Week 2 Lecture 2 - Western Washington...
Transcript of Week 2 Lecture 2 - Western Washington...
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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