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Course: Biology library > Unit 4
Lesson 2: Hydrocarbon structures and functional groupsHydrocarbon structures and isomers
Hydrocarbon structures and types of isomerism (structural isomers, cis/trans isomers, and enantiomers).
Introduction
Even though you likely see gasoline-powered vehicles everyday, you rarely see what gasoline itself looks like! To the naked eye, gasoline is a pretty uninteresting yellowish-brown liquid. At the molecular level, though, gasoline is actually made up of a striking range of different molecules, most of them hydrocarbons (molecules containing only hydrogen and carbon atoms).
Some of the hydrocarbons in gasoline are small and contain just four carbon atoms, while others are much larger and have up to twelve carbons. Some hydrocarbons form straight lines, while others have a branched structure; some have only single bonds, while others have double bonds; and still others contain rings. While the different hydrocarbons in gasoline often have very different properties, such as melting point and boiling point, they all produce energy when they’re burned in an engine.
Hydrocarbons are diverse!
As the gasoline example shows, hydrocarbons come in many different forms. They may differ in length, be branched or unbranched, form linear or ring shapes (or both), and include various combinations of single, double and triple carbon-carbon bonds. Even if two hydrocarbons have the same molecular formula, their atoms may be connected or oriented in different ways, making them isomers of one another (and sometimes giving the two molecules very different properties).
Each of these structural features can influence the three-dimensional shape, or molecular geometry, of a hydrocarbon molecule. In the context of large biological molecules such as DNA, proteins, and carbohydrates, structural differences in the carbon skeleton often affect how the molecule functions.
Branching, multiple bonds, and rings in hydrocarbons
Hydrocarbon chains are formed by a series of bonds between carbon atoms. These chains may be long or short: for instance, ethane contains just two carbons in a row, while decane contains ten. Not all hydrocarbons are straight chains. For example, while decane’s ten carbon atoms are lined up in a row, other hydrocarbons with the same molecular formula (start text, C, end text, start subscript, 10, end subscript, start text, H, end text, start subscript, 22, end subscript) have shorter primary chains with various side branches. (In fact, there are 75 possible structures for start text, C, end text, start subscript, 10, end subscript, start text, H, end text, start subscript, 22, end subscript!)
Hydrocarbons may contain various combinations of single, double, and triple carbon-carbon bonds. The hydrocarbons ethane, ethene, and ethyne provide an example of how each type of bond can affect the geometry of a molecule:
- Ethane (start text, C, end text, start subscript, 2, end subscript, start text, H, end text, start subscript, 6, end subscript), with a single bond between the two carbons, adopts a two-tetrahedron shape (one tetrahedron about each carbon). Importantly, rotation occurs freely about the carbon-carbon bond.
- In contrast, ethene (start text, C, end text, start subscript, 2, end subscript, start text, H, end text, start subscript, 4, end subscript), with a double bond between the two carbons, is planer (all of its atoms lie in the same plane). Furthermore, rotation about the carbon-carbon double bond is restricted. This is a general feature of carbon-carbon double bonds, so anytime you see one of these in a molecule, remember that the portion of the molecule containing the double bond will be planar and unable to rotate.
- Finally, ethyne (start text, C, end text, start subscript, 2, end subscript, start text, H, end text, start subscript, 2, end subscript), with a triple bond between the two carbons, is both planar and linear. As with the double bond, rotation is completely restricted about the carbon-carbon triple bond.
An additional structural feature that is possible in hydrocarbons is a ring of carbon atoms. Rings of various sizes may be found in hydrocarbons, and these rings may also bear branches or include double bonds. Certain planar rings with conjugated atoms, like the benzene ring shown below, are exceptionally stable. These rings, called aromatic rings, are found in some amino acids as well as in hormones like testosterone and estrogens (the primary male and female sex hormones, respectively).
Some aromatic rings contain atoms other than carbon and hydrogen, such as the pyridine ring shown above. Due to their additional atoms, these rings are not classified as hydrocarbons. You can learn more about aromatic compounds in the aromatic compounds chemistry topic.
Isomers
The molecular geometries of hydrocarbons are directly related to the physical and chemical properties of these molecules. Molecules that have the same molecular formula but different molecular geometries are called isomers. There are two major classes of isomers: structural isomers and stereoisomers.
Structural isomers
In structural isomers, the atoms in each isomer are connected, or bonded, in different ways. As a result, structural isomers often contain different functional groups or patterns of bonding. Consider butane and isobutane, shown above: both molecules have four carbons and ten hydrogens (start text, C, end text, start subscript, 4, end subscript, start text, H, end text, start subscript, 10, end subscript), but butane is linear and isobutane is branched. As a result, the two molecules have different chemical properties (such as lower melting and boiling points for isobutane). Because of these differences, butane is typically used as a fuel for cigarette lighters and torches, whereas isobutane is often employed as a refrigerant or as a propellant in spray cans.
