Download DNA RNA

!"#$"%&' !( )”*#& )”*+
DNA
(,-'( .&$#
.&*&-
#$&*&$
#$"%&'
5’ AGTACG 3’
3’ TCATGC 5’
RNA
!"*&/%5
#$"%&' *
:%/) DNA-% ($&+ *
thymine !&0$/ uracil
(&$12 %2 %'0.(% %&3" %/)) "%"+4-+5 3”#+/
7
3 2 21
15
70
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DNA
RNA
!"*&/%5
("&%. DNA-( .8"#)
DNA "#-&0 !"*&/%5/
!"#$"%&' *
&*"$) .&1$&5 = !"#$&*&$$ !"/3#&$ *
!"*&-& !"/# !"*/$ %/0% !"%4&7$ *
).( %- ”(+&/2( "7&7“ *
+&2& ,(*/$ ,!"$"8*) ,DNA-( .%'3( "3"%(./ !"/&-5 *
.!"*&/%5 .8.*"7& RNA-( 0&.2"-
DNA-$
Gallus gallus lysozyme (LYZ), gene, chromosome 1
TCCCGCTGTGTGTACGACACTGGCAACATGAGGTCTTTGCTAATCTTGGTGCTTTGCTTCCTGCCCCTGGCTGCTCTGGGGAAAGTCTTTGGACGATGTGAGCTGGC
AGCGGCTATGAAGCGTCACGGACTTGATAACTATCGGGGATACAGCCTGGGAAACTGTAAGTCTGTATTCTCATGATTTCCAGGGAGCACATGGGGTGGGAATTTCCA
TTTAACATGCTTCTTTAAAGTGAGCAGGTCTGCGTGATGTTGGAATGTAGATACTAAGAAGCCATCAGGTTAGTCCATCTCTGCTTGCACAGACTGCAGGTATTTTCTAC
AGATTTTCCCTCTGCCAGTCCTTTCCCTATCGTTCTTCCTCAGCTGAACTGAGATGTTGTCATCGGAAAGGTTTCCCAGAAGCAGCCTGTCCCGTCCTACCTCCTCAG
ATTCTAAGCGCCCTGGTTTTACTTGCTTCAATTCCTCTGCAGATGTCCCCAAGACTGTGGAGCAAGCAGGAGCAGAGTGCGGAGCCCCGCTGGGCAGAGACACTGG
TGTCAGGCTGGCTTGGTGGGCACTGCTACAAGGAGTAGTGGGGGAGAAGAGACGCTGAGCGTGCTGATGTGGGAAGGTCAGCCAGAAAGAAAGTGGGCTGAGAG
GGGATCATAGAAACAAGGAGTGAGGGGCCACTTTAAAGCTTCTTTCCTCTGGTGGGCACTGACAACAGATTATTGTTAAACCAATTTCCTTTGAGGGAAGCATGCGTG
CATTCTGTTCCCAGATCTGGAGAGCAATCCATGTCATGTTCACAGCTGAAACAGAAATCACTATCCCCATCCCTCCTCCTTCCTGCTGCCCTGACACGGATGCAGCAG
CATGTAAATAGGGCAAAATGAGGCCATCACAATGAGGCCACATAAAGTTTGAGCAGCTAAAATAACCCTCATTAAGGTGAGCAGGTACTGATGCAGAAAGAACGTCCA
AGGAGCGTGCCTGGCAGCAGAAGCAATATGAACAGCCCTGTTTGGATGCATCTGCACCGCTTGCCAAAAGCACCACCTGTGAGACCGTACTGGGGCTGCCCAAAG
CTTCCAAGAGTAGTAGGAGCTGTGCTGCAGAGCACAGCCTGCCCGCCAGCATCCTGAGGCATGATCTGTGTGTCTGTATATAGGGAGAAATGCACAAAAGCACGCTG
GAATTTATTTCTAAGGGTAGAAATCCTGTGCCAGGTTTACTAAGGACGTTTTGAAGTTAAGACACGTTGCACGTGTTTTTCACTCTTGGTTGGATTGGAAAAATGGTATG
