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Characteristic Chemical Reactions - Biology

Characteristic Chemical Reactions - Biology


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Characteristic Chemical Reactions

All chemical reactions begin with a reactant—the general term for the one or more substances that enter into the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. The one or more substances produced by a chemical reaction are called the product. **Note that there is some "hidden" excitement in the story about table salt involving water that we'll see soon.**

In chemical reactions, the atoms and elements present in the reactant(s) must all also be present in the product(s). Similarly, there can be nothing present in the products that was not present in the reactants. This is because chemical reactions are governed by the law of conservation of mass, which states that matter cannot be created nor destroyed in a chemical reaction. This means that when you examine a chemical reaction, you must try to account for everything that goes in AND make sure that you can find it all in the stuff that comes out!

Just as you can express mathematical calculations in equations such as 2 + 7 = 9, you can use chemical equations to show how reactants become products. By convention, chemical equations are typically read or written from left to right. Reactants on the left are separated from products on the right by a single- or double-headed arrow indicating the direction in which the chemical reaction proceeds. For example, the chemical reaction in which one atom of nitrogen and three atoms of hydrogen produce ammonia would be written as:

[N + 3H→NH_3.]

Correspondingly, the breakdown of ammonia into its components would be written as:

[NH3→N + 3H.]

Note that in either direction, you find 1 N and 3 Hs on both sides of the equation.

Reversibility

In theory, any chemical reaction can proceed in either direction under the right conditions. Reactants may synthesize into a product that later reverts back to a reactant. Reversibility is also a quality of exchange reactions. For instance, A+BC→AB+C could then reverse to AB+C→A+BC. This reversibility of a chemical reaction is indicated with a double arrow: A+BC⇄AB+C.

Synthesis reactions

Many macromolecules are made from smaller subunits, or building blocks, called monomers. Monomers covalently link to form larger molecules known as polymers. Often, the synthesis of polymers from monomers will also produce water molecules as products of the reaction. This type of reaction is known as dehydration synthesis or condensation reaction.

Figure 1. In the dehydration synthesis reaction depicted above, two molecules of glucose are linked together to form the disaccharide maltose. In the process, a water molecule is formed.

Attribution: Marc T. Facciotti (original work)

In a dehydration synthesis reaction (Figure 1), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers; for example, glucose monomers are the constituents of starch, glycogen, and cellulose.

In the carbohydrate monomer example above, the polymer is formed by a dehydration reaction; this type of reaction is also used to add amino acids to a growing peptide chain and nucleotides to the growing DNA or RNA polymer. Visit the modules on Amino Acids, Lipids, and Nucleic Acids to see if you can identify the water molecules that are removed when a monomer is added to the growing polymer.

Figure 2. This depicts, using words, (decorated with functional groups colored in red) a generic dehydration synthesis/condensation reaction.

Attribution: Marc T. Facciotti (original work)

Hydrolysis reactions

Polymers are broken down into monomers in a reaction known as hydrolysis. A hydrolysis reaction includes a water molecule as a reactant (Figure 3). During these reactions, a polymer can be broken into two components: one product carries a hydrogen ion (H+) from the water, while the second product carries the water's remaining hydroxide (OH–).

Figure 3. In the hydrolysis reaction shown here, the disaccharide maltose is broken down to form two glucose monomers with the addition of a water molecule. Note that this reaction is the reverse of the synthesis reaction shown in Figure 1 above.

Attribution: Marc T. Facciotti (original work)

Figure 4. This depicts using words (decorated with functional groups colored in red) a generic hydrolysis reaction.

Attribution: Marc T. Facciotti (original work)

Dehydration synthesis and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes. Note that both dehydration synthesis and hydrolysis reactions involve the making and breaking of bonds between the reactants—a reorganization of the bonds between the atoms in the reactants. In biological systems (our bodies included), food in the form of molecular polymers is hydrolyzed into smaller molecules by water via enzyme-catalyzed reactions in the digestive system. This allows for the smaller nutrients to be absorbed and reused for a variety of purposes. In the cell, monomers derived from food may then be reassembled into larger polymers that serve new functions.

Helpful links:

Visit this site to see visual representations of dehydration synthesis and hydrolysis.
Example of Hydrolysis with Enzyme Action is shown in this 3 minute video entitled: Hydrolysis of Sucrose by Sucrase.

Exchange/transfer reactions

We will also encounter reactions termed exchange reactions. In these types of reactions, "parts" of molecules are transferred between one another—bonds are broken to release a part of a molecule and bonds are formed between the released part and another molecule. These enzyme-catalyzed reactions are usually reasonably complex multistep chemical processes.

Figure 5. An exchange reaction in which both synthesis and hydrolysis can occur, chemical bonds are both formed and broken, is depicted using a word analogy.


