Physiology: Bicarbonate Buffer System and More

General Biochemistry Study Notes

• Biochemistry is the study of chemical processes within and relating to living organisms.
• It is a fundamental science that encompasses a wide range of topics, including the structure and function of biomolecules, metabolism, and the regulation of biological processes.
• Key concepts in biochemistry include:
• Structure & function of biomolecules (carbohydrates, lipids, proteins, and nucleic acids).
• Metabolic pathways (catabolism and anabolism).
• Enzyme kinetics and regulation.
• Cellular respiration and photosynthesis.
• Gene expression and protein synthesis.
• Cellular communication.
• Important biomolecules relate to the structure & function of living organisms.
• Knowledge of basic chemistry principles is crucial for understanding biochemical processes.

Acid-Base Concepts

• Acids are proton donors, increasing [H₃O⁺] in a solution.
• Bases are proton acceptors, increasing [OH⁻] in a solution.
• pKa is the negative logarithm of the acid dissociation constant (Ka).
• pKa indicates the strength of an acid in an aqueous solution.
• Buffers resist drastic changes in pH when acids or bases are added.
• They consist of a weak conjugate acid/base pair that maintains a relatively stable pH.
• The bicarbonate buffer is an important buffer in blood plasma.
• The blood's pH is controlled to maintain a healthy environment for metabolic functions.

Amino Acids

• Amino acids are the building blocks of proteins.
• They have an amino group (-NH₂), a carboxyl group (-COOH), and a side chain (R group) that varies between amino acids.
• Amino acids differ in their properties based on their side chains (R groups).
• These side chains can be classified as polar (hydrophilic), nonpolar (hydrophobic), acidic, basic, or aromatic.
• At a physiological pH, most amino acids exist as zwitterions with both positive and negative charges.
• Some amino acids are essential, meaning they must be obtained from the diet because the body cannot synthesize them.
• Essential amino acids include: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Others may be conditionally essential under certain circumstances, mainly for growing children.

Protein Structure I

• The flow of information from gene to protein involves the central dogma of molecular biology.
• First, information is transcribed from DNA into mRNA.
• Second, the mRNA is translated into a sequence of amino acids.
• Post-transcriptional modifications like splicing and capping/tailing can alter the sequence significantly.
• The mitochondria's proteome refers to the complete set of proteins found within the mitochondria.
• It is critical for energy production and various cellular processes.
• Most mitochondrial proteins are encoded by nuclear DNA and are synthesized in the cytoplasm, imported into mitochondria, and undergo processing.

Protein Structure II

• Primary structure is the linear sequence of amino acids in a polypeptide chain.
• Secondary structure involves local folding patterns (e.g., α-helices, β-sheets) stabilized by hydrogen bonds between backbone atoms.
• Tertiary structure describes the overall 3D structure of a single polypeptide chain, stabilized by interactions between side chains (R groups) such as hydrogen bonds, ionic bonds, disulfide linkages, and hydrophobic interactions.
• Quaternary structure describes the arrangement of multiple polypeptide chains (subunits) to form a functional protein complex, such as those found in hemoglobin.

Protein Structure III

• Post-translational modifications (PTMs) are chemical changes to proteins after synthesis, altering their structure, function, stability, localization, and interactions.
• PTMs include modifications such as phosphorylation, glycosylation, acetylation, ubiquitination, and carboxylation.

Protein Folding

• The folding mechanism of a globular protein involves multiple stages:
• Translation: ribosome assembles a polypeptide chain.
• Secondary Structure: localized folding into α-helices and β-sheets.
• Hydrophobic Collapse: hydrophobic amino acid side chains aggregate inside.
• Water Exclusion & Core Formation: Water is excluded from the hydrophobic interior.
• Domain Interactions: domains interact to guide final folding.
• Internal Packing: stable 3D conformation/structure is established.
• Quaternary Structure Assembly: formation of multimeric protein complexes.
• Molecular chaperones assist proteins during folding to prevent aggregation and ensure correct formation.

