Biology Test 4 Review SheetI. PROTEINS

A. Structure:• Properties of Protein ~

- Large complex organic molecules- All contain C, H, O, N and usually S- Amino Acid building blocks- made from amino acids (20 different amino acids)

• Typical Amino Acid- includes Carboxyl group, amino group, central carbon group, and the R variable group (20 variable group, any of the 20 amino acids)

• Peptide Bond- made by dehydration synthesis between “C” of the carboxyl group of one amino acid and “N” of the amino group of another amino acid. Peptide Bonds between Amino Acids ~

- Dipeptide- peptide bond (bond of multiple amino acids) with 2 amino acids- Tri-Peptide- peptide bond with 3 amino acids- Polypeptide- peptide bonds with many amino acids (I.e- proteins)

• Primary structure of a protein- string of amino acids. How do proteins differ from each other?

- Different order of amino acids - Different amino acid types- Different amount of amino acids, correct 3D structure

• 3D Structure— 3D shape of a protein held together primarily by ~

- Disulfide bonds of the cystine molecule (S-S)- Hydrogen bonds between “R” groups on the amino acids in different parts of the

amino acid chain/ Hydrogen bonds between negative side of one amino acid and the positive side of another

- Shape is crucial to the functioning of proteins, for the functions of enzymes, proteins, antibodies, protein receptors in the cell membrane, and protein carriers in the cell membrane

• Denaturation- change in 3D shape of protein (by breaking Hydrogen Bonds and S-S bonds) that destroy the function of a protein. The change in shape is caused by:

- Temperature (high heat)- pH- acid/base affects protein function- Substitution of amino acid for another amino acid in the primary structure of the

protein/ polypeptide chains making up the protein (i.e.- sickle cell anemia— glutamic acid is substituted for valine in Hemoglobin, 280,000,000 Hemoglobin in one red blood cell)

- Physical change (i.e.- egg white whipping changes shape)

• There are 8 amino acids that you cant make known as the essential amino acids. You eat them, and can get them from:

- Complete proteins- include all 8 essential amino acids (i.e.- meat, fish, milk, eggs, quinoa)

- Incomplete proteins- does not include all 8 essential amino acids (i.e.- tofu, beans, nuts, peas, rice, grains)

- Completing two incomplete proteins to get all 8 essential amino acids/Complementing Protein (i.e.- peanut butter on bread, rice and beans)

• Chemical Reactions done to form large organic compounds from building block molecules and break them down into their building block molecules ~

- Dehydration Synthesis— forming a larger organic molecule from smaller ones than a chemical reaction in which a molecule of H20 is removed, combines amino acids together to form polypeptide chains (takes the oxygen and hydrogen from the carboxyl group of one amino acid and the hydrogen from the amino group of

another amino acid to form H20, leaves the carbon and nitrogen needing to bond so they form peptide bonds)

- Hydrolysis— splitting a larger, more complex organic compound to smaller building block molecules by adding water, occurs when Golgi bodies break up proteins into individual amino acids, chemical digestion occurs through this process

B. Function• Various proteins discussed ~

- Examples of Functional Proteins— hormones, enzymes, muscles, antibodies (protections from infectious agents), protein receptors in the cell membrane (for recognition to identify cells to other cells and to target a cell for action by certain hormones), protein carriers in the cell membrane (allow certain molecules and ions through the cell membrane)

- Examples of Structural Proteins— keratin (nails and hair), muscle, cartilage, protein receptors in the cell membrane(for recognition to identify cells to other cells and to target a cell for action by certain hormones), protein carriers in the cell membrane (allow certain molecules and ions through the cell membrane), albumins, Hemoglobin (C302H4810O872N780S8Fe4)

II. ENZYMES (TYPE OF PROTEIN)A. Role as Catalysts:

• Speed up chemical reactions that with time would have happened on their own by lowering activation energy (amount of energy required for a chemical reaction to occur) at body temperature (chemical reaction being sped up is dehydration synthesis)

• How do enzymes lower the activation energy required to react? Pressure put on existing bonds allow them to break more easily and allows new ones to form

• Enzymes aren't used up or changed by the reaction, they just catalyze

• Enzymes are very specific, and a different enzyme is required for each different chemical reaction; if you don't have the correct enzyme, you can’t digest specific foods through dehydration synthesis; there are 1000s of different enzymes

• Substrate (chemical/s that will undergo reactions) and Enzyme (substrate complex) physically fit together (if correct enzyme for correct substrates) on the active sight (place on the enzyme where the substrate physically fits in)

