biochemistry

Atom: the elemental state of matter. It is the building block of everything around us.
Composition of an atom –

1. Nucleus: protons and neutrons.
2. Electron cloud: electrons circulating around the nucleus of the atom.
   Ion: a charged atom, meaning that it has lost/gained an electron.
   Electron configuration: the positioning of the electrons within an atom. This determines how the atom will react with other atoms.
   States of an electron –
3. Ground state: when electrons are in the lowest available energy levels.
4. Excited state: when electrons absorb energy and move to higher energy levels. c
   • The farther an electron is from the nucleus, the higher its potential energy.
   • Electrons always try to go back to their ground state after being excited.
   • If the e- changes, the charge will change. If the n0 changes, the mass will change.

Isotopes: The protons in an atom are its ID number; if the number changed, the atom changes too. Isotopes are atoms of the same element, meaning they carry the same number of protons, but have different amounts of neutrons. Isotopes will always try to go back to their ground state. The rate of radioactive isotopes decay is called the half-life.
For instance, the Isotopes of hydrogen are –

1. Protium: has zero neutrons. It’s the lightest.
2. Deuterium: has one neutron.
3. Tritium: has two neutrons. It is the heaviest since it has the most neutrons.
   As atoms get bigger and heavier, the nuclei get bigger and heavier too.

Importance of Isotopes in real life:
• The world around us is made up of stable isotopes. There are, however, such things are unstable isotopes.
• Unstable isotopes are radioactive, aka radio isotopes. They can be used as tracers or markers, and to kill malignant cancer cells.
• Nuclear medicine uses radioactive substances (isotopes) to test the function of organs in the body, to diagnose and treat diseases. They’re introduced into the patient’s body via swallowing, injection, or inhalation. They’re attracted to specific organs, bones, or tissues and emit radiation as they pass through the body. The radiation is captured by a camera.
Neutrons (radioactive decay):
• They provide stability for the atom by holding the protons together (via the nuclear force) and preventing the positive charges from repelling one another.
• The less neutrons an atom has, the more stable it is.
• When an atom has too much or too little neutrons/protons, the nucleus will try to arrange itself via radioactive decay.
• The more unstable a nucleus, the faster it will try to stabilize itself.
• Heavier elements tend to have more neutrons to hold the protons.

Covalent bonds: bonds that share electrons without passing on energy between atoms.
Based on the number of electrons Based on polarity and coordination
Single bond – when one electron bonds with another electron from another atom. Polar bond (hydrophilic) – in a polar bond, you might find some charged electrons around the atom, but the overall charge of the atom is zero. Dissolves in water.
Double bond – when two electrons bond with two other electrons. Non-polar bond (hydrophobic) – a hydrophobic bond. There are no electrons with positive charge. Dissolves in lipids.
Triple bond – when three electrons bond with three other electrons. Coordinate bond – a bond that’s formed as a result of an atom donating a pair of electrons.

Ionic bonds: one where electrons are being transferred (not shared) between atoms. There’s energy.
Ionic Bonds Covalent Bonds
Electrons are transferred – there’s energy. Electrons are shared peacefully – there’s no energy.
An atom that gains an electron becomes an anion. It has many bonds, both based on electrons and on polarity.
An atom that loses an electron becomes a cation. 1 bond requires 2 electrons. 2 bonds require 4. and 3 bonds require 6.
Properties of water:
• Composed of one oxygen atom and two hydrogen atoms. Oxygen is electronegative, and the periodic table shows that the electronegativity of elements increases from left to right. That’s because the number of protons increases, which allows the negative charges of the e- to get attracted to the center, which carries the positive charges of the p+. The element’s electronegativity also increases when it goes from down to up. Water will always be arranged so that the positive of the hydrogen faces the negative of the oxygen. The attraction between them is called a hydrogen bond.
• It’s a polar molecule – electrons are shared unequally.
• High specific heat is the fact that the temperature of water cannot be changed easily because to do so we’d have to break down the water’s molecules. Water’s cohesive property allows it to absorb a lot of thermal energy before it changes chemical states, allowing it to regulate the temperature of its surroundings.
• Solids usually sink, so why does ice float? Unlike most solids, ice is less dense than water. Water’s cohesive property allows for unique hydrogen bond interactions to occur when water is in a solid state, making ice (solid water) less dense than liquid water. If it sank, the earth would freeze. Also, ice keeps the water underneath it warm, allowing sea life to thrive.
• It’s a universal solvent. Water has high solubility and can dissolve anything with a similar composition to its own.
• Like dissolves like. Polar likes polar, and non-polar likes non-polar. Water dissolves sugar because they have similar charges. But water cannot dissolve a triglyceride compound because of their different elements and structure. Overall, water dissolves anything that’s polar.
• Water can have a significant amount of surface tension. That’s because the molecules of water are attracted to each other (cohesion). At the center of the water, one particle can be pulled to all sides because it’s surrounded by other particles. At the surface of the water, the molecules are less restricted than those at the center, allowing them to support a pressure, or a certain amount of weight, at the top. E.g., bugs “walking” on water, a needle “floating” on water.
• Cohesion: the attraction between the positive and negative which holds molecules together.
• Adhesion: when water (or any molecule) clings to another surface.
• Capillary action: the result of both the adhesive and cohesive properties of water. This is the same process by which water defies gravity by travelling up a tree’s stem. E.g., in plants, there are two types of tubes: Xylem, which is responsible for water transportation (via adhesion and cohesion) and Phloem, which transports food and nutrients (glucose) from the leaves to the plant.
What is pH?
It stands for ‘power of hydrogen.’ The pH of a solution is the concentration of hydrogen (H+) in it. When measuring a pH, you’re measuring the acidity/alkalinity of the solution. Higher H+ concentration translate to a small pH value (acidic). Lower H+ concentration/ more OH translate to higher pH value (alkaline). More H+ means more acidity. More Hydroxyl (OH) means more alkalinity.
The following must be memorized:
Stomach acidity 2 (acid)
Human blood 7.4 (neutral)
Acid rain 1.5 – 5.4 (acid)

