Friday, September 19, 2014

Special Newsletter: Gibbs Free Energy and Transition State Energy

Special Newsletter
Gibbs Free Energy and Transition State Energy

This goal of this newsletter is to help students navigate the complexity of Gibbs Free Energy (ΔG) and help avoid confusion about Gibbs Free Energy and Transition State Energy (Energy of Activation).

Gibbs Free Energy (ΔG) is a thermodynamics concept, and describes the thermodynamic potential of a system.  It measures the "work" that can be obtained from a system, for us a chemical reaction, if that system is held at constant temperature and pressure.  The goal is to determine whether a given reaction is spontaneous in the direction written, i.e., whether the reaction will proceed in the given direction without the input of energy.

Mathematically, Gibbs Free Energy is described as:

  • ΔG  The change in Free Energy
  • ΔH  The change in Enthalpy
  • ΔS   The change in Entropy
In biochemistry, the change in Enthalpy (ΔH) is the same as the change in internal energy.  Remember that ΔG is calculated based on a set of given conditions:  we are at constant temperature and pressure, and all variables have been taken into account (such as the solvent of the system).  If you change anything, you change the system, and thus the ΔG.

Gibbs free energy is a measure ONLY of the difference in free energy of the products and reactants, and does not tell us about the rate of the reaction.  It only tells us whether the reaction is Exergonic or Endergonic.
  • ΔG < 0   Exergonic:  The reaction is considered spontaneous in the direction written.
  • ΔG = 0   The system is in equilibrium
  • ΔG >0    Endergonic:  To carry out this reaction as written, there needs to be an addition of free energy (NOTE: this means that the reverse reaction is spontaneous).

Transition State Energy is not Gibbs Free Energy.
Gibbs Free Energy does not describe the path of transformation or the mechanism of transformation.  It does not describe the rate of transformation.  It only describes whether the reaction is spontaneous, non-spontaneous or at equilibrium.

The breakdown of the dissacharide sucrose to glucose and fructose has a ΔG of -5.5 kcal/mol.  This is a spontaneous (Exergonic) reaction in terms of ΔG.  Yet you can store sucrose in your kitchen and it remains sucrose.  There is no spontaneous degradation into monosaccharides.  Why?

Sucrose is a stable molecule.  In order to force the breakdown (catabolism) of sucrose, we need to destabilize the molecule.  This destabilization is the transition state of the reaction, and in a closed system, requires the input of energy.  This is termed the Activation Energy of the reaction (you will also hear this described as the Transition State Energy).  If we were to look at our breakdown of sucrose, we would see the following:

Sucrose   ⇄    Transition State   →   Glucose + Fructose

The energy of the transition state is noted as either Ea or ΔG.  These two expression are from different formula for calculating activation energy. ΔG is used in a formula that relates activation energy to Gibbs Free Energy (the Eyring equation).  In either case, the expression describe transition state energy (aka, activation energy).

In biochemistry, enzymes are used to reduce the activation energy (just like catalysts are used in chemistry).  Catalysts and Enzymes reduce the activation energy ΔG; they do not alter Gibbs Free Energy (ΔG).  This is a critical concept!

Transition state deals with the rate of the reaction.  By lowering the activation energy (transition state energy), you increase the rate of the reaction.  In essence, you are making the reaction more likely to happen.  But the enzyme does not change Gibbs Free Energy.
Original Image from ChemWiki,

Take home message:

Gibbs Free Energy (ΔG) describes whether a reaction is exergonic or endergonic.  It does not describe rate, and neither enzymes or catalysts will alter ΔG.

Activation Energy (ΔG) does not alter ΔG; it does not determine whether a reaction is spontaneous or non-spontaneous. Activation energy does help determine the rate of the reaction.

Tuesday, September 9, 2014

Daily Newsletter: September 10, 2014 - Codons, Anticodons & Amino Acids

Site LogoDaily Newsletter

September 10, 2014

Codons, Anticodons & Amino Acids

Translation is the process of "reading" mRNA, and using the code to construct a protein. But what is the code? The nucleotide language of mRNA can be divided into codons. Three sequential nucleotides that represent a genetic (nucleotide) word. So, how do you read this code or nucleotide language?
In the image to the right, you hav
e have sequential nucleotides divided up into codons. Notice that AUG is listed as Codon 1. This is important! AUG is the Universal Start Codon. Nearly every organism (and every gene) that has been studied uses the three ribonucleotide sequence AUG to indicate the "START" of protein synthesis (Start Point of Translation).

As we will see tomorrow, it takes more than a start codon to initiate transcription, but for now just remember that this is the codon that indicates the START point of the instructions on how to make a protein.
The start codon established the Reading Frame for translation. From the start codon, every three sequential nucleotides will be viewed as a codon. This is critical! Mutations can affect reading frames. For example, if a nucleotide is inserted between codon 2 and 3 (G G), would you have the same reading frame down stream? What if you deleted the first nucleotide of codon 4? What is the effect of changing the reading frame? What would happen to the resulting protein?