• Lock and Key/Induced Fit model- the enzyme/substrate model called this because it looks like a lock and key and because there is a different “key” for every “lock” (substrate/enzyme)

• 3D shape is crucial to enzyme function- if it's the wrong shape the substrate wing fit in and the reaction wing happen

• Factors that can affect the rate of enzyme action— pH, temperature, concentration of substrate present

• Coenzymes (organic, often are vitamins) are needed for many enzymes to function in order so that the active sight can fit the substrate

III. DNA / PROTEIN SYNTHESISA. Evidence that DNA is Genetic Material:

• Protein initially thought to be genetic material because it had lots of variety— 20 different amino acid variety

• Evidence that DNA was genetic material and not Protein ~- Fred Griffith Experiment— pneumococcus bacteria- S (smooth strain) killed the

mice, R (rough strain) didn't kill the mice, killed “S” didn't kill mice, but killed “S” + live “R” killed mice (unexpected because neither dead “S” nor live “R” killed mice individually)

- Avery/ MacLead/ McCarty— tested on the unexpected results of Griffith; asked question- “What if you crushed the dead ’S’, took extract where you would isolate just the protein, carbohydrate, lipid, and DNA?—

* Only the DNA resulted in Live “S” in the Live “R”* Why would there have been a live “S”? The DNA “transferred” the live “R” into live “S”.

- Hershey and Chase Experiment— experimented in Rockefeller University in 1952 to see if DNA was genetic material and not protein- set up two tests involving viruses and bacteriophages—

1. Test 1— the protein coats of bacteriophages (sends virus into bacteria) are radioactively labeled. After infected, no radioactivity entered the cell

2. Test 2— the DNA of bacteriophages are radioactively labeled (phosphorus). After infected, radioactivity entered the cell

* Established once and for all that DNA was the genetic material from the fact that it passed the radioactivity into the bacteria

B. DNA Structure:• Nucleotide polymers (many units bonded together) made of 4 different monomers

make up DNA. Each nucleotide consists of ~ - Phosphate group- Sugar (deoxyribose, ribose in RNA— able to distinguish between DNA and RNA)- Nitrogen bases- vary from adenine, guanine, cytosine, and thymine (uracil

instead of thymine in RNA)

• DNA polymer consists of a double-helix structure. Studies that contributed to discovery of the double helix structure ~

- Edwin Chargaff- 1947- said that adenine and thymine (uracil in RNA) correspond to each other and that guanine corresponds to cystine

- X- Ray Diffraction Studies- Rosalind Franklin, Maurice Wilkins in Kings College, London. Wilkins invited Franklin to help with X-ray diffraction. Franklin thought she would be partnered with Wilkins, but was actually just working in the lab. Franklin got the first picture of x-ray DNA which looked like this—

* We learn from this that DNA has a helix (3D wire like shape) structure.

* James Watson- 25 year old biologist. He and Francis Crick went to Franklin’s lecture that she gave on her DNA findings, but didn't take notes and therefore forgot the measurements to base his DNA model off of. Watson then asks Wilkins for the picture, and gets the measurements, studies them, and makes a model with Crick. They invite Franklin to see the model, she says that it’s wrong because the nitrogen bases were on the outside and the phosphate/sugar backbone was on the inside because because nitrogen bases are hydrophobic Watson and Crick make another model,

invite Franklin again (with phosphate/sugar backbone on the outside and the nitrogen bases are on the inside connecting with hydrogen bonds) and she validates it; Watson and Crick win nobel Prize for finding the structure of DNA in 1962.

- Linus Pauling- invented making models to study chemicals, called it “3D’ Experiments in Space— when you see it flat, it doesn't teach you anything so you need a 3D model of it

• Double Helix ~- The sugar phosphate “backbone” with nitrogen bases facing the inside (“rungs of

the ladder”)- One helix complements another in terms of base pairing (A complements T, G

corresponds with C)- The base pairs are bonded through hydrogen bonds, allows the helixes to be

unzipped easily- Each strand of the double helix is a DNA polymer (multiple phosphate-sugar-

nitrogen base groups bonded together)

C. DNA Function:• DNA must replicate itself exactly

• DNA controls which proteins are made by that cell/ protein synthesis, thus controlling the entire cell because the cell's job is determined by the protein that it makes, the proteins carry out the function of each cell

• Relationships of genes, DNA, and chromosome—DNA is the genetic material; genes are a sequence of bases in DNA that code for a particular protein (polypeptide); chromosomes are wound up DNA (one long double strand of DNA), 46 of them in the body (23 each from Mom and Dad);, those chromosomes are genetic material that determine your genes (I.e.- sex chromosome, Down syndrome) and your DNA depends on what genes you have

