Eukaryotic Genome Control Mechanisms for Gene Expression AP Biology Eukaryotic Genome Control Mechanisms for Gene Expression

What is the condition of DNA during transcription? It is loose What is this loose condition called? Chromatin Why is this condition necessary during transcription? It provides easy access for the RNA to get in to work and copy the DNA Like a bowl of spaghetti

What is the condition of the DNA during mitosis and meiosis? It is tightly wound up What is the tightly wound condition called? Chromosomes Why is this condition necessary during mitosis and meiosis? To allow for easy and equal separation of the DNA Chromosomes form an X shape

A description of prokaryote chromosomes is that they are ….. Circular The chromosomes of eukaryotes is…. Linear

What are histones? Proteins that DNA wraps around in order to condense more easily Why does DNA wrap around these proteins? Because DNA has a negative charge (because of the phosphate groups) The histone have a positive charge This attraction (like a magnet) causes the wrapping

Both eukaryotes and archaebacteria have histones Why do many scientists consider eukaryotes to be more closely related to archaebacteria than to eubacteria? Both eukaryotes and archaebacteria have histones histones

What is a nucleosome? The whole unit of the DNA wrapped around a group of histones

The process by which the DNA condenses from chromatin to chromosomes What is supercoiling? The process by which the DNA condenses from chromatin to chromosomes What is heterochromatin? DNA that remains condensed, even during interphase (different than normal) It is not active and no transcription can occur on it heterochromatin

The loose DNA (true) that is active during interphase What is euchromatin? The loose DNA (true) that is active during interphase Transcription actively take place on it euchromatin

What is cell differentiation or specialization? The process of making cells different How does this happen? Certain genes are “turned on” or “turned off” This is called differential gene experssion

What occurs when genes are “turned on”? They make proteins What happens when gene control does not work properly? Death or cancer can result

What are some gene control mechanisms that occur during transcription? DNA methylation Histone acetylation Enhancers and activators Repressors or silencers Coordinated control Micro RNA and small interfering RNA

What is DNA methylation? A heavy coat of methyl groups is put around the DNA This prevents transcription The methyl group attaches to the cytosine or adenine This is called genomic imprinting and effectively erases the information on the DNA at that point

What is histone acetylation? The attachment of acetyl groups to the histones This breaks the bond between the DNA and histone The positive charge is covered up, so there is no attraction any more This allows RNA Polymerase to attach to the DNA to free up the transcription process

What are enhancers and activators? They control the rate of transcription They move the transcription factory down the DNA faster Often called “pushers” because they are always in front of the gene being transcribed

What are repressors or silencers? They prevent transcription from occurring by sitting on the TATA box This represses the gene from being expressed They are also controlling the rate of transcription

What is coordinated control? One chemical signal can cause expression of multiple copies of the same gene This is referred to as the gene family This is like the bell signaling all classes to move at the same time

What is micro RNA (miRNA) and small interfering RNA (siRNA)? Little pieces of RNA that attach to the messenger RNA and control transcription

What is post transcription regulation? Controls that occur after transcription What is alternative RNA Splicing using splicesomones? Changing the primary mRNA into the secondary mRNA

What is cytoplasmic degradation? Removal of the caps and tails on the mRNA Then nucleotides are catabolized and recycled The longer the Poly A Tail, the longer the mRNA will survive in the cytoplasm

What are translation control mechanisms? Building the translation initiation complex Controls can occur in a step by step process If there is a faulty 5’cap, translation will not occur

What is post translation control mechanisms? Controls that function after the translation is complete What are some examples? Chaperonins Phosphorylation Proteosomes

What are chaperonins? Proteins that provide a safe, protected area for newly produced proteins to fold up

What is phosphorylation? Using an ATP molecule to add a phosphate group onto the protein

What determines the transport of the proteins? Whether they will remain in the cytoplasm or will go out of the cell If remaining in the cell, they will go to the chaperonin If leaving the cell, they will go to the RER

What are proteosomes? They are special lysosomes that will determine how long the protein will last They digest the A’s off the Poly A Tail

Chromatin vs. Chromosomes appearance within the cell.

Histone Proteins and Supercoiling 2 nm DNA double helix His- tones Histone tails Histone H1 10 nm Linker DNA (“string”) Nucleosome (“bead”) Nucleosomes (10-nm fiber)

Supercoiling of Chromatin

Euchromatin vs. Heterochromatin (The dark spots are the hetero)

DNA Control stages in Protein Synthesis Signal NUCLEUS Chromatin DNA Gene available for transcription Gene Transcription RNA Exon Primary transcript Intro RNA processing Tail Cap mRNA in nucleus Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Degradation of mRNA Translation Polypeptide Cleavage Chemical modification Transport to cellular destination Active protein Degradation of protein Degraded protein

Methylation

. Histone tails DNA double helix Amino acids available for chemical modification Histone tails protrude outward from a nucleosome Unacetylated histones Acetylated histones Acetylation of histone tails promotes loose chromatin structure that permits transcription

“Build the factory”

Enhancers Distal control element Activators Promoter Gene DNA Enhancer TATA box General transcription factors DNA-bending protein Group of mediator proteins RNA polymerase II RNA polymerase II Transcription Initiation complex RNA synthesis

Notice the different nucleotide control sequences (red vs, pink) Liver cell nucleus Lens cell nucleus Available activators Available activators Enhancer Promoter Control elements Albumin gene Albumin gene not expressed Crystallin gene Albumin gene expressed Crystallin gene not expressed Crystallin gene expressed Liver cell Lens cell

miRNA &siRNA Protein complex Degradation of mRNA Dicer OR miRNA Target mRNA Hydrogen bond Blockage of translation

Control of exons

How many As on the tail?

“Build the factory”

Chaperonin Protein will stay in the cell

RER Protein will leave the cell

Proteosomes Proteasome and ubiquitin to be recycled Ubiquitin Protein to be degraded Ubiquitinated protein Protein fragments (peptides) Protein entering a proteasome