Insertions and deletions can change reading frames, but point mutations can also occur. In this case, one nucleotide is change to a different nucleotide. What would happen if the final nucleotide of condon 3 were changed to a C? To an A? How about the second nucleotide in codon 4? Change the U to an A, what happens?

Each codon is a "genetic word," and refers to a specific amino acid (thus changes to these words can result in changes to final proteins). The tRNA is the agent of translation. On one end of the tRNA, you will find an anti-codon. Anti-codons are complimentary to codons. Example: Codon 1 reads AUG. The corresponding tRNA would have an anticodon reading UAC. (Question: Would these be antiparallel?). Codon 2 reads ACG, so the anticodon would read UGC. Oppisite the anticodon, you will find a binding site for a specific amino acid.

An amino acid can be attached to the free 3' end of the tRNA. There is a class of enzymes capable of attaching an amino acid to a tRNA: Aminoacyl tRNA Synthetase. Below is a very basic cartoon of how an amino acid is added to a tRNA.
Note that an ATP is needed to complete the binding. There is an Aminoacyl tRNA Synthetase for each tRNA-Amino Acid combination.
Below is a diagram showing the pairing of codon to anticodon. The diagram also contains a version of the Genetic Code table, showing the relationship between codon and amino acid.
Note that three codons are referred to as STOP codons: UAA, UAG, and UGA. These are used to terminate translation; they indicate the end of the gene's coding region. What would happen if you lost a Stop codon?

Daily Challenge

In an earlier newsletter, we discussed Hemoglobin, and how the change of one amino acid caused the configuration change in the protein.  Amino Acids are coded due to a codon.  If you recall, Valine (Val) is found in place of Glutamic Acid (Glu).  If we look at the sequences, we find that at the sixth codon, the wild type reads GAG, but the sickle type reads GUG.  This is a single nucleotide polymorphism.  Here is a video to explain SNPs (pronunciation: Snips)

Today, consider the consequence of a SNP.  What would happen if it occurred in a Start or Stop codon.  What would happen if an AAG upstream (before) the start codon had a SNP that changed the second nucleotide from an A to a U?  What would happen if CGC changed to CGG?  How about CAU to GAU?
After considering these, and looking at the above video, what are some of the consequences of a SNP?  How could a SNP either stop translation or prolong it?  Are all of the results harmful, or can they be neutral?

Link to Forum

Monday, September 8, 2014

Daily Newsletter: September 8, 2014 - Ground Rules for Gene Expression

Site LogoDaily Newsletter

September 8, 2014

Ground Rules for Gene Expression

(AKA Central Dogma)

Central Dogma, in broadest sense, encompasses the genetic mechanisms of Replication, Translation and Translation. In the strictest sense, Central Dogma describes gene expression: Information encoded in the nucleotides of DNA being use to construct proteins. The two core genetic processes involved in gene expression are Transcription (synthesis of RNA) and Translation (synthesis of proteins).
Central Dogma of Biology

Before digging into each process, let's talk a little about what is at stake here. DNA holds our genetic history. It holds codes on how to build an organism, but what does that really mean?

The basic unit of life is the cell, and cells are formed from phospholipids can naturally form bilayers. Furthermore, phospholipids can even natrually form spherical structures that create two fluid compartments, outside vs. inside.  The phospholipids that make up the cellular membrane form the most basic feature of the cell: a dividing point, separating the inside from the outside (more on this in the weeks to come).

Membranes though are passive. As a selectively permeable barrier, only certain materials can cross. Proteins add functionality to the membrane. By embedding proteins, you can chance the permeability of the membrane. This is how cells balance what is on the inside, and what is on the outside. Membrane proteins can also have enzymatic or signal functions. Proteins add functionality to the membrane.

A common expression is that DNA holds the code to make an organism. The meaning of this phrase lies in the concept that by making proteins, we make phospholipid membranes and cells functional. From DNA, cells can build proteins for metabolic pathways, to produce various chemical compounds, anchor with other cells, and in multicellular complex life, we even have the development of special cellular roles that work together to form a composit whole.

The concept of how we go from DNA to RNA and then Proteins is one of the most critical concepts in biology! Today we are going to focus on some of the basics, the Ground Rules, of genetics.

All genetic processes work due to base complementarity. If you know the base complementarity rules, then the foundations of genetics will make sense. At times, this may seem repetitious, but I really want you to get these terms and concepts.
Genes are sometimes referred to as the unit of heredity, and with good reason. A gene is a segment of DNA that holds the code to make a protein (NOTE: or functional RNA, such as trasfer RNA). In modern biology, we refer to gene products, which are just the expressed macromolecules coded by a gene.
Remember, a gene product can be either a proteins or functional RNA (e.g., tRNA). Functional RNA does not code for proteins, instead, these RNA strands have some function in cellular metabolism, most notably in the genetic process of Translation. Examples include tranfer RNA (tRNA), ribosomal RNA (rRNA), and small nuclear RNA (snRNA).