Isomers: molecules that have the same number of atoms and elements but have different structures. They share the same empirical formula but have different functions.
Their importance: Isomers are important in biology because they have different functions, meaning that their efficiency varies. For example, L-dopamine is effective in treating Parkinson, while D-dopa isn’t. Taste receptors can be sensitive to either cis or trans isomers but not both.

Organic molecules: molecules that contain carbon chemically joined with H+. Organic compounds include nucleic acids, carbs, proteins, fats, etc. The structure of molecules allows you know about its function.
Examples of organic molecules are:
• Carbohydrates: their main function is to fuel our body. They consist of repeated monomers of carbon, H+, and O2. They’re joined together by a glycosidic bond. There are three types:

1. Monosaccharides: glucose (plants), galactose, and fructose (fruits).
2. Disaccharides: glucose + glucose = sucrose. Two monosaccharides joined by glycosidic linkage.
3. Polysaccharides: Starch (storage in plants), cellulose (major part of cell wall), glycogen (storage in animals). Many repeated monosaccharides.
   Dehydration synthesis – when monomers join to form polymers via the removal of OH from one monomer and H+ from the other. The same process occurs for joining amino acids as well.
   Hydrolysis – when water is added to break polymers into monomers. The OH group attaches to one monomer, and the H+ group attaches to the other monomer.

• Lipids: it’s nonpolar and is composed of three fatty acid chains. Some are saturated and some are unsaturated – both determine by the shape. The three are linked to a glycerol (alcohol) backbone molecule and are connected to the hydrogen and carbon via a carboxyl group. They’re hydrophobic.

1. Saturated fats: the unhealthy fats. They are solid at room temperature, increase the levels of LDL (low-density cholesterol), and clog arteries. They only have single bonds.
2. Unsaturated fats: they’re the healthy fats (vegetable oils). They’re liquid at room temperature. Include HDL which “grabs” and helps break down LDL. They have double bonds.

Phospholipids: the main component of the cell membrane. It has a polar head (hydrophilic), a head with a slightly negative charge, and two hydrophobic tails, allowing the cell membrane to regulate what enters and leaves the cell. They’re called amphipathic.

• Cholesterol: a four ringed molecule present in the cell membrane. It keeps the cell membrane stable. When the temperature increases, phospholipids gain energy and move away from each other. The cholesterol keeps them together. When the temperature decreases, the phospholipids keep them apart, preventing the cell membrane from solidifying. It’s important in the making of many hormones, like testosterone, and vitamins, like vitamin D.

• Proteins: polymers made up of repeated amino acid monomers bonded together by peptide bonds. All amino acids have the same structure (as shown in the image); a carbon in the center connected to one hydrogen atom, one amino group, one carboxyl group, and one R-group. The R-group is what determines the type of amino acid. In protein synthesis, the amino acids are connected to each other from the carboxyl group’s side. All amino acids contain carbon, oxygen, nitrogen, hydrogen, and some contain sulfur. Selenocysteine is the only standard amino acid that contains a selenium atom.
Why are they important?
Proteins transport nutrients throughout the body, help speed up chemical reactions, build structures that make up living things, and more. As aforementioned, proteins are made up of repeated sequences of amino acids. The different types of amino acids include:

1. Hydrophobic amino acids: these contain carbon-rich r-variant group, causing them not to interact well with water. Nonpolar and uncharged.
2. Hydrophilic (polar) amino acids: these interact well with water. Polar and uncharged.
3. Charged amino acids: these interact well with oppositely charged amino acids or other molecules. Polar and charged.
   There are four types to the structure of a protein:
4. Primary Structure: this is the linear sequence of amino acids as encoded by DNA. The amino acids bond from the carboxyl group’s side, and a water molecule is released each time a peptide bond forms.
5. Secondary Structure: this structure has two main forms –

• Alpha Helix: a right-handed coil stabilized by hydrogen bonds between the amine and carboxyl of nearby amino acids.
• Beta Sheet: zigzags.

