Biology Chapter on Gene Expression

Principles of Biochemistry

• This subject covers DNA replication and transcription, enzymes, cofactors, ATP, and energy production.
• Lectures are based on those of Caroline Searing.

Introduction

• A lecture on biochemistry is given to explain how cosmetic products claim to affect skin processes using biochemically influencing compounds in a way that enhances or decreases the cellular activities.
• Some cosmetic products claim their effects influence biochemical processes in the skin.
• Others claim to supply compounds that decline with age or to either enhance or decrease the activities of cellular organelles.

What is Biochemistry?

• Biochemistry is the study of the chemical substances and vital processes occurring in living organisms.

Structure of an Animal Cell

• A diagram of an animal cell is presented with labelled component parts, including; membrane, nucleus, nucleolus, centrioles, mitochondria, peroxisome, secretory vesicle, ribosomes, Golgi complex, plasma membrane, lysosome, vacuole, smooth endoplasmic reticulum, and rough endoplasmic reticulum.
• Explanations for each part of the cell are on other slides (as noted on the diagram).

Human Cell – The Complex Bioreactor

• A human cell is a complex biochemical reactor responsible for essential processes for survival, growth, and reproduction in an organism.

Human Cell – The Complex Bioreactor (Detailed Diagram)

• A detailed diagram/map shows the various biochemical pathways and metabolic processes within a human cell.
• The diagram displays extensive pathways and processes involved in a human cell, including glycolysis, gluconeogenesis, amino acid metabolism, porphyrin synthesis, photosynthesis, lipid/fat metabolism, nucleotide metabolism, carbohydrate metabolism, vitamin/cofactor metabolism, secondary metabolite synthesis, nitrogen metabolism, and energy metabolism.

Biomolecules – Carbohydrates

• Carbohydrates include monosaccharides, disaccharides, oligosaccharides, and polysaccharides.
• They are a primary energy source, stored as glycogen in the liver and muscles.
• Found in cytoplasm and extra-cellular space.

Biomolecules – Lipids

• Lipids are organic molecules consisting of mostly hydrophobic chemical moieties.
• Important lipids include fatty acids, sterols, triglycerides, phospholipids, ceramides, cholesterol, testosterone, and estrogen, or steroids.

Biomolecules – Amino Acids, Peptides, and Proteins

• Proteins are composed of 20 amino acids and 9 essential amino acids (that must be obtained through diet).
• Proteins are characterized by an amine group, a carboxylic acid group, and a variable R-group. Proteins are built from amino acids linked together through chemical bonds, forming peptides and proteins.
• These proteins display a globular structure: their hydrophobic chains are pushed inside the core and hydrophilic chains are on the surface. Structure determines function in proteins (e.g., primary, secondary, tertiary, and quaternary).

Biomolecules – Other Small Molecules

• This category includes ATP, hormones (e.g., Camp, NO, hydrocortisone), vitamins (essential molecules that cannot be synthesized in the body), cofactors (helper molecules for enzymes), and degradation products (e.g., urea, glutathione).
• Certain minerals are physiologically relevant for the human body, including sodium, potassium, magnesium, chloride, zinc, calcium, iron, copper, and manganese.

Biomolecules – Nucleic Acids

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids.
• The structural unit of nucleic acids is a nucleotide.

Nucleotides

• Nucleotides are made up of a phosphate group, a pentose sugar (5-carbon sugar), and a nitrogenous base.
• The phosphate group is negatively charged.

The Nitrogenous Bases

• The nitrogenous bases include Adenine (A), Thymine (T), Cytosine (C), Guanine (G), and Uracil (U).
• A and G are large, two-ringed bases (purines).
• C, T, and U are smaller, single-ringed bases (pyrimidines).

DNA

• DNA is a double-stranded molecule, forming a double helix.
• The strands are joined by hydrogen bonds between complementary bases(A-T and C-G).
• The sequence of one DNA strand determines the sequence of the complementary strand (complementary base pairing).
• Alternating sugar and phosphate molecules form the DNA backbone.

RNA

• RNA is a single-stranded molecule with a sugar phosphate backbone.
• The sugar in RNA is ribose.
• The bases include A, U, C, and G, instead of thymine (T).
• Three types of RNA exist: transfer RNA (tRNA), ribosomal RNA (rRNA), and messenger RNA (mRNA).

Summary – DNA vs RNA

• A table summarizes the key differences between DNA and RNA; their function, sugar, bases, and structure.

