Lecture 1: Foundations of Biochemistry

What is biochemistry?

studying the essential structures/mechanisms/biochemical processes of all living things

Three areas of study in biochemistry

• Structural and functional biochemistry

• Informational biochemistry

• Bioenergetics

What is structural and functional biochem?

study 3D structure of molecules; understanding how structure informs protein function

What is informational biochem?

how biological info is passed on

What is bioenergetics?

how the flow of energy is transferred throughout processes

What does it mean to be alive at the molecular level?

1. function and dysfunction

2. drug discovery

3. mimicry

Function and dysfunction example

cystic fibrosis: mutation in CFTR = defective biosynthesis, with F508 (deletion of Phe at position 508) causing 70% of CF cases

drug discovery example

SARS-CoV-2; mutants cont. by infecting better and by blocking antibodies (bind well to ACE2 receptors on host cells to infect them), understanding pre-/post-fusion state structure/mechanism of spike protein F helped to develop vaccine

Mimicry example

Understanding chemical processes of living organisms can inform and advance biotechnology industries

Of the 90 naturally occurring elements, what makes up 98% of the atoms in any organism and why?

O, H = present in water

C = most common atom in biomolecules

4 major classes of biomolecules

proteins (amino acids), nucleic acids (nucleotides), lipids (fuels/membranes), carbohydrates (cell-cell interactions)

traits of biomacromolecules

• self assemble

• recognize and interact (weak and reversible interactions)

• three dimensions and shapes

Central Dogma principles

DNA → RNA → Protein; DNA replicated to form new DNA molecules, DNA transcribed to form RNA, mRNA translated into protein

How can you distinguish between different types of cells using cellular organelles?

eukaryotic cells have organelles while prokaryotic cells lack membrane bound compartments

organelles involved in the plasma membrane and endomembrane system

• nuclear envelope

• plasma membrane

• rough endoplasmic reticulum (RER)

• perixisome

• lysosome

• golgi complex

• smooth endoplasmic reticulum (SER)

nuclear envelope

segregates chromatin (DNA + protein) from cytoplasm

plasma membrane

separates cells from environment, regulates movement of materials into and out of cell

rough endoplasmic reticulum

site of protein synthesis

peroxisome (peroxides)

oxidizes fatty acidslys

osome

degrades intracellular debris

golgi complex

processes, packages, and targets proteins to other organelles or for export

smooth endoplasmic reticulum

site of lipid synthesis and drug metabolismge

gene expression organelles

ribosomes, rough ER, nucleolus

ribosomes

translate mRNA into proteins

nucleolus

site of ribosomal RNA synthesis

energy producing organelles

mitochondrion → oxidizes fuels to produce ATP

central challenge of biochemistry

the cytosol is very crowded

the foundations of biochemistry

1. There are a universal set of molecules for cellular processes in all living organisms

2. There are 4 important building blocks of macromolecules

3. Cellular organelles utilize membranes to compartmentalize different processes/control release of products

4. Generate and maintain biological order

   1. synthesis

   2. transport across membranes

   3. cellular movement

   4. waste removal