top of page

Biology
BIOCHEMISTRY

Atomic Structure

You will learn a lot more about atomic structure in Chemistry, but for right now, you need to understand the basic composition of atoms, the building blocks of matter. At the core of an atom lies its nucleus, which is composed of positively charged protons and neutral neutrons. The number of protons in the nucleus defines the element's identity and is referred to as the atomic number. Electrons are equal in magnitude to the negative charge of electrons in neutral atoms.  Negatively charged electrons orbit the nucleus in distinct energy levels or shells called their ground states.  Understanding basic atomic structure, particularly the behavior of electrons, is necessary to understand interactions between molecules, and also drives biological processes such as photosynthesis.

I'M MORE OF A MACRO TYPE OF PERSON.  I'D LIKE SOME HELP UNDERSTANDING THINGS ON A MICRO SCALE.

 

Ionic vs Covalent Bonding

Ionic and covalent bonding are two types of chemical bonds characterized by the mechanisms by which they occur.  Ionic bonding occurs after atoms have transferred electrons to one another, resulting in the formation of ions with opposite charges.  These oppositely charged ions then attract each other due to electrostatic forces, forming a stable bond.

In contrast, covalent bonding involves atoms donating electrons in such a way that each atom contributes to the formation of a shared electron pair. This sharing of electrons creates a strong bond between the atoms, holding them together in a molecule.

Intermolecular Forces (IMF’s)

It is important to understand the difference between IMF’s and chemical bonds.  Interpersonal relationships are relationships between two separate people.  Interstate highways are highways that run between separate states.  Intermolecular forces (IMFs) are interactions that occur between separate molecules.  All of this is to say that “inter” signifies an interaction “between” separate things.  They are NOT bonds holding atoms together in a molecule.  When IMF’s are disrupted or formed, absolutely nothing happens to the molecules themselves.  They are still intact, only the spacing between them changes.  For example, if you hug your mom and then let go, you are still you and your mom is still your mom.  Nothing about either of you has changed, but the interaction between you has.  In this way, IMF’s determine physical properties of molecules such as boiling point, melting point, and solubility, but do not change anything about the structure of the molecules involved.

Dipole-Dipole

Dipole-dipole interactions are a type of IMF that arises between polar molecules which are the result of differences in electronegativity.  The positive end of one polar molecule is attracted to the negative end of another polar molecule, creating a net attractive force between them.

Van der Waals

Van der Waals forces are temporary fluctuations in electron distribution within molecules, leading to short-lived dipoles which induce similar dipoles in neighboring molecules, thus causing an attraction between them.

Hydrogen Bonding

H-bonding is a specific and strong type of dipole-dipole interaction that occurs between molecules containing hydrogen covalently bonded to nitrogen, oxygen, or fluorine. In H-bonding, these hydrogens form interactions with nitrogen, oxygen, or fluorine on neighboring molecules.  Hydrogen bonding is responsible for many important phenomena in nature, including the unique properties of water and the stability of protein and DNA structures.

 

Properties of Water

Water exhibits several unique properties.  Firstly, it is a polar molecule, meaning it has a partial positive charge on one end (the hydrogen atoms) and a partial negative charge on the other end (the oxygen atom). This polarity allows water molecules to form hydrogen bonds with each other, resulting in cohesive forces that give water its high surface tension and ability to form droplets.  Additionally, water has a high specific heat capacity, meaning it can absorb and store a large amount of heat energy without a significant increase in temperature. This property is essential for maintaining stable environments, such as homeostasis in mammals. Moreover, water has a high heat of vaporization, meaning it requires a substantial amount of energy to change from liquid to vapor phase. This property is crucial for cooling mechanisms in organisms through processes like sweating and transpiration in plants. Another unique property of water is the density of ice. Unlike most substances, which become more dense when they solidify, water expands as it freezes, resulting in a lower density of ice compared to liquid water. This causes it to float, which insulates liquid water underneath and allows aquatic organisms to survive in cold environments.

