Biochemistry for dummies

Introduction

About this book

Conventions used in this book

What you're not to read

Foolish assumptions

How this book is organized:

Part 1: Setting The Stage: Basic Biochemistry Concepts

Part 2: Meat Of Biochemistry: Proteins

Part 3: Carbohydrates, Lipids, Nucleic Acids, And More

Part 4: Bioenergetics And Pathways

Part 5: Genetics: Why We Are What We Are

Part 6: Part Of Tens

Icons used in this book

Where to go from here

Part 1: Setting The Stage: Basic Biochemistry Concepts:

Biochemistry: what you need to know and why:

Why biochemistry?

What is biochemistry and where does it take place?

Types of living cells:

Prokaryotes

Eukaryotes

Animal cells and how they work

Brief look at plant cells

Seems so basic: water chemistry and pH:

Fundamentals of H2O

Let's get wet! The physical properties of water

Water's most important biochemical role: the solvent

Hydrogen ion concentration: acids and bases

Achieving equilibrium

Understanding the pH scale

Calculating pOH

Applying the Brønsted-Lowry theory

Buffers and pH control:

Identifying common physiological buffers

Calculating a buffer's pH

Fun with carbon: organic chemistry:

Role of carbon in the study of life

It's all in the numbers: carbon bonds

When forces attract: bond strengths:

Everybody has 'em: intermolecular forces

Water-related interactions: both the lovers and the haters

How bond strengths affect physical properties of substances

Getting a reaction out of a molecule: functional groups:

Hydrocarbons

Functional groups with oxygen and sulfur

Functional groups containing nitrogen

Functional groups containing phosphorus

Reactions of functional groups

pH and functional groups

Same content, different structure: Isomerism:

Cis-trans isomers

Chiral carbons

Part 2: Meat Of Biochemistry: Proteins:

Amino acids: the building blocks of protein:

General properties of amino acids:

Amino acids are positive and negative: the zwitterion formation

Protonated? pH and the isoelectric point

Asymmetry: chiral amino acids

Magic 20 amino acids:

Nonpolar (hydrophobic) and uncharged amino acids

Polar (hydrophilic) and uncharged amino acids

Acidic amino acids

Basic amino acids

Lest we forget: rarer amino acids

Rudiments of amino acid interactions:

Intermolecular forces: how an amino acid interacts with other molecules

Altering interactions by changing the pH

Combining amino acids: how it works:

Peptide bond and the dipeptide

Tripeptide: adding an amino acid to a dipeptide

Protein structure and function:

Proteins: not just for dinner

Primary structure: the structure level all proteins have:

Building a protein: outlining the process

Organizing the amino acids

Example: the primary structure of insulin

Secondary structure: a structure level most proteins have:

Helix

Pleated sheet

Turns and the loops

Tertiary structure: a structure level many proteins have

Quaternary structure: a structure level some proteins have

Dissecting a protein for study:

Separating proteins within a cell and purifying them

Digging into the details: uncovering a protein's amino acid sequence

Enzyme kinetics: getting there faster:

Enzyme classification: the best catalyst for the job:

Up one, down one: oxidoreductases

You don't belong here: transferases

Water does it again: hydrolases

Taking it apart: lyases

Shuffling the deck: isomerases

Putting it together: ligases

Enzymes as catalysis: when fast is not fast enough

All about kinetics:

Enzyme assays: fixed time and kinetics

Rate determination: how fast is fast?

Measuring enzyme behavior: the Michaelis-Menten equation:

Ideal applications

Realistic applications

Here we go again: Lineweaver-Burk plots

Enzyme inhibition: slowing it down:

Competitive inhibition

Noncompetitive inhibition

Graphing inhibition

Enzyme regulation

Part 3: Carbohydrates, Lipids, Nucleic Acids, And More:

What we crave: carbohydrates:

Properties of carbohydrates:

They contain one or more chiral carbons

They have multiple chiral centers

Sweet topic: monosaccharides:

Most stable monosaccharide structures:

Pyranose and furanose forms

Chemical properties of monosaccharides

Derivatives of monosaccharides

Most common monosaccharides

Beginning of life: ribose and deoxyribose

Sugars joining hands: oligosaccharides:

Keeping it simple: disaccharides

Starch and cellulose: polysaccharides

Aldose family of sugars

Lipids and membranes:

Lovely lipids: an overview

Behavior of lipids

Fatty acids in lipids

Fatty subject: triglycerides:

Properties and structure of fats

Cleaning up: breaking down a triglyceride

No simpletons here: complex lipids:

Phosphoglycerides

Sphingolipids

Sphingophospholidpids

Membranes: the bipolar and the bilayer:

Crossing the wall: membrane transport

Steroids: pumping up

Prostaglandins, thromboxanes, and leukotrienes: mopping up.

