B1.2 - proteins

What is the generalised structure of an amino acid?

All amino acids have the same structure in terms of an amine group;
and carboxyl group;
but different variable groups (R groups);

B1.2.2—How are amino acids linked together (what is the reaction?) to create longer chains of amino acids?

two amino acids are joined;
condensation reaction;
via carboxyl group of one amino acid;
and amine group of other;
creating a peptide bond;
and water

B1.2.3—What are the dietary requirements for amino acids?

Essential amino acids cannot be synthesized;
and must be obtained from food;
Non-essential amino acids can be made from other amino acids;
Vegan diets require attention to ensure essential amino acids are consumed;

B1.2.4—Why is there an infinite variety of possible polypeptide chains?

20 different amino acids can be used;
in any order;
long chains of amino acids can therefore have a huge number of different possible orders and combinations of the 20 amino acids;
even 2 amino acids gives 400 possible combinations;

B1.2.5—What is the effect of pH on protein structure?

proteins have an optimum pH in terms of maintaining their structure and activity;
extremes of pH effect the interactions holding protein structure together;
this means they lose their structure;
become insoluble;
in the process of denaturation;
most enzymes are proteins, so it can cause enzymes to lose their activity

B1.2.5—What is the effect of temperature on protein structure?

increased temperature away from optimum leads to higher kinetic energy;
this can lead to breaking of bonds holding protein structure together;
causing denaturing;
most enzymes are proteins, so it can cause enzymes to lose their activity;

B1.2.6 What are R-groups on amino acids? How are they responsible for the diversity of proteins?

R-groups are a variable group on amino acids;
R-groups determine the properties of assembled polypeptides;
R- groups are hydrophobic or hydrophilic;
hydrophilic R-groups are polar or charged, acidic or basic;
this leads to their interactions with other amino acids;
causing different shapes and structures to form;
accounting for the immense diversity of protein forms;

B1.2.7 What is the primary structure of a protein? How does it impact the conformation (shape) of proteins?

primary structure is the order of amino acids in a polypeptide or protein;
all other levels of structure are determined by the primary structure; because this determines which R-groups are present;
as the conformation (shape) is determined by interactions of the amino acids, which is determined by the sequence of amino acids;

B1.2.8 What is the secondary structure of a protein? How is it brought about? What are the two structures often formed?

Secondary structure is the folding patterns caused by nearby (local) interactions;
between amino acids;
e.g. Alpha helices are brought about by hydrogen bonding; in regular positions; which stabilise the structures;
beta-pleated sheets are also brought about by hydrogen bonding at regular positions;

B1.2.9 What is the tertiary structure of proteins? How is it brought about? What kinds of bonds stabilise it?

Tertiary is the folding pattern between more distant regions of the protein;
giving the three dimensional shape of the protein;
it is caused by hydrogen bonds;
ionic bonds;
disulfide covalent bonds;
between cysteines;
and hydrophobic interactions between amino acid R-groups;
amine (NH2) and carboxyl groups (COOH) in R-groups can become positively or negatively charged by binding or dissociation of hydrogen ions;
and they can then participate in ionic bonding.

B1.2.10—What is the effect of polar and non-polar amino acids on tertiary structure of proteins?

In proteins that are soluble in water, hydrophobic amino acids are clustered in the core of globular proteins;
with the hydrophilic amino acids facing outwards towards the water;
Integral proteins have regions with hydrophobic amino acids, helping them to embed in membranes; which have a hydrophobic central region;

B1.2.11 What is the quaternary structure of non-conjugated and conjugated proteins? Give an example of each

Quaternary structure is the interaction of more than one polypeptide chain to form the complete protein;
e.g. hemoglobin has two alpha subunits joined with two beta subunits;
hemoglobin is a conjugated protein, because it also requires the interaction with the heme group which has iron in it, as well as the polypeptide globin;
whereas insulin and collagen are non-conjugated proteins; because they are created by the interaction of more than one polypeptide chain; but no other groups or elements;
insulin

Nature of science - How has technology allowed us to visualise protein structure?

Cryogenic (freezing) electron microscopy has allowed us to image single protein molecules and their interaction with other molecules;

B1.2.12—What is a globular protein? What is the relationship of form and function in globular proteins?

Globular proteins have a roughly globe-like shape;
e.g. insulin;
this is caused by non-repetitive interactions giving a complex three dimensional shape;
they are soluble in water and are often enzymes;
held together by hydrogen bonding, disulphide bridges and ionic bonds;
leading to a specific shape that can bind to receptors allowing it to act as a hormone;

B1.2.12—What is a fibrous protein? What is the relationship of form and function in fibrous proteins?

What is a fibrous protein? What is the relationship of form and function in fibrous proteins?

what does the R-group do

gives each amino acid its specific properties, stabilizes protein structure

acidic amino acids

negatively charged bc extra carboxyl group loses H+ ion making COO-

basic amino acids

positively charged bc extra amine group gains H+ ion making -NH3+

nutrient

chemical substance found in foods used by the human body

essential

cannot be made by body must be obtained from diet

non-essential

can be made by the body or has a replacement that fulfills the same purpose

peptide bond

very strong covalent bond b/w carbon 2 of amino acid 1 and nitrogen of amino acid 2

word equation

amino acid + amino acid →\← dipeptide + water

diet lacking essential amino acids

causes deficiency disease

lysozyme

enzyme found in mucus, tears, blood or bacterial growth rich places (egg white), catalyzed hydrolysis reaction of the thought carbohydrate bacterial skin to make it burst

genetic code consists of…

triplets of RNA bases called codons

number of possible sequences for chain of n amino acids long

20^n

primary structure

sequence of amino acids held together by peptide bonds

proteins are made…

on ribosome found free in the cytoplasm or bound to the rough endoplasmic reticulum

THE ORDER OF AMINO ACIDS IN A PROTEIN IS

DETERMINED BY THE ORDER OF BASES IN THE DNA OF A GENE WHERE THREE BASES CODED FOR ONE AMINO ACID

primary structure determines…

3D shape of protein

change in one amino acid can

completely alter the structure and therefore function of a protein

soluble proteins

proteins w polar amino acids on exterior in contact w water to increase solubility and non polar amino acids hidden in the core to minimize contact w water

integral proteins

proteins that cross the bilayer → parts in contact w extra cellular fluid and cytoplasm have polar amino acids and parts in contact w fatty acid tails have non polar amino acids

channel proteins

protein that cross bilayer —> protruding parts and inner lining that are in contact w water have polar amino acids and non polar = hydrophobic fatty tails

collagen

3 polypeptide chains, repeating structure of gly, pro, hydroxyproline, fibrous

insulin

2 polypeptide chains, 17 amino acids, globular, hormone produced in beta cells in pancreas that regulate blood sugar levels by binding to receptors on muscle, liver, fat cells

hemoglobin

conjugated transport protein that transports oxygen from lungs to all repairing cells, 4 polypeptide chains, 2-alpha globin chains, 2-beta globin chains, non protein prosthetic heme grouo of Fe2+ for review or binding w O

fibrous proteins

• long narrow repeating

• structural support role → high stability to support tissues

• insoluble

• Fewer, repeating amino acids

• Very stable, high tensile strength

• e.g. collagen (main component of connective tissue

globular

• spherical irregular folding

• enzymes, transport, hormones, regulators

• soluble

• many variety of amino acids

• less stable

• e.g. insulin → hormone regulates blood sugar levels

denaturation

a structural change in a protein that results in an irreversible loss of tertiary structure and therefore biological properties