Biochemistry

By Peyton Kinon, Timothy

Cushman, and David Weild
Carbon
Carbohydrates -
Made up of hydrogen, oxygen, and carbon

Green plants, through photosynthesis, combine carbon dioxide, water

and sunlight to make carbohydrates (normally glucose in plants)

Carbohydrates store energy for your body to use

Protein Structure
Proteins -
Made up amino acids that contain hydrogen, oxygen, nitrogen, carbon

Proteins give cells structure and bind with molecules in the body
Carbon (cont.)
Lipids -
Made up of hydrogen, oxygen, and carbon

Fat soluble
Lipid Structure

Nucleic Acids-

Nucleic Acids are polynucleotides which are chainlike

molecules made up of nucleotides

Nucleotides are made of a nitrogen-containing base attached to

a pentose or five-carbon sugar and a phosphate group
Nitrogen
Nitrogen is an important compound in proteins and
nucleic acids

● In Proteins, the nitrogens are in the amino acids

○ They are in the Amino Group
○ The amino acids bond to make the primary structure of
proteins, the bond is called a peptide bond
○ Very important in determining shape and function of the protein
Nitrogen (cont.)
Nitrogen is also found in nucleic acids, such as RNA and DNA

● Nitrogen is found in Nitrogenous bases, which distinguish the different

nucleotides
○ The nucleotide sequence determines the trait that will be expressed
● There are two classes of nitrogenous bases purines and pyrimidines
Nitrogen Cycle
Phosphorus
Phosphorus is a very important component of nucleic
acids

● It is found in the Phosphate Backbone of nucleic

acids
○ The backbone is made of Phosphate (PO43-) and a sugar
(Deoxyribose in DNA, Ribose in RNA)
○ The phosphate backbone holds DNA and RNA together
● Phosphorus is also a very important component in
ATP
○ The phosphate-phosphate bonds are broken when ATP
turns into ADP which releases large amounts of chemical
energy which power many cellular functions
Phosphorus (cont.)
Phosphorus is also in phospholipids which make up
our cell membranes

● Phospholipids are made up of a phosphate ion

and two lipids
○ The phosphate ion is polar, so it bonds with the water
○ The lipids are nonpolar, so they repel the water
● The hydrophilic and hydrophobic qualities of
phospholipids determine the semi-permeability
of cell membranes
Phosphorus Cycle
 Cohesion
<=

Properties of Water
● Cohesion
○ Hydrogen bonds in water hold other water molecules together creating
○ This creates surface tension
● Adhesion
○ Water molecules like to stick to other substances that they can form hydrogen bonds
with
● High Specific Heat Capacity
○ Because there are so many hydrogen bonds in water, water has a ability to resist
temperature changes
○ It takes a lot of energy to break the hydrogen bonds and the the bonds need to be
broken for the temperature to rise.
○ This allows organisms to keep a constant body temperature
Properties of Water (cont.)

● Universal Solvent
○ Water is polar and its positive end is attracted to the negative sides of other polar
molecules, and its negative side is attracted the positive sides of other polar molecules
giving it the ability to be a good solvent
● Heat of Vaporization/ Heat of Fusion
○ To turn a solid into liquid or a liquid into a gas, many hydrogen bonds need to be broken
○ The heat of vaporization of water is 40.65 kJ/mol and heat of fusion for water is 6.02 kJ/mol
● Thermal Conductivity
○ Water is very thermally conductive because it takes a lot of energy to change its state
Matter in Biological Systems
Matter is necessary in biological systems

● All elements, compounds, and ions that make up biological systems are
made of matter
○ Without matter life would not be possible because the life giving chemical reactions
would not occur
○ There would be nothing, so the reactions couldn’t occur
Uses of Elements Biological Systems (C,H, and O)
● Carbon - is the building block of of carbohydrates, lipids, proteins, and
nucleic acids. It is used in forming cells
● Hydrogen - is a part of water and helps creates the structure of organic
molecules
● Oxygen - All organisms require oxygen. One component of water and of
the atmosphere.
Uses of Elements Biological Systems (N,P, and S)
● Nitrogen - is used in the building of proteins and nucleic acids
● Phosphorus - used in nucleic acids and some lipids
● Sulfur - used to help the body grow and repair. Also creates bonds
throughout proteins
Exchange of Matter
Water in Biological Systems
● Transport molecules, cells, and other substance throughout the body
● Cool and regulate the body’s temperature (high specific heat)
● Water in saliva acts as a lubricant for digestion
● Ensure joints and other body parts can move without friction
Structure and Function of Water Molecule
The polar structure and two hydrogens allow for
hydrogen bonds to form with other molecules

● The weak hydrogen bonds elongate when water

freezes, so the density lowers
● Water molecules creating hydrogen bonds between
other water molecules causes cohesion
○ The water molecules stick together
● Water molecules creating hydrogen bonds between
molecules that aren’t water causes adhesion
○ The water molecules stick to other materials
DNA
● Deoxyribonucleic Acid (DNA) is made up of two
strands of nucleotides arranged in a double
helix
● Each nucleotide is made up of
○ A five-carbon sugar - deoxyribose
○ A phosphate group
○ A nitrogen base pair
● Each base pair is made up of two of four
chemical bases
○ Adenine (A) and Thymine (T)
○ Guanine (G) and Cytosine (C)
● The ordering of the bases gives the information
for building and maintaining an organism
RNA
● Ribonucleic Acids (RNA) are made similarly
to DNA but made with ribose sugar
● One difference is that RNA uses the base
uracil (U) instead of thymine (T)
● Another difference is RNA has a hydroxyl
group attached to the sugar
● RNA is typically found in a single-stranded
form
DNA vs. RNA
The slight different in structure give DNA and
RNA different functions

