LEC 01 B - Intro - Chemical Foundations of Biochemistry

Summary

This lecture introduces two fundamental approaches to biochemistry: molecular structure and metabolic pathways. It emphasizes the importance of molecular structure in determining function, using proteins like myoglobin as examples. The class also explores metabolic pathways, such as the citric acid cycle, and delves into the roles of enzymes. The lecture covers the elements that constitute biomolecules, including bulk elements and trace elements, and their significance in cellular function. It discusses the Bohr model of electron configuration and how atoms bond, highlighting carbon's versatility in forming various bonds. The concept of resonance in organic chemistry is introduced, explaining the distribution of electron density in molecules like benzene and acetate. The lecture concludes with an overview of various functional groups containing oxygen, sulfur, and nitrogen, which are crucial for understanding biomolecule interactions.

Takeaways

• 🧬 **Structure and Function**: The class focuses on understanding molecular structure, particularly proteins, and how it relates to function.
• 🔬 **Biochemistry Approaches**: Two main approaches to studying biochemistry are discussed: molecular structure and metabolic pathways.
• 🌀 **Metabolic Pathways**: Metabolic pathways, such as the citric acid cycle, are explored to understand the transformation of molecules and the enzymes involved.
• 🌿 **Elements in Biomolecules**: Bulk elements like carbon, nitrogen, oxygen, hydrogen, phosphorus, and sulfur, as well as trace elements, are essential for biomolecule structure and function.
• 💧 **Water's Role**: Oxygen's high presence in the body is attributed to the abundance of water, which is a significant component of biological systems.
• 🌐 **Earth's Composition**: The human body's composition differs significantly from the Earth's crust, with carbon being a key element in biological systems.
• ⚛️ **Electrons and Bonding**: The Bohr model is introduced to explain how electrons dictate interactions and bonding between atoms.
• 🔗 **Carbon's Versatility**: Carbon's ability to form various bonds (single, double, triple) with different atoms is highlighted, leading to diverse molecular structures.
• 🔲 **Three-Dimensional Chemistry**: The importance of considering the three-dimensional nature of molecules, like cyclohexane, is emphasized.
• 🔍 **Resonance Structures**: The concept of resonance is introduced to explain the delocalization of electrons in molecules, leading to evenly distributed bonds.
• 📚 **Functional Groups**: Various functional groups containing oxygen, sulfur, and nitrogen, and their roles in biomolecules, are discussed.

Q & A

What are the two general approaches to biochemistry discussed in the class?

The two general approaches to biochemistry discussed are studying molecular structure and metabolic pathways. Molecular structure is important because it determines how biomolecules interact with each other and thus their function. Metabolic pathways, such as the citric acid cycle, are studied to understand the function of biomolecules in the context of biochemical processes.

Why is the molecular structure of proteins significant in biochemistry?

The molecular structure of proteins is significant because it dictates their function. The shape of a protein molecule determines how it interacts with other molecules, which in turn defines its role in biological processes.

What is the role of the citric acid cycle in the class's study of biochemistry?

The citric acid cycle is used as an example of a metabolic pathway in the class. Students will examine the intermediates, inputs, outputs, and the enzymes involved in the cycle, such as aconitase, which transforms citrate into isocitrate.

Which elements are considered bulk elements in biomolecules?

The bulk elements in biomolecules are carbon, nitrogen, oxygen, hydrogen, phosphorus, and sulfur.

What are the trace elements that are important for the human body and can be found in biomolecules?

Trace elements important for the human body and found in biomolecules include iron, cobalt, nickel, iodine, selenium, and magnesium.

Why is iodine added to salt, and what deficiency-related illness can result from not getting enough iodine?

Iodine is added to salt to ensure people get their daily required dose, as a deficiency in iodine can lead to the development of goiter and other thyroid-related illnesses.

How does the composition of the human body differ from that of geologic structures like rocks and sand?

The human body is composed of a higher percentage of carbon and oxygen, particularly due to the presence of water, whereas rocks and sand are composed mainly of silicon and other elements not as prevalent in biological systems.

What is the significance of the Bohr model in understanding how atoms interact in biochemistry?

The Bohr model is significant because it simplifies the understanding of electron configurations around the nucleus, which dictates how atoms will interact and bond with other atoms in biomolecules.

How does carbon's electron configuration affect its bonding capabilities in organic chemistry?

Carbon has four electrons in its outermost shell, needing four more to complete its octet. This allows carbon to form four single bonds with other atoms, contributing to the vast diversity of organic compounds.

What is the concept of resonance in the context of the phenyl group?

Resonance in the context of the phenyl group means that the double and single bonds are not fixed; instead, the electrons are delocalized and the bonds are of equal strength between single and double bonds, resulting in a symmetric structure.

Why is it incorrect to say that the acetate ion has one single bond and one double bond to oxygen in solution?

It is incorrect because the acetate ion exhibits resonance structures, meaning the electrons are delocalized and the bonds have characteristics between single and double bonds, rather than distinct single and double bonds.

What is the difference between an ether and an ester bond?

An ether bond consists of an oxygen atom in the middle of a chain, while an ester bond has a carbonyl group attached to the oxygen atom.