Protein+Synthesis

=Notes:= One gene- One polypeptide Hypothesis: · Garrod noticed that certain illnesses run in families · He analyzed a certain disorder, and hypothesized that it was caused by a lack of an enzyme, and that this deficiency was passed down through families · He hypothesized that hereditary material determines the presence of enzymes · Beadle & Tatum demonstrated Garrod’s hypothesis: o They exposed normal bread mold to UV light, mutating it   o By selectively adding to a minimal media they were able to determine where mutations occurred in a sequence by examining growth and accumulation

A à enz.1 à B à enz.2 à C à enz. 3 à D   · Ingram discovered that enzymes place certain amino acids accordingly · Messing up one amino acid can cause things like sickle cell anemia

Here is an animation that you might find useful for the history and discovery of this hypothesis: []

Protein Synthesis- Introduction: · Central Dogma: DNA à mRNA à polypeptide (protein)



· DNA stays inside the nucleus, so it must be transcribed into RNA to be used in the cytoplasm · mRNA (messenger RNA) moves from the nucleus to the ribosomes in the cytoplasm · ribosomes translate the message into polypeptides · Protein Synthesis has 2 main steps:

TRANSCRIPTION: · In nucleus · Copy DNA into mRNA: 1. __Initiation__: RNA polymerase binds to DNA 2. __Elongation__: RNA polymerase builds mRNA 3. __Termination__: A stop code is reached; ends process

TRANSLATION: · In cytoplasm · Building of protein from mRNA: 1. __Initiation__: ribosome recognizes a sequence on mRNA 2. __Elongation__: tRNA delivers amino acids to ribosome 3. __Termination__: a stop codon is reached; polypeptide is released

Ribonucleic Acid (RNA): · 5 carbon sugar ribose · 4 different nucleotides: adenine, guanine, cytosine, and uracil (in place of thymine) · Single stranded · Found in nucleus (mRNA) and cytoplasm (mRNA, tRNA, rRNA)

Here are some quizzes that you might want to take a look at: [] [] - -- (this one is really good, make sure to click and go through all the tabs at the top. They include brief summaries and activities, and a final quiz at the end) [] --- (this one has a bit of review of DNA synthesis at the beginning, up until about question 10) For Margaret, maybe not for this semester, but maybe next semester, here are a few activities that you might try: []

Sarah Dunn

5.2

**Codons:**
- sequence of 3 nitrogenous baes that codes for a specific amino acid - multiple codons code for one amino acids sometimes - AUG is usually start code - UAA, UAG, UGA are stop codons

=Lesson for 5.3 & 5.4. Transcription and Translation.= January 4, 2011 Christopher Chung

5.3 Transcription
- The process of creating an mRNA strand that is a copy of a gene

1. Initiation:

 * RNA polyermase binds to promoter (a set of A & T's that are upstream of the gene)
 * Opens up double helix
 * **Upstream**: Region of DNA before the start of gene

2. Elongation:
3. Termination:
 * Builds 5' to 3'
 * Uses a **template strand** -> leftover strand is coding strand
 * mRNA becomes clone of coding strand (with the exception of uracil)
 * Promoter not transcribed
 * Polymerase comes to terminator sequence where the mRNA then dissociates
 * RNA polymerase moves onto next promoter

Posttranscriptional Modifications:

 * In eukaryotes, the primary transcript (made in nucleus) needs modification.
 * These modifications are all done __inside the nucleus__

__**1.**__ **5' cap is added.**
 * made of modified guanine NTP
 * **protects** from nucleases and phosphatases in nucleus
 * also helps in starting translation

__**2.**__ **Poly-A-Tail is added.** - Final result is __mRNA transcript__ which is then ready to leave the nucleus []
 * 200 adenine ribonucleotides are added to 3'
 * **Prevents** from degradation
 * Uses poly-A-polymerase to attach
 * __3.__ Intron Splicing**
 * DNA has exons (coding regions) & introns (non-coding regions)
 * Introns are cut because if they were read, they would mess up folding of polypeptide
 * **Spliceosomes** cut introns and connect remaining exons
 * __Online Resources:__**

=5.4 Translation:=

**Ribosome:**

 * Consists of a large (60S) and small (40S) unit that sandwiches mRNA
 * Moves along mRNA in 5' to 3' direction
 * **Reading frame**: One of 3 possible phases which read the codons on mRNA

