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Proteins
Chapter 3
A. P. Biology
Mr. Knowles
Liberty Senior High School
Proteins are Most Common
Functions of Proteins1. Enzymes- Metabolism2. Structural- Collagen and Keratin3. Cell Recognition- proteins on
cellular surface.4. Regulation of Gene Expression-
Gene Repressors or Enhancers.5. Defense- Antibodies.
• An overview of protein functions
Table 5.1
Two Types of Proteins
1. Fibrous Proteins- rope-like, structural proteins; form shape of cells and tissues. Ex. Collagen-the most abundant protein of vertebrates.
2. Globular Proteins- have specific shapes for their functions. Ex. Enzymes and antibodies.
1. Proteins can be Structural
2. Proteins can be Globular
X-ray crystallography:Is used to determine a protein’s three-
dimensional structure. X-raydiffraction pattern
Photographic film
Diffracted X-raysX-ray
sourceX-ray beam
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern (b) 3D computer model
Figure 5.24
Papain
Proteins• Most diverse organic compound.
• Composed of amino acids- each with an amino group (NH2) and a carboxylic acid group (COOH).
• Different chemical group(s) attached to central C- R group .
Amino Acid Polymers• Amino acids
– Are linked by peptide bondsOH
DESMOSOMES
DESMOSOMESDESMOSOMES
OH
CH2
C
N
H
C
H O
H OH OH
Peptidebond
OH
OH
OH
H H
HH
H
H
H
H
H
H H
H
N
N N
N N
SH Side chains
SH
OO
O O O
H2O
CH2 CH2
CH2 CH2CH2
C C C C C C
C CC C
Peptidebond
Amino end(N-terminus)
Backbone
(a)
Figure 5.18 (b) Carboxyl end(C-terminus)
• 20 different amino acids make up proteins
O
O–
H
H3N+ C C
O
O–
H
CH3
H3N+ C
H
C
O
O–
CH3 CH3
CH3
C C
O
O–
H
H3N+
CH
CH3
CH2
C
H
H3N+
CH3
CH3
CH2
CH
C
H
H3N+ C
CH3
CH2
CH2
CH3N+
H
C
O
O–
CH2
CH3N+
H
C
O
O–
CH2
NH
H
C
O
O–
H3N+ C
CH2
H2C
H2N C
CH2
H
C
Nonpolar
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Methionine (Met) Phenylalanine (Phe)
C
O
O–
Tryptophan (Trp) Proline (Pro)
H3C
Figure 5.17
S
O
O–
O–
OH
CH2
C C
H
H3N+
O
O–
H3N+
OH CH3
CH
C C
HO–
O
SH
CH2
C
H
H3N+ C
O
O–
H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
O
C
C C
O
O–
NH2 O
C
CH2
CH2
C CH3N+
O
O–
O
Polar
Electricallycharged
–O O
C
CH2
C CH3N+
H
O
O–
O– O
C
CH2
C CH3N+
H
O
O–
CH2
CH2
CH2
CH2
NH3+
CH2
C CH3N+
H
O
O–
NH2
C NH2+
CH2
CH2
CH2
C CH3N+
H
O
O–
CH2
NH+
NH
CH2
C CH3N+
H
O
O–
Serine (Ser) Threonine (Thr)Cysteine
(Cys)Tyrosine
(Tyr)Asparagine
(Asn)Glutamine
(Gln)
Acidic Basic
Aspartic acid (Asp)
Glutamic acid (Glu)
Lysine (Lys) Arginine (Arg) Histidine (His)
Amino Acids• Are the monomers of proteins.• Only 20 naturally occurring amino
acids.• The R group gives each of the amino
acids its unique property.• All 20 amino acids can be grouped into
5 basic groups.
5 Groups of Amino Acids (Fig. 3.15)
1. Nonpolar- have R groups that contain CH2 and CH3.
2. Polar Uncharged- R groups that have O or only H.
3. Ionizable- have R groups that are acids and bases.
4. Aromatic- R groups that have organic rings.
5 Groups of Amino Acids (Fig. 3.15)
5. Special-function- amino acids that are only used for very specific functions; methionine begins protein synthesis, proline causes kinks in the protein polymer, cysteine links chains together.
The 20 Common Amino Acids (Fig. 3.15) Click
below for another view!
Proteins
• Are polymers of amino acids.
• Joined by peptide bonds.
• Di- Tri- and Polypeptides.
Globular Proteins• Are long amino acids chains
folded into complex shapes.• All of the internal amino acids are
nonpolar.• Water excludes nonpolar amino
acids – hydrophobic interactions.
Globular Proteins Have Four Levels of Structure
1. Primary- the specific sequence of amino acids in the polypeptide chain.
• R groups have no role in the backbone, so any sequence of amino acids is possible.
• Therefore, 100 amino acids may be rearranged in 20100 different possible sequences.
Primary Structure:
Is the unique sequence of amino acids in a polypeptide.
