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Department of Chemistry CHEM1020 General Chemistry *********************************************** Instructor: Dr. Hong Zhang Foster Hall, Room 221 Tel: 931-6325 Email: hzhang@tntech.edu. CHEM1020/General Chemistry _________________________________________ Chapter 15. (L15)-Biochemistry.

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Department of Chemistry

CHEM1020 General Chemistry

***********************************************

Instructor: Dr. Hong Zhang

Foster Hall, Room 221

Tel: 931-6325

Email: hzhang@tntech.edu

chem1020 general chemistry chapter 15 l15 biochemistry
CHEM1020/General Chemistry_________________________________________Chapter 15. (L15)-Biochemistry
  • Today’s Outline

..Peptide bond for peptides and proteins

peptides

peptide bond

..Protein structures

primary structure

secondary structure

tertiary structure

quaternary structure

four ways to link proteins

…Enzymes

chapter 15 l15 biochemistry
Chapter 15. (L15)-Biochemistry
  • Peptide bond

…Two amino acids can join together by the peptide bond:

O O O O

|| || || ||

H2N-CH-C-OH + HNH-CH-C-OH H2N-CH-C-NH-CH-C-OH

| | | |

R R’ R R’

+ H2O

…A peptide bond is an amide linkage as learned before.

Amino acids join together by means of condensation through removal of a H2O molecule.

chapter 15 l15 biochemistry4
Chapter 15. (L15)-Biochemistry
  • Peptides

…Peptides are small units of amino acids (AA) joined together by amide linkage through condensation.

So, peptides are small segments of proteins.

dipeptide: Gly-Ala

tripeptide: Gly-Ala-Cys

polypeptide: peptide with more than 10 AAs

…A great number of amino acids (102 or 103 or more) joined together form proteins (MW > 10000).

Naming peptides: see book on pp.444-445.

Proteins are also called polyamides.

chapter 15 l15 biochemistry5
Chapter 15. (L15)-Biochemistry
  • Sequence of proteins or peptides

…The sequence of a protein starts from the amino end called N-terminal to the carboxylic end called C-terminal.

…The amino acids sequence in a protein is very important.

The 20 or more basic amino acids are just like the 26 letters in English, which can form various words and sentences and paragraphs and pages and pages, and so on and on.

chapter 15 l15 biochemistry6
Chapter 15. (L15)-Biochemistry
  • Structures of proteins

…Proteins can have four levels of structures

-Primary structure: the amino acid sequence or chain formulized by the peptide bonds or amide linkage.

-Secondary structure: Arrangement of the protein polymer chain to form a higher level of structure held by hydrogen bonding between protein chains

-pleated sheet structure, held by hydrogen bond between chains and sheets, like in silk, etc.

-spiral right-handed called α-helix held by hydrogen bond inside the chain between N-terminals and

C-terminals, like in wool, hair, muscle

chapter 15 l15 biochemistry7
Chapter 15. (L15)-Biochemistry
  • Structures of proteins

…Proteins can have four levels of structures

-Tertiary structure: The folding of the helix in space

a 3-D structure, example: globular protein in a spherical shape

Example: myoglobin

-Quaternary structure: Different peptide units are arranged in an aggregate or assembly

Example: hemoglobin (each unit is like a myoglobin)

chapter 15 l15 biochemistry8
Chapter 15. (L15)-Biochemistry
  • Structures of proteins

Analogy by means of telephone cable cord (see pp. 447)

…Four types of interactions or “forces” or “bonding” to form the tertiary structure:

-hydrogen bond between the H from N-H and O from C=O and between the H from –OH and O from C=O

intramolecular, intermolecular

-ionic bond between “+” and “-” groups, also called salt bridges

-disulfide bond between two Sulfur atoms, covalent bond, strong to hold chains together

-dispersion force, inner non-polar portion, outer polar portion

chapter 15 l15 biochemistry9
Chapter 15. (L15)-Biochemistry
  • Enzymes

Enzymes are highly specialized class of proteins with special structures and functions.

biological catalysts speeding up or facilitating specific bioreactions at cell temperature

Some terminology:

-substrate: reacting substances

-active site: particular place in an enzyme where the substrate and the enzyme form an enzyme-substrate complex to lower the energy required for the reaction

chapter 15 l15 biochemistry10
Chapter 15. (L15)-Biochemistry
  • Enzymes

Some terminology:

-cofactor: a chemical component necessary for the proper function of the enzyme

..inorganic cofactors: metal ions, Zn2+, Mg2+, Mn2+, Fe2+, Cu2+

..organic cofactors: also called coenzymes

coenzymes are not proteins, just some organic molecules

many coenzymes are vitamins or derivatives of vitamins

chapter 15 l15 biochemistry11
Chapter 15. (L15)-Biochemistry

Quiz Time

Which of the following is a peptide bond

(a) CH2R-CONH-CHR’COO-;

(b) NH3+-CHR-CONH-CHR’COO-;

(c) NH3+-CHR-CONH-CH2R’;

(d) NH3+-CHR-COO-CH2-CHR’COO-.

chapter 15 l15 biochemistry12
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins are polymers made of the monomers of

(a) monosaccharides;

(b) ethylene;

(c) various amino acids;

(d) alkyl groups.

chapter 15 l15 biochemistry13
Chapter 15. (L15)-Biochemistry

Quiz Time

The N-terminal in a protein or peptide refers to

(a) the amide linkage;

(b) the carboxylic group;

(c) the amino group;

(d) none of above.

chapter 15 l15 biochemistry14
Chapter 15. (L15)-Biochemistry

Quiz Time

The C-terminal in a protein or peptide refers to

(a) the amide linkage;

(b) the carboxylic group;

(c) the amino group;

(d) none of above.

chapter 15 l15 biochemistry15
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins are polymers made by which bonding or linkage between two monomers?

(a) triple bond;

(b) double bond;

(c) ester bond;

(d) peptide bond.

chapter 15 l15 biochemistry16
Chapter 15. (L15)-Biochemistry

Quiz Time

A peptide bond is

(a) triple bond;

(b) double bond;

(c) an amide linkage;

(d) an ester bond.

chapter 15 l15 biochemistry17
Chapter 15. (L15)-Biochemistry

Quiz Time

A peptide bond is formed by

(a) addition of chlorine into the double bonds of the amino acids to form single bonds;

(b) elimination of a water molecule from the alcohol group and the carboxylic group to form an ester linkage;

(c) elimination of a water molecule from the amino group and the carboxylic group to form an amide linkage;

(d) none of above.

chapter 15 l15 biochemistry18
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins are polymers formed by connecting the monomers through

(a) dispersion force;

(b) elimination of double bonds;

(c) addition polymerization;

(d) condensation polymerization.

chapter 15 l15 biochemistry19
Chapter 15. (L15)-Biochemistry

Quiz Time

A peptide is

(a) a segment of cellulose;

(b) a segment of starch;

(c) a segment of Teflon;

(d) a chain of a small number of more than ten amino acids joined together, or a segment of a protein.

chapter 15 l15 biochemistry20
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins are amino acid polymers with their molecular mass generally

(a) < 5000;

(b) > 5000;

(c) < 10000;

(d) > 10000.

chapter 15 l15 biochemistry21
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins are amino acid polymers with the number of amino acids generally

(a) no more than three;

(b) a few;

(c) less than tens;

(d) more than hundreds or even thousands.

chapter 15 l15 biochemistry22
Chapter 15. (L15)-Biochemistry

Quiz Time

Proteins generally can have

(a) three levels of structures;

(b) four levels of structures;

(c) two levels of structures;

(d) one level of structure.

chapter 15 l15 biochemistry23
Chapter 15. (L15)-Biochemistry

Quiz Time

The primary structure of a protein is determined by

(a) the position of the N-terminal;

(b) the position of the C-terminal;

(c) its sequence of amino acid in the polymer chain;

(d) the number of amino acids.

chapter 15 l15 biochemistry24
Chapter 15. (L15)-Biochemistry

Quiz Time

The secondary structure of a protein refers to

(a) the arrangement of the protein chains in the form of cones;

(b) the arrangement of the protein chains in the form of pleated sheets or helixes;

(c) the arrangement of the protein chains in the form of closed rings;

(d) the arrangement of the protein chains in the random forms.

chapter 15 l15 biochemistry25
Chapter 15. (L15)-Biochemistry

Quiz Time

The secondary structure of a protein in the form of pleated sheets can be found in

(a) bone;

(b) silk;

(c) wool, muscle, hair;

(d) none of above.

chapter 15 l15 biochemistry26
Chapter 15. (L15)-Biochemistry

Quiz Time

The secondary structure of a protein in the form of helix can be found in

(a) bone;

(b) silk;

(c) wool, muscle, hair;

(d) none of above.

chapter 15 l15 biochemistry27
Chapter 15. (L15)-Biochemistry

Quiz Time

The helix structure of a protein is formed by

(a) hydrogen bonding between the N on the amino group and the H on the carboxylic group inside the spiral protein chain;

