For more information, please see full course syllabus of Molecular Biology
For more information, please see full course syllabus of Molecular Biology
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Biochemistry Review: Importance of Chemical Bonds
- Chemical bonds are forces that hold atoms together.
- Covalent bonds are very strong, and may be either polar or non-polar.
- Water is an important part of almost all biochemical reactions.
- Biochemical reactions flow based on the direction and magnitude of free energy.
- ssDNA absorbs more UV light than an equal amount of dsDNA.
Medium, 4 examples, 5 practice questions
Biochemistry Review: Importance of Chemical Bonds
- Hydrogen bond
- Ionic bond
- van der Waals forces
- Electric dipole
- O2
- H2O
- HCl
- NaCl
- Non-polar
- Polar
- Hydrophobic
- Lipid
- Equal to zero
- Less than zero
- Greater than zero
- Extremely small
- Covalent and polar
- Ionic and Hydrophobic interactions
- Hydrogen bonding and hydrophobic interactions
- van der Waals forces and hydrophilic interactions
*These practice questions are only helpful when you work on them offline on a piece of paper and then use the solution steps function to check your answer.
Answer
Biochemistry Review: Importance of Chemical Bonds
Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.
- Intro
- Lesson Overview
- Chemical Bonds
- Attractive Forces That Hold Atoms Together
- Types of Bonds
- Covalent Bonds
- Valence Number
- H O N C P S Example
- Polar Bonds
- Non-Polar Bond
- Non-Covalent Bonds
- Ionic Bonds
- Hydrogen Bonds
- Hydrophobic Interactions
- Van Der Waals Forces
- Example 1
- Properties of Water
- Chemical Reactions and Free Energy
- Transition State
- What Affect the Rate
- Forward and Reserve Reactions Occur Simultaneously But at Different Rate
- Equilibrium State
- Equilibrium Constant
- Example 2
- Chemical Reactions and Free Energy
- Activation Energy
- Energy Barrier
- Enzymes Accelerate Reactions by Decreasing the Activation Energy
- Enzymes Do Not Affect the Reaction Equilibrium or the Change in Free Energy
- Gibbs Free Energy Change
- Spontaneity
- Gibbs Free Energy Change Determines Final Concentrations of Reactants
- Endodermic vs. Exothermic Graph
- Example 3
- Properties of DNA
- Antiparallel Orientation
- Purine Bases Always Pairs Pyrimidine Bases
- Structure Images
- A, B, Z Forms
- Major and Minor Grooves
- Hydrogen Bonding and Hydrophobic Interactions Hold the Two Strands Together
- Denaturation and Renaturation of DNA
- Ways to Denature dsDNA
- Renature When Environment is Brought Back to Normal
- Hyperchromiicity
- Absorbs UV Light
- Spectrophotometer
- Graph Example?
- Example 4
- Intro 0:00
- Lesson Overview 0:14
- Chemical Bonds 0:41
- Attractive Forces That Hold Atoms Together
- Types of Bonds
- Covalent Bonds
- Valence Number
- H O N C P S Example
- Polar Bonds
- Non-Polar Bond
- Non-Covalent Bonds
- Ionic Bonds
- Hydrogen Bonds
- Hydrophobic Interactions
- Van Der Waals Forces
- Example 1 12:51
- Properties of Water 18:27
- Polar Molecule
- H-bonding Between Water H20 Molecules
- Hydrophobic Interactions
- Chemical Reactions and Free Energy 22:52
- Transition State
- What Affect the Rate
- Forward and Reserve Reactions Occur Simultaneously But at Different Rate
- Equilibrium State
- Equilibrium Constant
- Example 2 26:16
- Chemical Reactions and Free Energy 27:49
- Activation Energy
- Energy Barrier
- Enzymes Accelerate Reactions by Decreasing the Activation Energy
- Enzymes Do Not Affect the Reaction Equilibrium or the Change in Free Energy
- Gibbs Free Energy Change
- Spontaneity
- Gibbs Free Energy Change Determines Final Concentrations of Reactants
- Endodermic vs. Exothermic Graph
- Example 3 38:46
- Properties of DNA 39:37
- Antiparallel Orientation
- Purine Bases Always Pairs Pyrimidine Bases
- Structure Images
- A, B, Z Forms
- Major and Minor Grooves
- Hydrogen Bonding and Hydrophobic Interactions Hold the Two Strands Together
- Denaturation and Renaturation of DNA
- Ways to Denature dsDNA
- Renature When Environment is Brought Back to Normal
- Hyperchromiicity
- Absorbs UV Light
- Spectrophotometer
- Graph Example?
- Example 4 51:02
Molecular Biology Online Course
Section 1: The Beginnings of Molecular Biology | ||
---|---|---|
Biochemistry Review: Importance of Chemical Bonds | 53:29 | |
Mendelian Genetics & Foundational Experiments | 1:09:27 | |
Section 2: Structure of Macromolecules | ||
Structure of Proteins | 49:44 | |
Structure of Nucleic Acids | 1:02:10 | |
Section 3: Maintenance of the Genome | ||
Genome Organization: Chromatin & Nucleosomes | 57:02 | |
DNA Replication | 1:09:55 | |
DNA Mutations & Repairs | 1:13:08 | |
Homologous Recombination & Site-Specific Recombination of DNA | 1:14:27 | |
Section 4: Gene Expression | ||
Transcription | 1:19:28 | |
Translation | 1:15:01 | |
Section 5: Gene Regulation | ||
Gene Regulation in Prokaryotes | 45:40 | |
Gene Regulation in Eukaryotes | 1:06:06 | |
Section 6: Biotechnology and Applications to Medicine | ||
Basic Molecular Biology Research Techniques | 1:08:41 | |
Section 7: Ethics of Modern Science | ||
Genome Editing, Synthetic Biology, & the Ethics of Modern Science | 45:06 |
Transcription: Biochemistry Review: Importance of Chemical Bonds
Hello, and welcome to www.educator.com, today is our first lecture.0000
To start with molecular biology, first we have to do a little bit of biochemistry review and0005
we are specifically going to focus on the importance of the chemical bonds.0010
As an overview, first we are going to talk about chemical bonds.0016
We are going to talk about both covalent and non-covalent bonds, and the different types of each of those.0021
We will follow that up with the properties of water, as well as chemical reactions of free energy.0026
And then, we will have just a brief intro into the properties of DNA before we finish and move on to lecture 2.0032
Chemical bonds are attractive forces that hold atoms together, thereby making molecules at least two atoms together.0043
One type of chemical bonds are covalent, which are much stronger bonds.0056
They can be either polar or non polar.0063
One other class of bonds is the non-covalent bonds, which are much weaker than the covalent bonds.0066
However, when you have many non-covalent bonds together, they can become very strong.0072
The many types of non-covalent bonds, the ones we are going to talk about, ionic bonds, hydrogen bonds,0078
hydrophobic interactions, and finally Van Der Waals forces or Van Der Waals interactions.0086
Let us start off with covalent bonds, they are very strong.0096
They involve the sharing of an electron pair between two atoms.0101
Making and breaking covalent bonds usually requires the presence of an enzyme to catalyze that reaction.0106
The valence number of an atom determines the number of covalent bonds it can form.0119
What is that mean?0124
First of all, what is the valence number?0125
That is just a number of unshared electrons in an atoms outer shell.0136
The common atoms that we are going to see in molecular biology are hydrogen, oxygen, nitrogen, carbon, phosphorus, and sulfur.0165
How many valence electrons do each of these have?0191
Hydrogen has 1 valence electron, oxygen has 6, nitrogen has 5, carbon 4, phosphorus 5, and sulfur 6.0204
I said that the valence number of an atom determines the number of covalent bonds it can form.0225
How is that true, let me show you.0233
They key here is that all atoms other than hydrogen want to have a full octet, meaning a full 8 electrons in their outermost shell.0241
That will determine how many bonds it can make.0264
Hydrogen, I said was the only one that does not want 8, that is because hydrogen, its full electron shell cannot consist of 2 electrons.0276
Every bond is a sharing of a pair of electrons.0288
With hydrogen having a valence electron, 1 valence electron, and it only liking to have 2 to fulfill it, it can make one bond.0293
Oxygen, to have its full octet, can either accept 2 electrons from similar or give up 6 of its own, but it is more likely to take 2.0309
Therefore, by taking 2 electrons, each one of those is going to participate in a bond, that is 2 bonds for oxygen.0322
Nitrogen, to get its full octet would want 3 bonds.0331
Sometimes you can actually have 4 bonds.0339
Carbon, to get its full octet wants another 4 electrons, 4 bonds.0342
