Posted by: mrborden | February 1, 2015

Week 22 DNA Replication and Protein Synthesis


2/2/15
QFD: “It is better to be hated for what you are than to be loved for what you are not.” ― André Gide,
Essential Question of the day: If there is 14 percent thymine in a DNA strand, What percentage of the strand is Adenine?
Today’s learning objective: Students who demonstrate understanding can: HS-LS1 Use a model to illustrate the role of cellular division (mitosis) and differentiation in producing and maintaining complex organisms.
2/3/15
043.01
QFD:“You’ve gotta dance like there’s nobody watching, Love like you’ll never be hurt, Sing like there’s nobody listening,
And live like it’s heaven on earth.” ― William W. Purkey
Pyrimidines and Purines
Miss Crimson: Yes, Professor, I’m sure DNA transcription is very interesting, but let’s stick to the basic characteristics of DNA that pertain to the trial at hand. You were telling us about the nitrogenous bases.

Essential Question of the day: what are enzymes and how do they help DNA replicate?
Today’s learning objective: HS-LS3-1. Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring.


dnarep
proteincodonchart
1) webquest Cp PrepBiology_DynamicDNAWEB_Fullhart
2) webquest Honors dna_replication_webquest
2/4/15
QFD:“Love all, trust a few, do wrong to none.” ― William Shakespeare
Essential Question of the day: How are proteins made? what is the initial step ?
Today’s learning objective: HS-LS3-1. Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring.
1) quiz

2/5/15
QFD: “We accept the love we think we deserve.”
Essential Question of the day:
Today’s learning objective: HS-LS3-1. Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring.
dnamodel_4
Cytosine bonds with guanine and adenine bonds with thymine
Complementary Base Pairing
Professor Pear: You’re quite right. The bases can be categorized into two different groups. The single-ring nitrogenous bases, thymine and cytosine, are called pyrimidines, and the double-ring bases, adenine and guanine, are called purines. (Miss Crimson has a puzzled look.) I guess you might wonder how I can remember that, but it’s really quite simple. ‘All Gods are pure.’ Adenine and guanine are purines. And, by process of elimination, that means cytosine and thymine have to be pyrimidines. See?

Miss Crimson: Yes, yes. That’s a very nice mnemonic aid. Adenine and guanine are purines, but we’re getting off track. You were telling us why the chemical structure of nucleotides is important.

Complementary Base Pairing
The chemistry of the nitrogenous bases is really the key to the function of DNA. It allows something called complementary base pairing. You see, cytosine can form three hydrogen bonds with guanine, and adenine can form two hydrogen bonds with thymine. Or, more simply, C bonds with G and A bonds with T. It’s called complementary base pairing because each base can only bond with a specific base partner. The structures complement each other, in a way, like a lock and a key. C will only bond with G and A will only bond with T in DNA. Because of complementary base pairing, the hydrogen-bonded nitrogenous bases are often referred to as base pairs.
DNA Strands are Antiparallel
The sugar and phosphate ends of a DNA strand are referred to by their carbon numbers
Sugar and Phosphate Ends
Remember how I said that DNA polynucleotides look like half of a ladder? Well, hydrogen bonding completes the ladder. Since the nitrogenous bases can hydrogen-bond, one polynucleotide can bond with another polynucleotide, making the nitrogenous bases the rungs of the ladder. Each polynucleotide participating in this ladder is often referred to as a strand. Because the bases can only fit together in a specific orientation, a parallel orientation between the strands won’t work. The strands must be antiparallel, or upside-down, relative to one another.
The Double-Helix Model of DNA
The model that Watson and Crick proposed in 1953 to describe the molecular structure of DNA was a landmark discovery. But at the time, many scientists weren’t convinced that the model was right. Along with their structural model of DNA, Watson and Crick also proposed a model to describe how DNA is copied inside a cell. Many scientists thought their model of DNA production didn’t make sense, and it led some people to doubt whether they were even right about the double helix. Let’s learn more about the science behind DNA discoveries to find out how this problem was solved.