All genes have non-coding portions that are critical for the correct transcription (synthesis of RNA). These non-coding areas are critical for regulation and aligning the transcription enzymes (e.g., RNA polymerase). Below is a graphic that shows structure of a gene. The promoter of a gene is a sequence of DNA upstream of the actual code (coding region) that indicates the "Start" point for transcription. This is how your cell knows where to begin transcription. The loss of the promoter means that the gene will no longer be expressed.
In Eukaryotic cells, a common promoter is a DNA sequence that reads TATAAA, and is better known as the TATA-Box. In bacteria the promoter is known as the Pribnow Box (Pribnow-Schaller box).  In both cases, the promoter is found in the Major Groove of the DNA Major Groovemolecule. As can be seen in the image to the right, the major groove is wide enough to "see" the base pairs. The base pairs have an electrochemical profile, and thus can respond to other chemicals (via van Der Waals forces). Thus, the major groove is a place where proteins (and other compounds) can bind to specific sequences of DNA! The promoter sequences are found in the major groove. Major Groove with Initation FactorThe image to the right shows a bacterial promoter event. One of the factors needed to start transcription (by recognizing the promoter) has bound into the major groove. This recognition event is needed to identify the start point of a gene. The Transcription Initation Complex will then begin to form at this site, and begin the transcription of the gene. 

Many genes are regulated, meaning they can be turned on and off. Beyond a promoter, a regulated gene will typically have a non-coding region known as the Operator. The operator is located down stream of the promoter (meaning it will be between the promoter and the coding region). Regulatory proteins can bind to the operator, preventing transcription. Remember, cells are masters at energy conservation. They will not begin producing proteins that are unnecessary. Gene regulation is a common activity of Signal & Receptor systems. The image below is a good visual of the promoter & operator systems. Gene House keeping genes are those that are needed for the general function of the cell, and can include genes for glycolysis, citric acid cycle, and ribosomes. These genes are always ON, and are referred to as constituative genes

Messanger RNA (mRNA) is a molecule of RNA that cares the gene code for the construction of a protein. mRNA is sent to the Ribosome in order to produce a protein. The code for constructing a protein is in Nucleotide Language, meaning the code is a code of nucleotides. Specifically, the code in mRNA is in the ribonucleotide language (A, U, G, C). In order to make a protein, it is necessary to Translate the ribonucleotide language into the language of proteins, i.e., amino acid sequcences. 

In order to translate, you need an agent of translation. This agent of translation must be a molecule that contains both ribonucleotides and amino acids (think of it as the nucleotide-amino acid dictionary). A specific ribonucleotide sequence must directly correspond to an amino acid, just as in translating human languages requires word for word relationships. This concept of a direct nucleotide to amino acid relationship is the basis of the Genetic Code.

tRNAThe agent of translation is Transfer RNA (tRNA). In tRNA, there is a direct physical correspondence between a 3 nucleotide sequence (anti-codon) and an amino acid. To the right are common ways of illustrating tRNA, with the 3rd image being the most common way of drawing the molecule. In the image, each molecule has a region known as the anticodon; this region will interact with mRNA. At the 3' end of the molecule, a specific amino acid will be bound. 

On the mRNA, the code is broken down into codons (think of these as genetic words). Codons consist of 3 adjacent nucleotides. Codons are complimentary to anticodons found on tRNA. Each tRNA has a specific anticodon-amino acid relationship, so each codon then specifies an amino acid. The genetic code is NOT ambiguous. There is a direct correspondence between codon and amino acid; the tRNAs make sure of this.
The ribonucleic language is divided into 64 3-nucleotide words known as codons. Condons specify though tRNA an amino acid. The Genetic Code is thus the translation scheme between codons and amino acids. [NOTE: another way to describe the genetic code is in terms of a computer algorithm]. Below is a rather unique way of viewing the genetic code. It is an excellent way of visualizing the number of redundancies in the code.
Genetic Code Algorithm
The genetic code is redundant, which means that there are multiple codons (3 nucleotides) that specify the same amino acid. For example, around the 12 o'clock position of the above chart, you see the amino acid glycine. The codons GGU, GGC, GGA and GGG all specify Glycine. Phenylalanine is specified by UUU and UUC. There are only a few amino acids, such as methionine, that are specified by a single codon (in the case of methionine it is AUG).

The presence of redundancies means that some alterations in the gene sequence are silenced (silent mutation). For example, changing GGU to GGA does not change the specified amino acid (Glycine). This is a silent mutation. Changing UUC to UUA may cause a problem (point mutation), but both Leucine and Phenylalanine are hydrophobic, so the variation may be minor. Chaing CAC to CAG though has more impact as you are changing the positive histidine to a polar glutamine (you loose the full positive charge of histidine). Remember, chaning amino acids can easily change the way a protein folds. REMEMBER: The genetic code has redundancies, and this will limit some problems with mutation.