Phosphorus actually is kind of a little different, in the fact that it will more likely give up its 5 than take on 3, they will have 5 bonds.0348
Sulfur is a little bit weird, in the fact that it has a little more variety, it will make a possible 2, 4, or 6 bonds.0359
The number and types of bonds ultimately determines the geometry of what the molecule will look like.0376
Single covalent bonds, that would be, let us say this, for example, a nitrogen.0384
That would be a single covalent bond which is a sharing of 2 electrons.0391
A lot of rotation of the atoms around the bond meaning this can flip upside down, flip, maybe even curl a little bit.0396
Double and triple bonds, for example a double one that is a sharing of 4 electrons,0405
or triple bond a sharing of 6 electrons between there, do not allow any rotation around that bond.0412
Bond angles are actually determined by the number of atoms.0419
The whole goal is to space out the electrons, because the electrons are negatively charged.0424
If you have ever played with a magnet, you know that two things of a like charge will not attract. They push away, they repel.0429
Two negatives or two positives repel, a negative and a positive attract.0436
Chemical bonds can be broken down into your polar and your non-polar bonds.0444
Your polar bonds also called electric dipoles.0450
This is a bond between two nonmetal atoms with differing electron negativities.0454
What that basically means is that they are not sharing the bonding, they are not sharing the electrons equally.0463
Let us say for an example, one of the examples is hydrogen chloride.0474
They have just the bond right there, what we actually find is that the chlorine atom actually has a partial negative charge,0482
whereas the hydrogen atom has a partial positive charge0496
because the electrons are being pulled by chlorine because it has a higher electron negativity.0498
If you look at the periodic table, electron negativity decreases as you go downward and as you go leftward.0505
You decrease electron negativity, as you go down into the left.0520
A non-polar bond on the other hand is a bond between two middle atoms with similar or even equal electron negativity.0527
An example of that would be, let us go back to our nitrogen.0536
That would be an example of a non-polar bond because nitrogen,0541
if we have a nitrogen with an electron negativity of 3.04 and nitrogen with an electron negativity of 3.04,0545
they are exactly the same so electrons are evenly shared.0558
Whereas, this chloride, this is a 3.16 electron negativity, hydrogen over here is a 2.20.0563
Electrons will move toward the chloride.0575
Some examples of a non-covalent bonds, or what a non-covalent bond is.0588
They are not the same as the covalent bond.0594
They do not have that real nice sharing of the actual electrons, these are not electron sharing.0598
Ionic bonds, hydrogen bonds, hydrophobic interactions, and Van Der Waals forces, are all examples of non-covalent bonds.0607
Ionic bonds being the strongest, Van Der Waals forces being the weakest.0618
Ionic bonds form between charged groups or otherwise known as ions.0627
They are the strongest of the non-covalent interactions.0633
An example, let us say, our sodium ion, our chloride ion, coming together to make sodium chloride otherwise known as table salt.0636
Hydrogen bonds are a type of dipole-dipole interaction between a hydrogen atom and a highly electron negative atom,0652
usually being your oxygen, nitrogen, sulfur, and fluorine.0664
As I mentioned before in our example of a polar bond, I used hydrogen and chlorine, hydrogen chloride as being a polar bond.0671
Hydrogen and oxygen, hydrogen and nitrogen, those are not polar bonds, those are examples of hydrogen bonds.0682
We have non-covalent bonds, the other two left, we have hydrophobic interactions and0694
those occur between non polar molecules to limit their interaction with water.0702
Think of droplets of oil in the water and how they come together to form a bigger droplet, I will explain that a little bit.0707
Finally, Van Der Waals forces, these occur between all molecules as a result of unequal distribution of electrons.0718
These can be attractive or repulsive.0727
Altogether, when we are talking about these bonds, multiple weak bonds can have an additive effect to stabilize molecules.0732
We will see that throughout this course, especially for DNA.0741
Hydrogen bonds not very strong, Van Der Waals forces not very strong,0745
hydrophobic not very strong, but those together actually hold our DNA.0750
They hold the two strands of DNA together.0756
A lot of very weak bonds, added up over the length of the molecule can be very strong.0760
Let us get some examples of covalent and non-covalent bonds.0773
Covalent, we will do in blue.0777
Let us say polar, example of a polar one.0785
An equal distribution of electrons, we said before HCl.0790
I will give you another one, CH₄.0799
CH₄ looks like this.0806
There is equal sharing between the carbon and hydrogen in all of those.0813
A non-polar, we have the one that we talked about before, N₂, we have O₂.0818
Any diatomic molecule, you put them right here, hydrogen gas, sulfide gas.0835
Or even the carbon bond in an ethane molecule.0843
This is what ethane looks like.0849
We can even draw that out to look like this.0859
All the carbon hydrogen bonds are actually covalent, polar covalent.0871
The bond between the carbon and the carbon is actually a non-polar covalent bond.0879
The non-polar, let us put in green, this is actually non-polar.0886
Let us give some examples of, what else do we have.0898
Some examples of a non-covalent.0906
Let us say ionic, I gave you one already, sodium chloride.0919
That is going to be the strongest.0926
We have hydrogen bonds, those are going to be like the ones that I shown for water.0928
They are usually longer than covalent bonds.0937
Let us see you right here, if I can draw one out.0940
By the way, water those are covalent bonds between the hydrogen and oxygen.0949
It would be a polar covalent bonds.0955
I will even draw that one up here, H₂O.0958
These are polar bonds or covalent bonds.0974
If I draw another, water, this right here, the bond between the oxygen and0984
the hydrogen of two separate molecules is a hydrogen bond.1000
Now we have hydrophobic interactions.1006
Hydrophobic interactions that would be like water and oil droplets.1013
Van Der Waals, that just says that when any two molecules come together,1020
there is a point at which they are attracted, that point is 4 to 10 angstroms.1034
There is an attraction between 4 and 10 angstroms.1049
If you go below 4 angstroms, you start to get a repulsion.1053
If you go outside of 10 angstroms then there will becomes no attraction at all.1058
One thing I want to mention about Van Der Waals is that, Van Der Waals force is actually pretty cool.1067
Van Der Waals forces, as I said, occur between any molecule.1074
Van Der Waals forces are what is responsible not only for helping DNA stay together1077
but for geckos and spiders attach into the walls.1082
That is how they stick to walls, it is different than flies and other insects.1089
That is a different way that they utilize that.1094
But geckos and spiders, specifically, the way they attach to walls is through Van Der Waals forces.1098
I think that is pretty cool.1104
Let us move on to the properties of water.1109
First thing you need to know about water is that it is a polar molecule.1112
Which means we have oxygen which is highly electron negative, bound to hydrogen which are not very electron negative.1120
Therefore, we have a partial negative charge at the oxygen because it is trying to steal the electrons.1129
We have partial positive charges with the hydrogen.1141
This symbol here is a Δ, the Greek letter Δ.1147
Water is important because it is a solvent in which everything in the cell is dissolved.1154
We have to take into account water in anything in our living system.1161
Water can hydrogen bond, you can hydrogen bond several water molecules together.1171
A single water molecule can actually make 1, 2, 3, 4 different hydrogen bonds, with 4 different water molecules.1178
The oxygen of a water molecule can hydrogen bond with two different hydrogens from different water molecules.1197
Each hydrogen of that original water molecule can hydrogen bond with an oxygen of a different water molecule.1207
If you look here on your right, this is the cubic form.1217
