Week 2 Lecture 2

1. Weak chemical bonds2. Protein structure3. α-helix and β-sheet4. Levels of protein organization5. Protein domainsText: Chapter 2 pp. 58-65, 74-75, Chapter 4 pp 119-- 143Panels 2-2 (on water) and 2-7 (on noncovalent bonds)Panel 4-2 on pg 132: Four ways of depicting protein structure

Reading for upcoming lectures on enzymes:Chapter 3: pp 91-93 Figures 3-13, 3-14, 3-16Chapter 4 143-158, 91-94, 106-109

Hierarchical Structure of proteins:http://esg-www.mit.edu:8001/esgbio/lm/proteins/structure/structure.html

>gi|17384045|emb|CAD13147.1|Sex determining region Y [Homo sapiens]MQSYASAMLSVFNSDDYSPAVQENIPALRRSSSFLCTESCNSKYQCETGENSKGNVQDGVK

RPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPKNCSLLPADPASVLCSEVQLDNRLYRDDCTKATHSRMEHQLGHLPPINAASSPQQRDRY

primary structure: linear arrangement or sequence of amino acid residues that constitute thepolypeptide chains

The second level of biological information is encoded in proteinsProteins contain 3-dimensional information which is specified by the one-dimensional

information in the polypeptide polymer

HUH? The primary structure looks pretty one-dimensional

The polymer structure of polypeptides allows the formation of an almost limitless variety ofproteins with diverse 3-D shapes and diverse chemical properties and capacities

How is a polypeptide folded-up into a 3-D “object”?

02_31_protein fold.jpg

04_04_noncovalent.jpg

04_04_noncovalent.jpg

Hydrogen bonds: occurs when a hydrogen atomcovalently bonded to one electronegative atom (such asan oxygen or a nitrogen atom) is also attracted toanother electronegative atomThese bonds are critical in determining the overall shape and structure of polymerssuch as DNA and proteincovalent bond: when two atoms share a pair of valence electronspolar covalent bond: when one atom is more electronegative than another atomelectronegativity: the attraction of an atom for the electrons of a covalent bondThe more electronegative an atom is, the more is pulls shared electrons towards itself

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• Two models of protein conformation

(a) A ribbon model

(b) A space-filling model

Groove

Groove

Figure 5.19

04_10_1_alpha h. beta s.jpg

04_14_helix.jpg

The SRY protein binds non-covalently to specificsites on DNA and controls the expression of genes

that control the development of the testis

04_15_ahelix_lip_bilayer.jpg

04_10_2_alpha h. beta s.jpg

04_17_2 beta sheets.jpg

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Four Levels of Protein Structure

• Primary structure

– Is the unique sequence of amino acids in apolypeptide

Figure 5.20–

Amino acidsubunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeuAsp

AlaVal ArgGlySer

ProAla

Gly

lleSerProPheHisGluHis

AlaGlu

ValValPheThrAlaAsn

AspSer

GlyProArg

ArgTyrThr lle

AlaAla

Leu

LeuSer

ProTyrSerTyrSerThrThrAlaVal

ValThrAsnProLysGlu

ThrLysSer

TyrTrpLysAlaLeu

GluLle Asp

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

O C α helix

β pleated sheet

Amino acidsubunits NC

H

CO

C N

H

CO H

R

C NH

C

O H

CR

NHH

R CO

R

CH

NH

C

O HN

CO

R

CH

NH

H

CR

C

O

CO

C

NH

H

R

CCO

NH

H

CR

C

O

NH

R

CH C

ONH H

CR

C

ONH

R

CH C

ONH H

CR

C

O

N H

H C RN H O

O C N

C

RC

H O

CHR

N HO C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

CR

NH

CO

C

NH

R

CH C

ONH

C

• Secondary structure

– Is the folding or coiling of the polypeptide into arepeating configuration

– Includes the α helix and the β pleated sheet

H H

Figure 5.20

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• Tertiary structure

– Is the overall three-dimensional shape of apolypeptide

– Results from interactions between amino acidsand R groups

CH2CH

OHOCHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3CH3

H3CH3C

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

04_21_Serine proteases.jpg

04_19_functiondomains.jpg

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Quaternary structure

– Is the overall protein structure that results fromthe aggregation of two or more polypeptidesubunits

Polypeptidechain

Collagenβ Chains

α ChainsHemoglobin

IronHeme

02_32_Noncovalent bonds.jpg

04_22_protein subunit.jpg

02_33_macro complexes.jpg

04_29_Disulfide bonds.jpg