Unit 2 – Intro to Biochemistry Chapters 1 & 2 in text. In this chapter, we will overview the foundational chemistry of biology and how the chemical structure of biomolecules determines their properties.

Levels of Biology Last time we mentioned that the smallest unit of life is the cell. However, there are many levels below this that are important to biology even if they are not “alive” on their own. The most basic unit of matter we will cover is the atom. Atoms are the smallest unit of a element that still retains the properties of the element.

The Atom Atoms are very, very small. However, they are made up of three still-smaller components – protons, electrons and neutrons. Atoms can be envisioned as a central core of the positively-charged protons and neutral neutrons with the smaller and lighter negatively-charged electrons flying around this core in differing orbits. This core is called the nucleus.

The Atom

All atoms have a total net charge of 0. Thus, protons and electrons are cancelled out by having equal numbers of them. For atoms: electrons = protons

The Atom The atomic number of an element is defined as the number of protons present in an atom. The mass number of an element if defined as the number of protons and neutrons in a atom. Electrons are not counted as they weigh much less than either of the other particles.

The Atom Complete the table: # of protons# of electrons # of neutrons atomic number mass number

Ions The electrons of an atom determine how it will interact with other atoms. This determines if it will form bonds, and how strong they will be. Electrons come in sets called shells. Atoms are most stable when all their shells are full.

Ions Atoms will give up or take up electrons so that their shells are all filled. An atom that gains/loses electrons will now have a positive or negative charge as the protons and electrons are unequal. This is called an ion.

The Molecule When atoms link together by sharing electrons they form molecules. Which molecules combine and how determine the shape, size, weight, and other properties of the molecule. Carbon is exceedingly good at forming complex multi-atom structures and makes up most biological molecules. Carbon-based compounds are called Organic Compounds. All other compounds are called Inorganic.

Organic vs. Biological What’s the difference between organic chemistry and biochemistry? Organic chemistry deals with carbon-containing compounds, including many compounds that are not naturally occurring such as plastics. Organic compounds therefore do not have to have any relation to living things.

Organic vs. Biological Biochemistry covers the compounds that make up living things. Life on Earth is carbon-based, so essentially most biochemicals are also organic chemicals. Biochemistry also covers some inorganic compounds (compounds without carbon) that are used in life processes. For a compound to be both an organic chemical and biochemical, it must both contain carbon and be used by a living creature.

Biological Molecules Four very important biomolecules are: 1 – Carbohydrates – combinations of carbon, oxygen and hydrogen atoms. Can be linked together to form long chains. 2 – Lipids – mostly carbon and hydrogen atoms. Do not dissolve in water well (hydrophobic).

Biological Molecules 3 – Protein – carbon and nitrogen based with other atoms. Proteins are long chains of linked amino acids. Proteins are very diverse and can perform many roles as enzymes. 4 – Nucleic Acids – very special molecules that are used by cells to store information. The deoxyribonucleic acid (DNA) of cells hold all the information a cell needs to function.

Types of Reactions Many reactions will either convert many small things into large things or vice versa. Anabolic reactions build larger molecules from smaller reactants. (growth, repair, reproduction, etc) Catabolic reactions break down larger molecules into smaller ones. (digestion, shedding, etc)

Water Aside from organic compounds, water is the most important ingredient for life as we know it. Water can be formed in many ways from other elements and compounds – the simplest is forming water from oxygen and hydrogen. Chemical Reaction Formula:

Water In this reaction, hydrogen and oxygen are reactants and water is the product. Once made, water is not very reactive. For the most part it acts as a solvent (things dissolve into it).

Water Water’s combination of atoms ends up creating a molecule with a light positive and negative charge – water is polar. Polar molecules are great at interacting with charged molecules. This is how salts, electrolytes, acids, bases and some proteins and fats are able to dissolve in water.

Water At the same time, water is not strongly polar. This lets it be able to interact with neutral chemicals. This is how sugars, some proteins, certain fats and cholesterols, and other non-charged are able to also be dissolved in water. Most chemicals are either completely polar or non-polar. By having a light polar charge, water is able to dissolve a wider variety of chemicals than most other chemicals.

Water & Life Liquid water is needed for all life as we know it. Here are the four main traits of water that make it needed for life: 1 – Cohesion – water quite tightly sticks to itself. This allows easier forming of ponds and oceans, and is important for the continuous flow of liquids in systems like plant roots or animal blood vessels. 2 – High Heat Capacity – water can hold a lot of heat per gram. This allows water to stay at relatively stable temperatures easier, making it more hospitable for life.

Water & Life 3 – Density - Ice is less dense than Water. Most chemicals become tighter-packed when they form into solids. Water’s shape and polar charge prevent this. Ice being less dense if important for aquatic life as ice will form on the top first rather than on the seafloor first. 4 – Universal Solvent – water can dissolve a large variety of substances due to being partially polar.

Acid/Base/Buffer A combination of water and certain dissolved substances creates an acid or base. Acids donate extra hydrogen ions (H+) to the solution. Acids have a sour taste, pH under 7, neutralize bases, give off hydrogen gas when reacted with metals, conduct electricity, and turn litmus paper red. Bases accept H+, are often slippery, have a pH over 7 neutralize acids, conduct electricity and turn litmus paper blue. A Neutral solution is at pH=7.0 exactly. Perfectly pure water is neutral.