It is the crystal structure of the solid water which we know as ice.1223
Water also is going to undergo hydrophobic interactions.1233
Literally, what hydrophobic means is hydro water, phobic afraid.1237
It can be hydrophobic, afraid of water, hydrophilic water loving; philic - love.1245
We are going to talk about those terms, especially when we talk about proteins, later in this class.1251
Hydrophobicity, the not wanting to interact with water.1261
The hydrophobicity of non-polar molecules promotes aggregation,1265
they come in together by releasing water molecules in contact with their surfaces.1272
They released water to form more hydrogen bonds with other water molecules.1278
Imagine that this oil is in a aqueous solution of water, it is surrounded by water molecules.1284
The water wants to interact with other water molecules, we know that it did not want to interact with oil.1305
The oil desperately wants to interact with other things than water.1312
The oil wants to reduce its total surface area touching water.1319
What water will do is, it will come together to push water out.1325
It pushes all this water out to that surface area that is touching the water.1333
It will basically erase all that by becoming this big blob.1338
Of course, water still attached on the outside but it is pushed out a lot of water in the process.1345
It is better for the oil, now it is just touching less water, right.1351
It is better for the water because the water is touching more water.1357
This is a huge property of water and this is important.1361
We always think about our non polar molecules because of this.1366
Let us switch just a little bit to chemical reactions of free energy.1375
Any reaction, A + B going to C + D, there is always something called an intermediate or a transition state that we usually do not see.1380
That is the point that we call here AB, that is the point at which it is transitioning from the reactants A and B, to the products C and D.1390
It usually occurs via an enzyme.1402
The weight of the reaction is affected by the concentration of the reactant, as well as the concentration of the products.1408
The weight will also be affected by the energy barrier, the temperature,1419
as well as the pH of the solution in which the reaction is occurring.1425
When we are talking about chemical reactions, it is extremely important to know that1435
forward and reverse reactions are occurring simultaneously.1441
It is happening in both directions.1448
But the speed of reaction in the rightward direction vs. the leftward direction, differ.1452
That is what allows you to either make a bunch of products or stay with a bunch of reactants.1460
This equilibrium state is a very dynamic state, whether right of your forward and reverse reactions are equal.1470
It is important to note that forward in reverse reactions are still occurring but there is no net change of reactant or product.1480
If one reactant is being turned into a product then one product is being turned back into a reactant.1495
Forward reverse reaction is still occurring but at the same rate.1505
I have a zoomed out to macro view, nothing is changed.1509
We can measure the equilibrium because each reaction is going to have an equilibrium constant which is KEQ.1517
That is going to measure the extent to which reactants are converted into products.1527
It is a very simple measurement, it can get much more complex but I’m presenting you the simplified one.1532
Is that the KEQ is equal to the concentration of your products over the concentration of you reactants.1537
From here, you can understand that if you have your numerator bigger,1545
KEQ is going to be greater than 1, your reaction favors the products.1554
If you the denominator larger, you are going to have a number less than 1, that reaction is going to favor the reactants.1559
They are backwards.1569
As an example of these, I want to show a very cool aspect of chemical reaction.1575
In the following reaction equation, label the reactants and the products.1583
As we talked about before, I will work this through with you.1589
A + B going to C + D, you are starting with this.1593
These are going to be your reactants.1600
Your A and B you want in C and D, that is your going to be your products.1607
This is a double headed arrow that we see right here.1615
Here is a double headed arrow meaning this reaction is reversible, it can go on both directions.1628
In the other direction, C and D are your reactants, A and B are your products.1635
All 4, A, B, C, and D, are reactants and all 4 A, B, C, and D are products at one point or another, in this reaction.1650
Rightward reaction, A and B reactants.1661
Leftward reaction, C and B reactants.1664
Continuing on with our chemical reaction of free energy.1671
I want to introduce the concept of activation energy also shown as E sub a.1674
Activation energy is the minimum energy that is needed to the input to cause a chemical reaction.1680
In two reactants, let us say X + Y, clogged energy gets released.1691
It has to be greater than the energy barrier for the reaction to proceed.1696
Its energy barrier is that amount of energy required for the formation of the products.1702
This is your energy barrier or your activation energy.1708
Because this is the energy of your reactants and this is the energy of your products.1722
Even though your energy of your products are lower than your reactants,1732
you have to pass this hump, this threshold, to be able to get down to here.1735
Let us talk about enzymes, enzymes are biological catalysts.1747
They accelerate reactions by decreasing the activation energy.1753
Enzymes do not affect the reaction equilibrium, the KQ, or the change in the free energy.1762
But they can decrease this, let us say with an enzyme, my curve might look like this.1778
With, this is my activation energy with an enzyme.1802
This is my activation energy without an enzyme, which is much higher.1820
As we can see, this, the energy of the reactant and the energy of the product is unchanged.1836
Let us give a few statements about chemical reactions and free energy.1852
What is free energy, usually we talk about it as Gibbs free energy and as the change in Gibbs free energy, ΔG.1858
This is the difference between the free energy of the products - the free energy of the reactant.1868
As we saw back there on the previous slide, we had two different looking graphs.1878
This is reaction progress, this was free energy.1897
We know that the left tail, this is our reactant.1914
The right tail is our product.1922
We know that this is our activation energy or energy barrier.1927
If your products have a higher free energy, then your reactants, what do we have,1936
the difference between the free energy of the products.1945
What we are looking at is the G of our products - the G of our reactants.1948
That is our ΔG.1963
If our products have a higher energy state than our reactants, that ΔG is going to have a positive sign.1967
Meaning, you need to add in energy from the system, usually in a form of heat or ATP, to get up to this energy level.1983
That usually means that the reaction is non spontaneous.1994
It would not happen on its own, you need the input of energy.2000
This is also called an endorgonic reaction.2003
Let us look at the flip side, if our energy for our product is lower than our energy for our reactant,2013
we are going to have a -ΔG.2022
That means that it is actually going to give energy off to the system in the form of heat or ATP energy.2026
This will likely be spontaneous, meaning it can happen because you do not need to input in energy.2036
This is called an exorgonic reaction, it is likely to happen.2041
When your reactants and your products have the exact same amount of free energy,2050
That is when you are saying that that the reaction is at equilibrium.2062
You are no longer going one way or the other.2068
What is important here is that ΔG, ultimately only determines2072
the final concentrations of reactants to products but not the reaction rate.2078
The reaction rate is determined by the enzymes, by the activation energy.2090
Over here, remember, if we have the reactant, product, we have our activation energy.2103
This is endorgonic, you need to put in energy because the products have a higher energy than the reactants.2123
