PHSC1212 Biochemistry - Lecture 1 Introduction to Biochemistry

biochemistry

scientific discipline concerned with the molecules and chemical processes that sustain life

life

typically defined by characteristics including metabolism, growth and reproduction, response to external stimuli, and maintaining homeostasis

metabolism, growth and reproduction, response to external stimuli, homeostasis

four main characteristics of life

complex and dynamic, organized and self-sustaining, cellular, information based, adaptive

five common set of laws that life follows

homeostasis

maintaining a stable internal environment despite external changes

atom, molecule, organelle, cell, tissue, organ, organ system, organism

organization of life in a human being starting with the smallest unit and increasing

cells

smallest units that perform all vital physiological functions

autopoietic

characteristic of cells that means they are self-organizing, self-maintaining, and self-reproducing

self regulating network of thousands of biochemical reactions

What does cellular life rely on? (focus of the course)

bacteria

simplest living organism

single cell

What are bacteria composed of?

metabolism

sum of all chemical reactions in a living organism that maintain life

enzymes

catalyze most chemical reactions in a living organism that maintain life

acquisition and utilization of energy, synthesis of molecules needed for cell structure and function, growth and development, and removal of waste products

primary functions of metabolism

acquisition and utilization of energy

feature of metabolism that includes breaking down nutrients to release energy and capturing that energy in forms the cell can use, like ATP

synthesis of molecules needed for cell structure and function

feature of metabolism where cells build complex molecules like proteins, nucleic acids, lipids, and carbohydrates from simpler building blocks

biochemical pathway

series of reactions where a reactant molecule is modified into a product that can be used for a specific purpose

metabolic, energy transfer, signal transduction

three main types of biochemical pathways

metabolic pathway

biochemical pathway involving the building or breakdown of larger molecules

anabolic, catabolic

two types of metabolic pathways

anabolic reactions

type of metabolic reaction where larger molecules are built from smaller ones (biosynthetic)

catabolic reactions

type of metabolic reaction where larger molecules are degraded into smaller ones (degradative)

energy transfer pathways

biochemical pathway and specific type of catabolic pathway that captures and converts energy into useful forms, such as glycolysis

signal transduction

biochemical pathway that involves a cell receiving a signal that results in a series of metabolism reactions that ultimately produce a particular response inside the cell

reception, transduction, response

three parts of the signal transduction pathway

ATP, NADPH

used to drive biosynthetic (anabolic) reactions to build biomolecules needed for cellular maintenance and growth

biomolecules

living organisms composed of inorganic and organic molecules

carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur

six principal elements in biomolecules

Na+, K+, Cl-, Mg2+, Ca2+

other important elements relevent to biomolecules

water

solvent of life and where biochemical reactions take place

water insolubility and limited reactivity

Why are biomolecules composed of purely hydrocarbons extremely rare?

oxygen, nitrogen, sulfur, phosphorus

What can be added to most biomolecules to add water solubility and functionality?

water solubility

When a biomolecule has polarity, it has what?

polar, forms hydrogen bonds

alcohol/hydroxyl significance

polar, found in some sugars

aldehyde/ketone/carbonyl significance

polar, weakly acidic, negative charge when donating proton

carboxylic acid/carboxyl significance

polar, weakly basic, positive charge when accepts proton

amine/amino significance

polar but no charge

amide/amido significance

easily oxidized, readily forms disulfide bonds

thiol significance

polar, in certain lipid molecules

ester significance

acid

proton donor

base

proton acceptor

ionization

important for increasing water solubility

pka

acid dissociation constant, used to express strength of weak acid or base and determines whether an acid or base will be ionized or unionized at certain pH

when pH is above pKa

When are acidic functional groups ionized?

when pH is below pKa

When are basic functional groups ionized?

lower

pKa indicating stronger acid

higher

pKa indicating stronger base

percentage of acidic or basic molecules that are ionized at certain pH

What does pKa specifically determine?

Amino acids, Nucleotides, Sugars, Fatty acids and other lipids

4 major classes of biomolecules

peptide bonds

bonds used to link amino acids to form proteins

glycosidic bonds

bonds used to link sugars to form carbohydrates

phosphodiester bonds

bonds used to link nucleotides to form nucleic acids

breaking and forming covalent bonds

What do metabolism reactions involve?

electrostatic

forces between charged particles

non-covalent interactions

weak interactions individually, but vital role in biomolecules because of cumulative effects

Ionic interactions, Van der Waals forces, Hydrogen bonds

three most important non-covalent interactions

protein structure and protein interaction with other charged molecules

What do ionic interactions affect?

Van der Waals Forces

weak electrostatic interactions with three types

dipole dipole, dipole induced dipole, induced dipole induced dipole

three types of Van der Waals forces

dipole dipole

type of Van der Waals interaction that occurs between two polar molecules that each have permanent electric dipoles; positive end of one molecule is attracted to the negative end of another molecule

electric dipoles

regions of partial positive and negative charge

dipole induced dipole

type of Van der Waals interaction that occurs between polar and nonpolar molecules; electric field from polar molecule distorts the electron cloud of the nonpolar molecule, temporarily creating an induced dipole; permanent dipole then attracts this newly formed induced dipole.

induced dipole induced dipole

type of Van der Waals interaction that occurs between any molecules; arise from temporary fluctuations in electron distribution that create momentary dipoles. These temporary dipoles can induce dipoles in neighboring molecules, leading to weak attractive forces

hydrogen bonds

bond occurring between electronegative atoms (typically

O or N) and hydrogen atoms that are covalently

bonded to other electronegative atoms

electrostatic and covalent

What characteristics do hydrogen bonds have?

ionic and polar

What type of substances does water dissolve?

solvation spheres

shells of water molecules formed around ions

hydrophobic effect

polar water molecules attempt to minimize exposure to nonpolar molecules

droplets

What do nonpolar molecules aggregate into due to hydrophobic effect?

stable lipid membranes

What is the hydrophobic effect responsible for?

amphipathic molecules

molecules with both polar and nonpolar groups

micelles

formed by amphipathic molecules when mixed with water

polar portion

part of an amphipathic molecule that can form hydrogen bonds with water

nonpolar portion

part of an amphipathic molecule that aggregates together away from the water via hydrophobic interactions