Below is a more classic way to represent the genetic code, in the form of a table. The way the table is arranged, you can easily see the various redundancies in the system. In both representations, notice that there are three codons that specify STOP. These stop codons, UAA, UAG and UGA are essential for the termination of protein synthesis. In the image below, you will notice AUG has been tagged as the initiation (start) codon. All protein synthesis begins with the code AUG. We will talk more about this later in the the week.
Genetic Code

Daily Challenge

Today's newsletter helps to set the stage for our discussion of the central dogma of biology (gene expression).  In reading you find that DNA hold the codes to make various types of RNA and Proteins.  Most of the time, what concerns us is the production of proteins, as they will add functionality to our cells.
At the heart of the Central Dogma is the genetic code.  This code shows how you move from the language of nucleic acids to the language of proteins (aka, amino acids).  This code is Universal and Non-Ambiguous, but what does that mean?  Your goal today is to read, in your text and in the optional reading, and reflect on the concept of gene expression and the genetic code.  Why is it so important?  How do we use it?  How does this influence concepts from understanding hormonal changes at puberty, evolution and genetic engineering?

Link to Forum

Friday, September 5, 2014

Daily Newsletter: September 5, 2014 - DNA Replication

Site LogoDaily Newsletter

September 5, 2014 - DNA Replication

Textbooks have a tendency to make replication one of the most complext topics covered. With a tendency to throw all the current research and understanding at students, they rarely take a step back and try to explain it. This newsletters has two goals: 1) to help biology students understand DNA replication, and 2) to show you want is expected from a Biology Freshman/Sophmore.

Central Dogma of Biology
Before we get into replication, let's take a step back and look at the three core genetic processes, a.k.a., the Central Dogma. The central dogma describes the flow of genetic information in a cell. The core idea is INFORMATION. You may recall some of our early discussion on DNA, and about base complimentarity and the directionality of the molecule. This will become important rather quickly, but for just this moment, I want you to concentrate on the fact that DNA carries information. Information on how to build RNA and Proteins, both of which will produce the phenotype (expression) of the cell. For this reason, DNA, RNA and Proteins are considered Informational Macromolecules. This means that the sequence of monomers contains infomation, e.g., instructions on how to build RNA and Proteins. Since it is critical, the sequence of nucleotides carries information.
As you can see from the diagram of central metabolism shown above, there are three processes: Replication, Transcription and Translation. Think about those words. They are words used in reference to languages and documents. When you replicate a docuement, you want to ensure that you are getting a faithful (or even exact) copy of the original.

When you transcribe, you are moving from one medium, e.g., spoken word, to another medium, e.g., text. If you watch news shows, they will tell you that transcripts of the show are available. Court reports make transcripts of the trial. You are taking the language from one medium (in our case DNA) to another medium (RNA). The language is still the same (i.e., nucleic acid lanugae), just in a different form. Does the transcript have to be 100% correct? You want it to be, but it is not as exacting as a replication.
Translation is where you change languages. Unless you're fluent in another language, you will need somoene to help translate, or at least a good translation dictionary. Now you are moving the context from one language (nucleic acid) to another language (amino acids).

All of these processes rely on one key feature of nucleic acids: BASE COMPLIMENTARITY. In DNA: A complements T, and G complements C. In RNA: U complements A, and G still complements C.


In replication our goal is to take one molecule of DNA and make two daughter molecules of DNA that are identical to the first. Even the best replication processes can produce errors, but our goal is to be error free. This takes precision! As DNA is long, we also need this to be a fast process.

The enzyme that is ultimately responsible for replication is DNA Polymerase. [NOTE: there are multiple types of DNA Polymerase, but for now you just need to understand the core concept common to the DNA Polymerase family.] DNA polymerase is only one component of the Replication Complex, which is a complex association of proteins needed to successfully complete the replication event. Your goal at this time is to concentrate on DNA polymerase; we will talk about some of the other components later.
DNADNA is a double stranded molecule, in which the strands are anti-parallel. This means that one strand starts at the 5' end 3' end, while the the other strand is revered. This can be seen in the image to the right. A common way of saying this is that we read DNA in the 3' 5' direction. Why is this important? DNA Polymerase can only read DNA in the 3' 5' direction, and can only build a new strand in the 5' 3' direction. Before we go on, let's look another time at how deoxyribonucleotides are polymerized.

DNA Polymerization
To the left you will see a generic image showing DNA Polymerase adding nucleotides to a growing DNA strand. Look carefully: A deoxyribonucleotide triphosphate (dTTP) is being added. The 5' phosphate of the new nucleotide is what will be used to form the phosphodiester bond. DNA Polymerase requires a free 3' end on which to grow the new DNA strand. To the right is another image that will help you with this concept.Phosphodiester Bond Formation At this point, the critical thing to remember is that DNA Polymerase will need a free 3' end on which to add a new nucleotide.
This requirement to build in only one direction (5' 3') creates a problem for the DNA process: the two strands read in opposite directions, and each must be replicated. It was noticed that one strand appears to replicate continuously, while the opposite strand appears to replicate discontinuously.

The original strand that reads 5' 3' can be used by DNA polymerase to continuously produce the new 5' 3' strand (the antiparallel complement to the original strand). We refer to the continuous synthesis strand as the Leading Strand. The other original strand, which read 3' 5' cannot be copied continuously. A section will have to be exposed, replicated, and then another section exposed. This strand is constructed discontinuously, and is reffered to as the Lagging Strand.DNA ReplicationThe image above shows the leading and lagging strand. Notice that the leading strand is replicating toward the Replication Fork(where the original strands seperate). As more DNA unwinds and opens, DNA synthesis continues down the leading strand.
The lagging strand though has to build in a start-stop action, producing Okazaki fragments. These fragments have to be sealed (phosphodiester bonds) together before DNA can rewind into the α-helix.

