Molecular+genetics+notes


 * Biology 59 Class Notes **


 * Biology 59 Class Notes **
 * Date: Monday, December 5, 2011 **
 * Unit: Molecular Genetics **
 * Topic: Review! **
 * Notes By: Roshni Patel **

Today we had a review period, so I'll just be posting some links that you all might find helpful or fun.

Protein synthesis rap. 5 second quizzes (This website is really good, look around. The quiz forces you to answer things quickly. Don't be like me and think you need to answer in the computer though.)


 * Biology 59 Class Notes **


 * Biology 59 Class Notes **
 * Date: Tuesday, November 28, 2011 **
 * Unit: Molecular Genetics **
 * Topic: Mutations **
 * Textbook reference: p. 259-262 **
 * Notes By: Rejy Mae Gabaldon **

Mutations are any changes/error in a DNA sequence that can be inherited
 * __Main idea __**
 * Activity: Mutation stations to solve what type of mutations occurred **


 * __Vocabulary/definitions __**
 * //Silent mutation: //**<span style="font-family: Garamond,serif; font-size: 12pt;"> mutation that does not result in a change in the amino acid coded for


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Missense mutation //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> mutation that results when a base pair of a codon is altered & a different amino acid is expressed


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Nonsense mutation //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> mutation that converts an amino acid codon to a stop codon


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Frameshift mutation //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> mutation that causes reading frame of codons to change


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Point mutation //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> mutation on a specific base pair in the genome


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Translocation //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> transfer of DNA fragment from one site of the genome to another


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Transposable elements //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> DNA segments replicated as a unit from one location on the chromosome to another


 * //<span style="font-family: Garamond,serif; font-size: 12pt;">Inversion //****<span style="font-family: Garamond,serif; font-size: 12pt;">: **<span style="font-family: Garamond,serif; font-size: 12pt;"> Reversal of DNA segment within a chromosome


 * __<span style="font-family: Garamond,serif; font-size: 12pt;">Summary/notes __**


 * <span style="font-family: Garamond,serif; font-size: 12pt;">Mutations are errors in the DNA sequence that can be inherited
 * <span style="font-family: Garamond,serif; font-size: 12pt;">Frameshift mutation (reading frame changes)
 * <span style="font-family: Garamond,serif; font-size: 12pt;">Translocation (chunk of DNA is replaced with another sequence)
 * <span style="font-family: Garamond,serif; font-size: 12pt;">Point mutations (specific base pair is altered)
 * o <span style="font-family: Garamond,serif; font-size: 12pt;">Silent : no effect
 * § <span style="font-family: Garamond,serif; font-size: 12pt;">Mutation is in spliced intron; wobble position; various codons code for the same amino acid
 * o <span style="font-family: Garamond,serif; font-size: 12pt;">Missense : amino acids are changed
 * § <span style="font-family: Garamond,serif; font-size: 12pt;">Due to base pair insertion, deletion, or substitution
 * o <span style="font-family: Garamond,serif; font-size: 12pt;">Nonsense : early stop codon
 * § <span style="font-family: Garamond,serif; font-size: 12pt;">Due to base pair insertion, deletion, or substitution


 * <span style="font-family: Arial,sans-serif; font-size: 10pt;">Causes : **

> o <span style="font-family: Arial,sans-serif; font-size: 10pt;">Error in genetic machinery; faulty proofreading in DNA replication
 * <span style="font-family: Arial,sans-serif; font-size: 10pt;">Induced mutations
 * o <span style="font-family: Arial,sans-serif; font-size: 10pt;">Due to mutagenic agents :
 * § <span style="font-family: Arial,sans-serif; font-size: 10pt;">UV radiation – high energy causes point mutations
 * § <span style="font-family: Arial,sans-serif; font-size: 10pt;">X ray radiation – high energy can break DNA backbone; Can be annealed by enzymes but bases may be lost
 * § <span style="font-family: Arial,sans-serif; font-size: 10pt;">Natural radiation
 * § <span style="font-family: Arial,sans-serif; font-size: 10pt;">Chemicals
 * <span style="font-family: Arial,sans-serif; font-size: 10pt;">Pesticides
 * <span style="font-family: Arial,sans-serif; font-size: 10pt;">Ethidium bromide (used in gel electrophoresis) – binds to DNA and can cause mutations
 * Spontaneous mutations

