B1 1.2 Proteins

What are the components of an amino acid?

A central carbon atom called the alpha carbon, with a bond to the amine group, and carboxyl group. The carboxyl group is acidic and the amine group is basic. There is also a hydrogen and side chain called a R-group

How are dipeptides and polypeptides formed?

Dipeptides are 2 amino acids linked by condensation reaction, and polypeptides is when more than 2 are linked to together.

How do condensation reactions work in dipeptides and polypeptides and what breaks them apart?

They are linked by peptide bonds between the amine group and carboxyl group- amine group always linked to the end of the carboxyl group. Form from condensation reactions. Polypeptides are broken via hydrolysis reactions

Non essential and essential amino acids.

There’re 20 amino acids, essential ones need to be obtained by animals from their diet, while non-essential ones can be synthesized by an animal using metabolic pathways that transform 1 amino acids to another. Plants make all the amino acids

Essential amino acids in humans

9 are essential, other can be made in the human body from other amino acids. Vegan diets need attention to ensure all essential amino acids are being consumed

How to calculate diversity of polypeptides

20^n possibilities, with n being the number of amino acids in a polypeptide, based on the RNA sequences

Examples of polypeptides

beta endorphin, natural painkiller, insulin, a small protein, alpha amylase, digests starch in saliva, and titin, largest polypeptide

What is denaturation?

When the bonds and interactions between the R groups on amino acids are disrupted, it changes the 3D structure, or conformation of the proteins, causing denaturation

What does denaturation cause?

Denaturation is permanent, and causes soluble proteins to become insoluble because the hydrophobic R-groups in the center of the molecule become exposed

What can cause denaturation?

Heat, because it causes vibrations that break intermolecular bonds/interaction, extremes of pH, acidic and alkaline, can also cause it because the pos and neg charges on R-groups change, breaking ionic bonds or making new ones, and exposure to heavy metals- altering conformation

Diversity of R-groups

R-groups determine the chemical characteristics on an amino acid, as all the other parts of the amino acids are the same. R-groups can be hydrophobic or hydrophilic, and within the hydrophilic ones they can be pos or neg, by acting as an acid or a base

How can proteins have amino acids outside the 20?

Amino acids can be modified after a polypeptide has been synthesized, creating new amino acids

What is the primary level of organization of proteins?

linear sequence of amino acids in a polypeptide. The backbone of covalent bonds (-C-C-N-C-C-N-), the bonding angles allow rotations of the bond between alpha carbon atoms and the adjacent nitrogen and carbon atoms to rotate into 3D structures

What does the 3D shape of a polypeptide depend on?

Polypeptide’s assemble into a specific 3D conformation based on the amino acids sequence, which is dependent on the mRNA that comes from the DNA. Conformation determines function

What is the secondary level of proteins?

regular structures stabilized by hydrogen bonding within polypeptides

What stabilizes the secondary structure of proteins?

There’re C=O and N-H groups along the polypeptide chain, and are polar, with the oxygen being neg and hydrogen being pos, creating hydrogen bonds between the 2. Individually they’re weak, but there’s a lot so collectively they’re strong enough to stabilize conformation structures within polypeptides

What structures are stabilized by hydrogen bonding?

alpha-helix and beta-pleated sheets. Both can exist in a single protein

alpha helix

polypeptide is wound into a helical shape, with hydrogen bonds between the adjacent turns of the helix between the C=O and N-H groups

beta pleated sheets

2/more sections of polypeptide are arranged parallelly, with hydrogen bonds between them. The sections of polypeptide are in opposite directions, forming a pleated sheet due to bonding angles

Tertiary structure

whole polypeptide chain folding into a 3D structure, stabilized by R-group interactions, like ionic bonds, hydrogen bonds, disulfide bonds, and hydrophobic bonds

Ionic bonds in tertiary structure

between pos and neg R-groups. amine groups accept protons to become positive, carboxyl groups donate protons to become negative, forming ionic bonds. Because they bonds involve protons (hydrogen ions) they’re sensitive to pH changes

Hydrogen bonds

between polar R groups, when hydrogen forms a bond with a electronegative atoms like O or N, and after covalently bonding with them, they become slightly positive, and can form hydrogen bonds with other atoms

Disulfide bonds

disulfide bonds form between pairs of cysteines, or hydrophilic amino acids. These covalent bonds are the strongest

Hydrophobic interactions

hydrophobic interactions between the non-polar R-groups

How do amine and carboxyl groups become charged to form ionic bonds in tertiary structure?

Amine groups accept proton (-NH2 + H = -NH3), while carboxyl groups donate a proton (COOH = COO + H). They involve hydrogen ions to become charged to form ionic bonds

When does tertiary structure occur?

When polypeptide is synthesized by the ribosome, and within tertiary structures there can be parts with secondary structures. Produces wide range of 3D structures, most are globular. Elongated proteins don’t have a tertiary structure

How are amino acids organized in a protein in a aqueous solution?

amino acids can be polar/hydrophilic, or non-polar/hydrophobic, and most globular proteins are soluble in water, and have hydrophobic amino acids in the center, and hydrophilic ones on the outside. This stabilizes tertiary structure of proteins, with hydrophobic interactions between amino acids in the center, and hydrogen bonding between outer amino acids and water

How are amino acids of proteins organized in proteins in transmembrane/integral?

Integral proteins embedded in membranes have hydrophobic amino acids on the outside where they contact the non-polar hydrocarbon core of membranes. In transmembrane proteins the hydrophobic region is a belt, with hydrophilic regions inside and outside the cell in contact with aqueous solutions

What happens when proteins are in a hydrophobic/non-polar substance

they have hydrophobic amino acids over parts of their surface

Channel proteins

channel proteins in the membrane let hydrophilic substances get through the hydrophobic membrane core. They have a hydrophobic region in-between hydrophilic regions

Quaternary structure

the 3D arrangement of more than a single polypeptide as subunits is the quaternary structure of a protein. The polypeptides can have both alpha chains (from alpha helices) and beta chains (from beta pleated sheets)

Non-conjugated proteins

The quaternary structure only has polypeptide subunits- the subunits are linked by the same bonds as in the tertiary structure

Insulin and collagen.

a non-conjugated proteins. Insulin has 2 polypeptides linked by disulfide bonds, and collagen has 3 polypeptides wound together to form a rope-like structure and held together by hydrogen bonds

conjugated proteins

conjugated proteins have one or more non-polypeptide subunits along with polypeptide subunits, like hemoglobin, that have 4 polypeptide chains, each with a haem group, which binds to oxygen. Non-polypeptide components increase chemical and functional diversity of proteins. Many proteins have a non-polypeptide component to catalyze chemical reacions

Fibrous proteins

function of protein depends on form. Fibrous proteins are elongated polypeptides that don’t have tertiary folding or secondary structures. Quaternary structures are developed by linking together polypeptides chains into narrow fibers with hydrogen bonds holding them together

Collagen as a fibrous protein

fibrous proteins. Quaternary structure is 3 polypeptides wound in a triple helix, bound by hydrogen bonds. Special amino acids prevent alpha helixes from forming. Rope-like structure of collagen gives it high tensile strength, and variation in the R-groups facing outside triple helix creates different kinds of collagen, like for skin, tendons, and cartilage

Globular proteins

Globular proteins have a rounded shape from polypeptides forming, and stabilized by bonds between R-groups of amino acids. The conformation of the protein determines its structure

Insulin

insulin is a globular protein that has the exact conformation to bind to specific sites on insulin receptors to tell the body when blood sugar is too high. Its function depends on its conformation

oligopeptide

chain of less than 20 amino acids