Scientists had known for a very long time that organisms make copies of their DNA. Making extra copies of the instructions in DNA allows an organism to grow and reproduce. The scientific word for ‘copy’ is ‘replication.’ So when we talk about DNA making copies of itself, we call it DNA replication.

Let’s quickly review the things we’ve already learned about DNA. A DNA chain is composed of smaller components called nucleotides. Each nucleotide is composed of a sugar, a phosphate and a nitrogenous base. The nucleotides are arranged into two strands that link together like rungs on a ladder, and the ladder is twisted into a shape we call a double helix. Watson and Crick first proposed this structural model, and further scientific study has shown that they were basically correct. So, why were they challenged by the scientific community?
Three Different Models for DNA Replication
Watson and Crick had proposed that in order to copy itself, DNA would have to open down the center, sort of like a zipper coming apart, so that a new DNA strand could be built on top of the exposed strands. Following the rules of complimentary base pairing, adenine would pair with thymine, and cytosine would pair with guanine. This idea was called a template model, since one DNA strand serves as the template for a new one.

Watson and Crick figured that this model would result in two new double strands of DNA, each one with one strand of parent (or template) DNA and one strand of daughter (or newly-synthesized) DNA. They called this the semi-conservative model, because half of the parent DNA was conserved in each new DNA molecule.

Scientists looked at the double helix of DNA and wondered how in the world it could possibly open itself up without getting tangled or torn apart. So they thought up some other ideas about how DNA replication works. One hypothesis, called the dispersive model, suggested that DNA only copied itself for short chunks at a time, producing new strands that alternated parent and daughter DNA. Another idea, called the conservative model, argued that DNA didn’t split open at all, but somehow kept the parent strands intact while creating an entirely new and separate copy.

Nobody knew for sure how DNA replication really worked until two scientists named Matthew Meselson and Franklin Stahl devised an ingenious experiment in 1958. They realized that they could test all three models at once by keeping track of what happens to one parental DNA strand as it generates a series of copies.
DNA Helicase and Its Function in Replication
DNA helicase is an enzyme that unwinds the DNA double helix by breaking the hydrogen bonds between the complementary bases. It’s easy to remember the name because it has part of the word helix in it. You can imagine it sort of as a wedge that forces apart the two strands, just like the slider on a zipper wedges apart the two long rows of teeth. DNA helicase is responsible for taking apart our DNA double helix.

Just like a zipper makes a Y-shape with the two strands of teeth, the action of DNA helicase results in a Y-shaped fork in the molecule, which we call a replication fork. The enzyme attaches to the DNA at the origin of replication, which is the place where the process of DNA replication begins. As helicase moves down the length of the strand, the replication fork moves along in its wake. You can imagine that by the time it gets to the end of the strand, all the parent DNA had been split in two.
Review of DNA Polymerase
So far in our discussions about DNA replication, we’ve talked about a handful of enzymes that help us by changing and moving parts of the DNA molecules. One of the most important enzymes here is DNA polymerase. This enzyme is the one that carries the individual nucleotides to the site of replication. DNA polymerase builds the daughter strand by matching new nucleotides to their complementary bases on the parent strand.

DNA polymerase is the enzyme that builds the daughter strand one nucleotide at a time
DNA Polymerase Review
When scientists first began studying how DNA polymerase works, they assumed that it always added nucleotides in a continuous fashion. That is, they thought the enzyme always followed right behind the replication fork, laying down nucleotides as soon as the parent strands were exposed. But in the 1960s, a molecular biologist named Reiji Okazaki challenged that view. He and his colleagues had begun to think that the action of DNA polymerase was not always continuous. Their ideas stemmed from a combination of discoveries they’d made in the lab and a thorough knowledge of the structure of DNA.

Okazaki and the Antiparallel Problems
Okazaki understood the DNA molecule, and he knew that DNA backbones run in opposite directions. Remember that the strands in a DNA molecule are oriented antiparallel to one another. You can think of the two strands like arrows, with the arrowhead of one strand matching up with the tail of the other strand. Scientists name the ends of the DNA strands according to the carbons in the sugar ring. One end is called the 3′ end, and the other is called the 5′ end. So on any complete molecule of DNA, one strand will run from 3′ to 5′, and the other will run from 5′ to 3′.

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