notes!!!! textbook reading 1.3/1.4

Metabolism

1) Energy: the ability to do work

2) metabolism: the sum of all anabolic and catabolic processes in a cell or organism

3) anabolic reaction: reactions that produce large molecules from smaller subunits

4)Catabolic reaction: Reactions that break macromolecules into their individual sub units

5) kinetic energy: energy possessed by moving objects

6) Work: The transfer of energy from one body or place to another

7) THE FIRST LAW OF THERMODYNAMICS

• The total amount of energy in the universe is constant. Energy cannot be created or destroyed but only converted from on from into another.

8) THE SECOND LAW OF THERMODYNAMICS

• The entropy of the universe increase with any change that occurs.

9) Bond energy: the minimum energy required to break one mole of bonds between two species of atoms; a measure of the stability of a chemical bond.

• Bond formed = energy released
• Bond break = energy absorbed

10) Exothermic reaction: more energy released during bond formation -> net energy output -> exothermic reaction (ex. combustion) (negative delta H value)

11) Endothermic reaction: Energy absorbed in breaking bonds > energy released in formation of product bonds = net absorption energy (positive delta H value)

12) Entropy: A measure of the randomness or disorder in a collection of objects or energy symbolized by S

• ask Mr. Chung what favoured and not favoured means.

13) Free Energy (Gibbs Free energy): Energy that can do useful work

14) Exergonic reactions: A chemical reaction in which the energy of the products is less than the energy of the reactants; chemist call it an exothermic reaction

15) Endergonic reactions: A chemical reaction in which the energy of the products is more than the energy of the reactants; chemists call it an endothermic reaction

16) ask MR chung about reversible reactions -> why are dead cells reaching equilibrium

17) Hydrolysis: decomposition of a chemical compound by reaction with water

18) Polyphorylation: the process of attaching a phosphate group to an organic molecule

19) LEO GER: Leo (lion) says GER... losing election is oxidation.... gaining election is reduction. This is also known as a redox reaction.

ENZYMES

20)enzymes: protein catalyst

21) Catalyst: Allows reaction to proceed at suitable reates at moderate temperatures by reducing the activation energy (does not affect the free energy change of a reaction)

22) substrate: The reactant that an enzyme acts on when it catalyzes a chemical reaction

23) active site: the location where the substrate binds to an enzyme

24) cofactors: non protein component such as dissolved ions that are needed for some enzymes to function

25) coenzymes: organic nonprotein cofactors that are needed for some enzymes to function

26) competitive inhibitors: substances that compete with the substrate for an enzyme's active site

27) noncompetitive inhibitors: substances that attach to a binding site on an enzyme other than the active site, casing a change in the enzymes's shape and a loss of affinity for the substrate

28) allosteric sites: receptor sites, some distance from the active site or certain enzymes, that bind substances that may inhibit or stimulate an enzyme's activity

29) activator: a substance that binds to an allosteric site on an enzyme and stabilizes the protein conformation that keeps all the active sites available to their substrates

30) allosteric inhibitors: a substance that binds to an allosteric site on an enzyme and stabilizes the inactive form of the enzyme

31) ASK MR CHUNG TO RE EXPLAIN FEEDBACK INHIBITION

Still working on it (:

an order created by anabolic process is accompanied by an even greater disorder caused by energy yielding catabolic processes

Study notes for the Biotech Test

Blog 4: Top Ten Points I Need to Know About the Biotech Test

1) RFLP

Restriction Fragment Length Polymorphism

RFLP is the comparison of lengths of DNA. Restriction enzymes are used to completely digest the strands of DNA. Furthermore, using gel electrophoresis with a thick matrix, the differences

of the lengths of DNA amongst individuals can then be identified.

• involves the comparison between the length DNA fragnments between individuals.

2) PCR

Polymerase Chain Reaction

This is a method of DNA replication. It is used to make numerous copies of a desired gene fragment without placing it into a plasmid.