Meaning this is ΔG of positive, meaning endorgonic positive ΔG non spontaneous.2132
In this reaction, our reactants have a higher energy than the products.2152
Meaning they are giving energy off to the system, meaning it is exorgonic.2156
The ΔG is negative, it is likely to occur spontaneous.2162
One thing about spontaneous and not spontaneous, are –ΔG and +ΔG,2175
is that just because you have a +ΔG and it is a non-spontaneous reaction, it does not mean it will never occur.2182
Reaction coupling is what happens, meaning you can add a -ΔG to a +ΔG reaction to allow that +ΔG reaction to occur.2190
What happens is that, the second reaction consumes the products of the first reaction,2207
preventing reverse of the reaction which would otherwise be favored.2213
If you can, let say, here is our progress, here is the free energy.2217
What you could actually have here, this can be a reactant-product.2238
This can be a reaction 1, as we can see here, the products are much lower in energy.2259
The reactants, therefore, it is high -ΔG.2277
This can be coupled to another reaction where it is a +ΔG.2283
This product of reaction 1 now becomes the reactant of reaction 2.2300
That is how they can be coupled to force a +ΔG non spontaneous reaction to go forth.2317
Let us quiz you, based on the last couple of slides.2327
What information can be gained from a reaction with a –ΔG.2330
A –ΔG reaction is going to tell you that a reaction is spontaneous.2345
No energy input is needed, in fact it gives off energy to the system.2351
It will favor the formation of the products, -ΔG affects the equilibrium but not the rate.2358
It may be coupled with the +ΔG reaction to force that to proceed.2368
That is the biochemistry review that I wanted to do but I also want to introduce you to DNA.2380
We are going to go to DNA in much further detail in a few lectures but I wanted to introduce it to you first.2387
DNA stands for deoxyribonucleic acid, that is what the DNA stands for.2394
Let me write that out for you, deoxyribonucleic acid.2399
DNA is normally found in, let us call a double helix.2419
It is two stranded, as we can see over here.2423
It is in an anti parallel orientation.2428
Each strand has a 5 prime phosphate and a 3 prime hydroxyl end.2432
When it is in a double helical form, you have one strand, if we are just going to read this from top to bottom, going 5 prime to 3 prime.2448
It is bound to its complimentary strand in the opposite or2459
anti parallel orientation with 5 prime going up to the top of the page to the 3 prime hydroxyl end.2464
Purine bases and pyrimidine bases are two types of heterocyclic nitrogen bases that are parts of a nucleotide.2474
A nucleotide is the monomer of a nucleic acid.2484
Purines are two ringed heterocyclic nitrogen structures.2489
Pyrimidines are single in structure.2494
Purines and pyrimidines are always pair together.2498
Adenine is an example of a purine.2501
It will hydrogen bond to thymine which is an example of a pyrimidine.2506
Guanine is an example of a purine down here.2513
Cytosine is an example of a pyrimidine, they will hydrogen bond.2519
G’s and C’s always make 3 hydrogen bonds, as you can see here.2524
A’s and T’s always make 2 hydrogen bonds.2529
Under normal circumstances, A’s only bind with T’s in DNA.2533
G’s only bind with C’s in DNA.2539
Those bonds are on the inside.2545
On the outside is the phosphate backbone that links the nucleotides of the same chain together.2548
I said before that the bases on the inside making hydrogen bonds, 2 between A’s and T’s, 3 between G’s and C’s.2558
This right here is an example of a nucleotide.2572
These are the monomers of DNA, of the nucleic acid polymer.2579
It has to have a nitrogenous base, a purine in this case, a pyrimidine could also work.2585
Sugar, if it is DNA, it deoxyribose.2592
If it is going to be RNA, it would be an oxygen.2597
It must have a phosphate group.2609
Just a few other quick things on DNA.2615
It has several forms, A, B, and Z forms.2618
The normal is B form, that is found, there are 10.4 base pairs per turn of the helix in B DNA.2620
Let us say from here to here is one turn.2629
There are 10.4 base pairs, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.2636
There are both major and minor grooves on the surface of the helix.2648
We of the major groove, it goes this way.2652
The major groove and the minor groove.2658
These are important because as we will talk later, you can see more of the chemicals,2662
the atoms in the DNA, that helps for DNA binding of proteins.2673
What is important and I talked about, earlier in this unit is that hydrogen bonding and2679
hydrophobic interaction is also known as base stacking interactions, hold the two strands together.2684
Our DNA can be denatured and renatured, meaning you can break and remake the hydrogen bonds,2698
kind of as if nothing ever happened.2708
You are not breaking the molecule at all, you are just separating the two chains.2711
Think of it like an ice cream sandwich, the two cookie crust are your DNA S strands, your ice cream is your hydrogen bonds.2715
If you want denature your double stranded DNA, you just melt those hydrogen bonds.2729
A couple of ways to do it is actually with heat.2737
If you microwave your ice cream sandwich, which would just be a waste of an ice cream sandwich,2740
if you did, you would be able to pull apart this cookie crust very easily.2746
Another way to denature double stranded DNA is, if you put in a high PH environment or low salt concentration.2751
Or if you add metabolic enzymes that are made to break that open.2761
A cool thing about DNA is that the same complimentary DNA strands that were denatured can renature,2766
or reheal when the environment is brought back to normal, if you decrease the temperature,2773
if you decrease the PH, if you increases the salt, certain things like that.2778
DNA strands will anneal to what it should have anneal to, what are called complimentary sequences.2783
A’s and T’s will come back, G’s and C’s will come back to each other.2790
Speaking of the ability to denature and renature, I want introduce you to a concept called hyperchromiicity.2797
What hyperchromiicity is, it is just the increase of absorbent of a substance.2806
Single stranded DNA absorbs more UV ultraviolet light, then an equal amount of double stranded DNA, almost about 20% more.2818
If single stranded DNA, if you had 10 base pairs, it would be 10 bases, because it is single stranded.2830
You had 10 base pairs of DNA, this 10 bases of RNA would absorb about 20% more UV light than double stranded DNA.2841
That is because the actual nitrogenous bases, the A’s, G’s, and T’s,2856
they are purines and pyrimidines, are what is absorbing that UV light.2862
When it is in a double stranded helix, they are compact inside on the inner portion of the double helix.2866
Single stranded DNA or single stranded RNA, those flap out in solution.2873
What we can do, we can determine at a certain point, based on the absorbents.2881
If we have microscopic DNA we cannot see in solution, we will be able to tell if it is DNA or RNA,2887
or if it is double stranded specifically or single stranded.2899
How we do that is we use a machine called a spectrophotometer.2903
We make are reading, we take a reading, when we take a sample of DNA in the water or a buffer, put into a clear tube.2907
Put it in the machine, you shine light through the one side of the cuvette.2919
You have a detector on the other side, it will calculate how much of the original light came all the way through how much is captured.2924
They do that at a wave length of 260 nm.2934
At this low wavelength, at this wavelength, we are reading absorbent values.2939
An absorbent of 0 means that it is completely translucent, all the light went all the way through.2956
An absorbent of 100% that means it is completely blocked out,2964
not a single photon of light went from the light to the capturing device.2969
At this absorbents level, we have everything being double stranded.2975
As you increase the temperature, you start to denature the DNA.2981
You start to melt those bonds.2987
As you melt the bonds, the nitrogenous bases start being able to flap around the solution,2990
meaning it catches more UV light, it absorbs more.2996
Into the point where you are completely denatured, this is double stranded DNA.3000
Until you completely denatured and this is actually single stranded DNA, where it has before absorb it.3007
