Cell structure

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Cell structure
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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

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Construction, Part 3

• Bases Two types
• Pyrimidine Purine
• Derivatives

Cytosine, C
Uracil, U
Thymine, T
Adenine, A
Guanine, G
DNA ? C,T,A,G No U
RNA ? C,U,A,G No T
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dNTPs

• 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

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• 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
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Palindromes and DNA

• DNAs structure is inherently directional
• dNTPs have bonds on opposite ends that attach ?
  3 (OH) and a 5 (PO4)
• Direction of the code 3 ? 5

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DNA enzymes

• Restriction endonuclease cuts DNA at specific
  base combinations
• DNA ligase links DNA molecules
• DNA polymerase I attaches DNTPs, repairs DNA
• DNA polymerase II attaches DNTPs, proofreads
• DNA gyrase twists, coils DNA
• DNA Helicase DNA strand separation
• DNAse - degrades DNA to DNTPs

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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

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Transcription
RNA polymeraze takes the DNA and temporarily
unwinds it, templates the transfer RNA from that,
using ribonucleoside triphosphates to assemble
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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

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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.

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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.
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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 2nd base 2nd base 2nd base
U C A G
1stbase U UUU (Phe/F)PhenylalanineUUC (Phe/F)PhenylalanineUUA (Leu/L)LeucineUUG (Leu/L)Leucine UCU (Ser/S)SerineUCC (Ser/S)SerineUCA (Ser/S)SerineUCG (Ser/S)Serine UAU (Tyr/Y)TyrosineUAC (Tyr/Y)TyrosineUAA Ochre (Stop)UAG Amber (Stop) UGU (Cys/C)CysteineUGC (Cys/C)CysteineUGA Opal (Stop)UGG (Trp/W)Tryptophan
1stbase C CUU (Leu/L)LeucineCUC (Leu/L)LeucineCUA (Leu/L)LeucineCUG (Leu/L)Leucine CCU (Pro/P)ProlineCCC (Pro/P)ProlineCCA (Pro/P)ProlineCCG (Pro/P)Proline CAU (His/H)HistidineCAC (His/H)HistidineCAA (Gln/Q)GlutamineCAG (Gln/Q)Glutamine CGU (Arg/R)ArginineCGC (Arg/R)ArginineCGA (Arg/R)ArginineCGG (Arg/R)Arginine
1stbase A AUU (Ile/I)IsoleucineAUC (Ile/I)IsoleucineAUA (Ile/I)IsoleucineAUG (Met/M)Methionine, Start1 ACU (Thr/T)ThreonineACC (Thr/T)ThreonineACA (Thr/T)ThreonineACG (Thr/T)Threonine AAU (Asn/N)AsparagineAAC (Asn/N)AsparagineAAA (Lys/K)LysineAAG (Lys/K)Lysine AGU (Ser/S)SerineAGC (Ser/S)SerineAGA (Arg/R)ArginineAGG (Arg/R)Arginine
1stbase G GUU (Val/V)ValineGUC (Val/V)ValineGUA (Val/V)ValineGUG (Val/V)Valine GCU (Ala/A)AlanineGCC (Ala/A)AlanineGCA (Ala/A)AlanineGCG (Ala/A)Alanine GAU (Asp/D)Aspartic acidGAC (Asp/D)Aspartic acidGAA (Glu/E)Glutamic acidGAG (Glu/E)Glutamic acid GGU (Gly/G)GlycineGGC (Gly/G)GlycineGGA (Gly/G)GlycineGGG (Gly/G)Glycine
Anticodons the opposite sequence (G-C U-A) on
the transfer RNA
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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

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• Translation
• Protein Formation
• The code on mRNA determines the sequence of
  protein assembly
• Codon-anticodon?

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