In the image above, you will notice a number of enzymes on the lagging strand. These enzymes are required for the initiation of DNA polymerazation, and then sealing the fragments. Looking at the image, you will see an enzyme called Primase, and a structure in red known as a Primer. Another restriction on DNA polymerase is that it must have a free 3' end from which to start building. DNA Polymerase is prevented from building a DNA strand from nothing. Something (a primer) must be in place upon which DNA polymerase can build. The Primer is constructed from RNA, and is a temporary scaffold upon which DNA polymerase can start working.

Eventually the primer will need to be moved. This is where you need to learn a little more about DNA polymerase. There are multiple DNA polymerases in eukaryotic systems. The general work horse of replication is DNA Polymerase III (DNA pol III), which is used to make long strands of DNA. DNA Polymerase I (DNA pol I) is used to replace primers (it is also used in repair functions). Even after the RNA primer is replaced with DNA, there is still a gap between fragments. Ligase is the enzyme used to create a phosphodiester bond between fragments, thus sealing the new sugar-phosphate backbone of the synthesized strand.

The result of DNA replication is that one molecule one DNA was used to create two new molecules of DNA. The two strands of the original DNA molecule became the template from which to build new complimentary strands of DNA. This is referred to as semi-conservative replication, as each new molecule has one strand from the original molecule, and one freshly synthesized complimentary strand.

Daily Challenge

In your own words describe the purpose and process of replication.
Link to Forum

Thursday, September 4, 2014

Daily Newsletter: September 4, 2014 - Nucleotides

Daily Newsletter

September 4, 2014   Nucleotides

Nucleic Acids

Nucleotide Structure: The following image from wikipedia's image gallery shows the basic structure of the nucleotide and the five nitrogenous bases.
The central component of all nucleotides will be a pentose sugar (5-carbon sugar). We will either see ribose or 2'deoxyribose as the sugar (the second carbon has one less oxygen than ribose). Off of the 5' carbon of the sugar, you will find a phosphate group attached, while on the 1' carbon, you will find a nitrogenous base. [NOTE: remember the numbering of carbon atoms in carbohydrates from yesterday? Do you see why the numbering is important?]
There are five nitrogenous bases, divided into two categories: Purines and Pyrimidines. Notice that the purines are a composite of two ring structures, while the pyrimidines are a single ring structure. When you take organic chemistry and biochemistry, the importance and complexity of these ring structures will be further discussed. At present, just become aware of their respective shapes and sizes (and inclusion of nitrogen).

As with amino acids, the nucleotide contains a functional group: the nitrogenous base. Just like the side chain in an amino acid, the nitrogenous base will play an important part in the function of this biomolecule. The Sugar-Phosphate then becomes the backbone of the molecule (line the Amino-Chiral Carbon-Carboxyl of an amino acid). We will in later weeks that the sugar-phosphates of nucleotides will create the strands of DNA and RNA. The nitrogenous bases then playing an information role.

Base Complementarity:

The nucleic acids are referred to as informational biomolecules (biopolymers). This is because the sequence of nucleotides carries information on how to build RNA and Proteins. One of the central foundations of genetics (i.e., how it all works), is base complementarity. Here we are looking at the interactions between purines and pyrimidines:

A links with T through 2 hydrogen bonds.

G links with C through 3 hydrogen bonds.

A to T G to C

U has the binding properties of T, but is only found in RNA.
T is never found in RNA, only DNA.
NOTE: base complementarity is a critical concept to remember. All genetic processes rely on base complementarity!


When we get to genetics, we will be talking about the directionality of the nucleic acids. For example, we will talk about DNA being built from the 5' to 3'. This is in reference to the carbon atoms in the ribose or deoxyribose. The 5' holds a phosphate, while the 3' holds an open -OH (hydroxyl) group. This concept of directionality is critical, and you are warned to learn how it works, and what the terms represent.
As with all biopolymers, monomers are added together through dehydration synthesis, and separation is through hydrolysis. When synthesis occurs, the 5' phosphate links to the 3' -OH, forming a phosphodiester bond.

Daily Challenge

The challenge today is to understand the history of the discovery of DNA.  Look up the following researchers and read about their discovery, how it was done, and the importance the the discovery.  In addition, watch the TED Talk from James Watson "How we discovered DNA."  Write up a discussion about how these researchers contributed to our understanding of DNA.
Link to Forum


Wednesday, September 3, 2014

Daily Newsletter: September 6, 2013 - Carbohydrates and Lipids

Daily Newsletter

September 6, 2013    Carbohydrates and Lipids


While carbohydrates are mainly used as chemical energy storage, carbohydrates are also used as modifiers of proteins and in forming cellular receptors and anchors. One of your goals is to gain a good understanding of the structure of carbohydrates, and a little about their naming.

