DNA and Polypeptide Synthesis (HSC SSCE Biology): Revision Notes

Proteins in Living Things

Introduction to proteins

Proteins are the most abundant organic molecules found in cells. They perform two critical roles in living organisms. First, they create the fundamental structure of cells. Second, they carry out all cellular work by controlling chemical reactions that occur within cells.

Chemical structure of proteins

Elements in proteins

Proteins are composed of five chemical elements:

• Carbon (C)
• Hydrogen (H)
• Oxygen (O)
• Nitrogen (N)
• Sulfur (S) - sometimes present

These elements combine to form amino acids, which are the building blocks of all proteins.

Amino acids and polypeptides

There are approximately $20$ different amino acids. These can be arranged in chains containing up to $300$ amino acids. Each amino acid contains:

• An amino group ($\text{NH}_2$)
• An acid group ($\text{COOH}$)
• A variable 'R' group (hydrocarbon chain) that differs between amino acids

The diagram below shows the structure of two amino acids - proline and glycine:

Amino acids in a chain are connected by peptide bonds - chemical forces of attraction that hold the sequence together. A chain of amino acids linked by peptide bonds is called a polypeptide.

One or more polypeptides can twist together into a particular shape, creating the overall structure of a protein. The sequence and arrangement of amino acids determines the type of protein, similar to how letters of the alphabet combine to form words and sentences.

Physical structure of proteins

Proteins have a hierarchy of organisation described at four levels: primary, secondary, tertiary and quaternary structure.

Primary structure

The primary structure is the linear sequence of amino acids in a polypeptide chain. This is the most basic level of protein structure - simply the order in which amino acids are arranged.

Secondary structure

The secondary structure refers to the three-dimensional arrangement of the polypeptide chain. This structure forms when the amino acid chain becomes linked by hydrogen bonds.

There are two main types of secondary structure:

• Alpha helix: The polypeptide twists into a spiral shape. This is typical of fibrous proteins
• Pleated sheet: The polypeptide folds into a sheet-like structure held together by hydrogen bonds

Tertiary structure

The tertiary structure is seen in more complex proteins, particularly globular proteins. Further folding occurs when forces of attraction (such as disulfide bonds) form between different parts of the secondary structure. This causes the polypeptide to fold into a complex three-dimensional shape.

Quaternary structure

Quaternary structure occurs when a protein is made up of two or more polypeptide chains that link together to create an even more complex three-dimensional structure.

A single protein molecule may contain more than one type of structure. For example, spider silk contains pleated sheets joined by less ordered alpha helices.

Impact of amino acid changes

The primary structure (amino acid sequence) determines the secondary and tertiary structure of the protein. If an incorrect amino acid is inserted into a polypeptide chain, this may change the bonding properties of an essential part of the protein. This can alter the secondary, tertiary and quaternary structures, potentially changing or preventing the protein from functioning.

Occasionally, an amino acid change may improve protein function. Such changes are the source of random variation in populations that natural selection can act upon.

Types of proteins

Proteins can be classified into three main structural types based on their shape and composition.

Fibrous proteins

Fibrous proteins are long, stringy proteins that are insoluble in water. They form structural components of cells and tissues. Together with water, they create the basic structure of protoplasm (the cytoskeleton).

Examples:

• Collagen: A long, stringy protein that is coiled and very strong. Commonly found in skin, ligaments and tendons
• Elastin: Found in skin, ligaments and tendons alongside collagen
• Keratin: Found in hair and nails

The diagram below compares collagen (a fibrous protein) with haemoglobin (a globular protein):

Globular proteins

Globular proteins are usually spherical in shape, compact, and soluble in water. They typically perform functional roles rather than structural roles.

Examples:

• Haemoglobin: A transport protein in blood that carries oxygen
• Immunoglobulins (antibodies): Defence proteins that fight pathogens
• Hormones: Chemical messengers
• Enzymes: Catalysts that speed up biochemical reactions

Conjugated proteins

Some proteins are linked to a non-protein component called a cofactor. When the cofactor is tightly bound, it is termed a prosthetic group and may be organic or an inorganic metallic ion.

Functions of proteins

The biological properties of proteins depend on their interactions with other molecules. The tertiary structure and three-dimensional shape of a protein determines its ability to bind tightly and specifically with other molecules, and therefore determines its ability to function effectively.

Structural proteins - support and movement

Structural proteins provide support and enable movement in cells and organisms.

Support

Structural proteins are often fibrous and found in connective tissues such as:

• Skin, cartilage and bone
• Tendons and ligaments
• Shells in invertebrates
• Hair, nails and hooves in vertebrates

Tubulin (a protein in microtubules) forms the cytoskeleton, which maintains cell shape.

