Biochemistry

Weak bonds

• hydrogen bonds

  • attraction between positive Hydrogen and negative atom

Strong bonds

• covalent bonds

  • sharing electrons between two atoms

• ionic bonds 

  • Transfer of  electrons between two atoms

• Nonpolar covalent bond

Pair of electrons shared EQUALLY by 2 atoms. It is balanced, stable, and a good building block.

For example:  hydrocarbons = CxHx

• methane (CH4 ) 

Polar covalent bond

Pair of electrons shared unequally by 2 atoms.

For example:  Water = H₂O

• oxygen has stronger “attraction” for the electrons than hydrogen

• oxygen has higher electronegativity

• water is a polar molecule

  • positive vs negative poles

  • leads to many interesting properties of water…

Hydrogen bonding

• Polar water creates molecular attractions.

  • attraction between positive H in one H₂O molecule to negative O in another H₂O

  • Creates one molecule of H₂O

• Weak bond

  • but common in Biology 

• In liquid water hydrogen bonds are free to break/reform allowing molecules to be tightly packed = more dense

• In ice, 4 long-lasting hydrogen bonds form between water molecules; water molecules less tightly packed=less dense.

• Solid water is less dense than liquid water

• Water expands when it freezes

  • Due to the expansion, the density is lower than liquid water

    • Ice FLOATS on liquid water

Water is called the “solvent of life”

• When water is the solvent, the resulting mixture is called an aqueous solution

• In aqueous solutions, a small number of water molecules can break apart(dissociate) to form ions:

Dehydration synthesis (aka condensation) reactions join two monomers together into a polymer. A water molecule is removed in the process.

Hydrolysis reactions add a water molecule to cleave the covalent bond between two monomers in a polymer.

• The carbohydrates are known as the “quick energy” foods because they are very quickly converted to energy by the cells. 

• Living things use carbohydrates as their main source of energy. 

• Main functions = energy (glucose, glycogen, starch), structure (cellulose, chitin)

• Monosaccharides = carbohydrate monomers

  • Chains or rings, most often 5-6 C

  • End in -ose

• Polysaccharides = complex carbs (polymers)

• Bonds between monosaccharides are called glycosidic bonds

• Presence of O makes some carbs polar enough to dissolve in water

• structure is made up of rings

• Examples of polysaccharides include starch, glycogen, and cellulose, each serving distinct roles in biological systems.

• Polysaccharides function as energy storage molecules or structural components, demonstrating the diversity and importance of carbohydrates in living organisms.

Polysaccharides: Composed of many molecules of sugar bonded together. Formed by dehydration synthesis. Starch (pastas/bread)

Lipids

• These compounds are generally not soluble in water.

• There are two building blocks of lipids:  fatty acids and glycerol

• Examples of lipids are fats, oils, and waxes.

• Functions = energy storage, structure of the cell membrane

• All lipids are nonpolar and thus do not dissolve in water

• Triglycerides (fats) = three fatty acids + glycerol

• Phospholipids = two fatty acids + glycerol + phosphate group

• Steroids = four fused carbon rings

• They are used to store energy. (Saturated, Unsaturated)

• They are an important part of the cell membrane. (Phospholipids)

• They form waterproof coverings on feathers, fruits, leaves, etc. (Waxes)

• They cushion and insulate the internal organs. (Phospholipids)

• They are chemical messengers. (Steroids)
  
  

the differences between saturated and unsaturated fats are crucial for understanding their roles in biological systems. Saturated fats contain no double bonds between carbon atoms, leading to a straight structure that allows them to pack tightly, whereas unsaturated fats have one or more double bonds causing kinks in the chain, which prevents tight packing and results in a liquid state at room temperature. Unsaturated fats are healthy while saturated fats are not.

Lipids are hydrophobic due to being non-polar.

Nucleic Acids

• The building blocks of the nucleic acids are nucleotides.

• Nucleic acids store and transmit genetic information.