A topic that will come up throughout the semester is how carbons are numbered in carbohydrates. This is important as we will find carbohydrates being components of monomers and when we move through the carbohydrate catabolism. The following image from Rensselaer Polytechnic Institute shows the linear form of glucose, and the two possible cyclic (pyranose ring) isomers.
The formation is based on aldehyde chemistry, so we will leave some of this discussion to organic chemistry and biochemistry. For our purpose this semester, what is important is that we number carbons from the aldehyde. Notice in the above diagram that carbon 1 is to the left of the oxygen, we go around to carbon 5, and then carbon 6 is outside of the ring. If you see the expression 3', it is referring to the third carbon. 5' the fifth carbon. 6' the sixth carbon, and so forth.

Notice also, that when the ring was formed, there were differences in the groups coming off of carbon 1. These differences are important, and can influence how the sugar is metabolized. We say that these different forms are isomers (if you don't know what an isomer is, look it up and add the definition to your notebook).

One critical difference comes when linking two monosaccharides together to form disaccharides and polysaccharides. For instance (again from, here is maltose:
This is an α 1-4 glycosidic linkage. We have an α Maltose (look at carbon 1) bound from carbon 1 to carbon 4. Since the maltose on the left hand side is α at the 1 carbon, we form an α linkage. In comparison, look at cellobiose:
Cellobiose has a β 1-4 glycosidic linkage. The designation of β comes from the sugar unit that donates carbon 1 to the bond.

So, what is the big deal? Maltose is digestible by humans, cellobiose is not. Just this slight isomeric difference changes the metabolism.
All carbohydrate monomers are connected through glycosidic linkages, whether it is a disaccharide, oligosaccharide or a polysaccharide. Make sure that you learn the different types of carbohydrates.


Lipids are an odd group of biomolecules. Proteins, Carbohydrates and Nucleic Acids are all formed through polymerization reactions; they have monomeric units that join to make polymers. Lipids do not polymerize, and they have no monomers. Instead, Lipid is a word that defines a class of hydrophobic organic compounds found in living systems. There are a number of important groups of Lipids, such as the triglycerides, phospholipids and cholesterols. Today, we are going to concentrate on the triglycerides and the phospholipids.
Both triglycerides and phospholipids possess a glycerol molecule and fatty acids. GlycerolGlycerol is a 3 carbon compound that we will see from time to time. It acts as the backbone or schaffold of the triglycerides and phospholipids. As you can see, on each carbon atom, there is a hydroxyl group (-OH). This hydroxyl group is where other molecules can bond. Another thing to note is that there is free rotation around the carbon atoms. When you take organic chemistry, you will learn more about free rotation, why it is important, and how it can affect a molecule. For now, just note that there can be free rotation.
Fatty acids are long hydrocarbon chains with a carboxyl group (-COOH) at one end. To the left is a diagram of palmitic acid, a typical saturated fatty acid.Palmitic Acid In this diagram, each angle on the line represents a carbon atom, and off of these carbon atoms are hydrogens. This is one of many ways that organic palmitic acid molecular structurechemicals are depicted. Below the first depiction is a molecular model. Carbon atoms are in black, and the white balls are hydrogens. What you will begin to recognize in these diagrams is that there are only single bonds between the carbon atoms. This means that the maximum number of hydrogen atoms are attached to the fatty acid. In other words, they are saturated with hydrogen.
In contrast, an unsaturated fatty acid does not have the maximum number of hydrogen atoms. This occurs when double bonds (two electrons from each carbon are shared) occur in the carbon chain. To the right is a diagram of oleic acid. oleic acidNote that there is a double bond in the carbon chain. Notice that the chain is bent, or kinked. This creates a very different structure for lipids that carry unsaturated fatty acids.
As a general rule, saturated fatty acids are solid at room temperature, and unsaturated fatty acids are liquid in room temperature. But one thing is the same in both: the carbon chains are HYDROPHOBIC!
In a triglyceride, the carboxyl end of the fatty acid will react with the hydroxyl end of the glycerol. From you can see in the diagram, the two molecules are joined together through an oxygen molecule. As with other biosynthetic reactions, this is a dehydration synthesis (water is released). The resulting bond, as noted in the diagram, is an ester bond. You will learn more about this bond in organic chemistry, so for now I just want you to remember the general look of it. Why is this so critical? Because not all living organisms make triglycerides and phospholipids this way. Member of domain Archaea use an ether bond.
So, what is the difference between a triglyceride and a phospholipid? Recall the look of the glycerol, and note that there are three locations where an ester bond can be formed. In a triglyceride, a fatty acid will be bound to each of the carbon atoms by ester bonds. Tri- means three, so we have three fatty acids attached to the glycerol. The image to the right is an example of a triglyceride, and please note, you can have more than one type of fatty acid in a triglyceride.
The phospholipid in contrast only has two fatty acids. The third binding location will be used for a "phosphate head". This head contains a phosphate group and usually a diglyceride and some small charged organic structure. phospholipidPhosphytidyl choline is a commonly studied phospholipid that uses choline as the charged organic structure. NOTE: both the phosphate group and the organic structure carry a charge. This phosphate head is charged, thus it is hydrophillic (water loving). The phospholipid contains non-polar, hydrophobic fatty acids (usually referred to as the tails) and a polar, charged, hydrophillic head. This molecule is both hydrophobic and hydrophillic. Amphiphathic is the word we use to describe a molecule with both hydrophobic and hydrophillic properties. A main use for the phospholipid is in biological membranes, as shown in the image to the right.