Figure 5.20
–
Amino acid subunits+H3N
Amino end
o
Carboxyl end
oc
Gly Pro Thr Gly
Thr
Gly
GluSeuLysCysProLeu
Met
Val
Lys
Val
LeuAsp
Ala Val ArgGly
SerPro
Ala
Gly
lle
SerPro Phe His Glu His
Ala
Glu
ValValPheThrAla
Asn
Asp
SerGly Pro
ArgArg
TyrThr
lleAla
Ala
Leu
Leu
SerProTyrSer
TyrSerThr
Thr
Ala
ValVal
ThrAsn Pro
Lys Glu
Thr
Lys
SerTyrTrpLysAlaLeu
Glu Lle Asp
Globular Protein Structure
2. Secondary- folding or coiling of the chain into a pattern due to weak H bonds between amino acids.
• H bonds form between the main chain of amino acids.
• Two Kinds of Secondary Structure
Secondary Structures• Alpha Helix- H bonds between one
amino acid and another further down the chain. Pulls the chain into a coil.
• Beta Sheet- H bonds occur across two separate chains. If chains are parallel, they may form a sheet-like structure.
O C helix
pleated sheet
Amino acidsubunits N
C
H
C
O
C N
H
C
OH
R
C N
H
C
O H
C
R
N
HH
RC
O
R
C
H
N
H
C
OH
N
C
O
R
C
H
N
H
H
C
R
C
O
C
O
C
N
HH
R
C
C
O
N
HH
C
R
C
O
N
H
R
C
H C
O
N
HH
C
R
C
O
N
H
R
C
H C
O
N
HH
C
R
C
O
N H
H C R
N HO
O C N
C
RC
H O
CHR
N H
O C
R
CH
N H
O C
H C R
N H
C
CN
R
H
O C
H C R
N H
O C
R
CH
H
C
R
N
H
C
O
C
N
H
R
C
H C
O
N
H
C
Secondary Structure:– Is the folding or coiling of the polypeptide into
a repeating configuration.– Includes the helix and the pleated sheet.
H H
Figure 5.20
Alpha Helix- The First Type of Secondary Protein Structure
Beta Sheet- Another Type of Protein
Secondary Structure
Show me the levels of protein structure.
Secondary Structures• Some patterns of alpha helices
and/or beta sheets are very common in protein structures.
• When secondary structures are organized into specific structures within proteins-motifs. Ex. Β-Barrel or α-turn-α motifs
Β-barrel Motif in a Cell Membrane Protein
Globular Protein Structure3. Tertiary Structure- folding and
positioning of nonpolar R groups into the interior of the protein (hydrophobic interactions).
• Held together by weak van der Waal’s forces.
• Precise fitting of R groups within the interior. A change may destabilize a protein’s shape.
Tertiary Structure:– Is the overall three-dimensional shape of a
polypeptide.
– Results from interactions between amino acids and R groups.
CH2
CH
OH
O
CHO
CH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3C
H3C
Hydrophobic interactions and van der Waalsinteractions
Polypeptidebackbone
Hydrogenbond
Ionic bond
CH2
Disulfide bridge
Globular Protein Structure4. Quaternary Structure- two or more
polypepetide chains associate to form a protein.
• Each chain is called a subunit.• Subunits are not necessarily the same.• Ex. Hemoglobin = 2 α-chain subunits +
2 β-chain subunits.
Quaternary Structure:– Is the overall protein structure that results from
the aggregation of two or more polypeptide subunits.
Polypeptidechain
Collagen
Chains
ChainsHemoglobin
Iron
Heme
The four levels of protein structure
+H3NAmino end
Amino acid
subunits
helix
Quaternary Structure of Hemoglobin
Hemoglobin structure and sickle-cell disease
Fibers of abnormalhemoglobin deform cell into sickle shape.
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin A
Molecules donot associatewith oneanother, eachcarries oxygen.
Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen
10 m 10 m
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin S
Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.
subunit subunit
1 2 3 4 5 6 7 3 4 5 6 721
Normal hemoglobin Sickle-cell hemoglobin. . .. . .
Figure 5.21
Exposed hydrophobic
region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
Is Protein Folding Important?
Normal Prion Scrapie Prion
Reverse Transcriptase of HIV
Cobra Toxin
Shape of the Protein
• Tertiary and Quaternary structures provide shape.
• These structures are maintained by H bonds and other weak forces between R groups of amino acids.
Conditions that Affect Protein Shape
Can disrupt H bonds by:• High Temperature• pH Changes (Acidic or Basic)• Ion Concentration (Salt)Disrupting the 2°, 3°, 4° structure is
called denaturation.
Denaturation:
Is when a protein unravels and loses its native conformation.
Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
Enzymes:– Are a type of protein that acts as a
catalyst, speeding up chemical reactions.
Substrate(sucrose)
Enzyme (sucrase)
Glucose
OH
H O
H2O
Fructose
3 Substrate is convertedto products.
1 Active site is available for a molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds toenzyme.
22
4 Products are released.
Figure 5.16
Enzymes are Proteins• Organic catalysts - increase the rate of
chemical reactions in cells.
• Hold reactant molecules close together for reaction to occur- uses an active site.
• The active site is used to bind the reactant molecules-substrate.
Lock-and-Key Model
Show me the model, Luke!
Write your predictions!
Gelatin = Substrate
Pineapple = Papain (Enzyme)