**LINKSSSSS ! :)** [] []

**Date: Tuesday, November 24, 2011**

**Unit: Molecular Genetics**

**Topic: Transcription and Translation**


 * Textbook reference: p. 237-244 & 250 - 254V **


 * Notes By: Natasha Wood **

__ Main Idea __ To get a better understanding of how transcription and translation work between DNA and RNA

__Summary__ Did a simulation of transcription and translation following directions on a hand out. Here is what we did. __//Composed of many A's and T's//__ 2. mRNA strand created 3. What process have you just done? //__Transcription__// 4. Nucleotides 4-7 inclusive are now removed 5. In a real cell, name and describe two other things that would happen before translation //__A 5' cap is added to start the primary transript. It prevents mRNA from digestion by nucleases and phosphates as it exits the nucleus and exits the cytoplasm. The 3' is poly-A-tail which is a string of 200-300 adenine base pairs at the end of an mRNA transcript.__// 6.a) Amino acid sequences (Pg. 240) b) Give an specific, scientific way that this does not accurately reflect translation __//Does not travel through ignition, elongation, and termination//__ c)Translation part two: what is your resulting deep thought? (sentence on the back of the coded DNA from class) d) What else might happen to the polypeptide before it becomes active? //__The polypeptide folds and coils and things are added (phosphate groups) so it can become a protein__// 7. On mRNA a single deletion occured at the third place of the second codon a) What type of mutation is this? //__Frame shift__// b) Write out the resulting mRNA and animo acid sequences for the first five codons c) What are some possible results of a deletion? Why do mutation occur? //__Cancer and cystic fibrosis. Mutations occur from exposure to chemicals (i.e ethidium bromide), UV light, cosmic rays and X-rays.__//
 * 1) Copied down the template strand
 * Q#2 What function does this serve //__2 H-bonds, breaks easier to open up DNA__//
 * Q#1 What is the removed segment called? //__Intron__//
 * Q#2 What type of modification is this? //__Post transcriptional Modification__//

//Create a strand of DNA, find it's mRNA and the amino acid sequence. Once completed, rewrite the DNA strand that you created and insert a mutation somewhere in the strand. This will be used on Monday, for the class to try and detect where the mutation is occurring.// //Read 5.6 Pg 259-262 and summarize "causes"//
 * Homework**

**Date: Tuesday, November 23, 2011** **Unit: Molecular Genetics** **Topic: Transcription**
 * Biology 59 Class Notes **
 * Textbook reference: p. 242-248 **
 * Notes By: Paramveer Singh **

Decription of the process of transcription in which DNA is taken to create a complementary mRNA molecule.
 * __ Main idea __**

**__Vocabulary/definitions__** **//Upstream://** Region of DNA adjacent to the start of a gene


 * // Promoter //**** : ** Sequence of DNA that binds RNA polymerase upstream of a gene


 * // Terminator Sequence //**** : ** Sequence of bases at the end of a gene that signals the RNA polymerase to stop transcribing

RNA polymerase binds to DNA and opens the double helix. It then recognizes the promoter which is rich in A’s and T’s.
 * __ Summary/notes __**
 * // Stage I: Initiation //**

RNA polymerase builds mRNA in the direction 5’ to 3’. It uses only one strand of DNA to make it, called the ** template strand. ** The other strand is called the ** coding strand **.
 * // Stage II: Elongation //**




 * // Stage III: Termination //**

RNA polymerase recognizes a terminator sequence telling it to stop transcribing at the end of a gene. Both mRNA and RNA polymerase are released.


 * Posttranscriptional modifications **

The transcript (called the primary transcript at this stage) is then modified to prevent damage and degradation. A 5’ cap is added at the ‘top’ which also helps in the initiation of translation. Similarly, a poly A tail is added to the opposing end which also helps in the termination of translation. Processes are known as **capping** and **tailing**.


