Context Cell nucleus chromosome gene double helix

DNA vs RNA : Structure Double helix Deoxyribose A - T pair Single helix Ribose sugar A - U pair

DNA vs RNA : Function segments of the sequence - genes - code for polypeptides rewrites and translates the code into polypeptides (proteins)

Types of RNA Messenger, mRNA, is synthesized from a gene and carries the code into the cytoplasm for protein synthesis Si RNA is double stranded

Types of RNA amino acid Transfer (tRNA) loops of nucleotides, three of which form an anticodon. Also holds the amino acid coded for by the mRNA codon complement. The polypeptide is built by linking the amino acids of adjacent tRNA. Si RNA is double stranded anticodon

Types of RNA Ribsomal, rRNA, combines with protein in the cytoplasm to form a ribosome Synthesized in two sub units Si RNA is double stranded

Types of RNA Small, interfering RNA (siRNA) RNA interference (RNAi) small sequences of silencing RNA (siRNA) bind to cellular RNA, thereby interfering with the production of the encoded protein Si RNA is double stranded application

The Ribosome • The site of protein synthesis • holds mRNA/tRNA in position as the protein is synthesized tRNA sites mRNA site

Context Cell nucleus chromosome gene double helix

The Central Dogma gene expression Reading & expressing genes Genes in the DNA are transcribed into RNA which is translated into a sequence of amino acids Fundamental & universal to life on Earth overview

Peptide bonds link amino acids in order tRNA base pair with mRNA at ribosomes mRNA carries the gene code from the nucleus rRNA builds the ribosome subunits animation

Transcription is initiated when RNA polymerase binds at DNA ‘upstream’ of the gene, called the promoter http://www.nature.com/scitable/topicpage/dna-transcription-426 The first step in transcription is initiation, when the RNA polymerase binds to the DNA upstream (5′) of the gene at a specialized sequence called a promoter. In bacteria, promoters are usually composed of three sequence elements, whereas in eukaryotes, there are as many as seven elements. In eukaryotes, the "core" promoter for a gene transcribed by pol II is most often found immediately upstream (5′) of the start site of the gene. Most pol II genes have a TATA box (consensus sequence TATTAA) 25 to 35 bases upstream of the initiation site, which affects the transcription rate and determines location of the start site. The terms "strong" and "weak" are often used to describe promoters and enhancers, according to their effects on transcription rates and thereby on gene expression. Alteration of promoter strength can have deleterious effects upon a cell, often resulting in disease. For example, some tumor-promoting viruses transform healthy cells by inserting strong promoters in the vicinity of growth-stimulating genes, while translocations in some cancer cells place genes that should be "turned off" in the proximity of strong promoters or enhancers. Terminator sequences are found close to the ends of coding sequences. Elongation – polymerase adds nucleotides to transcribe the gene. Termination sequences near the end of the gene communicate a stop-transcription message

DNA as Template • The strand with the gene is the base-pair template (or anti-sense) for the mRNA nearly the same as mRNA code coding (sense) strand The template strand is ALWAYS read in the 3' to 5' direction (that is, starting from the 3' end of the template and reading the nucleotides in order toward the 5' end of the template). The new strand (since it is complementary) MUST BE SYNTHESIZED in the 5' to 3' direction (remember that both strands of a DNA molecule are described as being antiparallel). Polymerase catalyzes the formation of the hydrogen bonds between each arriving nucleotide and the nucleotides on the template strand. In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5' phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide (what we know is called a phosphodiester bond!). As a result, the new DNA strands can grow only in the 5' to 3' direction, and strand growth must begin at the 3' end of the template, anti-sense strand complementary to mRNA

3’ 5’ Template & Direction Nucleotides can only form phosphodiester bonds in the 5’ to 3’ direction. mRNA is thus built from 5’->3’, anti-parallel to a 3” -> 5” DNA template 5’? 3’? Numbered carbons in the nucleotide sugar 3’ 5’ Want more?

mRNA transcript built 5’ -> 3’ 5’ 3’ 5’ 3’ DNA template read from 3’ -> 5’

Template & Direction 5’ 3’ 3’ 5’ DNA template read from 3’ -> 5’ Template and mRNA are anti-parallel coding 5’ 3’ 3’ 5’ anti-sense The template strand is ALWAYS read in the 3' to 5' direction (that is, starting from the 3' end of the template and reading the nucleotides in order toward the 5' end of the template). The new DNA strand (since it is complementary) MUST BE SYNTHESIZED in the 5' to 3' direction (remember that both strands of a DNA molecule are described as being antiparallel). DNA polymerase catalyzes the formation of the hydrogen bonds between each arriving nucleotide and the nucleotides on the template strand. In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5' phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide (what we know is called a phosphodiester bond!). As a result, the new DNA strands can grow only in the 5' to 3' direction, and strand growth must begin at the 3' end of the template, (mnemonics: DNA = 3 write = 5) DNA template read from 3’ -> 5’ mRNA transcript built 5’ -> 3’

The code is redundant but never ambiguous 6 codons for serine! CCC = proline, only

Genes are modified before translation Introns are excised (cut out) Exons are spliced together splicesomes Can occur in multiple ways, creating many mRNA from one gene Ex: 30,000 genes, +100,000 proteins

Caps and tails are added to the mRNA, slowing destruction by enzymes STOP Codon START codon Methyl CAP at 5’ end Poly–A TAIL

Mutations in the DNA change the code and sometimes the protein Point mutation/substitution Potentially changes one amino acid - missense

Frameshift mutations result from insertion or deletion of nucleotides Alters the codons from that point on http://www.youtube.com/watch?v=kp0esidDr-c

siRNA can silence genes si = small interfering, or silencing aka RNAi, for interference small sequences of silencing RNA bind to RNA transcript, thereby interfering with the production of the encoded protein Si RNA is double stranded application

Summary of Differences Replication Transcription & Translation Copies both DNA helices Uses template strand of DNA to create RNA Leads to more cells Leads to proteins (gene expression) Entire molecule copied Single gene transcribed, exons spliced together DNA polymerase adds nucleotide RNA polymerase adds nucleotides RNA primer initiates sequencing Promoter on DNA initiates sequencing