The most common nucleotides

Image of the DNA

double-helix in a
space filling
model
Schematic representation of the DNA which illustrates its double helix structure
DNA under electron microscope
The cells of eukaryotes and prokaryotes. - This figure illustrates a typical human cell
(eukaryote) and a typical bacterium (prokaryote). The drawing on the left highlights the
internal structures of eukaryotic cells, including the nucleus (light blue), the nucleolus
(intermediate blue), mitochondria (orange), and ribosomes (dark blue). The drawing on
the right demonstrates how bacterial DNA is housed in a structure called the nucleoid
(very light blue), as well as other structures normally found in a prokaryotic cell,
including the cell membrane (black), the cell wall (intermediate blue), the capsule
(orange), ribosomes (dark blue), and a flagellum (also black).
DNA replication. In the first step, a portion of the double helix (blue) is unwound by a helicase.
Next, a molecule of DNA polymerase (green) binds to one strand of the DNA. It moves along
the strand, using it as a template for assembling a leading strand (red) of nucleotides and
reforming a double helix. A second DNA polymerase molecule (also green) is used to bind to
the other template strand as the double helix opens. This molecule must synthesize
discontinuous segments of polynucleotides (called Okazaki fragments). Another enzyme, DNA
ligase (violet), then stitches these together into the lagging strand.
James Watson in the Cavendish Laboratory at the University of Cambridge
Crick and Watson DNA model built in 1953, currently on display at the National
Science Museum in London.
 Francis Crick's first
sketch of the
deoxyribonucleic
acid double-helix
pattern

DNA replication
The chemical structure of DNA
This stylistic schematic diagram shows a gene in relation to the double helix structure
of DNA and to a chromosome (right). Introns are regions often found in eukaryote
genes which are removed in the splicing process: only the exons encode the protein.
This diagram labels a region of only 40 or so bases as a gene. In reality many genes are
much larger.
Thymine and Uracil were incorrectly depicted in the previous version. Guanine and
Adenine are still incorrect (Guanine has a C with 5 bonds and an H with 4 bonds;
Adenine has a C with 5 bonds). Better version of the image is needed.
RNA codons.
 This table shows the 64 codons and the amino acid each codon codes for.

2nd base
U C A G
UUU (Phe/F)Phenylalanine UCU (Ser/S)Serine UAU (Tyr/Y)Tyrosine UGU (Cys/C)Cysteine
UUC (Phe/F)Phenylalanine UCC (Ser/S)Serine UAC (Tyr/Y)Tyrosine UGC (Cys/C)Cysteine
UUA (Leu/L)Leucine UCA (Ser/S)Serine UAA Ochre (Stop) UGA Opal (Stop)
U UUG (Leu/L)Leucine, Start UCG (Ser/S)Serine UAG Amber (Stop) UGG (Trp/W)Tryptophan

CUU (Leu/L)Leucine CCU (Pro/P)Proline CAU (His/H)Histidine CGU (Arg/R)Arginine

CUC (Leu/L)Leucine CCC (Pro/P)Proline CAC (His/H)Histidine CGC (Arg/R)Arginine
CUA (Leu/L)Leucine CCA (Pro/P)Proline CAA (Gln/Q)Glutamine CGA (Arg/R)Arginine
C CUG (Leu/L)Leucine, Start CCG (Pro/P)Proline CAG (Gln/Q)Glutamine CGG (Arg/R)Arginine

1st
base AUU (Ile/I)Isoleucine, Start
2
ACU (Thr/T)Threonine AAU (Asn/N)Asparagine AGU (Ser/S)Serine
AUC (Ile/I)Isoleucine ACC (Thr/T)Threonine AAC (Asn/N)Asparagine AGC (Ser/S)Serine
AUA (Ile/I)Isoleucine ACA (Thr/T)Threonine AAA (Lys/K)Lysine AGA (Arg/R)Arginine
A AUG (Met/M)Methionine, Start
1
ACG (Thr/T)Threonine AAG (Lys/K)Lysine AGG (Arg/R)Arginine