CTCCGGACACAGTCATCTTCCAATTGAGAGAAGAGATGGAGAGCGCATCTTCATAAATAAGTCAGATACAGATTTAAAATAATAATCTTTGAGGGTTTTGTTTTCTTTTGA
ATGGAACTTCGACAGGGGTGTGTGCTGCAAAATTCGAGAGTAACTTCAACACCCAGGCTACAAACCGTAACACCGATGGGAGTACCGACTACGGAATCCTACAGATC
AACAGCCGCTGGTGGTGCAACGATGGCAGGACCCCAGGCTCCAGGAACCTGTGCAACATCCCGTGCTCAGGTGAGCTCAGTTTCTCAAGGCAACGAATGCCCTTC
CATAATCCGTGTGCAAGTAGACGAGCAAAGGGTGGTTACAACCCTATCTTTAGAACAAAGCAGAACAAAATCCAAACACACTCTTCTCATTTTCAAAAAGCAGATCTGC
ACTGTAGCCATGCACACGTGAGAGGAAAAAGTTATTCAGCGATAGGAACCGTGTTCCCCTGTCTACCCATCCGAATGTTTCTAGAGAAAAGAGGTTTCAGAGCAGCCA
TTTATTAATTAGCAGCAACACTACTCTCTGGAAAATTTTCTTTGAAGGTAGTAAAAGCTTGACCCTTGCAAAATATTGTCCCAAATGCCACTTTCCCATCCCACTAGTGAA
GGGGAGGAGAGGTGAACATATTCGCAAATCCCCCCTGGTTAGATTAAGGTGAAACGACACTCATGGTCTGTACATAAGAGGAAAAATCATCATTTTTAATAGGAGATTT
CTATGAAACAGTCATCCTATATGCATCAGCCCTCCCACAATTATATCTACCTAAGTACTGTCTATTACTGTACTGTACAAGTACTGTACAGTACTGAACAGTTGGATCAGG
TATTCTGGCAGCTGCACTGCCACACAACTTCGATAATGCATCCCTGCAATGCCTACTCATTTTGACAAGGACAAGAAATGCCTACACAGATAGCTAGGACCAACACATT
TGAGGGAAAATAATCAGTAGGCAGAGTGAAAACGGGACAGCAGCAGAGGTCAGAGTAACCATACTGTAACCGCAGGCTTTCTCATCAGCCTGTGTCCAGCCATTCTC
ACATCCTTTTAGTGAGGATTTCAGTGTTGATTTAAGTATGGGCGTTTAGACCAGTGCAATAACACTTTTGTCTTTCTAGAGCACAGCTGAGTGGATGGTTATCTGCCAAG
AAAGACAGTTAGTTACCATAGGCAAAACAGCTTGGCTGCAGATTAACCATAAAATGATGGCAGAAAGTAGTTTGCAGTCACACTAGTAGCCACATGCTGAATTCTAACT
CTATCTTCCAAAGACAAATGGATGAAATAGAGCTTCCTCTTGCAGCCCGGATTATTCTGCATCACTTGTGGCTTTGCTTCACTGGGTTTACTCTGCTTGCATTCTGATAG
CTGGAAGTCGCTAGAGGAAAATTCTTTCATTTTCCTTAGAAAGAGAGGAACAGAGAAACTGCCACACATCTCAGGGCTTCGTTCTTTACTATGAGAGTGGTGAGGTGC
TGGCATAGACTGCCCAGAGAGGTTGTAGATGCTCCATCCCTGGAGGCGTTCAGGGCCAGGTTGGATGGGGCCCTGGGCAGCCTGGTCTAGCATTAAATGGGGAGG
TTGGTGGCCCTGCCCACAGCAGGGGTGCTGGAGCTTCATGATCCTTGGGGTCCCTTCCAACCCGAGCATTCTTTGACTCTATGATCCCTTACCAAAGACCAGATAGA
