chp. 20-1 chemistry 121 winter 2009 la tech chapter 20. protiens sections… → the protein made by...

Chp. 20-1Chemistry 121 Winter 2009 LA Tech

Chapter 20. ProtiensChapter 20. Protiens

Sections…Sections…

→ The protein The protein made by spiders made by spiders to produce a to produce a web is a form of web is a form of silk that can be silk that can be exceptionally exceptionally strong.strong.


Chapter 20. ProteinsChapter 20. Proteins20.1 Characteristics of Proteins20.1 Characteristics of Proteins20.2 Amino Acids: The Building Blocks for Proteins20.2 Amino Acids: The Building Blocks for Proteins20.3 Chirality and Amino Acids20.3 Chirality and Amino Acids20.4 Acid-Base Properties of Amino Acids20.4 Acid-Base Properties of Amino Acids20.5 Cysteine: A Chemically Unique Amino Acid20.5 Cysteine: A Chemically Unique Amino Acid20.6 Peptide Formation20.6 Peptide Formation20.7 Biochemically Important Small Peptides20.7 Biochemically Important Small Peptides20.8 General Structural Characteristics of Proteins20.8 General Structural Characteristics of Proteins20.9 Primary Structure of Proteins20.9 Primary Structure of Proteins20.10 Secondary Structure of Proteins20.10 Secondary Structure of Proteins20.11 Tertiary Structure of Proteins20.11 Tertiary Structure of Proteins20.12 Quaternary Structure of Proteins20.12 Quaternary Structure of Proteins20.13 Fibrous and Globular Proteins20.13 Fibrous and Globular Proteins20.14 Protein Hydrolysis20.14 Protein Hydrolysis20.15 Protein Denaturation20.15 Protein Denaturation20.16 Glycoproteins20.16 Glycoproteins20.17 Lipoproteins20.17 Lipoproteins


Chapter 21. Protein and the Amino AcidsChapter 21. Protein and the Amino Acids

These are biopolymers that are constructed from a limited set of amino acids.

They are the most plentiful organic substances in the cell.

About half of the dry mass of a cell is composed of proteins.

They serve a wide range of functions.


Protein functionProtein functionEnzymesEnzymes biological catalysts.biological catalysts.

Immuno-Immuno- antibodies of immune system.antibodies of immune system.

globulinsglobulins

TransportTransport move materials around -hemoglobin for move materials around -hemoglobin for OO22..

RegulatoryRegulatory hormones, control of metabolism.hormones, control of metabolism.

StructuralStructural coverings and support -coverings and support -

skin, tendons, hair, bone.skin, tendons, hair, bone.

MovementMovement muscle, cilia, flagella.muscle, cilia, flagella.


Types of ProteinsTypes of Proteins


Amino acidsAmino acids

All proteins are composed of amino acids.

Twenty common amino acids.

All are -amino acids.

Except for proline, primary amino- group is attached to the carbon - the carbon just after the acid group.

GeneralStructure


Handedness/Chirality of Amino AcidsHandedness/Chirality of Amino Acids


Amino acidsAmino acidsBecause both acid and base groups are present, an Because both acid and base groups are present, an

amino acid can form a +/- ion.amino acid can form a +/- ion.

HH H H || ||

R-C-COOHR-C-COOH R-C-COO R-C-COO--

|| || NHNH22 NH NH33

++

The position of the equilibrium is based on pH and the The position of the equilibrium is based on pH and the

type of amino acid. Called atype of amino acid. Called a zwitterionzwitterion..


Some amino acid examplesSome amino acid examples

H |

HO-CHHO-CH22-C-COO-

| +NH3serine

H | HH-C-COO-

| +NH3glycine

OO H | || | |

HH22N-C-CHN-C-CH22-C-COO-

|

+NH3

asparagine

O O H | || | |-O-C-CHO-C-CH22-CH-CH22-C-COO-

| +NH3

glutamic acid


Groups of Amino AcidsGroups of Amino AcidsHydrophobic

Polar, neutral

Negatively charged-Acidic

positively charged-Basic


Non-polar Amino AcidsNon-polar Amino Acids


Ploar/Neutral Amino AcidsPloar/Neutral Amino Acids


Ploar Acidic/Basic Amino AcidsPloar Acidic/Basic Amino Acids


AbbreviationsAbbreviationsglycine glycine GlyGly G G

alanine alanine AlaAla A A

valine valine ValVal V V

leucine leucine LeuLeu L L

isoleucine isoleucine Ile Ile I I

methionine methionine MetMet M M

phenylalanine phenylalanine PhePhe F F

tryptophan tryptophan TrpTrp W W

Proline Proline ProPro P P


Primary protein structurePrimary protein structure

Proteins are polymers made up of amino Proteins are polymers made up of amino acids.acids.