 * Introns/Exons **
 * Introns are regions of DNA that do not code for anything
 * Exons are segments of DNA/mRNA that code for a specific protein

Introns do not allow the protein to fold and function properly which is why they are removed by proteins called **spliceosomes.** This results in a continuous coding region called the **mRNA Transcript.**




 * //__ HW __//**


 * Retrovirus: ** A type of virus whose genetic material is composed of RNA rather than DNA. They contain transcriptase which converts RNA into a double stranded DNA molecule when fused with the host cell’s hereditary material. Eg. HIV


 * __ Links/Videos: __**

[]

[]


 * Heads-up: ** Multiple Choice Questions are due this Friday. Email them to Kate the latest by Friday morning.


 * Biology 59 Class Notes **

**Date: Monday, November 21, 2011**

**Unit: Molecular Genetics**

**Topic: Overview of Protein Synthesis**


 * Textbook reference: p. 237-241 **


 * Notes By: Katie Scott **

-The central dogma of molecular genetics: DNA encodes RNA, encode proteins -DNA is located in the nucleus of the cell- it is not allowed to exit the nucleus because pieces can tangle and break and there are dangerous enzymes in the cytoplasm -Ribosomes are responsible for making proteins they access the genetic code from mRNA, which can leave the nucleus -DNA in the nucleus encodes for all proteins, which are synthesized in the cytoplasm -There are several steps and molecules involved to get from DNA to a finished protein product -Messenger RNA (mRNA) -provides a way for the genetic code to leave the nucleus -DNA is transcribed into a complementary RNA message, which is delivered to the ribosomes in the cytoplasm -RNA is then translated into polypeptide chains, which are processed into proteins The Central Dogma of DNA: replication (DNA)-->transcription-->RNA-->translation--> Protein -transcription carried out by RNA polymerase -translation is performed on ribosomes -replication is carried out by DNA polymerase reverse transcription (the exception to the central dogma) copies RNA into DNA

RNA -contains a ribose sugar (hydroxyl group on the 2' carbon) rather than deoxyribose -contains uracil rathe than thymine to pair with adenine -single stranded -three types: messenger, transfer, and ribosomal

Transcription Overview -three processes: initiation, elongation and termination -initionation: RNA polymerase (like DNA pol III in DNA replication) binds to DNA at the promoter -elongation: using DNA as a template, RNA pol puts together the ribonucleotides to build the mRNA transcript -termination: the RNA pol reaches a signal to stop, and the mRNA is released and exits the nucleus

Translation Overview -initation: ribosome binds to mRNA -elongation: ribosome moves along three nucleotides at a time -each three nucleotides represent one amino acid tRNA delivers the appropriate amino acid, elongating the polypeptide chain -termination: a stop signal is reached

The Genetic Code -universal in all organisms with few exceptions -Codon: a sequence of three bases that code for a particular amino acid -Start codon: AUG, signals the ribosome to begin translation -stop codons: signal the end of translation (do not code for an amino acid)

Redundancy in the genetic code -because there are three nucleotides for each of the four bases (4^3), there are 64 possible combinations 20 amino acids -this means more than one codon can code for an amino acid, meaning the code is redundant

short animations on DNA molecule, translation, transcription and other things we've talked about so far (and read in the biotechnology section): []

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Date: Tuesday, November 15, 2011 ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Unit: Molecular Genetics ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Topic: 1. DNA Introduction **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Biology 59 Class Notes **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Textbook reference: p. 206-214 **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Notes by Yi Lin **

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Introduction of molecular genetics
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Main idea **

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Vocabulary/definitions ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Antiparallel: parallel but running in opposite directions; the 5’ end of one strand of DNA aligns with the 3’ end of the other strand in a double helix

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Hammerling’s contribution to DNA research <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Conducted series of experiments using Acetabularia <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Conclusion: hereditary information in nucleus (in feet) <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">1st cap: intermediary 2nd cap: A.mediterranea
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Summary/notes **
 * 1) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">Remove cap -> grow new cap VS remove feet -> no new cap
 * 1) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">Grow 2 different species of Acetabularia by combining a stalk of A.crenulata and foot of A.mediaterranea

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Conclusion: instructions for specifying the type of cap and for directing the cellar substances to build it and found in the nucleus in the feet

