and L isomers for: cys.
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3) Use the following amino acids to answer the questions below:
Which amino acid is most polar? b. Which amino acid is most non-polar?
c. Which amino acid gives an acidic solution?
d. Which amino acid gives a basic solution?
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Primary protein structureProteins are polymers made up of amino acids.
Peptide bond - how the amino acids arelinked together to makea protein.
H |
H2NCCOOH
| R
+
H |
H2NCCOOH
| R’
H O | ||
H2N - C - C -
| R
H |N - C - COOH | |H R’ + H2O
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4) Draw the following:a) Dipeptide bond between ala and asp, and identify C- and N-terminal.
b) Tripeptide, ile-cys-thr, and identify N- ( left) and C-terminal(right).
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4) Continued….c) How many possible isomers are in the tripeptide formed with ile, cys and thr? Come up with a formula for linear chain with “ n” amino acids.
d) Give the IUPAC name of the tripeptide with the sequence, ile-cys-thr.
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5) Use the structure to answer the questions below:Use the structure to answer the questions below
a) Which letter arrow points the end of the peptide that is the "amine“ end-N-terminal?
b) Which letter arrow points the end of the peptide that is the "carboxyl" end, C-terminal?
c) Which letter arrow points to an amide or peptide bond?
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Four levels of protein structure1) Primary structureThe sequence of amino acids in a protein.
2) Secondary structureWay that chains of amino acids are coiled or folded
- (-helix, -sheet, random coil).
3) Tertiary structureWay -helix, -sheet, random coils fold and coil.
4) Quaternary structureWay that two or more peptide chains pack
together.
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Three levels of structure: telephone cord
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Summary of protein structure
primary secondary
tertiary quaternary
H O | ||H2N - C - C | R
H |N - C - COOH | |H R’’
H O | ||- NH - C - C - | R’
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6) Explain the differences between primary, secondary, tertiary, and quaternary protein structures by giving brief definitions of each. What types of bonding are used in each?
Primary Secondary Tertiary Quaternary
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7) Use the above structures to answer the questions below:
• a. Which two amino acids may link in a salt bridge in tertiary protein structure?
• b. Which two amino acids may link in hydrophobic interactions in tertiary protein structure?
• c. Which two amino acids may link in hydrogen bonding interactions in tertiary protein structure?
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Alpha Helix
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Alpha Helix
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Beta Pleated Sheets
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Beta Pleated Sheets
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8) Explain the difference between the alpha helix and the beta pleated sheet protein structures. What are the differences in the hydrogen bonding?