Right here at the inflection point is what we call that TN or the melting point.3013
The melting point is the point at which you have 50% of your DNA as double stranded and 50% as single stranded.3024
The TM, the melting temperature, is determined by the base sequence, as well as the salt concentration.3044
That can affect the shielding, salt concentration will affect if you denature or not.3049
For our last portion of this unit, I want to leave you with a very crude method3063
to approximate a melting temperature without using any type of absorbent device or techniques.3069
For example, the crude method is that for every AT base pair, that = to 2°C.3077
For every GC base pair, that is 4°C.3090
When we usually calculate this, when we are making primers for a polymerase chain reaction PCR,3097
which is another thing we will learn in this class.3103
I wanted to give you a sample problem.3107
For example, let us say we have this sequence AT, GC, AT, GC.3109
What would be the melting temperature of this 10 base pairs sequence be?3123
We have count up how many A’s and T’s, AT bonds are 1, 2, 3, 4, 5, 6.3133
That leaves us with how G’s and C’s, 1, 2, 3, 4.3145
6 AT bonds × 2°C = 12°C.3153
4 GC bonds × 4°C = 16°C.3163
Add those together that gives us a melting temperature of this sequent at 28°C.3172
As you will be able to see is that regions with higher GC content will have higher melting temperatures.3186
Regions with higher AT content will have lower melting temperatures comparatively.3196
Thank you for joining me at www.educator.com.3203
I hope you come back and see me in lecture 2, thank you.3207

Michael Philips
Biochemistry Review: Importance of Chemical Bonds
Slide Duration:Table of Contents
53m 29s
- Intro0:00
- Lesson Overview0:14
- Chemical Bonds0:41
- Attractive Forces That Hold Atoms Together0:44
- Types of Bonds0:56
- Covalent Bonds1:34
- Valence Number1:58
- H O N C P S Example2:50
- Polar Bonds7:23
- Non-Polar Bond8:46
- Non-Covalent Bonds9:46
- Ionic Bonds10:25
- Hydrogen Bonds10:52
- Hydrophobic Interactions11:34
- Van Der Waals Forces11:58
- Example 112:51
- Properties of Water18:27
- Polar Molecule13:34
- H-bonding Between Water H20 Molecules19:29
- Hydrophobic Interactions20:30
- Chemical Reactions and Free Energy22:52
- Transition State23:00
- What Affect the Rate23:27
- Forward and Reserve Reactions Occur Simultaneously But at Different Rate23:51
- Equilibrium State24:29
- Equilibrium Constant25:18
- Example 226:16
- Chemical Reactions and Free Energy27:49
- Activation Energy28:00
- Energy Barrier28:22
- Enzymes Accelerate Reactions by Decreasing the Activation Energy29:04
- Enzymes Do Not Affect the Reaction Equilibrium or the Change in Free Energy29:22
- Gibbs Free Energy Change30:50
- Spontaneity31:18
- Gibbs Free Energy Change Determines Final Concentrations of Reactants34:36
- Endodermic vs. Exothermic Graph35:00
- Example 338:46
- Properties of DNA39:37
- Antiparallel Orientation40:29
- Purine Bases Always Pairs Pyrimidine Bases41:15
- Structure Images42:36
- A, B, Z Forms43:33
- Major and Minor Grooves44:09
- Hydrogen Bonding and Hydrophobic Interactions Hold the Two Strands Together44:39
- Denaturation and Renaturation of DNA44:56
- Ways to Denature dsDNA45:28
- Renature When Environment is Brought Back to Normal46:05
- Hyperchromiicity46:36
- Absorbs UV Light47:01
- Spectrophotometer48:01
- Graph Example?49:05
- Example 451:02
1h 9m 27s
- Intro0:00
- Lesson Overview0:22
- Gregor Johann Mendel1:01
- Was a Biologist and Botanist1:14
- Published Seminal Paper on Hybridization and Inheritance in the Pea Plant1:20
- Results Criticized1:28
- Father of Modern Genetics1:59
- Mendel’s Laws2:19
- 1st Law: Principle of Independent Segregation of Alleles2:27
- 2nd Law: Principle of Independent Assortment of Genes2:34
- Principle of Independent Segregation (of Alleles)2:41
- True Breeding Lines / Homozygous2:42
- Individuals Phenotypes Determined by Genes3:15
- Alleles3:37
- Alleles Can Be Dominant or Recessive3:50
- Genotypes Can be Experimentally Determined by Mating and Analyzing the Progeny5:36
- Individual Alleles Segregate Independently Into Gametes5:55
- Example 16:18
- Principle of Independent Segregation (of Alleles)16:11
- Individual Genes Sort Independently Into Gametes16:22
- Each Gamete Receives One Allele of Each Gene: 50/50 Chance16:46
- Genes Act Independently to Determine Unrelated Phenotypes16:57
- Example: Punnett Square17:15
- Example 221:36
- The Chromosomal Theory of Inheritance30:41
- Walter S Sutton Linked Cytological Studies with Mendels Work31:02
- Diploid Cells Have Two Morphologically Similar Sets of Chromosomes and Each Haploid Gamete Receives One Set31:17
- Genes Are on Chromosome31:33
- Gene for Seed Color’s on a Different Chromosome Than Gene for Seed Texture31:44
- Gene Linkage31:55
- Mendel’s 2nd Law31:57
- Genes Said to Be Linked To Each Other32:09
- Linkage Between Genes32:29
- Linkage is Never 100% Complete32:41
- Genes are Found on Chromosomes33:00
- Thomas Hunt Morgan and Drosophila Melanogaster33:01
- Mutation Linked to X Chromosome33:15
- Linkage of White Gene33:23
- Eye Color of Progeny Depended on Sex of Parent33:34
- Y Chromosome Does Not Carry Copy of White Gene33:44
- X Linked Genes, Allele is Expressed in Males33:56
- Example34:11
- Example 335:52
- Discovery of the Genetic Material of the Cell41:52
- Transforming Principle42:44
- Experiment with Streptococcus Pneumoniae42:55
- Beadle and Tatum Proposed Genes Direct the Synthesis of Enzymes45:15
- One Gene One Enzyme Hypothesis45:46
- One Gene One Polypeptide Theory45:52
- Showing the Transforming Material was DNA46:14
- Did This by Fractionating Heat-Killed “S” Strains into DNA, RNA, and Protein46:32
- Result: Only the DNA Fraction Could Transform47:15
- Leven: Tetranucleotide Hypothesis48:00
- Chargaff Showed This Was Not the Case48:48
- Chargaff: DNA of Different Species Have Different Nucleotide Composition49:02
- Hershey and Chase: DNA is the Genetic Material50:02
- Incorporate Sulfur into Protein and Phosphorous into DNA51:12
- Results: Phosphorase Entered Bacteria and Progeny Phage, But no Sulfur53:11
- Rosalind Franklin’s “Photo 51” Showing the Diffraction Pattern of DNA53:50
- Watson and Crick: Double Helical Structure of DNA54:57
- Example 456:56
- Discovery of the Genetic Material of the Cell58:09
- Kornberg: DNA Polymerase I58:10
- Three Postulated Methods of DNA Replication59:22
- Meselson and Stahl: DNA Replication is Semi-Conservative1:00:21
- How DNA Was Made Denser1:00:52
- Discovery of RNA1:03:32
- Ribosomal RNA1:03:48
- Transfer RNA1:04:00
- Messenger RNA1:04:30
- The Central Dogma of Molecular Biology1:04:49
- DNA and Replication1:05:08
- DNA and Transcription = RNA1:05:26
- RNA and Translation = Protein1:05:41
- Reverse Transcription1:06:08
- Cracking the Genetic Code1:06:58
- What is the Genetic Code?1:07:04
- Nirenberg Discovered the First DNA Triplet That Would Make an Amino Acid1:07:16
- Code Finished in 1966 and There Are 64 Possibilities or Triplet Repeats/ Codons1:07:54
- Degeneracy of the Code1:08:53
49m 44s
- Intro0:00
- Lesson Overview0:10
- Amino Acids0:47
- Structure0:55
- Acid Association Constant1:55
- Amino Acids Make Up Proteins2:15
- Table of 21 Amino Acid Found in Proteins3:34
- Ionization5:55
- Cation6:08
- Zwitterion7:51
- Anion9:15
- Example 110:53
- Amino Acids13:11
- L Alpha Amino Acids13:19
- Only L Amino Acids Become Incorporated into Proteins13:28
- Example 213:46
- Amino Acids18:20
- Non-Polar18:41
- Polar18:58
- Hydroxyl19:52
- Sulfhydryl20:21
- Glycoproteins20:41
- Pyrrolidine21:30
- Peptide (Amide) Bonds22:18
- Levels of Organization23:35
- Primary Structure23:54
- Secondary Structure24:22
- Tertiary Structure24:58
- Quaternary Structure25:27
- Primary Structure: Specific Amino Acid Sequence25:54
- Example 327:30
- Levels of Organization29:31
- Secondary Structure: Local 3D29:32
- Example 430:37
- Levels of Organization32:59
- Tertiary Structure: Total 3D Structure of Protein33:00
- Quaternary Structure: More Than One Subunit34:14
- Example 534:52
- Protein Folding37:04
- Post-Translational Modifications38:21
- Can Alter a Protein After It Leaves the Ribosome38:33
- Regulate Activity, Localization and Interaction with Other Molecules38:52
- Common Types of PTM39:08
- Protein Classification40:22
- Ligand Binding, Enzyme, DNA or RNA Binding40:36