 

The pH Scale

The pH scale is a logarithmic scale used to measure the acidity or alkalinity of a solution. It ranges from 0 to 14, with 7 representing neutrality, where the concentration of hydrogen ions (H⁺) and hydroxide ions (OH⁻) are equal. Solutions with a pH below 7 are considered acidic, indicating a higher concentration of hydrogen ions, while solutions with a pH above 7 are alkaline or basic, indicating a higher concentration of hydroxide ions.

 

Biological Macromolecules

Biological macromolecules are large organic molecules essential for life processes, found in all living organisms. There are four main classes: carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates

Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1. They exist as simple sugars, such as glucose and fructose, as well as complex carbohydrates like starches and cellulose. At the simplest level, carbohydrates can be classified based on the number of sugar units they contain. Monosaccharides are single sugar units, disaccharides consist of two sugar units, and polysaccharides are composed of multiple sugar units. Monosaccharides, like glucose and fructose, are the building blocks of carbohydrates and serve as the primary source of energy for living organisms. They have a linear or ring structure, and can form chains or branches depending on their configuration. Disaccharides, such as sucrose and lactose, form when two monosaccharides undergo a condensation reaction, resulting in the loss of a water molecule and the formation of a glycosidic bond. Polysaccharides, including starch, glycogen, and cellulose, are long chains of monosaccharide units linked together by glycosidic bonds.

Starch and glycogen are energy storage molecules.  Starch is the primary energy storage molecule in plants. It consists of long chains of glucose molecules linked together by alpha glycosidic bonds. Starch exists in two forms: amylose, which is a linear polymer, and amylopectin, which is highly branched.  Glycogen is a polysaccharide and the main storage form of glucose in animals, particularly in the liver and muscles. It is structurally similar to starch but more extensively branched.

Cellulose, on the other hand, is a structural polysaccharide found in the cell walls of plants. It is composed of long, linear chains of glucose molecules linked together by beta glycosidic bonds which provide structural support and rigidity to plant cells, contributing to the strength and stability of plant tissues.

Proteins

Proteins are polymers made up of amino acid monomers linked together by peptide bonds. They have a wide range of functions, including structural support, enzymatic activity, immune response, and cell signaling. Proteins are crucial for the structure, function, and regulation of cells and tissues.

Amino Acids

An amino acid is a fundamental building block of proteins that consists of a central carbon atom (the alpha carbon) bonded to four different chemical groups: a hydrogen atom, an amino group (NH2), a carboxyl group (COOH), and a side chain (R group). There are 20 standard amino acids which differ in their R group configurations. These amino acids can be classified based on the properties of their side chains into categories such as nonpolar (hydrophobic), polar (hydrophilic), acidic, and basic. Amino acids are linked together by peptide bonds through condensation reactions between the amino group on one monomer and the carboxyl end on another.  The sequence of amino acids in a protein ultimately determines its three-dimensional structure and function.

Protein Structure

Proteins exhibit a hierarchical organization of structure, consisting of four levels: primary, secondary, tertiary, and quaternary.

Primary

The primary structure of a protein refers to the linear sequence of amino acids that make up its polypeptide chain. This sequence is determined by the genetic code encoded in the organism's DNA, and built up via translation in the rough endoplasmic reticulum.

Secondary

The secondary structure of a protein refers to the local folding patterns that arise within the polypeptide chain with are the result of H-bonding interactions between neighboring subunits of the backbone. Two common types of secondary structure are alpha helices and beta sheets. In an alpha helix, the polypeptide chain coils into a spiral shape. In beta pleated sheets, the polypeptide chain forms a sheet-like structure.

Tertiary

The tertiary structure of a protein refers to the three-dimensional arrangement of the entire polypeptide chain. This final folding is driven by interactions between R group side chains, such as hydrogen bonds, hydrophobic interactions, disulfide bonds, and electrostatic interactions. The tertiary structure of a protein determines its overall shape and specific functional properties, such as enzyme activity, ligand binding, or structural support.