Protein Structure IV

• Protein denaturation involves the loss of native structure.
• This can be caused by extreme pH values, heat, UV radiation or other denaturing agents.

Protein Families

• Protein families are groups of proteins with a shared evolutionary origin.
• They often have similar sequences and structures but different functions.
• Myoglobin and hemoglobin are examples of homologous proteins from a common ancestral globin gene.

The Ubiquitin-Proteasome System (UPS)

• The UPS is a cellular mechanism for targeted protein degradation, essential for maintaining cellular homeostasis.
• Proteins targeted for degradation are marked by ubiquitin tags.
• The 26S proteasome complex breaks down these ubiquitinated proteins.
• Ubiquitin is recycled for repeated use.

Amyloidosis

• Amyloidosis describes a group of diseases characterized by the abnormal deposition of insoluble amyloid fibrils in tissues and organs.
• These fibrils are formed by misfolded proteins that aggregate into ẞ-pleated sheets, stabilized by hydrogen bonds - causing damage and dysfunction in affected organs
• This abnormal deposition can occur in various parts of the body, leading to different forms of amyloidosis.
• The buildup of the amyloid deposits can disrupt normal brain function.

Describing Specific Proteins

• A detailed description of a specific protein requires identifying its: structure (amino acid sequence, domains, and 3D shape), function (enzymes, transport, regulation or other proteins), and location (where it's expressed, cellular compartment, or tissues).

Understanding Various Forms of Hb

• Various forms of hemoglobin exist due to differences in globin chains during human development (i.e., embryonic, fetal, adult).
• These forms have distinct oxygen-binding properties suited to the developmental stage.

Understanding Different Forms of Modified Hb

• Haemoglobin can be modified by a variety of chemical changes, affecting its function, such as carbaminohaemoglobin (CO2 transport), carboxyhaemoglobin (CO binding), or methaemoglobin (altered iron state).

Understanding the Differences between Polyclonal and Monoclonal Antibodies

• Polyclonal antibodies are derived from multiple B cell clones, producing a mixture of antibodies with assorted specificities.
• Monoclonal antibodies are derived from a single B-cell clone, resulting in a homogenous population of antibodies specific for one antigen or epitope.

Understanding Clonal Selection and the Antibody Response

• The clonal selection theory is the fundamental mechanism of the immune response; focusing on the recognition and reaction to foreign antigens.
• Naïve B cells are activated when encountering specific antigens, and are subsequently transformed into plasma cells; then produce and secrete large quantities of specific antibodies.

Channels and Transporters

• Channels facilitate the passive movement of ions or small molecules across cell membranes, while transporters move substances across using conformational changes that do not rely on diffusion alone; active transport also requires energy input from ATP.
• Channels and transporters show specificity and have unique structural features.

The Bohr and Haldane Effects

• These are important concepts for understanding how hemoglobin regulates O2 binding and release in response to changes in pO2, pH, and CO2 concentration.

Describe how bisphosphoglycerate (BPG) binds to Hb

• BPG plays a key role in regulating haemoglobin's oxygen-carrying function, ensuring efficient delivery of oxygen to tissues under various conditions (e.g., hypoxia, high altitudes).
• It binds to a specific cavity between the subunits of deoxyhemoglobin, stabilising the T state and promoting the release of oxygen in the tissues
• This process involves several distinct steps, and the mechanism plays a crucial role in oxygen transport in humans.

Explain how protein families exist, and their relationship

• Proteins related to a common ancestor gene are paralogs, which arise from gene duplication events.
• This evolutionary relationship is evident in proteins such as myoglobin and haemoglobin, which have analogous structures and functions despite differing evolutionary lineages.

Explain the various forms of tetrameric hemoglobin in development

• The synthesis of hemoglobin changes throughout development to optimise oxygen delivery at different stages.
• Embryonic, fetal, and adult forms exhibit unique globin chain combinations with varying oxygen affinities to better meet the needs of each developmental stage; supporting homeostasis and maintaining optimum cellular function.