● DNA stores genetic information

● RNA carries information about amino acid
sequence to the ribosomes to make
proteins
Protein Structures
● The primary structure is the sequence of amino acids in the polypeptide
chain
● The secondary structure is the three dimensional form of parts of
proteins
● The tertiary structures creates the overall shape of the protein
● The quaternary structure is the arrangement of more than one protein
molecule
● This overall three dimensional shape gives each protein a specific function
Diagram of Structure of Proteins
Lipids
● Most lipids are nonpolar
● The structure of phospholipids allows for
polar and nonpolar regions
○ Made up of a phosphate group on one end (head) and two
side-by-side chains of fatty acids (tails)
○ The phosphate group is negatively charged and makes the
phospholipid head polar
○ The lipid tails are uncharged and nonpolar
● The differing polarities allows for a
hydrophilic head and a hydrophobic tail
Carbohydrate Directionality
● Carbohydrates are made up sugar
monomers
○ The structures of these monomers help
determine the properties and functions of the
carbohydrates
● Ex. Starch and Cellulose
○ Both made up of glucose
○ In starch, each glucose unit is oriented in the
same direction
○ In cellulose, each glucose unit is rotated 180
degrees
Nucleic Acid Directionality
● Nucleic acids have ends, defined by the 3'
and 5' carbons of the sugar
● This determines the direction in which
complementary nucleotides are added
during DNA synthesis
● It also determines the direction in which
transcription occurs (from 5' to 3').
Protein Structure
● Proteins have an amino (NH2) end and a
carboxyl (COOH) end

● They consist of a linear sequence of

amino acids connected to the amino and
carboxyl groups of adjacent monomers
through the formation of peptide bonds
through dehydration synthesis
Carbohydrate Structure
● Carbohydrates are made up of subunits - monosaccharides, disaccharides
and polysaccharides
● The bonds between these sugars creating the different subunits give the
carbohydrates their

The nature of the bonding between carbohydrate subunits determines their

relative orientation in the carbohydrate, which then determines the secondary
structure of the carbohydrate.
Synthesis of Biological Macromolecules
● The hydrolysis of ATP creates ADP and Pi, as well as much energy that can
be put towards synthesizing molecules or activating new compounds.
○ These molecules are carbohydrates, lipids, proteins, DNA/RNA, etc.
How Structure Impacts Function
Polysaccharides
● Polysaccharides either store energy or are structural support. Starch and glycogen are highly compacted
polymers, making them good for energy storage. Cellulose and chitin are linear polymers, making them good
for structural support.

Proteins
● The underlying sequence of amino acids determines the shape of the protein. The shape of the protein is
what determines the function

Nucleic Acids
● The nucleotide sequence of the DNA or RNA determines what trait will be expressed
How the Structure of DNA Contributes to Protein Synthesis and Heritability

● The properties of nucleic acids allow for the coding of DNA.

● The specific ordering of the nucleotides that make up DNA polymers is what specifies the
directions for the DNA. The order of the bases in the chain determine the amino acid sequence
for which it codes.

● The specific Nitrogenous bases pairing allow for accurate replications of the DNA through the
Hydrogen bonds made between the bases. The double helix will unravel and completely
duplicate itself allowing for heritability.
DNA and RNA Information
● DNA is good at storing information because its unique double helix
formation allows it to have incredibly storage density.

● Because DNA is more stable, it is often used to store genetics long term,
while RNA is used for copying and moving outside of the nucleus specific
sets of instructions (mRNA)
Protein Structure and Amino Acid Sequence
The different elements, or more/less of a certain element leads to an
amino acid being more acidic, basic, and react differently with each other
and other structures.

Primary structure is just the amino acid sequence. There are also
peptide bonds.

Secondary structures form beta pleats and alpha helices.

Tertiary structure has more complex bonds, like H-bonds, ionic bonds,
and a disulfide bridge.

Quaternary structures can contain multiple tertiary structures bonded

together.
How a Protein’s Environment Could Affect Structure
● Every protein has an optimal pH zone and temperature zone. If a protein is in environment
with pH levels outside of the optimal zone or in an environment where the temperatures are
too high, it goes through a process called denaturation.

● During Denaturation, the hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic
interactions with break apart, leaving only the covalent bonds and destroying the structure of
the protein. What you are left with is the primary structure with covalent peptide bonds. Once
you lose this structure, you lose the function of the protein.
Structure of Lipids and Polarity
● Triglycerides are nonpolar because they have three hydroxyl groups which are
fatty acids and are nonpolar.
● Phospholipids have mixed polar & non-polar groups. Two fatty acids, a
phosphate group and a glycerol molecule are combined forming a hydrophilic
head and a hydrophobic tail.
● The hydrophilic head is polar while the hydrophobic tail is nonpolar.
● Steroids, having a large number of carbon-hydrogen bonds are nonpolar
Why Lipids are Useful in Biological Systems
● Phospholipids make up the plasma membrane. They are made of a glycerol, fatty acids, and a
phosphate group.
● They are also used to store large amounts of energy. About one gram of fat stores twice as
much as one gram of sugar/starch.
● The phospholipids are able to survive the aqueous solution by hiding the hydrophobic tail on
the inside of the bilayer. The tails want to be on the inside of the bilayer because of the
hydrophobic nature and like wants to be with like. This shape forms a bilayer compartment.
Phospholipids
Why Is Starch Easily Digested, But Cellulose Isn’t
● Starch is easily digested because it is able to be broken down by the enzyme Amylase whereas
cellulose is much harder to break down and must be done by bacteria.
● Cellulose has beta linkages and starch has alpha linkages. Alpha linkages are easily digested by
the human body because they are less stable and are weaker than Beta linkages.
Carbohydrates with Beta linkages are not easily digested by humans.