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Hershey & Chases’s contribution to DNA research <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Conducted experiment with bacteriophases (DNA + protein coat) <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Conclusion: Only DNA from phage, not the protein coat, enters the bacteria to direct the synthesis of new viral DNA and new viral protein coats <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Illustrate phosphorus-rich DNA was injected into bacteria cells <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Conclusion: DNA was accepted as the hereditary material
 * 1) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">Phage produces thousands of new virus and burst out of cell
 * 1) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">Tagged viral proteins with isotope of sulphur and DNA with isotope of phosphorus

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Chargaff’s rule <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Amount of Adenine = amount of Thymine <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Amount of Cytosine = amount of guanine <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Amount of ATGC=Total percentage = 100% <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Amount of purines = amount of pyrimidines

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Rosalind Franklin <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Produced a clear X-ray diffraction pattern using X-ray crystallography that suggested that DNA is helical in nature (2nm in diametre)

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Purines and Pyrimidines <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Adenine and Guanine are purines (2 rings) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Thymine and Cytosine are pyrimidines (1 ring) <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- A-T (2 H-bonds) G-C (3 H-bonds)

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">5 prime and 3 prime <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 5’ end is where a phosphate group resides <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 3’ end is where the hydroxyl group of deoxyribose sugar is found <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 5’ end of one strand aligns with 3’ end of the other stand

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Dimensions of double helix <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 2 nm in diameter <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 0.34 nm distance between each base pair <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- 3.4 nm is one complete turn of double helix (10 base pairs


 * <span style="font-family: 'Garamond','serif'; font-size: 16px;">Hand-backs: **<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> Photosynthesis Test
 * <span style="font-family: 'Garamond','serif'; font-size: 16px;">Heads-up: **<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> Quiz Monday

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Date: Wednesday November 16, 2011 ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Unit: Molecular Genetics ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Topic: DNA Replication **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Biology 59 Class Notes **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Textbook reference: p.217-222 **
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Notes by Yi Lin **

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">DNA is replicated through 3 steps: separating the DNA strands, building complementary strands and DNA repair <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">**<span style="font-family: 'Garamond','serif';">Vocabulary/definitions ** <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__Semi conservative replication:__ replication in which each new DNA molecule is composed of one parent strand and one newly synthesized strand. <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__Origin of replication:__ the region which attract protein (enzyme) to bind and unwound DNA strand to begin replication <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__DNA helicase:__ the enzyme that unwinds double-helical DNA by disrupting hydrogen bonds <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__Single-stranded binding proteins (SSBs):__ a protein that keeps separated strands of DNA apart <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__DNA gyrase:__ the bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__Replication fork:__ the region where the enzymes replicating a DNA molecule are bound to untwisted, single-stranded DNA <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">__Replication bubble:__ the region where two replication forks are in close proximity to each other, producing a bubble in the replicating of DNA
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Main idea **

<span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Result of mitosis and cytokinesis: 2 identical daughter cells exactly like the parent cell. <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Each strand to serve as a template for the other. The H bonds can be broken and a parent strand can be used to create 2 daughter stands (happens in interphase). <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Because the old strand and new strand are passed on, this is called semi conservative. <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- This model of DNA replication was developed by **Meselson and Stahl.** They labeled E. coli DNA with ­­N15. It was allowed to replicate until the entire DNA sample contained the heavy N. The N15 was allowed to reproduce with N14, a lighter isotope. The result is a mixture of heavy and light strands paired together. <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Diagram: <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Fig 4, p 220:
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Summary/notes **

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">

<span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- Fig. 8, p 222 <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> <span style="color: black; font-family: 'garamond','serif'; font-size: 16px;">- DNA pol III and I have the ability of proof reading and act as exonucleases to cut out incorrect nucleotides and replaces them. Otherwise mutation can be resulted from mistakes.

<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">[] <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">(video Kate showed in class)
 * <span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;">Related diagrams/links/videos **


 * <span style="font-family: 'Garamond','serif'; font-size: 16px;">Homework: **<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> p.221 Q#1-7
 * <span style="font-family: 'Garamond','serif'; font-size: 16px;">Heads-up: **<span style="color: black; font-family: 'Garamond','serif'; font-size: 16px;"> Biotech Assignment Package (Pt. B due Nov. 30. Pt. C due Dec. 1. Pt. D due Nov. 25th at noon) QUIZ MONDAY!