Stereoisomers
In stereoisomers, the atoms in each isomer are connected in the same way but differ in how they are oriented in space. There are many types of stereoisomers, but they can all be sorted into one of two groups: enantiomers or diastereomers. Enantiomers are stereoisomers that are non-superimposable mirror images of each other (“non-superimposable” means that the two molecules cannot be perfectly aligned one on top of the other in space). Enantiomerism is often seen in molecules containing one or more asymmetric carbons, which are carbon atoms that are attached to four different atoms or groups.
The molecules above are an example of an enantiomer pair. Both have the same molecular formula and are made up of a chlorine, a fluorine, a bromine and a hydrogen atom bonded to a central carbon atom. However, the two molecules are mirror images of one another, and if you try to place them on top of each other, you’ll find that there’s no way to make them fully line up. Enantiomers are often compared to a person's right and left hands, which are also mirror images that cannot be superimposed.
Most amino acids, the building blocks of proteins, contain an asymmetric carbon. Below, you can see space-filling models of the two enantiomers of the amino acid alanine. Historically, enantiomers in biology were distinguished using the prefixes L and D, and biologists often still use this terminology for amino acids and sugars. However, in the wider world of chemistry, the D/L system has been replaced by another naming system, the R/S system, which is more precise and can be applied to all enantiomers. You can learn more about enantiomers and the R/S naming system in the organic chemistry section.
The difference between a pair of enantiomers may seem very small. In some cases, though, two enantiomers may have very different biological effects. For example, the D form of the drug ethambutol is used to treat tuberculosis, while the L form actually causes blindness!start superscript, 1, end superscript Additionally, there are many cases where only one enantiomer is produced by the body or found in nature. For example, typically only the L forms of amino acids are used to make proteins (although the D forms of amino acids are occasionally found in the cell walls of bacteria). Similarly, the D enantiomer of the sugar glucose is the main product of photosynthesis, while the L form is rarely seen in nature.
Remember that all stereoisomers can be classified as either enantiomers or diastereomers. Diastereomers are any stereoisomers that are not enantiomers. One common example of a diastereomer is a cis-trans isomer. Cis-trans isomers can occur when atoms or functional groups are situated on either end of a rigid carbon-carbon bond, such as a double bond. In this case, restricted rotation about the double bond means that the atoms or groups attached to either end can exist in one of two possible configurations. If either carbon is attached to two of the same atoms or groups, then this won't matter; however, if both carbons are attached to two different atoms or functional groups, then two different arrangements are possible.
For example, in 2-butene (start text, C, end text, start subscript, 4, end subscript, start text, H, end text, start subscript, 8, end subscript), the two methyl groups (start text, C, H, end text, start subscript, 3, end subscript) can occupy different positions relative to the double bond central to the molecule. If the methyl groups are on the same side of the double bond, this is called the cis configuration of 2-butene; if they are on opposite sides, this is the trans configuration.
In the trans configuration, the carbon backbone is more or less linear, whereas in the cis configuration, the backbone contains a bend, or kink. (Some ring-shaped molecules can also have cis and trans configurations, in which attached atoms are trapped on the same or on opposite sides of the ring, respectively)
In fats and oils, long carbon chains called fatty acids often contain double bonds, which can be in either the cis or trans configuration (shown below). Fatty acids that contain cis double bonds are typically oils at room temperature. This is because the bends in the backbone caused by cis double bonds prevent the fatty acids from packing tightly together. In contrast, fatty acids with trans double bonds (popularly called trans fats), are relatively linear, so they can pack tightly together at room temperature and form solid fats.
Trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have eliminated their use in recent years. Fats with trans double bonds are found in some types of shortening and margarine, while fats with cis double bonds may be found in oils, such as olive oil and canola oil. See the article on lipids to learn more about the different types of fats.
Want to join the conversation?