- All Other Functions40:53
- Some Functions: Contraction, Transport, Hormones, Storage41:34
- Enzymes as Biological Catalysts41:58
- Most Metabolic Processes Require Catalysts42:00
- Most Biological Catalysts Are Proteins43:13
- Enzymes Have Specificity of Reactants43:33
- Enzymes Have an Optimum pH and Temperature44:31
- Example 645:08
1h 2m 10s
- Intro0:00
- Lesson Overview0:06
- Nucleic Acids0:26
- Biopolymers Essential for All Known Forms of Life That Are Composed of Nucleotides0:27
- Nucleotides Are Composed of These1:17
- Nucleic Acids Are Bound Inside Cells2:10
- Nitrogen Bases2:49
- Purines3:01
- Adenine3:10
- Guanine3:20
- Pyrimidines3:54
- Cytosine4:25
- Thymine4:33
- Uracil4:42
- Pentoses6:23
- Ribose6:45
- 2' Deoxyribose6:59
- Nucleotides8:43
- Nucleoside8:56
- Nucleotide9:16
- Example 110:23
- Polynucleotide Chains12:18
- What RNA and DNA Are Composed of12:37
- Hydrogen Bonding in DNA Structure13:55
- Ribose and 2! Deoxyribose14:14
- DNA Grooves14:28
- Major Groove14:46
- Minor Groove15:00
- Example 215:20
- Properties of DNA24:15
- Antiparallel Orientation24:25
- Phosphodiester Linkage24:50
- Phosphate and Hydroxyl Group25:05
- Purine Bases Always Pairs Pyramidine Bases25:30
- A, B, Z Forms25:55
- Major and Minor Grooves26:24
- Hydrogen Bonding and Hydrophobic Interactions Hold Strands Together26:34
- DNA Topology - Linking Number27:14
- Linking Number27:31
- Twist27:57
- Writhe28:31
- DNA Topology - Supercoiling31:50
- Example 333:16
57m 2s
- Intro0:00
- Lesson Overview0:09
- Quick Glossary0:24
- DNA0:29
- Gene0:34
- Nucleosome0:47
- Chromatin1:07
- Chromosome1:19
- Genome1:30
- Genome Organization1:38
- Physically Cellular Differences3:09
- Eukaryotes3:18
- Prokaryotes, Viruses, Proteins, Small Molecules, Atoms4:06
- Genome Variance4:27
- Humans4:52
- Junk DNA5:10
- Genes Compose Less Than 40% of DNA6:03
- Chart6:26
- Example 18:32
- Chromosome Variance - Size, Number, and Density10:27
- Chromosome10:47
- Graph of Human Chromosomes10:58
- Eukaryotic Cell Cycle12:07
- Requirements for Proper Chromosome Duplication and Segregation13:07
- Centromeres and Telomeres13:28
- Origins of Replication13:38
- Illustration: Chromosome13:44
- Chromosome Condensation15:52
- Naked DNA to Start16:00
- Beads on a String16:13
- Mitosis16:52
- Start with Two Different Chromosomes17:18
- Split Into Two Diploid Cells17:26
- Prophase17:42
- Prometaphase17:52
- Metaphase19:10
- Anaphase19:27
- Telophase20:11
- Cytokinesis20:31
- Cohesin and Condensis21:06
- Illustration: Cohesin and Condensis21:19
- Cohesin21:38
- Condensin21:43
- Illustration of What Happens21:50
- Cohesins27:23
- Loaded During Replication and Cleaved During Mitosis27:30
- Separase27:36
- Nucleosomes27:59
- Histone Core28:50
- Eight Histone Proteins28:57
- Octamer of Core Histones Picture29:14
- Chromosome Condensation via H130:59
- Allows Transition to Compact DNA31:09
- When Not in Mitosis31:37
- Histones Decrease Available Binding Sites32:38
- Histone Tails33:21
- Histone Code35:32
- Epigenetic Code35:56
- Phosphorylation36:45
- Acetylation36:57
- Methylation37:01
- Ubiquitnation37:04
- Example 238:48
- Nucleosome Assembly41:22
- Duplication of DNA Requires Duplication of Histones41:50
- Old Histones Are Recycled42:00
- Parental H3-H4 Tetramers Facilitate the Inheritance of Chromatin States44:04
- Example 346:00
- Chromatin Remodeling48:12
- Example 453:28
1h 9m 55s
- Intro0:00
- Lesson Overview0:06
- Eukaryotic Cell Cycle0:50
- G1 Growth Phase0:57
- S Phase: DNA & Replication1:09
- G2 Growth Phase1:28
- Mitosis1:36
- Normal Human Cell Divides About Every 24 Hours1:40
- Eukaryotic DNA Replication2:04
- Watson and Crick2:05
- Specific Base Pairing2:37
- DNA Looked Like Tetrinucleotide2:55
- What DNA Looks Like Now3:18
- Eukaryotic DNA Replication - Initiation3:44
- Initiation of Replication3:53
- Primer Template Junction4:25
- Origin Recognition Complex7:00
- Complex of Proteins That Recognize the Proper DNA Sequence for Initiation of Replication7:35
- Prokaryotic Replication7:56
- Illustration8:54
- DNA Helicases (MCM 2-7)11:53
- Eukaryotic DNA Replication14:36
- Single-Stranded DNA Binding Proteins14:59
- Supercoils16:30
- Topoisomerases17:35
- Illustration with Helicase19:05
- Synthesis of the RNA Primer by DNA Polymerase Alpha20:21
- Subunit: Primase RNA Polymerase That Synthesizes the RNA Primer De Navo20:38
- Polymerase Alpha-DNA Polymerase21:01
- Illustration of Primase Function Catalyzed by DnaG in Prokaryotes21:22
- Recap24:02
- Eukaryotic DNA Replication - Leading Strand25:02
- Synthesized by DNA Polymerase Epsilon25:08
- Proof Reading25:26
- Processivity Increased by Association with PCNA25:47
- What is Processivity?26:19
- Illustration: Write It Out27:03
- The Lagging Strand/ Discontinuing Strand30:52
- Example 131:57
- Eukaryotic DNA Replication - Lagging Strand32:46
- Discontinuous32:55
- DNA Polymerase Delta33:15
- Okazaki Fragments33:36
- Illustration33:55
- Eukaryotic DNA Replication - Okazaki Fragment Processing38:26
- Illustration38:44
- When Does Okazaki Fragments Happen40:32
- Okazaki Fragments Processing40:41
- Illustration with Okazaki Fragments Process Happening41:13
- Example 247:42
- Example 349:20
- Telomeres56:01
- Region of Repetitive Nucleotide Sequences56:26
- Telomeres Act as Chromosome Caps by Binding Proteins57:42
- Telomeres and the End Replication Problem59:56
- Need to Use a Primer59:57
1h 13m 8s
- Intro0:00
- Lesson Overview0:06
- Damage vs. Mutation0:40
- DNA Damage-Alteration of the Chemical Structure of DNA0:45
- DNA Mutation-Permanent Change of the Nucleotide Sequence1:01
- Insertions or Deletions (INDELS)1:22
- Classes of DNA Mutations1:50
- Spontaneous Mutations2:00
- Induced Mutations2:33
- Spontaneous Mutations3:21
- Tautomerism3:28
- Depurination4:09
- Deamination4:30
- Slippage5:44
- Induced Mutations - Causes6:17
- Chemicals6:24
- Radiation7:46
- Example 18:30
- DNA Mutations - Tobacco Smoke9:59
- Covalent Adduct Between DNA and Benzopyrene10:02
- Benzopyrene10:20
- DNA Mutations - UV Damage12:16
- Oxidative Damage from UVA12:30
- Thymidine Dimer12:34
- Example 213:33
- DNA Mutations - Diseases17:25
- DNA Repair18:28
- Mismatch Repair19:15
- How to Recognize Which is the Error: Recognize Parental Strand22:23
- Example 326:54
- DNA Repair32:45
- Damage Reversal32:46
- Base-Excision Repair (BER)34:31
- Example 436:09
- DNA Repair45:43
- Nucleotide Excision Repair (NER)45:48
- Nucleotide Excision Repair (NER) - E.coli47:51
- Nucleotide Excision Repair (NER) - Eukaryotes50:29
- Global Genome NER50:47
- Transcription Coupled NER51:01
- Comparing MMR and NER51:58
- Translesion Synthesis (TLS)54:40
- Not Really a DNA Repair Process, More of a Damage Tolerance Mechanism54:50
- Allows Replication Past DNA Lesions by Polymerase Switching55:20
- Uses Low Fidelity Polymerases56:27
- Steps of TLS57:47
- DNA Repair1:00:37
- Recombinational Repair1:00:54
- Caused By Ionizing Radiation1:00:59
- Repaired By Three Mechanisms1:01:16
- Form Rarely But Catastrophic If Not Repaired1:01:42
- Non-homologous End Joining Does Not Require Homology To Repair the DSB1:03:42
- Alternative End Joining1:05:07
- Homologous Recombination1:07:41
- Example 51:09:37
1h 14m 27s
- Intro0:00
- Lesson Overview0:16
- Homologous Recombination0:49
- Genetic Recombination in Which Nucleotide Sequences Are Exchanged Between Two Similar or Identical Molecules of DNA0:57
- Produces New Combinations of DNA Sequences During Meiosis1:13
- Used in Horizontal Gene Transfer1:19
- Non-Crossover Products1:48
- Repairs Double Strand Breaks During S/Gs2:08
- MRN Complex Binds to DNA3:17
- Prime Resection3:30
- Other Proteins Bind3:40
- Homology Searching and subsequent Strand Invasion by the Filament into DNA Duplex3:59
- Holliday Junction4:47
- DSBR and SDSA5:44
- Double-Strand Break Repair Pathway- Double Holliday Junction Model6:02
- DSBR Pathway is Unique6:11
- Converted Into Recombination Products by Endonucleases6:24
- Crossover6:39
- Example 17:01
- Example 28:48
- Double-Strand Break Repair Pathway- Synthesis Dependent Strand Annealing32:02
- Homologous Recombination via the SDSA Pathway32:20
- Results in Non-Crossover Products32:26
- Holliday Junction is Resolved via Branch Migration32:43
- Example 334:01
- Homologous Recombination - Single Strand Annealing42:36
- SSA Pathway of HR Repairs Double-Strand Breaks Between Two Repeat Sequences42:37
- Does Not Require a Separate Similar or Identical Molecule of DNA43:04
