Topic 2.4 - Protein
amino acids, amino acids, condensation reactions, amino acids, peptide bond, dipeptide, amino acids, ribosomes
Fill in the blanks: Polypeptides are polymers of ________ . _______ are joined by _________ reactions. Two ________ are linked by a _______, forming a _________. More ________ are added to form a polypeptide. Polypeptides are synthesized by ________ in the cytoplasm.
Fibrous: long and narrow, structural, repetitive sequence, less sensitive to change in pH and temperature, generally insoluble in water, example: collagen Globular: round and spherical, functional, irregular amino acid sequence, more sensitive to changes in pH and temperature, generally soluble in water, example: insulin
Compare fibrous proteins and globular proteins
alpha helix
A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.
The proteome is all the proteins produced by a cell, tissue, or individual. Proteins are coded by genes. Any genetic differences (in genes) between individuals will result in them coding slightly different proteins. Hence, a different genome will lead to a different proteome. In addition, the proteome can change during development or in response to environmental factors. The proteome can be visualized by two-dimensional gel electrophoresis.
Define the term proteome. Why do all individuals have a unique proteome?
Because there are 20 different amino acids that can be assembled in any order, there are so many different shapes proteins can have. The shape of the protein determines its function. Example: The shape of hemoglobin enables it to move through human veins and arteries transporting oxygen and carbon dioxide.
Explain how the structure of proteins allow for their biological functions.
The carboxyl group of one amino acids joins with the amine group of the other amino acid. A peptide bond is formed between two amino acids. One molecule of water is produced. The next amino acid would join onto the carboxyl group of the dipeptide.
Explain how two amino acids join.
Each protein has a pH range in which it has its normal three dimensional shape. Changes away from this pH range cause intramolecular interactions between non adjacent amino acids (those involved in protein folding) to break. Denaturation caused by mild changes to pH can be reversible.
How do changes in pH cause a protein to denature?
A gene is a sequence of DNA which encodes a polypeptide sequence. It is either converted via transcription or translation.
How does a gene convert into a polypeptide?
The structure of the R group determines the unique properties of amino acids. Depending on the R group, amino acids can have traits of being polar, non polar, acidic, basic, charged, or aromatic.
How does the structure of the 'R' group affect the properties of a particular amino acid?
The sequence of amino acids in a polypeptide is determined by the sequence of DNA nucleotides in a gene. A polypeptide is a single chain of amino acids. A protein comprises one or more polypeptides. Most proteins are single polypeptides. Some proteins combine two or more polypeptides.
How is the sequence of amino acids in a polypeptide determined? Distinguish the terms polypeptide and protein.
beta pleated sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
quaternary structure
Only found in proteins with more than 2 polypeptides chains. Hydrophobic reactions that help determine structure. Much more efficient and functional.
Twenty different amino acids are found in all living organisms. They vary at the R group only. R groups have different properties. These include: Hydrophilic (polar or charged) R groups. Hydrophobic R groups. The finding that all organisms use the same 20 amino acids (coded by the same genetic code) to build polypeptides supports the theory that all organisms on Earth evolved from a single, common ancestor. However, three non-standard amino acids have been discovered. For example, pyrrolysine is found in some archaea and one bacterium that produces methane.
Outline differences between amino acids that are found in the polypeptides of living organisms.
Polypeptides fold up into three-dimensional structures after being synthesized. Most proteins fold into a compact, globular shape. Each different polypeptide has a unique three-dimensional shape (or conformation). The three-dimensional conformation gives a protein its specific function. The way a protein folds up depends on the sequence of amino acids. Intramolecular bonds link non-adjacent amino acids to form a stable, three-dimensional shape. If a protein is soluble, amino acids with hydrophilic R groups are usually positioned on the outside of the structure and amino acids with hydrophobic R groups in the center. The same polypeptide will always fold up in an identical way.
Outline how the sequence of amino acids in a protein determines its three-dimensional shape.
Rubisco - Enzyme - Catalyzes the fixation of inorganic carbon dioxide from the atmosphere into carbon compounds. This is the first major step in the production of organic compounds by photosynthesis. Insulin - Hormone - Regulates blood glucose levels. A messenger that is secreted by the pancreas and transported in the blood. Immunoglobulins - Antibody - Helps to destroy pathogens. Produced as part of a specific immune response. Rhodopsin - Pigment - A light sensitive pigment present in rods, a type of photoreceptor. Collagen - Structural - Collagen is a protein made of three polypeptide chains twisted around each other. It is strong and flexible and used in ligaments, tendons, and blood vessels. Spider silk - Structural - Spiders use silk to suspend themselves and make webs to catch prey. It can stretch without breaking.
Proteins have diverse functions in living organisms. Outline the range of functions using the following proteins as examples: Rubisco Insulin Immunoglobulins Rhodopsin Collagen Spider silk
When a protein is denatured, it loses its three-dimensional shape. This results in the loss of function. Heat causes the atoms within the protein to vibrate. If the vibrations are great enough, intramolecular interactions between non adjacent amino acids (those involved in protein folding) break. This usually results in a permanent loss of shape.
What happens when a protein becomes denatured?How does heat cause a protein to denature?
Polypeptides are made from 20 different amino acids. The composition and order of amino acids can vary. The length of the polypeptide can also vary. A typical polypeptide is 300 amino acids long but they range from 100 to over 30,000 amino acids in length. The unlimited variety of polypeptides allows them to be an extremely diverse group of molecules with a wide range of functions.
Which features give polypeptides unlimited variety?
Because they have many different functions based on their structure. The structure of a protein depends on the sequence of amino acids and there are 20 different amino acids, which can be assembled in any order, so there are a lot of ways a protein can be folded. This is why proteins have many functions which are categorized into 7 main functions: defense, transport, support, enzyme catalysis, motion, regulation, and storage
Why are proteins the most complex biological molecules?
Gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene. Proteins may be modified following translation to phosphorylated further variations
Why is the proteome always larger than the number of genes?
Primary structure of Protein and bonds involved
a sequence of amino acids are bonded together through dehydration synthesis to create peptide bonds between two amino acids. The peptide bonds act as a partial double bond and inhibit free rotation, which affects the structural character of the coils and other shapes formed by chains of amino acids.
Secondary structure of proteins and bonds involved
amino acids are in a helix/pleated form due to the hydrogen bonds between amino acids, causing there to be more structure in the protein
tertiary structure
bends itself to become stable due to sulfide bridges and hydrogen bonds between R groups, determined by the interactions between the variable side chains (hydrogen bonds, disulphide bridges, ionic interactions, polar associations)
Transcription
making an mRNA transcript based on a DNA template (occurs in the nucleus)
fibrous proteins
protein structure which are generally composed of long and narrow strands and have a structural role. (they are something)
globular proteins
protein structure which are more compact and rounded shape and have functional roles (they do something)
Translation
using the instructions of the mRNA transcript to link amino acids together (ribosome)