The second picture in the article, showing various ring formations, and how they compare includes pyridine. From what I have previously seen here on Khan Academy, it was my understanding that one aspect of hydrocarbons is that they are comprised of chains made up of only carbon and hydrogen. Because of this, wouldn't pyridine be discluded from the hydrocarbon classification because it contains an atom of nitrogen? Thank you much for the clarification!(17 votes)
Good question! Pyridine is not a hydrocarbon, as hydrocarbons can only contain hydrogen and carbon atoms, by definition. I think the point he was trying to make by showing that molecule is that hydrocarbons can take on ring-shaped forms to form more diverse molecules, which could potentially include other atoms. I hope that makes things more clear! :)(18 votes)
how many carbons can be bonded in chain ( maximum) ?(4 votes)
When carbon bonds to itself to form a matrix, there is no limit. Organic molecules formed from a carbon chain can grow quite large and complicated, forming the basis for the complex machinery of living organisms.(7 votes)
What can determine an atoms stability?I mean that it was written that Benzene is exceptionally stable. I am speaking general.(4 votes)
Stability suggests than an atom is very unreactive. For this to happen, the atom needs to be completely neutral. For example, Neon is a nobel gas that rarely reacts with anything else because it has a fully complete outer shell of electrons (which is what every atom "wants".) Sodium however has only one electron in its outer shell, so it would "like" to donate that electron to get rid of it. Chlorine has seven outer electron, so it wants to gain an electron to be stable. Therefore, Sodium and Chlorine easily react together to make table salt.(7 votes)
- In the paragraph after the heading Cis-trans (geometric) isomers, it says that linear molecules have single carbon-carbon bonds and can rotate freely. This kinda conflicts with the video that goes with this pdf because I thought linear carbon-carbon bonds were triple bonded and does not allow rotation. Only tetrahedrons can do that. Is this a mistake?(4 votes)
Linear is being used two different ways here, which I agree is a bit confusing.
The first use doesn't really mean linear in a geometric sense, but it is intended to mean "unbranched and not circular".
Note that this is analogous to how we often use line — e.g. "The line for tickets was so long it went around the block!".(4 votes)
How do we know what shape these molecules take and second - How can we control, or is it possible to control the shape of the molecules?(3 votes)
The configuration of the bonds around each carbon can be easily determined - this is known as the geometrical configuration and depends on the electron hybridisation (sp, sp2, sp3) of the carbon and other atoms. What can be harder to predict is the overall shape of a large organic molecule because there is rotation around single bonds so a large number of different shapes are possible and a molecule can cycle through all the different configurations, although some will be energetically more stable than others.
Interactions between different parts of the molecule (e.g., hydrogen bonds, ionic interactions, lone pair repulsions, steric hindrance, etc) are responsible for some configurations being more energetically favourable than others.(4 votes)
Is the psa isomers reference Prostate Specific Antigen? If not, what is it?(3 votes)- Perhaps it was an error that was removed, because I can't find the item you are referring to.(2 votes)
- Why cannot we superimpose enantiomers of L and D? In the example, carbon with F, H, Br, and Cl, if you superimpose back to back it exactly aligns.(2 votes)
Try to think of this in terms of laying your left hand on top of your right hand. They may seem to line up, but your left palm is showing. Therefore, your hands still wouldn't be the same. Also, keep in mind that most Carbon Enantiomers are 3 dimensional in a tetrahedral shape with some of the atoms revolving.(3 votes)
- what is a carbon backbone?(1 vote)
Most organic molecules have a carbon backbone, meaning that their structure is made up of carbon atoms bonded to other carbon atoms.(4 votes)
- Are the D forms of amino acids found in good bacteria, bad bacteria, or both?(2 votes)
While it is true that our bodies prefer L-amino acids which are just result of an evolutionary process, does not mean D-amino acids would harm us.
L.amino acids are alreday present in nature in biological systems.
On the flip side, bacteria did develop a metabolic pathway for D-amino acids. For example, spore germinating bacteria (such s Bacillus) utilize D-amino acids. D amino acids are present also in peptidoglycan (e.g. Mycoplasma).
So the answer is both, in all kind of bacteria (they all have peptidoglycan, and in some sporulating etc, forming a biofilm.
You can find sporulating and biofilm producing bacteria species among pathogens, opportunistic pathogens, beneficial microbiota.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037491/(1 vote)
- Can somebody explain the last two pictures? They label it like they are different molecules but all they are is the same molecule just turned 180 degrees. Are they saying that you get a different molecule from the direction you observe it?(1 vote)
- They look very similar, yes, but they are not just turned 180 degrees. They are actually mirror images of each other. If you tried to turn one you couldn't get it to line up with the other. The molecules have the same physical properties, such as melting point etc, and will react the same way with molecules that are symmetric. However they will interact differently with other molecules that are not symmetrical.
The best way to see the difference is to make a model in 3D and moving them around. But otherwise you can try rotating them on a computer, like here, but it is harder to see. http://www.bluffton.edu/homepages/facstaff/bergerd/classes/NSC105/enantiomers.htm
If you are interested for more information there is a whole section on stereochemistry on khan academy, maybe take a look at the beginning of that
https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic
Or chemguide has some good diagrams where you can see the difference more clearly too (I'm talking about the coloured ones and the ones with the mirror plane drawn in - the end gets complicated looking at rings and cholesterol). https://www.chemguide.co.uk/basicorg/isomerism/optical.html(3 votes)