CACAATAAACATCCCAGAGATGAATAAGGATCTCTTGAGTAGTCAGGCTACAGAACGGGTATCTGGAAGCCCATGGTGGCTGCACGGCCGCTCCCAGGCTTCCCTTT
CCCCAGGTCGTGGTGTATCACTTACTCTTCTCCCTCACGCTGTGTCTGTCCGTGTGTGCTGCACACACACCGGCACTGCTCTGCTCGTCCAGCACGTCGGCGTCTG
GTTTAAGCAGACACCGTGTGGGCCCACGGGAGTGGGGAGCAAACCGGCCAACACCAACACGCACTGAAGTAAAAACACGACGTGACGTGTTTCCCCCTTCCTTTCT
TAAGCCCTGCTGAGCTCAGACATAACAGCGAGCGTGAACTGCGCGAAGAAGATCGTCAGCGATGGAAACGGCATGAACGCGTGGTAGGTGGCGGGGGGTTCCCAG
GAGAGCCCCCAGCGCGGACGGCAGCGCCGTCACTCACCGCTCCGTCTCCCTCCGCCCAGGGTCGCCTGGCGCAACCGCTGCAAGGGCACCGACGTCCAGGCGT
GGATCAGAGGCTGCCGGCTGTGAGGAGCTGCCGCGCCCGGCCCGCCCGCTGCACAGCCGGCCGCTTTGCGAGCGCGACGCTACCCGCTTGGCAGTTTTAAACG
CATCCCTCATTAAAACGACTATACGCAAACGCC
32338217
E. coli chromosome
~6,000,000 bp
~4mm
mRNA-%
Gallus gallus lysozyme (LYZ), mRNA
TCCCGCTGTGTGTACGACACTGGCAACATGAGGTCTTTGCTAAT
CTTGGTGCTTTGCTTCCTGCCCCTGGCTGCTCTGGGGAAAGTC
TTTGGACGATGTGAGCTGGCAGCGGCTATGAAGCGTCACGGAC
TTGATAACTATCGGGGATACAGCCTGGGAAACTGGGTGTGTGTT
GCAAAATTCGAGAGTAACTTCAACACCCAGGCTACAAACCGTAA
CACCGATGGGAGTACCGACTACGGAATCCTACAGATCAACAGC
CGCTGGTGGTGCAACGATGGCAGGACCCCAGGCTCCAGGAAC
CTGTGCAACATCCCGTGCTCAGCCCTGCTGAGCTCAGACATAA
CAGCGAGCGTGAACTGCGCGAAGAAGATCGTCAGCGATGGAA
ACGGCATGAGCGCGTGGGTCGCCTGGCGCAACCGCTGCAAGG
GTACCGACGTCCAGGCGTGGATCAGAGGCTGCCGGCTGTGAG
GAGCTGCCGCACCCGGCCCGCCCGCTGCACAGCCGGCCGCT
TTGCGAGCGCGACGCTACCCGCTTGGCAGTTTTAAACGCATCC
CTCATTAAAACGACTATACGCAAACGCC
6&/%5%
)”5 %- !"#$"%&' !( !"*&/%5
(1"/ !"8&8"%
!"*&/%5 .8,*"7& !"$&8&/"#
!&8&/"#/ 6&/%5% !4#&.$ RNA-(
KVFGRCELAAAMKRHGLDNY
RGYSLGNWVCAAKFESNFNT
QATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPC
SALLSSDITASVNCAKKIVS
DGNGMNAWVAWRNRCKGTDV
QAWIRGCRL
rRNAs- "#0"2( /"3#$( ,.&+"5" .. 2
!"*&/%5 .8,*"7& !"$&8&/"#
!"*&/%5 .8,*"7& !"$&8&/"#
!&8&/"#/ 6&/%5% !4#&.$ RNA-(
!""). 9&. !"*&#/) !( !"$&8&/"#(
",*4( +&0(
"+",'' #-0 .#"1"
(!"*&+&0) .&-%-/ )#0* mRNA-(
!G°’ ! +10 kJ/
mol !