Acid/Base/Buffer Buffers are special compounds that help a system resist pH change. In the event that a small amount of acid or base is added, the system will not change pH radically. Buffers can be overpowered by large amounts of acid/base. Buffers are very important because most biochemicals are very fragile and can be damaged or altered by slight changes in the chemical environment.

Polymers Many biological molecules are made from smaller units called monomers. Monomers combine to make a polymer. Linking monomers will result in a water molecule being released so it is named dehydration synthesis.

Polymers In the same way, to split a polymer into smaller units requires the addition of water and is therefore called hydrolysis.

Polymers Most polymers are recycled and rebuilt in new ways. When animals eat another organism, they break down the polymers in the food by hydrolysis into the base monomers. These monomers are then rebuilt into parts of the animal. Protein in food is used to build protein in the animal that ate it.

Carbohydrates Carbs are a family consisting of sugars. Carbs are used for energy as well as structure and messaging. Monosaccharides are a single lone sugar monomer (glucose, fructose, etc). Disaccharides are sugar polymers made of two monomers. (maltose, etc).

Carbohydrates Polysaccharides consist of many sugar monomers linked together. Up to as many as Most are either made of a single monomer, or have a repeating pattern of monomers. Three important polysaccharides: Cellulose – important structural part of plants. It’s structure makes it so that the human digestive system cannot break it down easily so it passes through the body as fiber.

Carbohydrates Three important polysaccharides: Glycogen – another all-glucose polymer found in the liver of animals to store energy. This is how the body can fuel itself and raise blood glucose levels easily during fasting. Starch – long branched chains of glucose. Stores energy in plants. Unlike cellulose, this can be digested and the glucose used.

Lipids Lipids, unlike most biomolecules, are hydrophobic and dislike water (think of how oil and water do not mix). Lipids is a large category, including vital molecules such as fats and steroids. Fats typically come in the form of triglycerides. These are made of three fatty tails attached to a head. The tails can be taken off to be broken down for energy.

Lipids The fatty acid tails of lipids come in two forms: Saturated fat – tails are simple carbon and hydrogen. Very flexible and regular, so they stack together tightly. Found in animal fats. Unsaturated fats – fats where the carbons are double or triple bonded to each other, lowering the number of hydrogen atoms. These bonds give the tails kinks and turns, making them pack together much looser. Found in plant fats.

Lipids – Steroids Steroids are another type of lipid but have a very different structure than fats. Steroids are made up of rigid rings of atoms and thus become stiff and flat, rather than the free-moving tails of fats. All steroids are not bad, nor are they all synthetic (human-made). Normal substances like cholesterol, testosterone, estrogen and other hormones are steroids. Anabolic steroids are synthetic imitations of testosterone to gain extra muscle-building potential. These are dangerous and prohibited in professional sports.

Lipids – Steroids Fat (Triglyceride)Steroid (Cholesterol)

Protein Amino acids are the monomers of protein. Amino acids link together using a peptide bond and therefore chains of amino acids are known as polypeptides. Many proteins are hundreds and thousands of amino acids long, these large structures preform chemical reactions (enzymes), can carry other substances (hemoglobin) as well as can offer structure (keratin). Short polypeptides are used for many roles such as signalling (insulin).

Protein Amino acids come in a variety of shapes and sizes. Each one effects how the final chain. Bulky amino acids will cause the chain to be inflexible, smaller amino acids allow more motion. Some amino acids are charged positively or negatively, or are neutral. All of these will determine how that part of the chain will interact with the rest of the chain, and with the environment.

Protein An important factor in determining a protein’s function is its final three-dimensional shape. Proteins begin to fold up as they are made because certain amino acids will induce bends or attach to one another. The basic sequence of the chain is called the primary structure. This is just the order of amino acids in a line.

Protein Eventually small sections of the protein form small sub-structures such as sheets or helices. This is secondary structure. Finally, all the sub-structures give a protein its characteristic shape. This is tertiary structure. Above that, many proteins will group together to form a working complex. The interactions between each protein may alter the proteins’ shape. This is known as quaternary structure.

Protein

Nucleic Acids Nucleic acids are complex polymers that all life forms use to store information. The order of the monomers makes a code that is used to tell a cell how to make certain proteins. Two of the most important nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Nucleic Acids The monomer of a nucleic acid is called a nucleotide. Nucleotides are made of three parts: A sugar (ribose in RNA, deoxyribose in DNA) A Phosphate group A nitrogenous (nitrogen- containing) base. These are the actual coding pieces.

Nucleic Acids The nitrogenous base actually determines the code of the DNA. There are four bases possible in DNA and like letters, they form “words” that code for specific amino acids in a protein chain. The bases are: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). Each one is different structurally so that they can be “read”.

Nucleic Acids DNA is normally found with two stands locked together. The bases from one strand pair up with bases from the other to link the strands. The sugar-phosphate backbone bends to create a double helix.

Nucleic Acids Due to their shape, only C-G and A-T bonds are possible. This allows the cell to know what should be opposite of any base if part of the other strand goes missing or is damaged.

Nucleic Acids The fact that G-C and A-T bonds are the only combination possible allows for easy replication of the DNA. During replication, the two original DNA strands are separated, and each has a new second strand built upon them. The cell knows what bases to use on the new strands because there is only one base that could be across from each base on the original strand.

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