credit: modification of work by NIH Chapter 15 General Biology I BSC 2010 Genes and Proteins credit: modification of work by NIH

credit: National Human Genome Research Institute Genes credit: National Human Genome Research Institute Genes are tangible molecular entities composed of DNA and capable of replication, expression, and mutation.

Download for free at http://cnx.org/content/col11448/latest/ The Central Dogma Download for free at http://cnx.org/content/col11448/latest/

The Central Dogma a sequence of DNA nucleotides colinear DNA a sequence of DNA nucleotides RNA polymerase does transcription. RNA a sequence of RNA nucleotides Ribosomes and transfer RNA do translation. polypeptide protein a sequence of amino acids

The Genetic Code is Degenerate, Universal, and Unambiguous Codons are 3-letter RNA sequences. The reading frame is maintained as long as no nucleotides (letters) are inserted or removed. credit: modification of work by NIH credit: modification of work by NIH

Frameshift Mutations Disrupt the Reading Frame Download for free at http://cnx.org/content/col11448/latest/

Polypeptides are Chains of Amino Acids Download for free at http://cnx.org/content/col11448/latest/

Prokaryote Transcription Download for free at http://cnx.org/content/col11448/latest/ Prokaryotes typically have a single chromosome where the genes are located. They may also have plasmids (short circular pieces of DNA containing a few “bonus” genes). Transcription occurs for individual genes. Not all genes are “expressed” (transcribed) at all times.

Transcription Begins at the Promoter of a Gene Download for free at http://cnx.org/content/col11448/latest/ The promoter is a region of the DNA having a specific sequence. It is “upstream” of the gene’s coding region. There are consensus sequences at -10 and -35.

Three Phases of Transcription Initiation – RNA polymerase attaches to the promoter. Elongation – RNA polymerase uses the DNA as a template to assemble a complementary sequence of RNA nucleotides. Note: RNA that is eventually translated to make a polypeptide is called “messenger” RNA (mRNA). Termination – RNA polymerase and the new RNA dissociate from the DNA.

Prokaryotic Transcription video link DNA Non-Template (coding) strand DNA Template strand Download for free at http://cnx.org/content/col11448/latest/ Termination, the end of transcription, is a mechanical phenomenon involving collision (Rho-dependent termination) or hairpin structures (Rho-independent termination).

Multiple Polymerases Can Transcribe a Single Gene Download for free at http://cnx.org/content/col11448/latest/

Eukaryote Transcription is Similar to Prokaryote Transcription Eukaryotes have multiple nuclear chromosomes where the genes are located. They also have mitochondrial DNA. Transcription occurs for individual genes. Not all genes are “expressed” (transcribed) at all times. Download for free at http://cnx.org/content/col11448/latest/

Eukaryotic RNA Polymerases Download for free at http://cnx.org/content/col11448/latest/

Eukaryotic Genes Have Promoters The TATA box at -30 has the sequence TATAAA. Regulation of transcription is complex, involving many transcription factors. Download for free at http://cnx.org/content/col11448/latest/

Eukaryotic mRNAs Must Undergo Splicing and Processing Download for free at http://cnx.org/content/col11448/latest/ Eukaryotic mRNA contains introns that must be spliced out. A 5’ cap and poly-A tail are also added.

mRNA Splicing Splicing involves precise removal of introns. Spliceosomes recognize sequences at the 5’ and 3’ end of the intron. Alternative splicing is possible. Download for free at http://cnx.org/content/col11448/latest/

Translation Involves tRNAs (transfer RNAs) tRNAs have amino acid attachment sites and anticodons. They can translate the mRNA nucleotide language into the protein amino acid language, according to the genetic code. Many copies of up to 60 types of tRNAs exist in the cytoplasm. Download for free at http://cnx.org/content/col11448/latest/

Aminoacyl tRNA Synthetases are Enzymes A tRNA becomes “charged” when an aminoacyl tRNA synthetase adds an amino acid to it. They use ATP energy to charge the tRNA. They are able to “read” the tRNA anticodon and select the corresponding amino acid (based on the genetic code).

Translation Happens at Ribosomes Translation has initiation, elongation, and termination phases. In E. coli, the Shine- Dalgarno sequence in the mRNA attaches to the ribosome. Ribosome small and large subunits assemble together around the mRNA. Download for free at http://cnx.org/content/col11448/latest/

Ribosome Structure Parts of the ribosome are made of rRNA (ribosomal RNA). Other parts are made of protein. There are two subunits (large and small). An important part is the enzymatic portion called peptidyl transferase.

Peptide Bonds Link the Amino Acids Amino end of chain Carboxyl end of chain Download for free at http://cnx.org/content/col11448/latest/ Peptide bonds are covalent bonds, created by the peptidyl transferase of the ribosome. Protein synthesis involves making “polypeptide” chains.

Protein Folding, Modifications, and Targeting Recall that polypeptide chains fold into secondary and tertiary shapes. They may also be involved in quaternary structures. Modification examples include addition of functional groups (as in phosphorylation) and cleavage into smaller pieces. In targeting, polypeptides are directed to specific cellular locations via a signal sequence at the end of the chain.

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