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 m long in bacteria, while the organism is on the order of 1 m 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 Adenine, A Guanine, G

DNA C,T,A,GNo U

RNA C,U,A,GNo T

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…

DNA

RNA

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 – formationof RNA from DNA

• Translation – formationof proteins from RNA information

TranscriptionRNA 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 mRNAmRNA 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 chain2nd 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

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

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

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

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?