(b) hydrogen bonding between the N on the amino group and the O on the carboxylic group inside the spiral protein chain;

(c) hydrogen bonding between the H on the amino group and the O on the carboxylic group inside the spiral protein chain;

(d) hydrogen bonding between the O on the amino group and the H on the carboxylic group inside the spiral protein chain.

chapter 15 l15 biochemistry28
Chapter 15. (L15)-Biochemistry

Quiz Time

The helix structure of a protein is

(a) a γ-helix;

(b) a β-helix;

(c) an α-corn;

(d) an α-helix.

chapter 15 l15 biochemistry29
Chapter 15. (L15)-Biochemistry

Quiz Time

An α-helix of a protein is

(a) left-handed;

(b) right-handed;

(c) either left- or right-handed;

(d) none of above.

chapter 15 l15 biochemistry30
Chapter 15. (L15)-Biochemistry

Quiz Time

The tertiary structure of a protein refers to

(a) left-handed helix structure of a protein;

(b) the variation of the sequence of the amino acids;

(c) the folding of the protein helix in a certain way in the space;

(d) none of above.

chapter 15 l15 biochemistry31
Chapter 15. (L15)-Biochemistry

Quiz Time

The quaternary structure of proteins refers to

(a) the aggregate of several peptides in a certain way in the space;

(b) the aggregate of several amino acids in a certain way in the space;

(c) the aggregate of several protein helix subunits in a certain way in the space;

(d) none of above.

chapter 15 l15 biochemistry32
Chapter 15. (L15)-Biochemistry

Quiz Time

The forces holding the various levels of the structures of proteins include

(a) gravitation, dipole force, ester-linkage, and magnetic attraction;

(b) H-bond, salt-bridge, dipole force, and gravitation;

(c) hydrogen bond, ionic attraction, disulfide covalent bond, and dispersion force;

(d) none of above.

chapter 15 l15 biochemistry33
Chapter 15. (L15)-Biochemistry

Quiz Time

The ionic attraction or salt-bridge in a protein occurs between

(a) the negative N-terminal of a side chain and the positive C-terminal of a side chain;

(b) the positive N-terminal of a side chain and the negative C-terminal of a side chain;

(c) the zero-charged N-terminal of a side chain and the negative C-terminal of a side chain;

(d) the positive N-terminal of a side chain and the zero-charged C-terminal of a side chain.

chapter 15 l15 biochemistry34
Chapter 15. (L15)-Biochemistry

Quiz Time

Enzymes are

(a) a highly specialized class of amines;

(b) a highly specialized class of amino acids;

(c) a highly specialized class of peptides;

(d) a highly specialized class of proteins.

chapter 15 l15 biochemistry35
Chapter 15. (L15)-Biochemistry

Quiz Time

Enzymes function as

(a) biosolvents;

(b) biological catalysts to speed up specific bioreactions at the temperatures of biosystems;

(c) bio-matrixes for animals;

(d) biological catalysts to increase the temperatures at which bioreactions occur in biosystems.

chapter 15 l15 biochemistry36
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, substrates refer to

(a) the reaction media;

(b) the solvents;

(c) the products;

(d) the reactants or reacting substances.

chapter 15 l15 biochemistry37
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, the active site of an enzyme refers to

(a) the site where the enzyme becomes excited;

(b) the site where an enzyme-substrate complex forms to catalyze the specific bioreaction;

(c) the site where the enzyme cannot function well;

(d) the site where the enzyme decomposes.

chapter 15 l15 biochemistry38
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, the cofactor refers to

(a) another important type of enzymes;

(b) a special matrix for bioreactions;

(c) a special solvent for bioreactions;

(d) a chemical component necessary for the proper function of the enzyme.

chapter 15 l15 biochemistry39
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, the common inorganic cofactors are

(a) water molecules;

(b) inorganic anions such as SO42-, NO3-, and Cl-;

(c) metal cations such as Zn2+, Mg2+, Mn2+, Fe2+, and Cu2+;

(d) non-polar water molecules.

chapter 15 l15 biochemistry40
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, the organic cofactors are called

(a) comolecules;

(b) comonomers;

(c) coenzymes;

(d) copeptides.

chapter 15 l15 biochemistry41
Chapter 15. (L15)-Biochemistry

Quiz Time

In biochemistry, many organic cofactors or coenzymes are

(a) water molecules;

(b) vitamins and derivatives of vitamins;

(c) metal ions;

(d) salts.