During this method, heat i used to separate the strands of DNA. DNA is subjected to temperature between 94-96 degrees Celsius, causing the hydrogen bonds to break down and separate. The temperature is then brought down to about 50- 60 degrees Celsius. A 5'-3' DNA primer is then added to anneal with the template DNA. After a Taq Polymerase DNA is added at 72 degrees. It adds DNA nucleotides until it reaches the end of the DNA. The processes is repeated until an exponential amount of DNA has been produced.

Heat -> brek hydrogen bond -> cool -> primers -> heat

• Required during PCR
• Taq polymerase + 2 DNA primers + dNTPs (Deoxynucleoside triphosphate) + PCR machines

3) Sangers method of Sequencing

This was a method to sequences the genome of a DNA.

First the DNA template must be replicated several times. then a Radioactive primer must be placed on to the strands. then placed into four reaction tubes. Each tube containing a full supply of nucleotides in form of all four dNTPs.

Now in each of these 4 tubes, each one should have a low concentration of the same ddTTP.

the dideoxy analogue blocks further growth of the chain. After placing these sequences

through a gel electrophoresis. we are able to sequence them.

4) Vector cloning

• Isolate the DNA from the organism with the desired gene.
• Then the DNA is fragmented with restriction enzymes, generating cuts with sticky ends
• DNA fragments are incorporated in to bacterial plasmids
• The plasmid is cut with the same restriction enzyme that generates the same cohesive ends
• the cohesive ends of the gene and the cut at on the plasmid are joined together by DNA ligase used to form covalent bonds
• place the plasmid back into the bacterial host.
• the cells can now be grown or placed in the organism of desire

PCR vs Vector cloning and DNA sequencing

compare and contrast the following two methods in biotechnology. Provide 5 points in how they are similar to and/ or different from each other.

(a) PCR vs. Vector cloning.

-the difference between PCR and vector cloning is that protein is important in Vector cloning. In vector cloning, the proteins the desired gene codes for is very crucial. Whereas PCR's function is only to duplicate the amount of desired genes

- both of these methods duplicate the gene of desire

-PCR uses the knowledge of temperatures + Taq polymerase + 2 DNA primers + dNTPs + PCR machines in order to multiply the dna

where as Vector cloning multiplies DNA from the offspring of the "infected cells"

(b) PCR vs DNA sequencing

- DNA sequencing require alot of DNA in order to accurately sequence the DNA

- PCR is often done before DNA squencing

Study notes for the test!

DNA test

5’ g cap- Guanine cap at the 5’ end of the RNA

Anticodon - base pairs with a complementary codon on the mRNA

Base- Pair substitution - when the point mutation results in replacement of a pair of complimentary nucleotides with another nucleotide pair

Chargaff- Noticed a ratio between the nucleotides bases (A=T C≡G) where A and G both have 2 rings

DNA - (Deoxyribonucleic acid) Backbone of DNA is the alternating phosphates and sugars. It is a double helical structure. And the two strands are anti parallel. See Glycosyl Phosphodiester, and hydrogen bonds

Frameshift Mutations - Mutations that dont happen in multiples of 3, improperly group codons.

Extrons - The coding regions

Gene - Sequence that can be transcribed and translated into proteins

Glycosyl (Intramolecular) - Sugar + nitrogenous base

Griffith - 1928 studied bacterium and developed the phenomenon called transformation. experimental observations led to scientist to suspect that protein is not the hereditary material.

Gyrase - Releases the tension

Introns - noncoding segment

Helicase - An enzyme untwists and separates the strand

Hershey and Chase - 1952, helped confirmed that DNA was the genetic material using viruses and bacteria. The bateriophages were radioactive on the protein coat. However the genetic material was uncontaminated. However when the genetic material was radioactive, the host it infects is also radioactive

Hydrogen Bonds (intermolecular) - Between Nitrogenous base

intermolecular- Between

intramolecular- with in

Ligase - Joins phosphate backbone together

Missense Mutation - Code for an amino acid but change the indicated amino acid

Morgan - Showed that Morgan’s group showed that genes are located on chromosomes.

pre-mRNA - (RNA transcript, primary transcript)

Nonsense Mutations - Change an amino acid codon into a stop codon nearly always leading to a nonfunctional protein.