Characteristic Chemical Reactions - Biology

Functional groups refer to specific atoms bonded in a certain arrangement that give a compound certain physical and chemical properties.

Learning Objectives

Define the term “functional group” as it applies to organic molecules

Key Takeaways

Key Points

  • Functional groups are often used to “functionalize” a compound, affording it different physical and chemical properties than it would have in its original form.
  • Functional groups will undergo the same type of reactions regardless of the compound of which they are a part however, the presence of certain functional groups within close proximity can limit reactivity.
  • Functional groups can be used to distinguish similar compounds from each other.

Key Terms

  • functional group: A specific grouping of elements that is characteristic of a class of compounds, and determines some properties and reactions of that class.
  • functionalization: Addition of specific functional groups to afford the compound new, desirable properties.

The Role of Functional Groups

In organic chemistry, a functional group is a specific group of atoms or bonds within a compound that is responsible for the characteristic chemical reactions of that compound. The same functional group will behave in a similar fashion, by undergoing similar reactions, regardless of the compound of which it is a part. Functional groups also play an important part in organic compound nomenclature combining the names of the functional groups with the names of the parent alkanes provides a way to distinguish compounds.

The atoms of a functional group are linked together and to the rest of the compound by covalent bonds. The first carbon atom that attaches to the functional group is referred to as the alpha carbon the second, the beta carbon the third, the gamma carbon, etc. Similarly, a functional group can be referred to as primary, secondary, or tertiary, depending on if it is attached to one, two, or three carbon atoms.

Classification of alcohols: Alcohols are a common functional group (-OH). They can be classified as primary, secondary, or tertiary, depending on how many carbon atoms the central carbon is attached to.

Functional Groups and Reactivity

Functional groups play a significant role in directing and controlling organic reactions. Alkyl chains are often nonreactive, and the direction of site-specific reactions is difficult unsaturated alkyl chains with the presence of functional groups allow for higher reactivity and specificity. Often, compounds are functionalized with specific groups for a specific chemical reaction. Functionalization refers to the addition of functional groups to a compound by chemical synthesis. Through routine synthesis methods, any kind of organic compound can be attached to the surface. In materials science, functionalization is employed to achieve desired surface properties functional groups can also be used to covalently link functional molecules to the surfaces of chemical devices.

In organic chemistry, the most common functional groups are carbonyls (C=O), alcohols (-OH), carboxylic acids (CO2H), esters (CO2R), and amines (NH2). It is important to be able to recognize the functional groups and the physical and chemical properties that they afford compounds.

Organic chemistry functional groups lesson: This video provides a great overview of the various functional groups in organic chemistry.


Functional Groups and Naming

Functional groups are specific groups of atoms or bonds within molecules. They are responsible for the characteristic chemical reactions of those molecules.

Functional groups are attached to the carbon backbone of organic molecules. They determine the characteristics and chemical reactivity of molecules.

The same functional group undergoes the same chemical reactions regardless of the size of the molecule it is a part of.

Functional groups are less stable than the carbon backbone. They are more likely to take part in chemical reactions.

Some common functional groups are:

Identify the functional groups in the tetracycline molecule shown below.

Starting from the left hand ring and going clockwise around the carbon backbone, the functional groups are:

Benzene ring
Alcohol
Amine
Alcohol (this one has a special name — an enol)
Alkene
Amide
Ketone
Alcohol
Alcohol
Alkene
Ketone
Alcohol (this one has a special name — a phenol)


MATERIALS AND METHODS

Benchmark RNAs and their SHAPE probing data

To identify the characteristic SHAPE patterns for hairpin, internal, and bulge loop motifs, we analyzed a dataset consisting of 11 RNAs with known structures as determined by crystallography or NMR and with low-throughput SHAPE reactivities publicly available ( 12, 37–39) ( Supplementary Table S1 ). These RNAs include nine short RNAs and two long rRNAs (Escherichia coli 16S and 23S). The two long rRNAs were divided into 10 domains for structural prediction following the published strategies ( 40, 41).

Identification of characteristic SHAPE patterns

Hairpin, internal, and bulge loops with two flanking base pairs were extracted from the benchmark RNAs (Table 1). Loops involved in pseudoknot structures were removed. A loop motif was defined as any loops with the same length and type (hairpin, bulge, or internal), irrespective of their sequences. We applied paired Wilcoxon signed-rank tests ( 42) to detect significant differences in SHAPE reactivities between any two positions in each loop motif (Figure 1A). Among the pairs under comparison, if the P-value was <0.05 and was ranked as the top two smallest P-values for that loop motif, the pair was selected as a characteristic SHAPE pattern of that specific motif ( Supplementary Figure S1 ). We also attempted to identify SHAPE patterns for multi-branch loops however, such data were too diverse for a statistical analysis ( Supplementary Table S2 ).


Watch the video: Was passiert bei exothermen und endothermen Reaktionen?! (January 2023).