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HAZEL SIVE: All right. Let's move on to the second topic of our discussion today, which we will start today and then continue on Friday. And this is a discussion of the proteins. The proteins, probably the most fascinating class of macromolecules, 55% of the dry mass of a cell, and proteins function everywhere. They do almost everything. Strictly speaking, proteins are not hereditary information, although Professor Jacks will talk with you about a class of proteins called prions, which kind of are hereditary information. So not hereditary info, but they do almost everything else. They form the structure of the cell. They form a major class of catalysts called enzymes that we will talk about on Friday. They function in defense as in the immune system. They allow cells to move, dot, dot, dot. Okay? We'll talk about proteins on and on and on as major players in the fabric of life. Their monomer is an amino acid that is abbreviated AA or little aa. And it has a partic...

HAZEL SIVE: Another truism of biochemistry is that many of the molecules within cells are very large. And they're called macromolecules, to indicate this. So macromolecules. So these are often -- Biological molecules are often macromolecules. And these macromolecules are often polymers-- not always-- where a polymer is some kind of repeat of a monomer "n" times. And in formation of macromolecules, there are two kinds of reactions that you need to know. They are called condensation and hydrolysis reactions. And they go something like this. Condensation reactions form bonds. Hydrolysis reactions break bonds. And condensation reactions go something like this. If we call the monomer M, there would be a monomer with a hydroxyl group that interacts with another monomer that has a hydroxyl group. And the outcome of that would be a bond between the two monomers, with the release of water. And the flip of that, during a hydrolysis reaction, is exactly the opposite, w...

HAZEL SIVE: All right. After your class exercise that has to do with vectors and ligation, you should be able to find compatible ends and figure out whether or not they will ligate or not. And you should understand the concept of a vector and how this is used to carry a piece of DNA and to amplify a piece of DNA that you are interested in. I want now to move to our last topic in this discussion today. And that has got the acronym, or the abbreviation, PCR. PCR stands for polymerase chain reaction, polymerase chain reaction, PCR. And it is a very cool technique that allows one to exponentially amplify DNA in a test tube in the lab. Exponential amplification or synthesis of DNA in the lab-- why do we care about this? Why is PCR of interest? It's of interest because it means that you can take a tiny, tiny amount of starting DNA and you can make lots, and lots, and lots, and huge amounts of it. When we talked about molecular cloning, you also amplify DNA a great deal. But...

HAZEL SIVE: From your class exercise about restriction endonucleases, you should now be able to manipulate a piece of DNA to reveal blunt ends or sticky ends. You should know whether or not it's a 5-prime overhang or a 3-prime overhang. And this will set us up for the next topic I want to discuss, which is the question of the vector and ligation. Let's set the stage for this topic by looking back at the overall view that I gave you on cloning and using a gene of interest. We've talked about cutting the DNA now. And we haven't talked about how you exactly isolate your gene of interest. But we'll not worry about that for the moment. What we need to talk about now is the next step, how you're going to put your gene of interest into some kind of carrier DNA molecule that will allow it to replicate to high copy number. And the reason that this can occur is because of these things called vectors. A vector is really a virus that grows in bacteria. It may ...

HAZEL SIVE: Welcome back to Getting Up to Speed in Biology. Today is our last discussion. And the topic today is building with DNA. We're going to cover four topics today. And I think you will find them both interesting and useful. The first is genetic engineering. I'll talk about what that is. We'll then talk about something called restriction endonucleases. We'll talk about vectors and ligation. And then we'll talk about something that has the abbreviation PCR. Let's start with the topic of genetic engineering. I bet you've heard of this. Another word for genetic engineering is recombinant DNA technology, recombinant DNA technology. And what it really means is making DNA constructions in the lab. Building with DNA, the title of our discussion today, DNA construction in the lab-- something that people do to build DNA molecules. And one of the aspects of genetic engineering, the subtopic that is really crucial, is called molecular cloning. And ...

HAZEL SIVE: We're well along our sequence of molecular information transfer. The thing that I want to talk with you about now is kind of the culmination of information transfer. And that is the process of translation. Translation refers to a process that produces protein from an RNA template. If we think about DNA replication and transcription, they are, in a way, quite similar. DNA replication is just copying one language into the same language. Transcription is kind of like changing fonts in your Word document. You go from Calibri to Georgia. The letters are the same. You can recognize them. There's a U, the UT, thing. But otherwise, the letters are the same. You're in the same language with RNA transcription from DNA. Translation is different. We're producing a protein here that's made of amino acids, its own language, from a different language, the language of nucleic acids. And that sense of how does nucleic acid encode protein, a different langua...

[SQUEAKING] [RUSTLING] [CLICKING] HAZEL SIVE: Welcome back to Getting Up to Speed in Biology. This is lecture three, class three, because you're going to participate in the class with a number of exercises, as you have been doing. Today we're going to talk about information transfer in biology. Information transfer and molecular biology are some of the most key, crucial aspects of modern biology, and you need to know this material very carefully in order to understand anything at a higher level in biology. It is very cool stuff. Understanding information transfer explains lots and lots of things. For example, why babies look like their parents, how you control the number of fingers, how a bird gets its colors, and how pathogens, including viruses, make us ill. This is just the tip of the iceberg when we think about what information transfer and molecular biology can teach us. Today I want to cover four aspects. We're going to talk about the gene and some rules...

HAZEL SIVE: In this part of our class organization of the cell, you should now have some familiarity with the notion of a lipid bilayer and some familiarity with the organelles that the cell contains and that indeed makes the cell a cell. Let's go on then to the last topic we're going to cover in our class, which is the topic of cell division. One of the really cool things about cells is that they make more of themselves. Cell division makes more cells. And this is one of the attributes of life that is not true for inanimate objects, of course. When we think of cells making more cells, you should be familiar with something called the cell division cycle, which briefly has two parts. This involves firstly replication and making more of the DNA, taking the DNA, the genes that are in one cell, making a whole other set of them. So you've now got two sets. So DNA replication, which makes two sets of the genes-- since as we discussed, the genes are DNA-- and secondl...

HAZEL SIVE: In conclusion of our first topic today, cellular chemistry, you should now be familiar with condensation and hydrolysis reactions. You should know what free energy means and be able to predict whether a reaction will proceed spontaneously or not. And you should know something about how biological pathways are put together. Let us move on then to our next topic, which is organization of the cell. Last time we talked about the cell as the building block of life, a little package of chemical reactions and macromolecules that can be used kind of like a brick to build a living organism. So let us consider this further in topic 2, cellular organization, and let us talk about the cell as some kind of building block. If you like, you can add of life next to it. So how do you get a building block? When you think about anything that is some kind of brick or some kind of package, it has some kind of surrounding material. And for the cell, this is the cell membrane. So th...

HAZEL SIVE: Let's talk a little bit more about some of the parameters that govern the chemical reactions in a cell, and indeed, any chemical reaction. All chemical reactions are governed by something called free or usable energy. So let us write that. Reactions are governed by free energy where free really means usable. And this free energy gets a special symbol. It is called G. And the difference in free energy is what's really important, and so we write delta G. Delta G comes from a key thermodynamic equation such that the difference in the free energy of a reaction has to do with a difference in enthalpy or total energy minus temperature times the difference in useless energy. So this is the free energy. This is the total energy, and this is the temperature multiplied by the unusable energy or entropy. So this delta G equals delta H minus T delta S is an equation that you should have seen and at least know the terms associated. When we think about a chemical re...