Transfer RNA (tRNA):
1. Initiation: 2. Elongation: 3. Termination :
 * small, single stranded nucleic acid that resembles a cloverleaf
 * Delivers amino acid
 * Has complimentary anticodon to mRNA ie. mRNA: UAU tRNA: AUA
 * tRNA is specific to codon -> stop codons don't have complimentary tRNA
 * amino acid attaches to 3' end
 * Ribosome subunits sandwich mRNA by recognizing 5' cap
 * AUG (methionine) is start codon
 * Ensures that ribosome is reading in right direction
 * Ribosome has 2 sites: -> A (Acceptor) and P (Peptide)
 * 1) tRNA with methionine enters P site
 * 2) 2nd tRNA enters A site with another amino acid
 * 3) Ribosome moves one codon over and first tRNA is released
 * 4) Amino acid from first tRNA makes a peptide bond with 2nd amino acid
 * 5) tRNA #2 now in P and 3rd tRNA goes into A
 * 6) Continues until stop codon where there is no complimentary
 * Elongation stops @ stop codon (UGA, UAG, UAA)
 * Release factor protein helps release polypeptide
 * Endoplasmic reticulum folds polypeptide
 * Ribosome disassembles


 * __Online Resources:__**

This youtube video is good for imagining what it looks like when the P & A sites are being used. However, they don't specify where the P & A sites are. The P site is the one that first recieves a tRNA.

media type="youtube" key="OabrAXr_9rg?fs=1" height="385" width="480"

This one is good for narration and visualization though it can be a tad bit confusing because it's 3D

media type="youtube" key="41_Ne5mS2ls?fs=1" height="385" width="480"

[]

=5.5: Control Mechanisms= January 5, 2011 Scott Mastromatteo

__Important terms__

housekeeping genes : are genes that are always being transcribed and translated because they are essential for an organism to live

gene regulation : is the process of controlling which genes are "on" based on the requirements of the organism

β-galactosidase : is the enzyme that breaks up lactose into its monomers (glucose/galactose)

operon : is a segment of DNA that contains a promoter, an operator and a set of genes

operator : is a segment of DNA to which a repressor protein binds to prevent a set of genes from being transcribed

repressor protein : binds to an operator to prevent an operon from being transcribed

inducer - binds to a repressor protein, causing a change in conformation and the repressor protein to fall off the operator

__In General__

There are about 42000 genes that code for proteins in human, but not all these proteins are needed all the time. The body has ways of regulating which proteins are needed. Some genes need to constantly be transcribed and translated. These genes, known as housekeeping genes, are essential for the organism to live. Gene regulation is the process of controlling which genes are "on" based on the requirements of the organism.

Eukaryotic cells can control genes at four levels: 1. transcriptional - controlling either the the rate of the transcription of a gene or whether or not a gene gets transcribed at all 2. posttranscriptional - controlling the changes that happen in the nucleus before translation occurs 3. translational - controlling how rapidly or how often mRNA will be translated into polypeptides by controlling how quickly mRNA will be destroyed 4. posttranslational - controlling the ability to pass through the membrane or the mechanisms required for the protein to become functional

__The //lac// Operon__

This is an example of a control mechanism in **a prokaryote organism only**. β-galactosidase is the enzyme that breaks up lactose into its monomers (glucose/galactose). If lactose is not present, then there is no need for an organism to produce the enzymes to break it down. A negative control system is used to stop the production of β-galactosidase if there is no lactose. β-galactosidase is a part of an operon. An operon is a segment of DNA that contains a promoter, an operator and a set of genes. An operator is a segment of DNA to which a repressor protein binds to prevent a set of genes from being transcribed. (see Figure 1). The //lac// operon is a set of three genes that code for three protein involved in the breakdown of lactose. A Lactl protein is a repressor protein that binds to the lactose operator to prevent the genes from being transcribed. When the repressor protein is binded to the operator, RNA polymerase cannot transcribe the genes because the repressor acts as a kind of roadblock. When lactose becomes present, the genes controlled by the operan need to be turned on. Lactose acts a a inducer, binding to the Lacl protein and changing its conformation. The protein falls off and RNA polymerase can transcribe the genes.

//Figure 1: An operon//

__Other Operons__

Some operons work the opposite way the //lac// operon does; an example is the //trp// operon. The //trp// operon controls the producion of the amino acid tryptophan. If there is enough tryptophan present in the organism, the amino acid will bind to a repressor protein and change its conformation to allow it to bind to the operator. Essentially, it's the opposite of how the //lac// operon works.