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Cell structure
Nucleoid
• Single strand of DNA, usually circular, usually
looks like a big ball of messed up twine…
• Size – smallest organism yet discovered
(Nanoarchaeum equitans) 490,889 base pairs; e.
coli 4.7 Mbp, most prokaryotes 1-6 million base
pairs (1-6 MBp); Humans 3300 MBp
• DNA is around 1000 mm long in bacteria, while the
organism is on the order of 1 mm long – special
enzymes called gyrases help coil it into a compact
form
Construction, Part 3
• Bases – Two types:
Pyrimidine
Purine
• Derivatives
Cytosine, C
Uracil, U
Thymine, T
DNA  C,T,A,G
No U
Adenine, A
RNA  C,U,A,G
No T
Guanine, G
dNTP’s
• Deoxyribonucleotide triphohosphate
• ATP (the energy-generating molecule) is
the same and the ‘A’ building block – also
GTP, CTP, UTP, TTP
• These react to chain lengthen and form
RNA or DNA – lose 2 of the PO4 groups in
the process
•DNA is double-stranded (double helix), while RNA is single stranded
•RNA has a slightly different sugar backbone – ribose instead of
deoxyribose
•RNA has a lot of turns and kinks, more chaotic structure, but some
sections are closer to the outside than others…
RNA
DNA
Palindromes and DNA
• DNA’s structure is inherently directional
• dNTP’s have bonds on opposite ends that
attach  3’ (OH) and a 5’ (PO4)
• Direction of the ‘code’ 3’  5’
DNA enzymes
• Restriction endonuclease – cuts DNA at specific
base combinations
• DNA ligase – links DNA molecules
• DNA polymerase I – attaches DNTP’s, repairs DNA
• DNA polymerase II – attaches DNTP’s, proofreads
• DNA gyrase – twists, coils DNA
• DNA Helicase – DNA strand separation
• DNAse - degrades DNA to DNTP’s
Data copying inside a cell
• Polymerases – proteins that catalyze different
components of DNA, RNA replication
• DNA replication – occurs by unwinding, copying
each strand, and putting 2 identical pairs
together
• Transcription – formation
of RNA from DNA
• Translation – formation
of proteins from RNA
information
Transcription
RNA polymeraze takes the DNA and temporarily unwinds it, templates the
transfer RNA from that, using ribonucleoside triphosphates to assemble…
Ribosome
• The ribosome is the site of translation of messenger
RNA into protein. It is composed of two subunits.
• In prokaryotes, the large subunit is called 50S and the
small subunit is called 30S. The 30S subunit consists of
a single strand of RNA (the 16S rRNA, 1542 bases), and
21 proteins ranging in molecular weight from 9 kD to 61
kD.
• The 30S subunit is the site of translation initiation.
• Measured by a ‘sedimentation coefficient’ – 16S rDNA is
associated with a 16S sized small subunit of the RNA
translating ribosome
RNA and protein construction
• The nucleotide base sequence of mRNA is encoded
from DNA and transmits sequences of bases used to
determine the amino acid sequence of the protein.
• mRNA (“Messenger RNA”) associates with the ribosome
(mRNA and protein portion).
• RNA (“Transfer RNA”) also required
• Codons are 3 base mRNA segments that specify a
certain amino acid.
• Most amino acids are coded for by more than one
codon.
• Translation ends when ribosome reached “stop codon”
on mRNA.
Ribosomal RNA
• Ribosomal RNA is single stranded
• RNA is a single stranded nucleic acid
– mRNA- messanger RNA – copies information from DNA
and carries it to the ribosomes
– tRNA – transfer RNA – transfers specific amino acids to
the ribosomes
– rRNA – ribosomal RNA – with proteins, assembles
ribosomal subunits
DNA is transcribed to produce mRNA
mRNA then translated into proteins.
Codons
• 64 combinations of bases – 61 of these code for amino
acids, 3 of them signal the end or start of the chain
2nd base
U
1st
ba
se
C
A
G
U
UUU (Phe/F)Phenylalanine
UUC (Phe/F)Phenylalanine
UUA (Leu/L)Leucine
UUG (Leu/L)Leucine
UCU (Ser/S)Serine
UCC (Ser/S)Serine
UCA (Ser/S)Serine
UCG (Ser/S)Serine
UAU (Tyr/Y)Tyrosine
UAC (Tyr/Y)Tyrosine
UAA Ochre (Stop)
UAG Amber (Stop)
UGU (Cys/C)Cysteine
UGC (Cys/C)Cysteine
UGA Opal (Stop)
UGG (Trp/W)Tryptophan
C
CUU (Leu/L)Leucine
CUC (Leu/L)Leucine
CUA (Leu/L)Leucine
CUG (Leu/L)Leucine
CCU (Pro/P)Proline
CCC (Pro/P)Proline
CCA (Pro/P)Proline
CCG (Pro/P)Proline
CAU (His/H)Histidine
CAC (His/H)Histidine
CAA (Gln/Q)Glutamine
CAG (Gln/Q)Glutamine
CGU (Arg/R)Arginine
CGC (Arg/R)Arginine
CGA (Arg/R)Arginine
CGG (Arg/R)Arginine
A
AUU (Ile/I)Isoleucine
AUC (Ile/I)Isoleucine
AUA (Ile/I)Isoleucine
1
AUG (Met/M)Methionine, Start
ACU (Thr/T)Threonine
ACC (Thr/T)Threonine
ACA (Thr/T)Threonine
ACG (Thr/T)Threonine
AAU (Asn/N)Asparagine
AAC (Asn/N)Asparagine
AAA (Lys/K)Lysine
AAG (Lys/K)Lysine
AGU (Ser/S)Serine
AGC (Ser/S)Serine
AGA (Arg/R)Arginine
AGG (Arg/R)Arginine
G
GUU (Val/V)Valine
GUC (Val/V)Valine
GUA (Val/V)Valine
GUG (Val/V)Valine
GCU (Ala/A)Alanine
GCC (Ala/A)Alanine
GCA (Ala/A)Alanine
GCG (Ala/A)Alanine
GAU (Asp/D)Aspartic acid
GAC (Asp/D)Aspartic acid
GAA (Glu/E)Glutamic acid
GAG (Glu/E)Glutamic acid
GGU (Gly/G)Glycine
GGC (Gly/G)Glycine
GGA (Gly/G)Glycine
GGG (Gly/G)Glycine
Anticodons – the opposite sequence (G-C U-A) on the transfer RNA
Translation
• mRNA is coded for one or more specific
amino acids and moves to the ribosome to
assemble amino acids into proteins
• On mRNA, codons are 3 bases, coded to
specific amino acids
• On tRNA, the anticodon
latches to the codon
on the mRNA
Translation =
Protein Formation
•
The ‘code’ on
mRNA determines
the sequence of
protein assembly
•
Codon-anticodon?