D. DNA Replication:• DNA unwinds/unzips at the (weak) hydrogen bonds between opposite base pairs

• New DNA nucleotides base pairs “fall in”/hydrogen bond along both strands of DNA. The original two strands of DNA are like “templates” for how the new strands form

• As a reaction of these two procedures, in the end, the DNA replicates into two double helixes identical to the original helix

E. Protein Synthesis:• RNA nucleotides include— ribose (not deoxyribose— makes it recognizable), uracil

(not thymine), single strand (not double helix)

• Types of RNA- tRNA (transfer), mRNA (messenger), rRNA (“ribosomal”- part of the actual structure of the ribosome itself)

• The mRNA is copied off of the DNA “sense strand”, RNA nucleotides “fall in”/ hydrogen bond in opposite DNA nucleotides on the “sense strand”/Template Strand

• RNA polymerase does dehydration synthesis to attach the RNA nucleotides together and build the mRNA (Transcription- mRNA is being “built” off of DNA sense strand)

• mRNA goes out to the ribosome to be “read”, the mRNA code determines the sequence of Amino Acids in a particular protein (Translation- translating mRNA code in an Amino Acid sequence of a growing polypeptide)

• Codon- triplet form of 3 bases on an mRNA that code for a particular amino acid

• tRNA recognizes on one end of the particular amino acid and on its other end it “recognizes” the codon and has the opposite base pairing, or the anticodon, which carries the amino acid needed and those are combines through dehydration synthesis to produce a polypeptide bond. The anticodon (which consists of bases that form hydrogen bonds opposite the codon on mRNA) is on one side of the tRNA and the amino acid attaches to the other side of the tRNA to make a polypeptide chain (bond through dehydration synthesis)

• For the test, know how to transcribe DNA to mRNA and how to translate (chart that will be provided) mRNA into a growing polypeptide chain (protein)

• Mutations- Gene Mutations- permanent change in DNA that is passed on to the succeeding cells ~

- Deletion = when one or more of the nucleotides is zapped/deleted from the DNA

- Addition = when one or more nucleotides is added to the DNA- Substitution = when one or more nucleotides is substituted for another in the

DNA

* Effects of Mutation are more harmful when a nucleotide is either added or deleted from the DNA because it changes the order of the nucleotides which changes the codons from that point which changes the entire sequence of amino acids. It is not as harmful when a nucleotide is added/deleted at the end because it is not affecting as much in the sequence but it is still harmful (opposite- when a nucleotide is added/deleted at the beginning it is very harmful because it affects the entire sequence)

* Substitution not so harmful because the same number of nucleotides will be on the DNA and therefore only the amino acid produced from the codon that a nucleotide is being substituted from can change. Although it can result in a new protein being produced, it is not as harmful as Deletion or Addition.

F. Genetic Engineering:• Genetic Engineering- ability to move a section of DNA from one organism to another

to make a new form of DNA

• Recombinant DNA- DNA composed of DNA from 2 different organisms (would happen by taking cell, identifying where the gene is, what chromosome it's on, and snip the chromosome of the DNA and take bacteria whose DNA is in the cytoplasm and plasmid and cut them open and stick the DNA into the plasmid (I.e.- growth hormone), they multiply in a Petri dish, and you can use it

• Insulin (example of recombinant DNA)- people make insulin from human bacteria in order to make it more applicable and not have as many effects as ones from animals, you can have unlimited of the human one

• Gene therapy- harmless, uses a virus (vaccinia), engineer the piece of DNA for making that membrane protein into the virus's DNA. In order for it to affect the body, have the patient breathe in the engineered virus hoping that the virus will infect its DNA that now has human DNA into the respiratory system cells of the person

- Cystic Fibrosis- gene on chromosome number seven that has information for making protein, deletes one codon that codes for one amino acid which changes the shape of the protein which also results in the fact that the Cl- (chloride ion) can't move through the respiratory system membranes which results in mucus building up through the respiratory tubes

• You “cut out”/splice genes from a human DNA by using restriction enzymes. Restriction enzymes are enzymes that are found in/produced by bacteria, they chop up DNA

• Ethical Question Example- why are we altering someone's natural being if some of the stuff that we are altering it with is not needed (ex- growth hormone), why are we changing someone's natural being in the first place

G. DNA and Cell Differentiation:• If all Cells have the same DNA, how do they differentiate? Cell Differentiation (cell

specialization)- cells specialize by most of the DNA “unlocking” from its normal “locked up” state, unlocking them can change their specialization