Introduction to Biochemistry – Lecture Review

Matter: Elements and Compounds

• Matter: Anything that occupies space and has mass.

  • Makes up the physical component of the universe.

  • Matter is composed of elements.

Elements and the Periodic Table

• Elements: Cannot be broken down into other substances by chemical means.

• Elements are organized into the Periodic Table

Elements: Atoms

• Elements are made of atoms.

• All atoms of a given element are identical.

• Atoms are the smallest particle of an element which retain the chemical properties of that element.

• The atoms of different elements have different properties.

Atoms & Bonding

• Chemical Bond: An attraction between atoms that enables them to stay close together.

• Types of Chemical Bonds:

  • Ionic Bonds: Sodium (Na) + Chlorine (Cl) = Sodium Chloride (NaCl)

  • Covalent Bonds: Water (H2O)

Atoms & Ionic Bonding

• Ion: An atom that has acquired an electrical charge by either losing or gaining an electron.

• By definition, an atom is neutral (number of protons = number of electrons), (p+ = e-).

Ionic Bonds

• Ionic Bonds: The attraction between oppositely charged ions.

• Electrons are transferred (not shared).

• Ions: Atoms that are electrically charged as a result of gaining or losing electrons.

Covalent Bonds

• Covalent Bonds: Two atoms share one or more pairs of outer shell electrons.

• Molecule: Atoms held together by covalent bonds.

Electron Dot Formula = Lewis Dot Structure (Valence shell diagram)

• Carbon (C) tends to share electrons to form covalent bonds.

• Sodium (Na) and Chlorine (Cl) tend to lose or gain electrons, respectively, to form ionic bonds.

Covalent or Ionic Bonding Checkpoint

• C-H bonds indicate covalent bonding.

• H + Cl à H+ + Cl- indicates ionic bonding.

Checkpoint: Ions

• When a neutral atom loses an electron, it becomes a positively charged ion.

• Example: K + Cl à K+ + Cl-: Potassium loses its electron to chlorine to become a positively charged potassium ion.

Reaction Types

• Endergonic: Energy in.

• Exergonic: Energy out.

• Reduction: Gain of electrons.

• Oxidation: Loss of electrons.

• Anabolic: Build-up.

• Catabolic: Break down.

Enzymes

• Enzymes are proteins.

• Function: To allow for chemical reactions to happen that would otherwise take too long (a catalyst).

• Enzymes lower a reaction’s activation energy.

• Example: Sucrase breaks down sucrose into glucose and fructose: Sucrose à glucose + fructose.

Enzymes & Chemical Reactions

• Catalyst: A substance that lowers the activation energy, but is not used up itself.

• Activation Energy: The amount of energy the reactants in the reaction must absorb to start the reaction.

Enzymes & Chemical Reactions: Types of Reactions

• Catabolic reaction: Break down substances.

• Anabolic reaction: Put two substances together.

Enzyme Examples

• Luciferase: Breaks down luciferin molecules (catabolic enzyme).

• Sucrase: Breaks down sucrose into glucose and fructose (catabolic enzyme).

• Carboxypeptidases: Help put together molecules to create insulin, help in blood clotting, growth hormones, and others (anabolic enzyme).

How do Enzymes Work?

• Active Site: The region of an enzyme where the substrate fits for the reaction to occur.

• Substrate: The reactant specific to that enzyme.

• Example: Enzyme for Cellular Respiration = Dehydrogenase.

Acids, Bases and pH

• Acid: A chemical that donates H^+ (hydrogen ions) to solutions.

• Base: A chemical that donates OH^- (hydroxyl ions) to solutions.

Checkpoint: pH

• Which has a higher [H^+]? A solution with pH 5.

• Which is more acidic? A solution with pH 5.

• ↑ [H^+] ↓pH

• ↑ acidic

Biological Molecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

Building and Breaking Down Biomolecules Processes or Reaction

• Dehydration synthesis: Links monomers together to form polymers.

• Hydrolysis: Breakdown of polymers with water into monomers.

Carbohydrates

• Function: Energy source.

• Types:

  • Monosaccharides

  • Disaccharides

  • Polysaccharides

Carbohydrate Structure: Monosaccharides (a.k.a. simple sugars)

• Monomers of other carbohydrates

• Examples: glucose, fructose, galactose

Carbohydrate Structure: Monosaccharides

• Glucose, fructose, and galactose have the same number of each type of atom, but arranged differently

• Type # C; # H; # O

• glucose 6; 12; 6

• fructose 6; 12; 6

• galactose 6; 12; 6

Carbohydrate Structure: Disaccharides

• Constructed from two monosaccharides

• Examples:

  • Maltose (Glucose + Glucose)

  • Lactose (Glucose + Galactose)

  • Sucrose (Glucose + Fructose)

• Dehydration synthesis forms a disaccharide.