1. Tertiary Structure: the 3D shape of the protein chain. This shape is determined by the characteristics of the amino acids forming the chain. The function of a protein relies on its 3D shape.
2. Quaternary Structure: when two or more polypeptide chains form one functional molecule with several subunits.

How does the structure affect the function? Here are examples.

1. Defense. Antibodies have flexible arms that allow them to recognize and bind to pathogens to target them for destruction.
2. Communication. Insulin is a stable molecule that can maintain its shape while travelling through the blood to regular blood-glucose levels.
3. Enzymes. Alpha-amylase begins the digestion of starches in saliva.
4. Transportation. Calcium pump, aided by magnesium and powered by ATP, moves calcium ions back to the sarcoplasmic reticulum after each muscle contraction.
5. Storage. Ferritin is a spherical protein with channel that allow iron atoms to enter and exit depending on the organism’s needs.
6. Structure. Collagen forms a strong triple helix that’s used throughout the body for structural support.

Side notes:
• Most proteins are smaller than the wavelength of light. E.g., hemoglobin is only 6.5 nanometers. It is highly concentrated in red blood cells – one red blood cell has approximately 280 million hemoglobin proteins.
• The bigger a protein gets, the more it coils. Hydrogen bonds keep the coils of the protein. If the protein uncoiled, it would be too big for our cells.
• Proteins are affected by any increase in temperature, changes in pH and salt concentration. These might cause a protein to denature.
• A decrease in temperature will cause the protein to slow down and, eventually, stop functioning. This protein will be stored, not denatured, and if the original temperature is restored, the protein will function again.

Nucleic acids encode all hereditary information. They’re made up of repetitive monomers called nucleotides.
Composition of nucleotides:
The backbone, which contains a phosphate group and a 5-carbon sugar.
The ‘rungs of the ladder’, which are nitrogenous bases (A, T, C, G). There are two hydrogen bonds between A and T, and three hydrogen bonds between C and G.
DNA is negatively charged. This negative polarity comes from the phosphate group.
DNA vs. RNA: They differ in the type of sugar – DNA has deoxyribose, while RNA has ribose.
The nitrogenous bases are held together by hydrogen bonds to allow the DNA’s strands to be separated easily. The backbone, however, is connected via covalent bonds. The covalent bond between the phosphate and sugar is named Phosphodiester.

As shown in the image, Adenine and Guanine are both two-ringed nitrogenous bases, while Uracil, Thymine, and Cytosine are one-ringed nitrogenous bases.

COLLEGE BOARD VIDEO NOTES

Video 1 (1.1): Structure of water and hydrogen bonding
The subcomponents of biological molecules determine the properties of that molecule. Let’s take water for example.
• Water is composed of two elements – 1 oxygen and 2 hydrogens.

• Covalent vs. Ionic – The bond with which atoms share electrons is a covalent bond. A bond where atoms transfer electrons is an ionic bond.

• Why is water Polar? Oxygen is more electronegative compared to hydrogen, resulting in an unequal sharing of electrons between oxygen and hydrogen. This results in water’s polarity.

• What’s a hydrogen bond? A hydrogen bond is a weak bond interaction between the negative and positive regions of two separate molecules. Water can form hydrogen bonds with other water molecules or with other charged molecules.

• When two of the SAME molecules form a hydrogen bond, it’s called cohesion.

• When two DIFFERENT molecules form a hydrogen bond, it’s called adhesion.

• The hydrogen bonds between water molecules can result in surface tension.

• Cohesion, adhesion, and surface tension allow for water to demonstrate additional chemical behaviors known as emergent properties. Life depends upon these water properties.

Video 2 (1.2): Element of Life
Living systems require a constant input of energy, and the law of conservation of energy states that energy cannot be created nor destroyed – only transformed. All living systems follow the laws of energy.
Living systems require an exchange of matter. Atoms and molecules (monomers) from the environment are necessary to build new molecules (polymers). For example, the following monomers make up their respective polymers:

1. Carbon – used to build carbohydrates, proteins, nucleic acids, and lipids.
2. Nitrogen – used to build proteins and nucleic acids.
3. Phosphorus – used to build nucleic acids and certain lipids.

Carbon skeleton: the shape that forms when carbon atoms bond together.