Carboxy (C-)
terminus
Amino (N-)
terminus
"+",'' #-0 .#"1"
!."1# )%- ($ %3
&*"$) .&1$&5 %2 .2+%
"%%3 (*/$
.&#/&5$ )”5 10,000 %3% .5) .&2, - ((&/4 +&)$ 0&"+ .$# *
:.&)"4- 6&0".& (0"+/ 9"%(.$ ()1&.3 %”*( 0&"+( .$# *
(2ATP ,!"/%- "*-) tRNA-% )”5( #&-"0/ %3% GDP-% 2GTP .!&8&/"#/ mRNA % tRNA( .$).( .0"+// .!"$").$ )% )”5-tRNA 0&%"7% .'7&*=/ ("4#*) ."+",'' #-0
Common amino acids
11/06/2005 07:44 PM
Common amino acids
Glycine (Gly) Alanine (Ala)
Aspartate (Asp)
Serine (Ser)
Valine (Val)
Asparagine (Asn)
Threonine (Thr)
Lysine (Lys)
Phenylalanine (Phe)
Leucine (Leu)
Glutamate (Glu)
Methionine (Met)
Arginine (Arg)
Tyrosine (Tyr)
20
.&1$&5
&*"$)(
”.&1&'*”(
!"*&/%5/
Isoleucine (Ile)
Glutamine (Gln)
Cysteine (Cys)
Histidine (His)
Proline (Pro)
Tryptophan (Trp)
Close
Other amino acids
11/06/2005 07:47 PM
Other amino acids
L-Ornithine
L-Homocysteine
N-(L-Arginino)succinate
L-Homoserine
3,4-Dihydroxy-Lphenylalanine
Triiodothyronine
beta-Alanine
D-Alanine
4-Aminobutylate
D-Leucine
3-Sulfino-Lalanine
3-Iodo-L-tyrosine
L-Thyroxine
N-(L-Arginino)Taurine
D-Valine
L-Citrulline
3,5-Diiodo-L-tyrosine
L-Selenocysteine
(R,S)-3-Amino-2-methylpropanoate
D-Isoleucine
&*"$) .&1$&5
.”.&#5)”
.&-$-$
)1&$ "#$&53
!8"%&/,$/
!"#$&5 %6&43 !"*&!"+",&)%0&*
+5&"$/ .&*"*2$ )”5 ($3
http://www.genome.ad.jp/kegg/catalog/cpd_amino.html
Pyrrolysine
64&*.$/ ()1$*
Methanosarcina
!.++&0$ ,barker
!3”+/ ,UAG "”2
stop
Page 1 of 1
Selanocystein
-&*%7/ ()1$*
!.++&0$ ,!"*&/%5
!3”+/ ,UGA "”2
stop
D-Aspartate
(S)
D-Asparagine
D-Methionine
D-Gulutamate
D-Cysteine
D-Glutamine
D-Lysine
D-Serine
D-Arginine
D-Threonin
D-Histidine
Bing et al 2002
Gayathri et al 2002
http://www.genome.ad.jp/kegg/catalog/cpd_other_amino.html
Page 1 of 2
Methionine
%3/ (*&-)#( )”5(
!"0+""5 .6&/%5
-/ 3”+/ !"%"5.$
formylmethionine
!?6"*&".$/ !"%"5.$ !"*&/%5( %3
!"8&8"%
.&"%#"3 6( )”5
KVFGRCELAAAMKRHGLDNYRGYSLGNW
VCAAKFESNFNTQATNRNTDGSTDYGIL
QINSRWWCNDGRTPGSRNLCNIPCSALL
SSDITASVNCAKKIVSDGNGMNAWVAWR
NRCKGTDVQAWIRGCRL
ATGAGGTCTTTGCTAATCTTGGTGCTTTGCTTCCTGCCCCTGGCTGCTCTG
MetArgSerLeuLeuIleLeuValLeuCysPheLeuPheLeuAlaAlaLeu
M R S L L I L V L C F L P L A A L
AAAGTCTTTGGACGATGTGAGCTGGCAGCGGCTATGAAGCGTCAC...
GlyLysValPheGlyArgCysGluLeuAlaAlaAlaMetLysArgHis...
G K V F G R C E L A A A M K R H ...