Quaternary

The quaternary structure of a protein refers to the arrangement of multiple polypeptide chains (subunits) that come together to form a functional protein complex. Some proteins consist of a single polypeptide chain and do not exhibit quaternary structure, while others are composed of multiple subunits that assemble to form a larger, functional protein complex. The interactions between subunits in a quaternary structure are similar to those involved in tertiary structure, including hydrogen bonds, hydrophobic interactions, and disulfide bonds.

Enzymes

Enzymes are biological catalysts that accelerate the rate of chemical reactions by lowering the activation energy required for the reaction to proceed.  They achieve this by binding to specific molecules, known as substrates, and facilitating their transformation into products. The specificity of enzymes for their substrates is crucial for their function, as it ensures that only specific reactions are catalyzed, preventing unwanted side-reactions, and maintaining metabolic pathways.

Induced Fit Mechanism

The induced fit mechanism describes the dynamic interaction between an enzyme and its substrate during the formation of an enzyme-substrate complex.  Initially, the enzyme and substrate are in an open conformation, where the active site of the enzyme is not fully complementary to the substrate. When the substrate binds to the enzyme, both the enzyme and the substrate undergo conformational changes leading to a tighter fit between the two.  As a result, the binding interactions between the enzyme and substrate become stronger, enhancing the catalytic activity of the enzyme. 

Denaturing

Remember that higher levels of protein structure are determined primarily by IMF’s and not bonds.  When these interactions are disrupted, enzymes can be denatured, or “unravel” losing their native structure and function.  High temperatures cause atoms and molecules to vibrate which can disrupt backbone and R-group interactions, causing the enzyme to unfold and lose its activity. Conversely, extremely low temperatures can also affect enzyme activity by slowing down molecular movements necessary for catalysis.

Additionally, enzymes have an optimal pH range at which they function most efficiently. Deviations from this can disrupt the ionic interactions and hydrogen bonding within the enzyme, leading to changes in its structure and loss of activity.

Enzyme Control

Enzyme inhibition refers to the process regulating enzyme activity. There are several types of enzyme inhibition, including irreversible, competitive, allosteric, and feedback inhibition.

Irreversible Inhibition

Irreversible inhibition occurs when a molecule irreversibly binds to the active site or another crucial part of the enzyme, rendering it permanently inactive. This type of inhibition is often caused by molecules that covalently modify the enzyme, such as certain drugs or toxins. Once irreversible inhibition occurs, the enzyme cannot function again.

Competitive Inhibition

Competitive inhibition occurs when a molecule, known as the inhibitor, competes with the substrate for binding to the active site of the enzyme. The inhibitor typically resembles the substrate and binds reversibly to the active site, preventing the substrate from binding and undergoing catalysis. Competitive inhibitors can be overcome by increasing the concentration of the substrate, which effectively outcompetes the inhibitor for binding to the active site.

Allosteric Inhibition

Allosteric inhibition occurs when a molecule binds to a site on the enzyme, known as the allosteric site, which is separate from the active site. This binding induces a conformational change in the enzyme that reduces its catalytic activity.  Allosteric inhibitors can be either reversible or irreversible and can either enhance or inhibit enzyme activity, depending on the specific molecule involved.

Feedback Inhibition

Feedback inhibition is a type of allosteric regulation in which the product of a metabolic pathway binds to an enzyme early in the pathway, inhibiting its activity. This process helps regulate metabolic pathways by preventing the overproduction of certain substances. As the concentration of the product decreases, the inhibition is relieved, allowing the pathway to resume activity.