GUU (Val/V)Valine GCU (Ala/A)Alanine GAU (Asp/D)Aspartic acid

GUC (Val/V)Valine
GUA (Val/V)Valine
G GUG (Val/V)Valine, Start
2
GCC (Ala/A)Alanine GAC (Asp/D)Aspartic acid GGU (Gly/G)Glycine
GCA (Ala/A)Alanine GAA (Glu/E)Glutamic acid GGC (Gly/G)Glycine
GCG (Ala/A)Alanine GAG (Glu/E)Glutamic acid GGA (Gly/G)Glycine
GGG (Gly/G)Glycine

1The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's
coding region is where translation into protein begins.
2This is a start codon for prokaryotes only.
 This table shows the 20 amino acids used in proteins, and the codons that
code for each amino acid.

Ala A GCU, GCC, GCA, GCG Leu L UUA, UUG, CUU, CUC,
CUA, CUG
Arg R CGU, CGC, CGA, CGG, AGA, AGG Lys K AAA, AAG
Asn N AAU, AAC Met M AUG
Asp D GAU, GAC Phe F UUU, UUC
Cys C UGU, UGC Pro P CCU, CCC, CCA, CCG
Gln Q CAA, CAG Ser S UCU, UCC, UCA, UCG,
AGU,AGC
Glu E GAA, GAG Thr T ACU, ACC, ACA, ACG
Gly G GGU, GGC, GGA, GGG Trp W UGG
His H CAU, CAC Tyr Y UAU, UAC
Ile I AUU, AUC, AUA Val V GUU, GUC, GUA, GUG
Start AUG, GUG Stop UAG, UGA, UAA
Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). Side
and front view.
(1) Head. (2) Platform. (3) Base. (4) Ridge. (5) Central protuberance. (6) Back. (7)
Stalk. (8) Front.
Figure 2 : Large (1) and small (2) subunit fit together
Figure 3 : Translation of mRNA (1) by a ribosome (2) into a polypeptide chain (3).
The mRNA begins with a start codon (AUG) and ends with a stop codon (UAG).
The "life cycle" of an mRNA in a eukaryotic cell. RNA is transcribed in the nucleus;
once completely processed, it is transported to the cytoplasm and translated by the
ribosome. At the end of its life, the mRNA is degraded.
The structure of a mature eukaryotic mRNA. A fully processed mRNA includes a 5'
cap, 5' UTR, coding region, 3' UTR, and poly(A) tail.
Structure of tRNA
Detection of Plant Viruses

Molecular biological assay

RNA or DNA based assay

Polymerase Chain Reaction

(PCR)
Viral RNA
cDNA

DETEKSI SECARA PCR

Viral RNA
cDNA
Denature, 94 C
Anneal,50-55 C
Extension,72 C
Viral RNA
cDNA
Denature, 94 C
Anneal,50-55 C
Extension,72 C

Chain Reaction
Viral RNA
cDNA
Denature, 94 C
Anneal,50-55 C
Extension,72 C

Chain Reaction

PCR DNA
Use electrophoresis to detect PCR DNA
M TSWV M

1700
1600

1016

516
 CuYV RNA 1

ORF 1 ORF 2 ORF 3 ORF 5 ORF 7

p59
5` CPd 3`
4 HSP70 9 CP
ORF 4 ORF 6

A 529 bp C
529 kDa
Primer CP-5
B ataggatccGACGTTTTGAACACTCAGG(+)
Primer CP-6 ataaagcttCATAAGAAGCCAATTGGG ( - )

Schematic diagram of BPYV-CP expression construct (A);primers CP-5 and CP-6 with BamHI and HindIII
restriction site (underline), respectively (B); and RT-PCR-amplified product of CP.
Consensus TCAAACCGCT TTATGTCGTG AAATTAGTAG GGAATGATGT CTATTWWACT GGTGTGAACA 60
CuYV-Japan .......... .......... .......... .......... .....AT... .......... 60
CuYV-Indonesia .......... .......... .......... .......... .....TA... .......... 60
CuYV-Vietnam .......... .......... .......... .......... .....TA... .......... 60

