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​UNIT 1 - BIOCHEMISTRY

​Overview of Chemistry

 

Ionic bonds = an atom donates electrons to another atom, creating a bond

Covalent bonds = two atoms share electrons

 

  • Bond polarity, molecular polarity, and electronegativity

EX:  Water is very polar.  Oxygen is a very electronegative element, hogging electrons to itself

 

  • Hydrogen bonds

EX:  Water molecules form many hydrogen bonds with each other.  This is a cool simulation that shows how hydrogen bonds form.  You can actually move around the molecules

Hydrogen bonds will come up again and again throughout biology; keep an eye out for it!

Properties of water - ap biology

Properties of Water

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  • Emergent properties of water (which are all due to its ability to hydrogen bond):

    1. Cohesion, adhesion, surface tension

    2. Keeps temperatures moderate through evaporative cooling and a high specific heat

    3. Ice floats on top of liquid water

    4. Acts as a universal solvent

 

  • Acids = increase the concentration of H+ ions in solution
    EX:      Ocean acidification.  Carbon dioxide dissolves into the ocean, creating carbonic acid
     

  • Bases = decrease the concentration of H+ ions in solution
     

  • Buffers = a substance that limits any significant changes in H+ concentration.  We have natural buffers inside our bodies. 
    EX: carbonic acid in our blood, which regulates our blood pH

       

Diamond

Versatility of Carbon

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  • Organic compounds = compounds that contain carbon

  • Organic chemistry is the study of how organic compounds interact

  • Shapes and types of organic molecules:
     

    • Carbons are usually the central atom in organic molecules.  They can form single, double, or triple bonds with other atoms
       

    • Hydrocarbons = organic molecules that contain only carbon and hydrogen
       

    • Organic molecules can be branched, straight chains (such as hydrocarbons), or rings
       

    • Functional groups: be familiar with their general structure and special properties.  The key groups to know are hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.  You will see these groups come up throughout the course
      EX:  The crucial molecule ATP (adenosine triphosphate) has 3 phosphate groups.  ATP is what our cells use for energy

      *Use this cheatsheet to study the functional group chemical structures       and properties

Diamonds are made of pure carbon and they are known as the hardest substance on Earth becuse of the special crystal structure (called diamond cubic) holding the carbon atoms together

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Image by Pille-Riin Priske

Rice is full of starch.  If you keep cooked rice in your mouth for a couple of minutes, it will actually start tasting very sweet because enzymes in your mouth are breaking down the starch into glucose molecules

Macromolecules
 

  • Macromolecules synthesis and breakdown

  • Know the general structure and functions of each of the four macromolecules listed below
     

  • Types of macromolecules:
    *Here is a study guide with the key points to know for each of the macromolecules
     

  • Carbohydrates

    • ​Glycosidic linkages = covalent bonds linking monosaccharides together in a polysaccharide

    • Main polysaccharides to know (including the function of each): starch, glycogen, cellulose, chitin, peptidoglycan.  Also know that glycogen and starch are branched, while cellulose is linear in structure

    • Disaccharides to know:  sucrose, maltose, lactose

    • Monosaccharides to know:  glucose, fructose, galactose
       

  • Proteins (more details below)
     

  • Nucleic acids (DNA, RNA) 

    • DNA has the sugar deoxyribose, the nitrogenous bases A, T, C, and G, and a sugar-phosphate backbone.  It is typically a double-stranded helix

    • RNA has the sugar ribose​ and the nitrogenous bases A, U, C, and G.  It also has a sugar-phosphate backbone and is usually single-stranded

    • DNA and RNA store hereditary information that can be passed on to offspring
       

  • Lipids​

    • ​Triacylglycerol = important source of energy in animals.  Made of 1 glycerol and 3 fatty acid chains

    • Phospholipids = the building block of the cell membrane lipid bilayer.  The phosphate head is hydrophilic, while the two fatty acid tails are hydrophobic

    • Steroids = the structure consists of 4 fused carbon rings.  Examples include cholesterol and steroid hormones, such as estrogen

    • Cholesterol = a type of steroid that is found in the cell membrane; important for maintaining membrane fluidity
       

  • More about proteins:

    • Amino acids = the building blocks of proteins.  There are 20 unique amino acids, and each has a unique side chain (also known as an R group) which gives a unique set of chemical properties
       

    • Proteins are extremely diverse and have a wide range of structures and functions.  The key functions include:  enzymes (biological catalysts that speed up reactions), structural support, transport (like ion channels), hormones, receptors, motor proteins, and defensive proteins such as antibodies from the immune system
       

    • Four Stages of protein structure:
       

  1. Primary structure = the sequence of amino acids in the peptide chain.  The primary structure indirectly determines the ultimate 3D structure of a protein
     

  2. Secondary structure = hydrogen bonds form between the peptide chain backbone, creating either alpha pleated sheets or a beta-helix
     

  3. Tertiary structure = chemical interactions between side chains create more of the 3D structure.  Can include disulfide bridges, hydrogen bonding, and Van der Waals interactions.  All of these occur between the side chains of amino acids.  Tertiary structure directly determines the 3D structure of a protein
     

  4. Quarternary structure = present in some, but not all proteins.  This is when multiple peptide chains join together to form a whole protein.  Hemoglobin is an example of a protein with a quaternary structure

    *The infographic below is a summary of the four levels of protein structure

four levels of protein structure - ap biology.PNG

want to test yourself?

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