Peptide bondPeptide bond - - how the amino acids arehow the amino acids are

linked together to makelinked together to make

a protein.a protein.

HH ||

HH22NCCOOHNCCOOH

|| RR

++

HH ||

HH22NCCOOHNCCOOH

|| R’R’

H H O O | | ||||

HH22N - C - C -N - C - C -

|| RR

HH ||N - C - COOHN - C - COOH | | | |H H R’ R’ + H2O


Four levels of protein structureFour levels of protein structurePrimary structurePrimary structure

The sequence of amino acids in a protein.The sequence of amino acids in a protein.

Secondary structureSecondary structure

Way that chains of amino acids are coiled or Way that chains of amino acids are coiled or folded - (folded - (-helix, -helix, -sheet, random coil).-sheet, random coil).

Tertiary structureTertiary structure

Way Way -helix, -helix, -sheet, random coils fold and coil.-sheet, random coils fold and coil.

Quaternary structureQuaternary structure

Way that two or more peptide chains pack Way that two or more peptide chains pack together.together.


Three levels of structure: telephone cord Three levels of structure: telephone cord


Summary of protein structureSummary of protein structure

primary secondary

tertiaryquaternary

H H O O | | || ||

HH22N - C - C N - C - C

|| RR

HH ||N - C - COOHN - C - COOH | | | |H H R’’ R’’

H H O O | | || ||- NH - C - C -- NH - C - C - || R’R’


All proteins have the same covalent backbone.All proteins have the same covalent backbone.

Part of a protein.Part of a protein.

Primary structurePrimary structure

H H O O | | || ||

HH22N - C - C N - C - C

|| RR

HH ||NH - C - COOHNH - C - COOH || R’’’R’’’

H H O O | | ||||- NH - C - C -- NH - C - C - || R’R’

H H O O | | ||||- NH - C - C -- NH - C - C - || R’’R’’


Separation of three amino acidsSeparation of three amino acids

Separation of Lys, Phe, and Glu using electrophoresis after Separation of Lys, Phe, and Glu using electrophoresis after hydrolysis of proteinhydrolysis of protein


Secondary structureSecondary structure

Long chains of amino acids commonly fold or curl into Long chains of amino acids commonly fold or curl into a regular repeating structure.a regular repeating structure.

Structure is a result of hydrogen bonding between Structure is a result of hydrogen bonding between amino acids within the protein.amino acids within the protein.

Common secondary structures are:Common secondary structures are:

- helix- helix

- pleated sheet- pleated sheet

Secondary structure adds new properties to a protein Secondary structure adds new properties to a protein like strength, flexibility, ...like strength, flexibility, ...


-helix-helix

H|N

C||O

H|N

C||O

H|N

C||O

C||OH

|N

C||O

H|N

C||O

H|N

C||O

C||O

C||O

H|N

H|N

H|N Every amide hydrogen

and carbonyl oxygen is involved in a hydrogen bond.


Representations of the helix secondary structureRepresentations of the helix secondary structure


-helix-helix One common type ofsecondary structure.

Properties of an -helix include strength and low solubility in water.

Originally proposed byPauling and Corey in 1951.


The coiled-coil structuresThe coiled-coil structures

The coiled-coil The coiled-coil structure of the structure of the fibrous protein beta fibrous protein beta kerotin.kerotin.


CollagenCollagenFamily of related proteins.Family of related proteins.

About one third of all protein in humans.About one third of all protein in humans.

Structural proteinStructural protein

Provides strength to bones, tendon, skin, blood Provides strength to bones, tendon, skin, blood vessels.vessels.