Nucleotides - (Sugar: deoyribose Phosphate Base: ATCG) molecules that consist of a five carbon sugar with a nitrogenous base attached to their 1’ carbon and a phosphate group attached to their 5’ carbon. The phosphate group is negatively charged.

Nucleoside - Contains only a sugaar and a nitrogen base

Okazaki Fragments: Single stranded DNA on the Lagging Strand

Phosphodiester (intramolecular)- Sugar + phosphate

Point Mutation - Chemical Change in just one base pair of a gene

Polymerase l - proofreads and replaces the primers with DNA Nucleotide.

Polymerase III - Elongates new DNA strand by adding on to the 3’ end

Primase: An RNA polymerase that links ribonucleotides that are complementary to the DNA temperate into the primer. Create RNA primers that serve as a signal to DNA Polymerase III

Primer: A short chain segment of RNA (10 nucleotides long in Eukaryotes)

Promotor: The “Upstream region” where transcription begins, binding site for RNA polymerase and several dozen nucleotides upstream of the start point

Purine - The A and G in the Nitrogenous bases

Pyrimidine - The T and C in the nitrogenous bases

Ribose (RNA) - single ringed sugar that has an extra hydroxyl (OH) group on the 2’ carbon ring than the deoxyribose sugar in DNA

RNA polymerase II - Separates the DNA Strands at the appropriate point and bonds the RNA nuceotides as they base-pair long the DNA template

Semiconservative replication: the two strands of the parental molecule separate and each functions as a template for synthesis of a new complementary strand

Silent Mutation: Alterations of nucleotides still indicate the same amino acids because of redundancy in the genetic code

Single stranded Binding Protein - Keeps the single stranded DNA Stabilized

snRNP - has several protein molecules and a small nuclear RNA molecule (snRNA)

Spliceosome - Contains several proteins and several small nuclear ribonucleoproteins (snRNPs)

Terminator: Signals the end of Transcription

tRNA - Transfer RNA

Transcription Factors - Proteins that recognize the promotor region and bind to it (5’TATA3’ box)

Transformation - introduction of foreign DNA usually by a plasmid or virus, into a bacterial cell

Watson and Crick - 1950 Discovery of the double helix by building models to conform to X-ray data

Wobble - allows for the third position to have a different nucleotide but code for the same amino acid

Replication
Acts	Names	Characters	Roles
1	Initiation	-Helicase -Single stranded Bonding Protein -Gyrase -Primase
2	Elongation	-DNA Polymerase III
3	Termination	-DNA Polymerase I -Ligase

Transcription
Acts	Names	Characters	Roles
1	Initiation	5’ TATA 3’ on template Transcription Factors RNA Polymerase II used for mRNA	This is the Transcription Initiation Complex Eukaryotes are different cause they have 3 different types of RNA polymerase
2	Elongation	- RNA Polymerase II
3	Termination	AAUAA on RNA AATAA on the Sense/Coding Strand	In Prokaryotes RNA polymerase stop transcription right at the end of the terminator
*at the end of the process the pre-mRNA has to be modified to put a Guanine cap at the 5’ end. As well at the 3’ there is and enyzme that adds about 50-250 adenine nucleotides, Poly (A) tail.(protects from hydrolytic enzymes)

Translation
Acts	Names	Characters	Roles
1	Initiation (prokaryotic)	- 5‘AUG 3’ 30s Ribosomal Subunit 50s Ribosomal Subunit tRNA	Translation begins at the P site
2	Elongation	tRNA	- mRNA is read 5’ ->3’ Amino acids join togther by a petide bond E site releases tRNA New tRNA enters through the A site
3	Termination	-DNA Polymerase I -Ligase	Stop Codons (UAA, UGA, UAG)