... ATCAGAGGCTGCCGGCTGTGA
... IleArgGlyCysArgLeuStop
... I R G C R L Stop
6&*"" "/1$ ($3/ .&"(% .&%&3" )”5
pK ~ 2.2
“cationic”
pK ~ 9.4
“zwitterionic”
“anionic”
!""2/,( !"*&/%5( %3 ,2$3
L-amino acids !""&-2
...($% #&#/ )%
",#' (#0$ (8 6"1"%4 %/)
Table of a-Amino Acids Found in Proteins
pK2
pK1
pK R Group
(COOH) (NH2)
Structure*
Amino Acid
Symbol
Glycine
Gly - G
2.4
9.8
Alanine
Ala - A
2.4
9.9
Amino Acids with Aliphatic R-Groups
Valine
Val - V
2.2
9.7
Leucine
Leu - L
2.3
9.7
Isoleucine
Ile - I
2.3
9.8
Non-Aromatic Amino Acids with Hydroxyl R-Groups
Serine
Ser - S
2.2
9.2
~13
Threonine
Thr - T
2.1
9.1
~13
1.9
10.8
8.3
2.1
9.3
Amino Acids with Sulfur-Containing R-Groups
Cysteine
Cys - C
Methionine
Met-M
.&"%"70&/#0( .&1&/0( %3 %- pK-( *
~2 )&( (COO/H)
.&"*"$)( .&1&/0( %3 %- pK-( *
~9 )&( (COOH)
.&$&75 (10( .&1&/0 /&# 6&/%5/ *
."++1( (1&/0( 63%& "+",''( #-0/
.2/&0- )"(
Aspartic Acid
Asp - D
2.0
9.9
Asparagine
Asn - N
2.1
8.8
Glu - E
2.1
9.5
2.2
9.1
Glutamine
Gln - Q
3.9
Arg - R
1.8
9.0
12.5
Lys - K
2.2
9.2
10.8
6.0
Histidine
His - H
1.8
9.2
Phenylalanine
Phe - F
2.2
9.2
Tyrosine
Tyr - Y
2.2
9.1
Tryptophan
Trp-W
2.4
9.4
2.0
10.6
Hydrophobic
• Aromatic
• Hydroxyl Containing
Basic Amino Acids
Lysine
• Aliphatic (non aromatic)
• Sulfur Containing
4.1
Arginine
Amino Acid Categories (R is… )
• Cyclic
Acidic Amino Acids and their Amides
Glutamic Acid
&*"$) .&1$&5 6&"$
• Acidic and their amides
Amino Acids with Aromatic Rings
Polar
• Basic
10.1
Imino Acids
Proline
Pro - P
*Backbone
25
of the amino acids is red, R-groups are black
Amino (N-)
terminus
Aliphatic amino acids
Carboxy (C-)
terminus
Aromatic amino acids
pK ~ 10.5
Hydrophobicity
Hydrophobicity
Only the aromatic amino acids have strong
absorption in the UV-Vis range
Cyclic amino acids…only one, actually
! !-amino acid -$$ )%
Hydrophobicity
Oxidation
pK ~ 8.4
Reduction
Cys residues can form a crosslink - a
disulfide
Sulfur containing amino acids
Hydroxyl containing amino acids
Acidic amino acids and their amides
pK ~ 3.9
Polar
Polar
Basic amino acids
pK ~ 10.5
pK ~ 12.5
Polar
pK ~ 4.0
Basic amino acids
pK ~ 6.0
pK ~ 10.5
pK ~ 12.5
Polar
pK ~ 6.0
A proteins primary (1°) structure is
its sequence
!"#$%&' (#%)
)”5 :1# - "*&-)#
;-sheet -& !-Helix - "*&"*%'&0$ - "*&-"%!"#$&4"%&) - "*&2"/#&
A tetrapeptide (or oligopeptide):
GluGlyAlaLys
EGAK
A
polypeptide
41
Protein primary sequence can involve crosslinks
and other chemical modifications
Bovine Insulin
(synthesized as a single polypeptide!)
The peptide bond does not freely
rotate
O
O
C
N
C
H
Some Common Chemical Modifications
N
H
Protein 2° Structure:
the "-helix
•
•
•
•
Specific H-bonding pattern: i, i+4
Right handed helix
0.15 nm/residue
3.6 residues/turn
Amino acid side chains are on outside
of the "-helix
Side
view
End
view
Protein 2° Structure: the #-sheet
Side
view
?;-sheet-& !-helix )0&&+ ($%
The peptide bond does not freely
rotate
O
O
C
N
C
H
Peptide bonds highly prefer to be
trans, with one exception…
H
Torsion Angles of the polypeptide
backbone - Phi and Psi
R2
R1
HC"1
HC"2
C
N
H
O
HC"2
C
HC"1
ci
s
Keq = [trans] /
[cis]
R2
O
R1
N
N
H
tran
s
All but Pro*:
"
Keq ! 1000
Pro*:
"
Keq ! 4
* When Pro contributes N-
1950s
"
"
"
"
- Linus Pauling
• Model Building
• Allow on only $ and % to vary
• Look for conformations that
maximize H-bonding
Steric clash between the carbonyl-O
and the amide-H
A Ramachandran Diagram
C"3
Amide H
Carbonyl
C"2
C"1
Pro and Gly are not strictly
confined to these areas…
Zinc finger
Leucine zipper
Helix-Loop-Helix
55