Carbohydrate Structure: Polysaccharides

• Complex carbohydrates: Long chains of monosaccharides

Lipids

• Function

  • Store energy

  • Insulation

  • Protect and cushion vital organs

  • Building blocks for cell membranes

  • Steroid function?

• Types of Lipids

  • Fats

  • Phospholipids

  • Steroids

Lipids: Fats (a.k.a. Triglycerides)

• Made up of 1 glycerol molecule and 3 fatty acid molecules.

• Making fats: Dehydration synthesis

• Saturated and Unsaturated fats

Lipids: Phospholipids

• Made up of phosphate group and 2 fatty acid molecules

• Found in cell membranes.

• Hydrophilic = Water “loving”

• Hydrophobic = water “fearing”

Lipids: Steroids

• Structure: Skeleton is bent to form 4 fused rings

• Examples of steroids:

  • Cholesterol LDL/HDL

  • Sex hormones

Lipids: Steroids (cont.)

• Cholesterol – Important for cell membranes, hormones, etc.

  • LDL = low-density lipoprotein

    • Too much = build up on artery wall, can cause heart attack

  • HDL = high-density lipoprotein

    • Carries excess cholesterol away

Lipids: Steroids (cont.)

• Sex hormones: Estrogen and Testosterone

Lipids: Steroids (cont.)

• Steroids - Anabolic steroids: Made from testosterone

Proteins

• Structure depends on Function

• Function

  • Transport

  • Structural (collagen)

  • Storage

  • Contractile

  • Enzymes

  • Defensive

  • Signaling (hormones)

  • (Energy) only during starvation

Proteins (cont.)

• Generally huge polymers

• Constructed from amino acid monomers.

Proteins (cont.) Monomer Structure

• Monomers = amino acids

• All amino acids have a central carbon atom + a hydrogen atom

  • Amino group

  • Carboxyl group

  • Side group (a.k.a. “R” or functional group)

    • 20 different R groups

    • Hydrophobic or hydrophilic

    • Positively or negatively charged

Proteins (cont.)

• Peptide Bond: The covalent bond between adjacent amino acids

• Polypeptide: A chain formed by 3 or more amino acids

Protein Structure

• Primary (1°): polypeptide (amino acid) chains in sequences unique to a given protein

• Secondary (2°): coiling or folded sheets held together by hydrogen bonds between neighboring amino acids

• Tertiary (3°): three-dimensional structure of coils or sheets, held together by amino acid side groups

• Quaternary (4°): some proteins may be formed by including 2 -4 tertiary structures (subunits)

Checkpoint: Protein Monomers

• What are the monomers of proteins?

  • Amino acids

Checkpoint: Protein Bonds

• What type of bond holds the secondary structure of a protein together?

  • Hydrogen bonds

Checkpoint: Overall Shape

• Which structural level ultimately dictates the overall shape of a protein?

  • Tertiary (3º)

Checkpoint: Protein Structure

• What level of protein structure is exhibited in Green Fluorescent Protein (GFP)?

  • Tertiary (3º)

Checkpoint: Hemoglobin

• What level of protein structure is exhibited in hemoglobin?

  • Quaternary (4º)

Nucleic Acids

• Two types of nucleic acids

  • DNA(Deoxyribonucleic acid)

  • RNA (Ribonucleic acid)

• Function: Information storage molecules that provide the information for building proteins

Nucleic Acids (cont.)

• Structure: Monomer = nucleotide

• Nucleotide consists of 3 parts:

  • 5 Carbon Sugar

  • Phosphate group

  • Nitrogenous base (varies)

Nucleic Acids (cont.)

• Each DNA nucleotide has 1 of the following Nitrogenous bases:

  • Adenine (A)

  • Guanine (G)

  • Cytosine (C)

  • Thymine (T)

• RNA has Uracil (U), instead of Thymine (T)

Nucleic Acids (cont.)

• A single DNA strand -- polymer of nucleotides linked to a sugar-phosphate backbone

• DNA – 2 strands held together by H-bonds between N-bases

DNA vs. RNA

• Similarities : Both have nucleotides made of phosphate, sugar, nitrogenous bases

• Differences:

  • DNA

    • Double-stranded

    • Nitrogenous bases include: A, G, C, (T) Thymine

    • Sugar = deoxyribose

  • RNA

    • Single-stranded

    • Nitrogenous bases include: A, G, C, (U) Uracil

    • Sugar = ribose

Checkpoint: DNA Bonds

• What type of bond links nucleotides along the sugar-phosphate backbone of DNA?

  • Covalent bonds

Checkpoint: DNA Bonds

• What type of bond links nucleotides between the nitrogenous bases of the double strand of DNA?

  • Hydrogen bonds

Checkpoint: DNA Structure

• What type of bond links nucleotides along the sugar-phosphate backbone of DNA?

  • Covalent bonds