- Only Requires a Single DNA Duplex43:25
- Considered Mutagenic Since It Results in Large Deletions of DNA43:42
- Coated with RPA Protein43:58
- Rad52 Binds Each of the Repeated Sequences44:28
- Leftover Non-Homologous Flaps Are Cut Away44:37
- New DNA Synthesis Fills in Any Gaps44:46
- DNA Between the Repeats is Always Lost44:55
- Example 445:07
- Homologous Recombination - Break Induced Replication51:25
- BIR Pathway Repairs DSBs Encountered at Replication Forks51:34
- Exact Mechanisms of the BIR Pathway Remain Unclear51:49
- The BIR Pathway Can Also Help to Maintain the Length of Telomeres52:09
- Meiotic Recombination52:24
- Homologous Recombination is Required for Proper Chromosome Alignment and Segregation52:25
- Double HJs are Always Resolved as Crossovers52:42
- Illustration52:51
- Spo11 Makes a Targeted DSB at Recombination Hotspots56:30
- Resection by MRN Complex57:01
- Rad51 and Dmc1 Coat ssDNA and Promote Strand Invasion and Holliday Junction Formation57:04
- Holliday Junction Migration Can Result in Heteroduplex DNA Containing One or More Mismatches57:22
- Gene Conversion May Result in Non-Mendelian Segregation57:36
- Double-Strand Break Repair in Prokaryotes - RecBCD Pathway58:04
- RecBCD Binds to and Unwinds a Double Stranded DNA58:32
- Two Tail Results Anneal to Produce a Second ssDNA Loop58:55
- Chi Hotspot Sequence59:40
- Unwind Further to Produce Long 3 Prime with Chi Sequence59:54
- RecBCD Disassemble1:00:23
- RecA Promotes Strand Invasion - Homologous Duplex1:00:36
- Holliday Junction1:00:50
- Comparison of Prokaryotic and Eukaryotic Recombination1:01:49
- Site-Specific Recombination1:02:41
- Conservative Site-Specific Recombination1:03:10
- Transposition1:03:46
- Transposons1:04:12
- Transposases Cleave Both Ends of the Transposon in Original Site and Catalyze Integration Into a Random Target Site1:04:21
- Cut and Paste1:04:37
- Copy and Paste1:05:36
- More Than 40% of Entire Human Genome is Composed of Repeated Sequences1:06:15
- Example 51:07:14
1h 19m 28s
- Intro0:00
- Lesson Overview0:07
- Eukaryotic Transcription0:27
- Process of Making RNA from DNA0:33
- First Step of Gene Expression0:50
- Three Step Process1:06
- Illustration of Transcription Bubble1:17
- Transcription Starting Site is +15:15
- Transcription Unit Extends From the Promoter to the Termination Region5:40
- Example 16:03
- Eukaryotic Transcription: Initiation14:27
- RNA Polymerase II Binds to TATA Box to Initiate RNA Synthesis14:34
- TATA Binding Protein Binds the TATA Box14:50
- TBP Associated Factors Bind15:01
- General Transcription Factors15:22
- Initiation Complex15:30
- Example 215:44
- Eukaryotic Transcription17:59
- Elongation18:07
- FACT (Protein Dimer)18:24
- Eukaryotic Transcription: Termination19:36
- Polyadenylation is Linked to Termination19:42
- Poly-A Signals Near the End of the pre-mRNA Recruit to Bind and Cleave mRNA20:00
- Mature mRNA20:27
- Dissociate from Template DNA Strand21:13
- Example 321:53
- Eukaryotic Transcription25:49
- RNA Polymerase I Transcribes a Single Gene That Encodes a Long rRNA Precursor26:14
- RNA Polymerase III Synthesizes tRNA, 5S rRNA, and Other Small ncRNA29:11
- Prokaryotic Transcription32:04
- Only One Multi-Subunit RNA Polymerase32:38
- Transcription and Translation Occurs Simultaneously33:41
- Prokaryotic Transcription - Initiation38:18
- Initial Binding Site38:33
- Pribnox Box38:42
- Prokaryotic Transcription - Elongation39:15
- Unwind Helix and Expand Replication Bubble39:19
- Synthesizes DNA39:35
- Sigma 70 Subunit is Released39:50
- Elongation Continues Until a Termination Sequence is Reached40:08
- Termination - Prokaryotes40:17
- Example 440:30
- Example 543:58
- Post-Transcriptional Modifications47:15
- Can Post Transcribe your rRNA, tRNA, mRNA47:28
- One Thing In Common47:38
- RNA Processing47:51
- Ribosomal RNA47:52
- Transfer RNA49:08
- Messenger RNA50:41
- RNA Processing - Capping52:09
- When Does Capping Occur52:20
- First RNA Processing Event52:30
- RNA Processing - Splicing53:00
- Process of Removing Introns and Rejoining Exons53:01
- Form Small Nuclear Ribonucleoproteins53:46
- Example 657:48
- Alternative Splicing1:00:06
- Regulatory Gene Expression Process1:00:27
- Example1:00:42
- Example 71:02:53
- Example 81:09:36
- RNA Editing1:11:06
- Guide RNAs1:11:25
- Deamination1:11:52
- Example 91:13:50
1h 15m 1s
- Intro0:00
- Lesson Overview0:06
- Linking Transcription to Translation0:39
- Making RNA from DNA0:40
- Occurs in Nucleus0:59
- Process of Synthesizing a Polypeptide from an mRNA Transcript1:09
- Codon1:43
- Overview of Translation4:54
- Ribosome Binding to an mRNA Searching for a START Codon5:02
- Charged tRNAs will Base Pair to mRNA via the Anticodon and Codon5:37
- Amino Acids Transferred and Linked to Peptide Bond6:08
- Spent tRNAs are Released6:31
- Process Continues Until a STOP Codon is Reached6:55
- Ribosome and Ribosomal Subunits7:55
- What Are Ribosomes?8:03
- Prokaryotes8:42
- Eukaryotes10:06
- Aminoacyl Site, Peptidyl tRNA Site, Empty Site10:51
- Major Steps of Translation11:35
- Charing of tRNA11:37
- Initiation12:48
- Elongation13:09
- Termination13:47
- “Charging” of tRNA14:35
- Aminoacyl-tRNA Synthetase14:36
- Class I16:40
- Class II16:52
- Important About This Reaction: It Is Highly Specific17:10
- ATP Energy is Required18:42
- Translation Initiation - Prokaryotes18:56
- Initiation Factor 3 Binds at the E-Site19:09
- Initiation Factor 1 Binds at the A-Site20:15
- Initiation Factor 2 and GTP Binds IF120:50
- 30S Subunit Associates with mRNA21:05
- N-Formyl-met-tRNA22:34
- Complete 30S Initiation Complex23:49
- IF3 Released and 50S Subunit Binds24:07
- IF1 and IF2 Released Yielding a Complete 70S Initiation Complex24:24
- Deformylase Removes Formyl Group24:45
- Example 125:11
- Translation Initiation - Eukaryotes29:35
- Small Subunit is Already Associated with the Initiation tRNA29:47
- Formation of 43S Pre-Initiation Complex30:02
- Circularization of mRNA by eIF431:05
- 48S Pre-Initiation Complex35:47
- Example 238:57
- Translation - Elongation44:00
- Charging, Initiation, Elongation, Termination All Happens Once44:14
- Incoming Charged tRNA Binds the Complementary Codon44:31
- Peptide Bond Formation45:06
- Translocation Occurs46:05
- tRNA Released46:51
- Example 347:11
- Translation - Termination55:26
- Release Factors Terminate Translation When Ribosomes Come to a Stop Codon55:38
- Release Factors Are Proteins, Not tRNAs, and Do Not Carry an Amino Acid55:50
- Class I Release Factors55:16
- Class II Release Factors57:03
- Example 457:40
- Review of Translation1:01:15
- Consequences of Altering the Genetic Code1:02:40
- Silent Mutations1:03:37
- Missense Mutations1:04:24
- Nonsense Mutations1:05:28
- Genetic Code1:06:40
- Consequences of Altering the Genetic Code1:07:43
- Frameshift Mutations1:07:55
- Sequence Example1:08:07
45m 40s
- Intro0:00
- Lesson Overview0:08
- Gene Regulation0:50
- Transcriptional Regulation1:01
- Regulatory Proteins Control Gene Expression1:18
- Bacterial Operons-Lac1:58
- Operon2:02
- Lactose Operon in E. Coli2:31
- Example 13:33
- Lac Operon Genes7:19
- LacZ7:25
- LacY7:40
- LacA7:55
- LacI8:10
- Example 28:58
- Bacterial Operons-Trp17:47
- Purpose is to Produce Trptophan17:58
- Regulated at Initiation Step of Transcription18:04
- Five Genes18:07
- Derepressible18:11
- Example 318:32
- Bacteriophage Lambda28:11
- Virus That Infects E. Coli28:24
- Temperate Lifecycle28:33
- Example 430:34
- Regulation of Translation39:42
- Binding of RNA by Proteins Near the Ribosome- Binding Site of the RNA39:53
- Intramolecular Base Pairing of mRNA to Hide Ribosome Binding Site40:14
- Post-transcriptional Regulation of rRNA40:35
- Example 540:08
1h 6m 6s
- Intro0:00
- Lesson Overview0:06
- Eukaryotic Transcriptional Regulations0:18
- Transcription Factors0:25
- Insulator Protein0:55
- Example 11:44
- Locus Control Regions4:00
- Illustration4:06
- Long Range Regulatory Elements That Enhance Expressions of Linked Genes5:40
- Allows Order Transcription of Downstream Genes6:07
- (Ligand) Signal Transduction8:12
- Occurs When an Extracellular Signaling Molecule Activates a Specific Receptor Located on the Cell8:19
- Examples9:10
- N F Kappa B10:01
- Dimeric Protein That Controls Transcription10:02
- Ligands10:29
- Example 211:04
- JAK/ STAT Pathway13:19
- Turned on by a Cytokine13:23
- What is JAK13:34
- What is STAT13:58
- Illustration14:38
- Example 317:00
