• 4 calories per gram of energy → Similar in energy to carbs

• Most diverse molecules in living organisms

  -- Structural support (muscle)

  -- Storage (center of glycogen)

  -- Transport (hemoglobin; on RBC which transport oxygen)

  -- Signalling (hormones and steroids)

  -- Cell response (receptor proteins)

  -- Movement (contractile proteins)

  -- Defense (antibodies, latching onto antigens and identifying pathogens and things that shouldn’t be there)

  -- Catalysis of reactions (enzymes)

  -- and more!

• The body can’t store protein

  • Extra protein is converted to energy and/or stored as fat (triglycerides, anything in excess is converted to triglycerides)

• Proteins aren’t mostly our main source of energy, but we need their amino acids

Amino Acids

• Monomers of proteins (building blocks of proteins)

• They are amphiprotic - they have both an acidic and basic component

  • The carboxyl group is acidic and the amino group is basic

• There are 20 different side chains and thus 20 different amino acids

  • 9 are essential amino acids which mean that we need them in our food (must be consumed) because our bodies cannot manufacture them ourselves

• Non polar: are non polar because of ∆EN

  • C–H and C–C bonds are non polar

• Polar: polar because of their functional groups

  • more hydrophilic

    • SH on cysteine is a functional group called sulfhydryl – its polarity is debated, it is very weakly polar covalent though some consider it non polar

      • Creates bonds with other cysteine

• Electrically charged: side groups are charged

  • charged carboxyl = negative charge

  • charged amino = positive charge

  Amino acids to know how to draw

Amino acids to note

Cysteine

• Contains S in side chain sulfhydryl FG

• The S forms disulfide bridges (bonds) with other cysteines

  • Helps hold chains together

  • 2 cysteines close enough will bond

Proline

• Side chain forms a ring with itself

  • Side chain bonds to base/foundation of the molecule

• Causes bends in the polypeptide chain

• Proline kink = a bend in the strand

Amino acid formation

• Monomers (amino acids) attach to each other by forming peptide bonds

• They form these peptide bonds between the amino group of one amino acid and the carboxyl group of another amino acid

A protein is hundreds of amino acids strung together

When counting amino acids, count by side chain (every amino acid has one side chain)

Polypeptides

• When over 50 amino acids are strung together it forms a polypeptide (many = poly)

• The order of amino acids is determined by an organism’s DNA (instruction manual)

• Once the polypeptide chain has been formed, it has to be folded into a specific shape in order to properly function

• Structure determines function

  • If there is something wrong with the DNA then an improper protein will be made. Cystic fibrosis is caused by a single protein being wrong

4 levels of folding (only the first 3 are required to reach full protein status)

1. Primary structure: sequence of amino acids (aka residues)

2. Secondary structure: coils and folds

3. Tertiary structure: supercoiling

4. Quaternary structure: subunit interaction

Primary Structure

• Starts at the N (amino) terminus and ends at the C (carboxyl) terminus

• Order of amino acids determines how the protein will be folded

• A single mistake can cause a huge change in a protein (e.g. sickle cell anemic which causes the RBC to be half moon shaped and causing them to get stuck)

• A single mistake in DNA causes a single amino acid in the protein sequence to be different, leading to a serious change in the shape of RBC

  

  Secondary Structure

• Coils and folds

• Stabilized by Hydrogen bonding between amino and carboxyl groups

α-helices

• H bonding is forming amino groups to other carboxyl groups

• Forms a coil

• The carboxyl bonds to amino ~4 carbons away

β-pleated sheets

• Carboxyl and amino

  • Instead of the strand staying straight, it will turn a corner and make an S-like curve

Different parts of the protein can coil and sheet (as seen in the bottom image)

Tertiary Structure

• Super coiling occurs at the tertiary level when side groups (R) on the amino acids interact with each other and cause another level of folding

  • Disulfide bridges (if there is a cysteine amino acid)

  • Hydrophobic interactions (non polar)

  • Hydrogen bonding (different in tertiary structure, between side groups (as opposed to the base of an amino acid in secondary))

  • Ionic bonding (between acidic and basic)

• Can be a fully functioning protein at this level

• Can be a fibre or globular

Quaternary Structure

• Not all proteins have this -- if a protein is made up of more than 1 polypeptide strand

• Some proteins are made of more than one polypeptide (2 or more subunits interacting)

• Hemoglobin: has quaternary structure because one hemoglobin is made of 4 polypeptide chains together

  • Has an accessory molecule – vitamins and minerals: this is called heme and it is made of iron (Fe) → prosthetic group

• Some proteins with quaternary structures also have prosthetic groups (non protein components)

  • Hemoglobin: 4 heme groups which carries 4 oxygen

  • People with anemia faint, are pale, and are tired. They take iron supplements to attract the oxygen

Summary

Types of proteins

1. Globular

   • One or more polypeptide chains that take on a round spherical shape (forms a blob)

   • E.g. antibodies, enzymes

   • Hemoglobin are globular

   • Can be one or many chains

2. Fibrous

   • Long strands or sheets of polypeptide chains

   • E.g. actin and myosin (muscle contractions), silk, collagen (skin), and keratin (hair)

   • Pile up to form fibrous tissue (doesn’t ball up, more of a linear structure)

Changing of proteins

• Proteins can only function in their optimal shape

• Their shape can be impacted by their environment

• The 3D shape of a protein can be changed by changes in temperature, pH, or ionic concentration

• The loss of shape is called denaturation (if it isn’t in its native conformation/optimal shape)

• Therefore proteins have optimal ranges for temperature, pH, and ionic concentration within the function’

• Can be rendered useless if the shape is too altered and cannot be reversed if the primary structure is altered (if slightly changed it can still be sort of useless)

  

• Small proteins denatured by heat or chemicals usually return to their original shape when the cause is removed

• As long as the amino acid sequence must remain intact (primary structure)

• Native conformation = functional form of a protein found under normal biological conditions

  • Enables recognition to/of other molecules (e.g. enzyme-substrate, antigen-antibody)

  • When not in native conformation, protein either doesn’t function or works less effectively

  • Denaturation is the reason that an egg becomes solid when boiled