Video 3 (1.3): introduction to biological macromolecules
Monomers: chemical subunits used to create polymers.
Polymers: macromolecules (large molecules) made up of monomers.
How are monomers connected? A covalent bond forms between two interacting monomers – that connects them together.
Polymers are specific to the monomers that they consist of. Specific monomers make up specific polymers.
Monomer Polymer
Monosaccharide Carbohydrate
Amino acid Protein
Nucleotide Nucleic acid
*Fatty acid Lipids
*Lipids don’t have true monomers.
Dehydration synthesis: the process that creates macromolecules. Water is a byproduct.
Hydrolysis: when a polymer is being digested (the bonds between the polymer are being hydrolyzed). Water is added back in this case to help break down the bonds.

Video 4 (1.4): Properties of biological molecules
Function is related to structure. Living systems are organized in a hierarchy of structure levels. A change in structure generally results in a change in function.
Nucleic acids: biological macromolecules composed of monomers called nucleotides.
All nucleotides have a phosphate group, a 5-carbon sugar, and a nitrogenous base. However, not all nucleic acids are the same.
DNA vs. RNA
While they’re both nucleic acids, there are two main differences between them:

1. The type of sugar they have is different. DNA has deoxyribose while RNA has ribose.
2. Nitrogenous base differences. DNA contains Thymine, while RNA contains Uracil.
   Although they both store biological information, these differences cause them to have specific functional differences.
   Similarly, differences in the structure of proteins cause them to have different functions.
   Proteins are composed of amino acids. All amino acids contain a carbon connected to a carboxyl group and an amino group.
   A polypeptide, the primary structure of a protein, consists of a specific order of amino acids and determines the overall shape the protein can achieve. Therefore, though all amino acids are the same, the way they’re arranged, or their order, can affect their functionality.
   Furthermore, amino acids each have an r-group, which is a group of atoms that can be hydrophobic, hydrophilic, or ionic. This determines whether the entire protein takes on certain chemical behaviors.

Video 5 (1.5): structure and function of biological macromolecules (nucleic acids)
Not only composition affects function, but directionality does as well. Directionality of the subcomponents influences the structure of nucleic acid polymers.
The linear sequence of all nucleic acids is characterized by a 3’ hydroxyl and 5’ phosphate of the sugar in the nucleotide.
DNA’s strands are antiparallel. 5’-3’ direction.
A and T are bonded by 2 hydrogen bonds. C and G are bonded by 3 hydrogen bonds. The number of bonds is significant because the more bonds there are, the more stable that molecule is overall.
The number of Adenine bases is always equal to that of Thymine’s, and the number of Guanine bases is always equal to that of Cytosine’s.
The linear sequence of nucleotides encodes biological information. Any change in that sequence may lead to a change in the encoded information.
During the synthesis of a nucleic acid, nucleotides can only be added to the 3’ end. Covalent bonds are used to connect free nucleotides to the strand.

Video 6 (1.5): structure and function of biological macromolecules (proteins)
Proteins comprise linear chains of amino acids that have directionality with an amino terminus (NH2) and a carboxyl terminus (COOH). Amino acids are connected by the formation of covalent bonds at the carboxyl terminus of the growing peptide chain.
To fit into our cells, proteins must coil. They undergo the following structures:

1. Primary structure – the sequence of amino acids held together by covalent bonds. Proteins are not yet functional at this level – additional folding is needed.
2. Secondary structure – arises through local folding of the amino acid chain into elements such as alpha-helices and beta-sheets. Proteins still aren’t functional at this level.
3. Tertiary structure – the overall 3D shape of the protein. Various types of bonds and interactions stabilize the protein at this level. Many proteins are functional here.
4. Quaternary structure – arises from the interactions between multiple polypeptide units.
   Regardless of the 3D shape and functionality of the protein is, it all starts with the primary structure, the sequence of amino acids, and the chemical properties that each of those possess.

Video 7 (1.5): structure and function of biological macromolecules (carbs)
Carbohydrates comprise linear chains of sugar monomers connected by covalent bonds.
Small directional changes in the components of a molecule can result in functional differences.
Carbohydrates can be linear or branched.

Video 8 (1.6): nucleic acids
DNA and RNA’s similarities:

1. They’re both compromised of nucleotide subunits.
2. The nucleotides in both have similar structures (phosphate group, sugar, and nitrogenous base).
3. In both, the nucleotide monomer is connected by covalent bonds between the sugar-phosphate backbone.
4. The bond between the phosphate and the sugar, in both, is a covalent bond called the phosphodiester bond.
   Each linear strand has directionality. The nitrogenous bases are perpendicular to the sugar-phosphate backbone.
   DNA vs. RNA
5. The sugar. DNA has deoxyribose and RNA has ribose.
6. Nitrogenous bases. DNA has Thymine, RNA has Uracil.
7. DNA is double-stranded, RNA isn’t.
8. In DNA, the strands are antiparallel.