Forms triple helix -Forms triple helix - tropocollagentropocollagen..


CollagenCollagen


-Pleated sheets-Pleated sheetsAnother secondary structure for protein.Another secondary structure for protein.

Held together by hydrogen bonding Held together by hydrogen bonding between adjacent sheets of protein.between adjacent sheets of protein.

C|R

R|C

R|C

R|C

R|C

C|R

C|R

C|R

C|R

C|R

N|H

N|H

N|H

O||C

O||C

O||C

O||C

C||O

C||O

C||O

C||O

H|N

H|N

H|N

H|N

N|H

The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage.


-Pleated sheets-Pleated sheetsSilk fibroin Silk fibroin - - main protein of silk is an example main protein of silk is an example

of a of a pleated sheet structure. pleated sheet structure.

Composed primarily of glycine and alanine.

Stack like corrugated cardboard for extra strength.


-Pleated sheets-Pleated sheets


Tertiary structure of proteinsTertiary structure of proteins

Fibrous proteinsFibrous proteins• insoluble in water

• form used by connective tissues

• silk, collagen, -keratins

Globular proteinsGlobular proteins• soluble in water

• form used by cell proteins

• 3-D structure - tertiary


Tertiary structure of proteinsTertiary structure of proteins

Results from interaction of side chains.Results from interaction of side chains.

The protein folds into a tertiary structure.The protein folds into a tertiary structure.

Possible side chain interactions:Possible side chain interactions:

Similar solubilitiesSimilar solubilities

Ionic attractionsIonic attractions

Electrostatic attraction between Electrostatic attraction between ++ and and -- sidechainssidechains

Covalent bondingCovalent bonding


Tertiary StructureTertiary Structure


Tertiary Structure of ProteinsTertiary Structure of Proteins

- S - S -

Saltbridge

Sulfidecrosslink

Hydrogenbonding

Hydrophobicinteraction

-COO- H3N+-

-O

\

H

-O \

H


Four types of interactions between amino acid R groupsFour types of interactions between amino acid R groups


Quaternary structure of proteinsQuaternary structure of proteinsMany proteins are not single peptide strands.

They are combinations of several proteins- aggregate of smaller globular proteins.

Conjugated protein - incorporate another type of group that performs a specific function.

prosthetic group


Quaternary structure of proteinsQuaternary structure of proteins

Aggregate Aggregate structurestructure

This example shows four different proteins and two prosthetic groups.


Hemoglobin and MyoglobinHemoglobin and Myoglobin

HemoglobinHemoglobin

Oxygen transport protein of red blood cells.Oxygen transport protein of red blood cells.

MyoglobinMyoglobin

Oxygen storage protein of skeletal muscles.Oxygen storage protein of skeletal muscles.

As with the cytochrome example, both proteins As with the cytochrome example, both proteins use heme groups. It acts as the binding site use heme groups. It acts as the binding site for molecular oxygen.for molecular oxygen.


HemeHeme

myoglobinmyoglobin

1 heme group1 heme group

hemoglobinhemoglobin

4 heme groups4 heme groups


MyoglobinMyoglobin

HemeHeme


HemoglobinHemoglobin

4 heme

2 chains

2 chains


Oxygen TransportOxygen Transport


Example - cytochrome C 550Example - cytochrome C 550

Aggregate of proteins andother structures.

Heme structure

Contains Fe2+

Used in metabolism.


Sickle cell anemiaSickle cell anemia

Defective gene results in production of mutant hemoglobin.

Still transports oxygen but results in deformed blood cells - elongated, sickle shaped.

Difficult to pass through capillaries. Causes organ damage, reduced circulation.

Affects 0.4 % of African-American.


Comparison of normal and sickle cell hemoglobinComparison of normal and sickle cell hemoglobin

Normal Sickle


Denaturation of ProteinsDenaturation of Proteins

The loss of secondary, tertiary, and quaternary The loss of secondary, tertiary, and quaternary structuresstructures

1) pH extremes.

2). Heat -

3). Mechanical Agitation (foaming)

4). Detergents

5). Organic Solvents

6). Inorganic Salts -


Heat-Denaturation of ProteinsHeat-Denaturation of Proteins


Permanent for HairPermanent for Hair

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