Movement

Several proteins enable movement:

Microtubules: These allow movement in cells. For example:

• Cilia and flagella move as microtubules slide along each other
• Spindle fibres contract by a similar mechanism during cell division

Contractile proteins: In muscle, the protein actin slides along another protein called myosin, allowing the muscle to contract. This is shown in the diagram below:

Actin is also found in microfilaments in cells. These are responsible for:

• Contraction of the cytoplasm, allowing the cell membrane to pinch off during cytokinesis in animal cells
• The crawling movement of protists such as amoeba

Enzymes - control of biochemical reactions

Enzymes are protein molecules involved in all biochemical aspects of cellular metabolism. They catalyse (speed up) reactions such as:

• Chemical respiration pathways
• Digestion
• DNA replication, repair and transcription

Proteins for cell communication, cell signalling and biological recognition

Cells communicate using chemical signals. Many of these signals involve proteins.

Membrane transport proteins

Some proteins embedded in cell membranes form channels to transport substances between cells and their environment. The diagram below shows the fluid mosaic model of the cell membrane with various embedded proteins:

Cell signalling

Some proteins act as chemical messengers between cells:

• Hormones: Signal changes in cell functioning
• Neurotransmitters: Transmit signals between nerve cells

These messengers communicate information to cells about their environment and trigger responses in the target cell's functioning.

Biological recognition

Receptor proteins in cell membranes receive chemical signals. These proteins must have a shape that is exactly complementary to the shape of the molecule they bind with.

Some receptors on cell surfaces are genetically determined and act as markers. These allow the body to:

• Recognise its own cells
• Identify foreign invaders (pathogens) that need to be destroyed

Antibodies (also called immunoglobulins) are defence proteins. They recognise foreign invaders by detecting different proteins on the surfaces of pathogen cells (called antigens). Antibodies bind with these antigens to signal to other defence cells that the invading antigens need to be destroyed.

Transport and storage proteins

Some proteins bind to and carry or store chemicals in the body. These are termed ligand-binding proteins and must be able to bind easily with the chemical (ligand) and release it when and where needed.

Transport proteins

Haemoglobin is an excellent example. It has an affinity (attraction) for oxygen, particularly when oxygen is present in high concentrations (such as in the lungs). Haemoglobin loses its affinity for oxygen in areas with low oxygen concentration and high carbon dioxide concentration (such as in active tissues).

Storage proteins

Some proteins store chemicals for use by the organism:

• Ferritin: Stores iron
• Albumin: Found in egg whites, stores amino acids
• Casein: Found in milk, stores amino acids

Sensory proteins - responding to stimuli

Some proteins change their shape or biochemical activity in response to stimuli (changes in the environment).

Technology and protein research

Proteomics and genomics

Today, we can predict expected amino acid sequences in proteins because we understand how nucleotide sequences in DNA are decoded.

Genomics is the field of sequencing the nucleotides of complete sets of genes in organisms.

Proteomics is the large-scale study of sets of proteins produced in an organism or biological system. This research aims to understand how proteins in different cell types work together.

Bioinformatics

Bioinformatics is the field that combines computer science and genetics. People working in this field develop methods and software for analysing and interpreting biological data. It combines:

• Biology
• Computer science
• Mathematics
• Statistics
• Engineering

X-ray crystallography and synchrotrons

X-ray crystallography has been used for over a century to study molecular structures. Over the past $60$ years, it has been applied to study biological macromolecules like proteins.

Initially, progress was slow because X-ray diffraction technology needed to evolve to produce sufficiently strong X-ray beams. Collecting data for large molecules like proteins took many days or weeks.

The first complete protein structure (myoglobin) was published in $1958$. By $1971$, the Protein Data Bank (PDB) was created, containing seven protein structures determined using X-ray diffraction.

Because one protein may have between $5$ and $50$ different modified forms (each with a different function), progress was slow. What was needed were:

• High-brilliance X-ray radiation sources to speed up diffraction measurements
• Methods to analyse data quickly

The development of the synchrotron (a particle accelerator) brought about this change. A synchrotron emits electromagnetic radiation by accelerating charged particles to speeds close to the speed of light. By the $1990$s, third-generation synchrotrons provided the high-resolution images required.

Today, detailed analysis of protein structure is assisted by 3D visualisation computer technology. Programs can sort protein structures by:

• Arrangement of particular chemical elements
• Bonding patterns
• Sequence of atoms
• Overall structure and shape

This is extremely useful for exploring how changes in amino acid sequences affect protein structure. Many proteins targeted in cancer research are currently being studied using these methods and big data analysis.

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