Daily Challenge

Proteinscarbohydrates and nucleic acids have the ability to form complex polymers.  Proteins and nucleic acids have their function is determined by the sequence of monomers.  Phospholipids can spontaneously form sealed spheres that create an inside vs. an outside.  All life functions rest upon the diversity of these chemicals.  The basics of biochemistry that you have learned this week will be expanded upon throughout the coming weeks.  You will see further examples of proteinscarbohydrates, nucleic acids and lipids.

Your goal is to start building mental models of what they are and how they interact.  Draw out the structures, write out a full dehydration synthesis or hydrolysis.  What factors cause proteins to fold?  What would occur if you used saturated fatty acids in a phospholipid?  What about non-saturated fatty acids?  Take some time and really build an idea about each of these molecules, and appreciate the diversity.
After spending time, write in the discussion forum your thoughts and ideas about these biochemicals.  (This is a free form discussion where you can write about proteins,carbohydrates and lipids.  The focus is for you to express your understanding of the structure and function of the three biochemical categories, but you are also welcome to pose questions regarding what you do not understand about these chemicals.)
Link to Discussion Forum

Tuesday, September 2, 2014

Daily Newsletter: September 2, 2014 - Protein Folding

Daily Newsletter

September 2, 2014 - Protein Folding

Yesterday's newsletter focused on amino acids, how these monomers are polymerized, and the importance of their R (functional) group. Today we are going to further examine the importance of functional groups by discussing how they help form the working shape of a protein by causing a chain of amino acids to fold.

The primary structure of a protein is a chain of amino acids. Due to how proteins form, one end of the chain will end in an amino group (N-terminus), which the other end will have a carboxyl group (C-terminus). In Between these two terminal points will be a wide variety of amino acids.
The side chains of neighboring amino acids will begin to interact. They could be pulled toward each other, be repelled, or have nothing happen. Remember that the functional groups can twist around the chiral (central) carbon of the amino acid, so repulsion may just force the side chains to opposite sides of the chain (remember, you are dealing with 3-D structures here). The amino groups and carboxyl groups, even though they are part of the back bone, also retain polarity. Thus they can also be involved in the folding.

These interactions start the formation of the secondary level of protein structure. The two most common types of secondary structures are the alpha helix and the beta pleated sheet. These two types of secondary structures will help explain how the amino acid side chains start the folding process.
The α-helix relies on neighboring amino acids. Through the polarity of amino and carboxyl groups, the backbone of the molecule begins to twist and hold due to electrostatic interaction (van der Waals forces). The image to the left is an example of an alpha helix. The alpha represents the direction of the twist, and you will learn more of the naming of these in organic chemistry. Illustration of the hydrogen bonding patterns, represented by dotted lines, in an antiparallel beta sheet. Oxygen atoms are colored red and nitrogen atoms colored blue.found at that in the image there are yellow dashed lines. These represent hydrogen bonds (van der Waals forces) between amino acids. The green ribbon represents the backbone of the amino acid chain (amino-chiral-carboxyl connected to amino-chiral carboxyl and so on). So the interactions (notably from polar partially charged side chains has produced a twist in the primary structure.

In contrast, β-pleated sheet, shown on the right, has interactions between different regions of the primary structure. While only one amino acid chain is involved, in this case the chain is not twisting. Instead, neighboring regions become attracted to each other. Also, the electrostatic interaction is between amino and carboxyl groups, not R groups. Multiple regions can be brought together to form these sheets as indicated in the diagram below. Portion of outer surface Protein A of Borrelia burgdorferi complexed with a murine monoclonal antibody.  Found at: this diagram, the red arrows represent a portion of the primary structure that has begun to form β-pleates. Notice that six red arrows are arranged together. The purpose of this diagram is to show the placement of the β-pleated sheet. Consider a sheet. It is flat with two sides. Why do you think it would be important for a protein to fold in such a way as to create a relatively "flat" surface with two sides?

Notice that with the α-helix and β-pleated sheet we have altered the structure of the protein. It is no longer a linear chain, but has greater dimensionality. We have either turned the protein into a rope/cord (α-helix) or into a "plane" with two faces(β-pleated sheet). Now areas that were once distant have been brought closer together. Now side chains can start interacting with each other.
In the tertiary structure, different regions of the protein are brought into association. Electrostatic and hydrophobic interactions will force more conformational (structural) changes onto the protein. This will lead to a 3-dimensional structure. In the following diagram to the left, you can see an example of From
a protein in primary and then tertiary structure.

Notice that the secondary structures are visible, but even these have been folded into each other.
The forces that govern this are found in the R (functional) groups of the amino acids. Hydrophobic areas cluster together. Positive and Negative charges attract, while like charges repel. Polar partially charged side chains further interact, either with each other, or with full charged. We also have a new interaction. Found at amino acid cystine contains a thiol (-SH). The thiols of two cystines can react to form a disulfide bond. This is a covalent bond. Question: Which is stronger individually, a covalent bond or a hydrogen bond (electrostatic interaction)? The disulfide bond is utilized to stabilize the 3-dimensional structure of the protein.