DNA → RNA → Amino Acids

• DNA is the master blueprint for protein synthesis in a cell.
• Genes are segments of DNA coding that codes for a polypeptide chain with the genetic information encoded as a sequence of bases.
• This genetic information is expressed by sequences of three bases called codons, which identify specific amino acids.
• Processes include transcription (encoding DNA information into RNA) and translation (decoding RNA information into amino acid sequences/assembling a polypeptide chain).

The Central Dogma of Molecular Biology

• The central dogma explains how genetic information flows from DNA to RNA to proteins.
• It involves two fundamental processes, transcription and translation.

Transcription – RNA Synthesis

• DNA remains in the nucleus, but RNA copies of the genes (mRNA) are made and leave the nucleus to carry the instructions to the cytoplasm for protein synthesis.

Translation – Protein Synthesis

• Translation occurs in the ribosomes.
• Transfer RNA (tRNA) carries specific amino acids.
• tRNA pairs with mRNA’s codons and adds amino acids to the growing polypeptide chain.
• The polypeptide chain is formed and folds into the final protein.

Mechanism of Enzyme Activity

• Enzymes have 3 basic steps in the process of enzyme activity:
• locating a substrate at the enzyme’s active site.
• enzyme-substrate complex undergoes rearrangement that forms the product
• product released, and enzyme is free to repeat the activity.
• This process is analogous to a key (substrate) locking into a lock (enzyme) to make a reaction occur

Lock and Key Theory

• The 3D shape of an enzyme's active site is critical for specific binding with a substrate, like a lock-and-key interaction;
• Substrate shape must fit the enzyme's active site for a reaction to proceed;
• This specificity determines which reactions the enzyme will catalyze/act on.

Factors Affecting Enzyme Activity

• Factors that affect enzyme activity include:
• Temperature (denaturing above optimum temp)
• pH (enzyme function/effectiveness is impacted at different pH levels)
• Substrate and Enzyme concentrations (limiting rates)
• Inhibitors (reversible or irreversible, and affecting the rate of reactions).

Enzyme Cofactors

• A table of enzyme cofactors, listing cofactors and corresponding enzymes.

Enzymes and Collagen Synthesis

• Collagen is the most abundant protein in the body.
• It’s a major component of connective tissue (skin, bone, cartilage).
• Collagen has a triple helical structure.
• Di-oxygenase enzymes are required to form hydroxyproline (by hydroxylating specific proline residues).

ATP and Energy Production

• ATP is the main energy currency in the body.
• It captures and stores energy from food.
• Its molecular weight is 507 Da.
• ATP is water-soluble.

Cellular Respiration

• Cellular respiration is the process of converting glucose into ATP (energy).
• This process involves glycolysis, the citric acid cycle, and oxidative phosphorylation.
• The diagram shows how ATP is produced through cellular respiration in a simplified view, highlighting the transition steps.

Co-enzyme Q10 (ubiquinone)

• Co-enzyme Q10 is a fat-soluble compound found in respiring cells.
• It’s part of the electron transport chain, is an essential part of cellular energy production in eukaryotic cells.
• It’s primarily found in the mitochondria.

Components of an Animal Cell (various components)

• Lists different parts of a typical animal cell like;
• centrioles, peroxisomes, smooth ER, rough ER, and their functions;
• Golgi complex/apparatus and their functions (including the processing, sorting, and secretory pathways inside a cell).
• Lysosomes, vacuoles, mitochondria (energy), nucleus (genome and control center), and nuclear envelope/membrane (separating nucleus from cytoplasm).

Gene Regulation

• Gene expression is regulated in many ways, including transcription factors.
• Products regulation can be exerted at several points along the pathways for protein or RNA synthesis control (several steps);
• Cellular regulation impacts the body’s response to external stimuli/internal factors.
• Upregulation and Downregulation – this process involves either increasing or decreasing gene product output.

Upregulation and Downregulation

• Upregulation is the process that increases the quantity of a cellular component.
• Down-regulation decreases the quantity of a cellular component in response to an external stimulus.

Genome vs Epigenome

• Genome contains the cell’s genetic information.
• Epigenome is a set of chemical compounds. It modifies or marks the genome, and thus alters the instructions from DNA (it is not encoded directly in the DNA).

Epigenetics Continued

• Epigenetic factors influence skin repair, response to UV radiation, and antioxidant activity.
• Specific products like green tea polyphenols and others may have epigenetic effects.