- Seven-Spanner Receptors20:49
- Illustration: What Is It21:01
- Ligand Binding That Is Activating a Process21:46
- How This Happens22:17
- Example 424:23
- Nuclear Receptor Proteins (NRPs)28:45
- Sense Steroid and Thyroid Hormones28:56
- Steroid Hormones Bind Cytoplasmic NRP Homodimer29:10
- Hormone Binds NRP Heterodimers Already Present in the Nucleus30:11
- Unbound Heterodimeric NRPs Can Cause Deacetylation of Lysines of Histone Tails30:54
- RNA Interference32:01
- RNA Induced Silencing Complex (RISC)32:39
- RNAi33:54
- RISC Pathway34:34
- Activated RISC Complex34:41
- Process34:55
- Example39:27
- Translational Regulation41:17
- Global Regulation41:37
- Competitive Binding of 5 Prime CAP of mRNA42:34
- Translation-Dependent Regulation44:56
- Nonsense Mediated mRNA Decay45:23
- Nonstop Mediated mRNA Decay46:17
- Epigenetics48:53
- Inherited Patterns of Gene Expression Resulting from Chromatin Alteration49:15
- Three Ways to Happen50:17
- DNA Sequence Does Not Act Alone in Passing Genetic Information to Future Generations50:30
- DNA Methylation50:57
- Occurs at CpG Sites Via DNA Methyltransferase Enzymes50:58
- CpG Islands Are Regions with a High Frequency of CpG Sites52:49
- Methylation of Multiple CpG Sites Silence Nearby Gene Transcription53:32
- DNA Methylation53:46
- Pattern Can Be Passed to Daughter Cells53:47
- Prevents SP1 Transcription Factors From Binding to CpG Island54:02
- MECP254:10
- Example 555:27
- Nucleosomes56:48
- Histone Core57:00
- Histone Protein57:03
- Chromosome Condensation Via J157:32
- Linker Histone H157:33
- Compact DNA57:37
- Histone Code57:54
- Post-translational Modifications of N-Terminal Histone Tails is Part of the Epigenetic Code57:55
- Phosphorylation, Acetylation, Methylation, Ubiquitination58:09
- Example 658:52
- Nucleosome Assembly59:13
- Duplication of DNA Requires Duplication of Histones by New Protein Synthesis59:14
- Old Histones are Recycled59:24
- Parental H3-H4 Tetramers58:57
- Example 71:00:05
- Chromatin Remodeling1:01:48
- Example 81:02:36
- Transcriptionally Repressed State1:02:45
- Acetylation of Histones1:02:54
- Polycomb Repressors1:03:19
- PRC2 Protein Complex1:03:38
- PRC1 Protein Complex1:04:02
- MLL Protein Complex1:04:09
1h 8m 41s
- Intro0:00
- Lesson Overview0:10
- Gel Electraophoresis0:31
- What is Gel Electraophoresis0:33
- Nucleic Acids0:50
- Gel Matrix1:41
- Topology2:18
- Example 12:50
- Restriction Endonucleases8:07
- Produced by Bacteria8:08
- Sequence Specific DNA Binding Proteins8:36
- Blunt or Overhanging Sticky Ends9:04
- Length Determines Approximate Cleavage Frequency10:30
- Cloning11:18
- What is Cloning11:29
- How It Works12:12
- Ampicillin Example12:55
- Example 213:19
- Creating a Genomic DNA Library19:33
- Library Prep19:35
- DNA is Cut to Appropriate Sizes and Ligated Into Vector20:04
- Cloning20:11
- Transform Bacteria20:19
- Total Collection Represents the Whole Genome20:29
- Polymerase Chain Reaction20:54
- Molecular Biology Technique to Amplify a Small Number of DNA Molecules to Millions of Copies21:04
- Automated Process Now21:22
- Taq Polymerase and Thermocycler21:38
- Molecular Requirements22:32
- Steps of PCR23:40
- Example 324:42
- Example 434:45
- Southern Blot35:25
- Detect DNA35:44
- How It Works35:50
- Western Blot37:13
- Detects Proteins of Interest37:14
- How It Works37:20
- Northern Blot39:08
- Detects an RNA Sequence of Interest39:09
- How It Works39:21
- Illustration Sample40:12
- Complementary DNA (cDNA) Synthesis41:18
- Complementary Synthesis41:19
- Isolate mRNA from Total RNA41:59
- Quantitative PCR (qPCR)44:14
- Technique for Quantifying the Amount of cDNA and mRNA Transcriptions44:29
- Measure of Gene Expression44:56
- Illustration of Read Out of qPCR Machine45:23
- Analysis of the Transcriptome-Micrarrays46:15
- Collection of All Transcripts in the Cell46:16
- Microarrays46:35
- Each Spot Represents a Gene47:20
- RNA Sequencing49:25
- DNA Sequencing50:08
- Sanger Sequencing50:21
- Dideoxynucleotides50:31
- Primer Annealed to a DNA Region of Interest51:50
- Additional Presence of a Small Proportion of a ddNTPs52:18
- Example52:49
- DNA Sequencing Gel53:13
- Four Different Reactions are Performed53:26
- Each Reaction is Run in a Lane of a Denaturing Polyacrylamide Gel53:34
- Example 553:54
- High Throughput DNA Sequencing57:51
- Dideoxy Sequencing Reactions Are Carried Out in Large Batches57:52
- Sequencing Reactions are Carried Out All Together in a Single Reaction58:26
- Molecules Separated Based on Size59:19
- DNA Molecules Cross a Laser Light59:30
- Assembling the Sequences1:00:38
- Genomes is Sequenced with 5-10x Coverage1:00:39
- Compare Genomes1:01:47
- Entered Into Database and the Rest is Computational1:02:02
- Overlapping Sequences are Ordered Into Contiguous Sequences1:02:17
- Example 61:03:25
- Example 71:05:27
45m 6s
- Intro0:00
- Lesson Overview0:47
- Genome Editing1:37
- What is Genome Editing1:43
- How It Works2:03
- Four Families of Engineered Nucleases in Use2:25
- Example 13:03
- Gene Therapy9:37
- Delivery of Nucleic Acids Into a Patient’s Cells a Treatment for Disease9:38
- Timeline of Events10:30
- Example 211:03
- Gene Therapy12:37
- Ethical Questions12:38
- Genetic Engineering12:42
- Gene Doping13:10
- Synthetic Biology13:44
- Design and Manufacture of Biological Components That Do Not Exist in Nature13:53
- First Synthetic Cell Example14:12
- Ethical Questions16:16
- Stem Cell Biology18:01
- Use Stem Cells to Treat or Prevent Diseases18:12
- Treatment Uses19:56
- Ethical Questions20:33
- Selected Topic of Ethical Debate21:30
- Research Ethics28:02
- Application of Fundamental Ethical Principles28:07
- Examples28:20
- Declaration of Helsinki28:33
- Basic Principles of the Declaration of Helsinki28:57
- Utmost Importance: Respect for the Patient29:04
- Researcher’s Duty is Solely to the Patient or Volunteer29:32
- Incompetent Research Participant30:09
- Right Vs Wrong30:29
- Ethics32:40
- Dolly the Sheep32:46
- Ethical Questions33:59
- Rational Reasoning and Justification35:08
- Example 335:17
- Example 438:00
- Questions to Ponder39:35
- How to Answer40:52
- Do Your Own Research41:00
- Difficult for People Outside the Scientific Community41:42
- Many People Disagree Because They Do Not Understand42:32
- Media Cannot Be Expected to Understand Published Scientific Data on Their Own42:43
1 answer
Mon Apr 27, 2020 2:26 PM
Post by Monicasong on April 26, 2020
What does covalent bonds mean, professor, I can't figure out its meaning.
By the way, I like your lessons, they're quite interesting.
0 answers
Post by Mei Gill on July 6, 2018
what types of things we mainly need to know about chemical bonds?
1 answer
Wed Feb 8, 2017 3:14 PM
Post by Firebird wang on November 2, 2016
Professor, I know that AP Statistics is not your subject, but I just wonder if you are able to watch the two videos which called "Practice Test 2013 AP Statistics" and "Practice Test 2014 AP Statistics" in the AP Statistics content? Both videos showing network error, I dont know why. I already tried in different computers already.
1 answer
Tue Dec 29, 2015 1:39 PM
Post by Christoph Bader on December 16, 2015
Isn't CH4 non-polar? That is the electronegativity difference is negligible.
2 answers
Tue Dec 8, 2015 10:28 AM
Post by Professor Michael Philips on December 1, 2015
Hi Apolonia,
First of all, it is great to hear how passionate you are about science! As for your intended undergraduate major, biochemistry, microbiology molecular biology, genetics, or immunology would all give you a great foundation of knowledge that could help you succeed. If you truly want to do research, you would likely enter a graduate program, at which point you would then choose a more narrow focus (such as virology, genetics, etc.). Hope that helps. Best of luck!
1 answer
Tue Dec 1, 2015 11:25 PM
Post by Apolonia Gardner on November 24, 2015
Hello,
I am a high school senior about to send off my applications for college. I am stuck on one thing – my intended major. Biology and chemistry have been my favorite courses throughout high school, and I would like to get a college degree that will enable me to perform research with viruses. My lifetime goal is to find a cure for a disease. From your experience, what undergraduate major should I shoot for? Biochemistry? Microbiology? Molecular Biology? Immunology? Chemical Biology? Organic Chemistry? Pharmaceutical Science? Any guidance is appreciated.