Many proteins are functional at the tertiary structure. Here you will see either globular or linear proteins Found at collagen). There is a final level of structure. Some functional proteins are actually made up of multiple individual proteins. A great example of this is hemoglobin. The hemoglobin molecule, seen to the left, is composed of four individual proteins: 2 α-hemoglobin (red) and 2 β-hemoglobin (blue). The green structure is Heme, a prosthetic group that is used to hold oxygen, and is attached by electrostatic interactions (van der Waals forces) to the proteins.

NOTE: Some proteins are functional in the tertiary structure, but others are only functional when you have multiple individual proteins forming the quatrenary structure.
Denaturation: The protein is held together primarily through electrostatic interactions. What happens when a protein warms up? It starts to unfold. Why? The electrostatic interactions weaken as kinetic movement of the atoms increases. Acids and bases, with their charged H+ and OH- also disrupt these electrostatic interactions. Secondary and tertiary structures begin to change conformation. Most notably, they unfold. To denature a protein is to unfold it....but....
What if you only apply a mild heat, let's say your muscles warm up due to exercise. What happens to the proteins? What happens to hemoglobin when it passes through a warm temperature? Your muscles are also metabolizing, and as we will see, produce acids. What does this do? So, is denaturation all or nothing?

The tertiary and quatrenary structures all have a specific electrochemical profile.
What happens if you add a charged particle/compound to a protein?   What happens if I add a new positive charge? Answer: The protein will change shape (conformation).
What will this due to the function of the protein? It could actually active the protein, but it could also deactivate the protein. This will be a discussion a little later in the semester, but I want you to start thinking of the implications.

Example: Hemoglobin
Adult hemoglobin is a quaternary protein, composed of two α-subunits (tertiary proteins) and two β-subunits (tertiary proteins).  Each subunit contains a heme group which bears an Fe+2.  The heme is a prosthetic group of the individual proteins; without the heme, the subunit is non-functional.  We will see further examples of prosthetic groups and other factors as we go through the semester.  NOTE:  We are looking at adult hemoglobin.
animation of hemoglobin t-r state transformation, made by en:User:BerserkerBen
To the left is an animated image of hemoglobin.  Notice that the configuration (shape) of the protein changes when Oxygen is bound (Oxy) and when no oxygen is bound (deoxy).  MEME:  When something binds to a protein, it changes shape.  In the image, you can also see the various subunits (each a tertiary protein) with their associated Heme groups (heme groups are in red).

The folding of the protein is critical to its function.  Even a small error in the primary structure can cause significant changes to the overall structure, and therefore changes to the  function.

A well known condition with hemoglobin is Sickle Cell Anemia.   The condition is based upon a mutation of the gene that codes for the β-hemoglobin.  The switch from an Adenine to Thymine causes a change in the primary sequence of the protein.  In wild type (non-mutant) β-hemoglobin, there is a glutamic acid (charged, negative) at position 6, but in Sickle Cell Anemia, the sixth position holds valine (non-polar).  At low oxygen levels (such as in your tissues after exercise), the hemoglobin takes on an abnormal shape:

The quaternary protein has now changed shape by opening up.  Sickle hemoglobin has the ability to bond to other sickle hemoglobins.  This is due to electrostatic interactions.  The image blow shows the result of this interaction between sickle hemoglobin:  clumping.

The clumping of sickle hemoglobin in low oxygen environments causes the distinctive change in shape seen in sickling red blood cells, and is all due to changing one amino acid in the primary structure.  Below is an image showing normal vs. sickle red blood cells.
Normal RBC vs Sickle RBC

Daily Challenge:

Pick your challenge!  Decide if you want to work on Discussion 1 or Discussion 2.  Understand that you are responsible for considering both, and information from both could appear on future quizzes.

Discussion 1

Hemoglobin is a protein that is constantly changing shape due to the presence or absence of oxygen.  It also changes shape when in acidic environments or hot environments (think of your muscles after a work out). The effects of temperature and pH are described in the Oxygen Dissociation Curve.  Temperature and pH disrupt electrostatic interactions, allowing for proteins to denature.  Using the concept of denaturation, explain why more oxygen is released when the pH lowers and temperature increases.  How would this be of benefit to the body?

Discussion 2

Antibodies help to defend the body against infections.  They work by binding foreign chemical markers called antigens.  The diversity of antigens is staggering, and cells that make them (B lymphocytes) have the ability to undergo somatic recombination (programed changes to DNA) to increase the variability of antibodies.  Of specific importance is the variable domain:

In the above diagram, look at the Variable Domain of the Light Chain (VL).  Notice 3 areas drawn in red, and referred to as the Loops that Bind Antigens.  These are the areas where Somatic Recombination can change the nucleotides present in the gene.  If I change the nucleotides (as with hemoglobin above), I can change the amino acids in the primary sequence.  Explain how changing the primary sequence in these loop regions can change the binding affinity of an antibody to an antigen, and why this is beneficial to the body.