Consensus AGGGTTTCTC TTGTACCTAT ACAGTCAAAC AACTCATTCT TCTATTTATT GATACGATGG 120

CuYV-Japan .......... .......... .......... .......... .......... .......... 120
CuYV-Indonesia .......... .......... .......... .......... .......... .......... 120
CuYV-Vietnam .......... .......... .......... .......... .......... .......... 120

Consensus TAAGGTTGTT TTCAAAAACA AATRATTTAA ATATTATTAG TCTTAATGTC TCTGTCCCGG 180

CuYV-Japan .......... .......... ...A...... .......... .......... .......... 180
CuYV-Indonesia .......... .......... ...A...... .......... .......... .......... 180
CuYV-Vietnam .......... .......... ...G...... .......... .......... .......... 180

Consensus CAGATTATAA GTGCAAACAA CGAATGTTCA TGAAATCAGT TTGTGATTCG TTGAACTTTT 240

CuYV-Japan .......... .......... .......... .......... .......... .......... 240
CuYV-Indonesia .......... .......... .......... .......... .......... .......... 240
CuYV-Vietnam .......... .......... .......... .......... .......... .......... 240

Consensus CACTCCGGAG AATAATTAAT GAACCGTCTG CWGCAGCGAT TTATTCCGT 289

CuYV-Japan .......... .......... .......... .A........ ......... 289
CuYV-Indonesia .......... .......... .......... .T........ ......... 289
CuYV-Vietnam .......... .......... .......... .A........ ......... 289

Gambar 3. Perbandingan sekuen dari fragmen gen HSP70 (289 nukleotida)

dari tiga isolat CuYV, Jepang, Indonesia dan Vietnam.
 670 680 690 700 710 720
TTCTTTTGGATTTTATTCTTAGTCATAAACACGATGCAAGCGAAGGTGGGTTTGGACTTT
F F W I L F L V I N T M Q A K V G L D F
S F G F Y S * S * T R C K R R W V W T L
F L L D F I L S H K H D A S E G G F G L

730 740 750 760 770 780

GGTACAACTTTCAGTACCATTAGTTCTTTCACCAATGGAGAGATGAAGACTCTGTATGTG
G T T F S T I S S F T N G E M K T L Y V
V Q L S V P L V L S P M E R * R L C M *
W Y N F Q Y H * F F H Q W R D E D S V C

790 800 810 820 830 840

AACAACTCACCTTACATCCCCACTTGTTTGTCCATTTCATCTGAAGGTGATGTGATCATT
N N S P Y I P T C L S I S S E G D V I I
T T H L T S P L V C P F H L K V M * S L
E Q L T L H P H L F V H F I * R * C D H

850 860 870 880 890 900

GGGAGCGCCGCACAAGTCATCGATGAGTCAGAAGTTAAATCTTGTTACTTTTATGATCTC
G S A A Q V I D E S E V K S C Y F Y D L
G A P H K S S M S Q K L N L V T F M I S
W E R R T S H R * V R S * I L L L L * S
 0 5 10 15 20 kb

P-PRO MTR HEL P6 P64 CP P21

BYV (15.5 kb) RdRp HSP70 CPd P20

P-PRO MTR HEL P33 P6 P61 CP P13 P23

CTV (19.3 kb) RdRp HSP70 CPd P18 P20

P-PRO MTR HEL P4 P64 CPd P27

LChV-1 (16.9 kb) RdRp HSP70 CP P26

RNA1 RNA2
P-PRO MTR HEL P32 P5 P59 CPd

LIYV (15.3 kb) RdRp HSP70 P9 CP P26

RNA2 RNA1
P-PRO MTR HEL P4 P59 CPd

CuYV (15.5 kb) RdRp HSP70 P9 CP P26

Fig. Comparison of the genome organization of CuYV with BYV, CTV, LChV-1 and LIYV. Boxes
represent ORFs, and homologous genes are shade similarly. Open boxes indicate ORFs that
encoded proteins whose functions are unknown or that are not statistically similar to other virus
proteins. The scale indicates size in kb.