• There are two kinds of nucleic acids:  DNA and RNA

  • DNA: Deoxyribonucleic acid

  • RNA: Ribonucleic Acid

• DNA is structured as an antiparallel double helix, meaning each strand runs in opposite directions

• Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds

• Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds

RNA (ribonucleic acid) is a single-stranded molecule made of a sugar-phosphate backbone attached to four nitrogenous bases: adenine (A), cytosine (C), guanine (G), and uracil (U)

Proteins

• Proteins are macromolecules needed by the body for growth & repair

• The building blocks of proteins are amino acids

• There are 20 different amino acids

• Functions = structure, signaling, catalysis, and more

• Monomers are amino acids

• Directionality: amino (-NH₂) terminus and carboxyl (-COOH) terminus 

• R groups are categorized by chemical properties (hydrophobic, hydrophilic, or ionic)

• Interactions of R groups determine structure and function of regions of proteins

Proteins are IMPORTANT!

There are many, many uses for proteins:

• Enzymes (substances that speed up chemical reactions)

• Hormones (help control how cells & organs work)

• Transport proteins such as hemoglobin (in red blood cells)

• Contractile proteins such as in muscle tissue

• Antibodies (protects organisms against virus/bacteria)

• Membrane proteins (help cells move & connect)

• Structural proteins such as bones and muscles

Enzymes

• Enzymes are proteins that speed up the chemical reactions of the cell.

• Enzymes do not cause reactions to happen.  They simply speed up reactions that will already occur.

• Without enzymes the reactions of the cell would proceed so slowly that the cell would die. 

Extra info:

Hydrolysis is the chemical reaction your body uses during digestion to break down food.

When proteins get too hot, they denature. This means they lose their 3D shape and unfold. Because a protein's shape determines its function, a denatured protein stops working.

• The Two Types: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid).

• The Three Parts: Nucleic acids are made of chains of nucleotides. Every nucleotide consists of a sugar (deoxyribose or ribose), a phosphate group, and a nitrogenous base (Adenine, Thymine/Uracil, Cytosine, Guanine).

Three Functions of Proteins

• Structure: Building components like keratin in hair/nails and collagen in skin/bones.

• Enzymes: Speeding up chemical reactions (like amylase breaking down carbs in saliva).

• Transport: Moving molecules around the body (like hemoglobin carrying oxygen in your blood).

Activation Energy

• Every chemical reaction between molecules involves bonds breaking and bonds forming.

• The activation energy (E_A) is the initial amount of energy needed to start a chemical reaction. 

• This energy is typically supplied in the form of heat from the surroundings

Enzymes

• Enzymes are proteins that act as biological catalysts.

  • A catalyst is a chemical that speeds up a reaction without being consumed by the reaction

• Enzymes speed up metabolic reactions by lowering the activation energy.

Enzymes

• The reactant an enzyme binds to is known as the enzyme’s substrate.

• The binding of the enzyme and substrate forms an enzyme-substrate complex.

• The region on the enzyme where the substrate binds to is called the active site.

• The binding of a substrate(s) to the active site creates an induced fit, in which the enzyme changes shape to embrace the substrate(s) to ensure it does not detach until the reaction is complete. 

Enzyme Specificity 

• Enzymes have a specific shape and active site that only binds to a specific substrate. Thus, enzymes control very specific reactions. Lock and key model.

• For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme.

Enzyme Specificity 

• The name of an enzyme often ends with the suffix “-ase” and typically refer to the substrate they bind to or the type of reaction they catalyze.

  • EX: Lactase catalyzes the hydrolysis of lactose into glucose and galactose. 

  • EX: ATP Synthase catalyzes the reaction that synthesizes ATP in the cell.

Increasing Substrate Concentration

• The rate of enzyme activity can be sped up by increasing the substrate concentration in a solution.

• When all enzyme molecules in a solution are bonded with substrate, the enzyme is saturated.

• At enzyme saturation, reaction speed can only be increased by adding more enzyme.

Optimal Temperature and pH

• Enzymes have optimal environmental conditions in which they work best, such as temperature and pH.

• Increasing temperature generally increases the rate of a reaction, because it causes molecules to move faster and increases the number of collisions between enzymes and their substrate.

  • However at some point, the increased temperature will affect the stability of the enzyme (denaturing). 

Optimal Temperature and pH

• The optimal pH values for most enzymes fall in the range of pH 6-8, but there are some exceptions.

The active site is on the enzyme