 

Lipids

Lipids include fats, oils, phospholipids, and steroids. They serve as energy storage molecules, components of cell membranes, and signaling molecules. The basic structure of lipids consists of fatty acids which are long non-polar hydrocarbon chains or rings bonded to a polar head. Triglycerides, the most common type of lipid, are composed of three fatty acid molecules bonded to a glycerol molecule through ester linkages.  Phospholipids have a structure similar to triglycerides but with two fatty acid chains and a phosphate group attached to a glycerol molecule. The phosphate group is hydrophilic (water-attracting), while the fatty acid chains are hydrophobic (water-repelling), making phospholipids amphipathic. In aqueous environments, phospholipids arrange themselves into bilayers, with the hydrophobic tails facing inward and the hydrophilic heads facing outward, forming the basis of cell membranes. This phospholipid bilayer provides a selectively permeable barrier that regulates the passage of substances in and out of cells, maintaining cellular integrity and facilitating cellular communication. Overall, lipids, including triglycerides and phospholipids, play essential roles in energy storage, structural integrity, and cellular function in living organisms.

Cholesterol in the Plasma Membrane

Cholesterol molecules have a polar head like triglycerides and phospholipids do. However, their nonpolar hydrocarbons are in ring form.  This means they interact with both the hydrophilic heads and hydrophobic tails of phospholipid bilayers which make up cell membranes.  One of their key functions is to regulate membrane fluidity by preventing the phospholipid molecules from packing too closely together, thereby preventing the membrane from becoming too stiff.

 

Nucleic acids

Nucleic acids, such as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are polymers of nucleotide monomers. DNA carries genetic information and serves as a blueprint for the synthesis of proteins, while RNA plays roles in protein synthesis and gene regulation.

Nucleotides

A nucleotide is the basic building block of nucleic acids.  It is composed of three main components: a phosphate group, a pentose sugar, and a nitrogenous base. The phosphate group consists of a phosphorus atom bonded to four oxygen atoms and carries a negative charge, contributing to the overall negative charge of nucleic acids. The pentose sugar is a five-carbon sugar molecule that serves as the part of the backbone of a nucleotide chain.. In DNA, there are four nitrogenous bases: adenine (A), thymine (T), cytosine (C), and guanine (G).  In RNA, thymine is replaced by uracil (U).  Nucleotides bind together through phosphodiester bonds to form the polynucleotide chains of nucleic acids.

DNA vs RNA

DNA and RNA are different from each other in several distinct ways. The primary structural difference between DNA and RNA lies in their sugar molecules. DNA contains the sugar deoxyribose, while RNA contains ribose. Deoxyribose lacks one oxygen atom compared to ribose, hence the prefix "deoxy" in DNA. Additionally, DNA is typically double-stranded, forming a stable double helix structure, whereas RNA is usually single-stranded.  As mentioned above, Both DNA and RNA contain four nitrogenous bases where RNA contains uracil (U) instead of thymine (T) present in DNA. This difference is crucial for base pairing during replication and transcription.

Purines and Pyrimidines

Purines and pyrimidines are two types of nitrogenous bases that are classified by the number of rings they contain.  Purines are double-ring nitrogenous bases that consist of a six-membered ring fused to a five-membered ring. The two most common purines found in nucleic acids are adenine (A) and guanine (G). Adenine.  Pyrimidines, on the other hand, are single-ring nitrogenous bases composed of a six-membered ring. The three pyrimidine bases found in nucleic acids are cytosine (C), thymine (T; in DNA only), and uracil (U; in RNA only).

Complementary Base Pairing

Complementary base pairing in DNA refers to the specific purine-pyrimidine H-bonding interactions between the two DNA strands forming a stable double helix structure. Adenine (A) always pairs with thymine (T), forming two hydrogen bonds, while cytosine (C) always pairs with guanine (G), forming three hydrogen bonds. Similarly, during transcription, complementary base pairing between DNA and RNA allows for the synthesis of an RNA molecule that is complementary to one of the DNA strands. This RNA molecule serves as a template for the synthesis of proteins during translation.

bottom of page