Nucleic acids and the code of life:

Nucleotides: the guts of DNA and RNA:

Reservoir of genetic info: nitrogen bases

Sweet side of life: the sugars

Sour side of life: phosphoric acid

Tracing the process: from nucleoside to nucleotide to nucleic acid:

First Reaction: Nitrogen base + 5-carbon sugar = nucleoside

Second Reaction: Phosphoric acid + nucleoside

nucleotide

Third Reaction: Nucleotide becomes nucleic acid

Primer on nucleic acids:

DNA and RNA in the grand scheme of life

Nucleic acid structure

Vitamins: both simple and complex:

More than one-a-day: basics of vitamins

To B or not to B: B complex vitamins:

Vitamin B1, (thiamine)

Vitamin B2, (riboflavin)

Vitamin B3 (niacin)

Vitamin B6 (pyridoxine)

Biotin

Folic acid

Pantothenic acid

Wonders of vitamin B12

Vitamin A

Vitamin C

Vitamin D

Vitamin E

Vitamin K

Hormones: the body's messengers:

Structures of some key hormones:

Proteins

Steroids

Amines

Now and later: prohormones:

Proinsulin

Angiotensinogen

Fight or flight: hormone function:

Opening the letter: hormonal action

Models of hormonal action

Part 4: Bioenergetics And Pathways:

Life and energy:

ATP: the energy pony express:

ATP and free energy

ATP as an energy transporter

It's relative: molecules related to ATP:

Nucleoside triphosphate family

As easy as 1, 2, 3: AMP, ADP, and ATP

Where it all comes from

ATP: the body's monetary system:

Metabolism 1: Glycolysis:

Glucose: where it all starts

Releasing the power: energy efficiency

Going in reverse: Gluconeogenesis

Alcoholic fermentation: we'll drink to that

Metabolism 2: Citric acid (Krebs) cycle:

Let's get started: synthesis of acetyl-CoA

Three's a crowd: tricarboxylic acids

Oxidative decarboxylation

Production of succinate and GTP

Oxaloacetate regeneration

Amino acids as energy sources

Electron transport and oxidative phosphorylation:

Electron transport system

Oxidative phosphorylation

Proposed mechanisms

ATP production

Involving the fats: b-oxidation cycle

Not so heavenly bodies: ketone bodies

Investing in the future: biosynthesis:

Fatty acids

Membrane lipids

Amino acids

Smelly biochemistry: nitrogen in biological systems:

Ring in the nitrogen: purine

Biosynthesis of purine

How much will it cost?

Pyrimidine synthesis:

First Step: Carbamoyl phosphate

Next Step: Orotate

Last Step: Cytidine

Back to the beginning: catabolism:

Nucleotide catabolism

Amino acid catabolism

Heme catabolism

Process of elimination: the urea cycle

Amino acids once again

Metabolic disorders:

Gout

Lesch-Nyhan syndrome

Albinism

Alkaptonuria

Phenylketonuria

Part 5: Genetics: Why We Are What We Are:

Photocopying DNA:

Let's do it again: replication:

DNA polymerases

Current model of DNA replication

Mechanism of DNA repair

Mutation: the good, the bad, and the ugly

Restriction enzymes

Mendel rolling over: recombinant DNA

Patterns: determining DNA sequences:

Getting charged up about gel electrophoresis

Determining the base sequence

Butler did it: forensic applications

Genetic diseases and other DNA testing applications:

Sickle cell anemia

Hemochromatosis

Cystic fibrosis

Hemophilia

Tay-sachs

Transcribe this! RNA transcription:

Types of RNA

RNA polymerase requirements

Making RNA: the basics:

Promoting transcription of RNA

Prokaryotic cells

Eukaryotic cells

Not a secret any longer: the genetic code:

Codons

Alpha and omega

Models of gene regulation:

Jacob-Monod (operon) model

Regulation of eukaryotic genes

Translation: protein synthesis:

Hopefully not lost in translation:

Why translation is necessary

Home, home in the ribosome

Translation team:

Team captain: rRNA

Here's the snap: mRNA

Carrying the ball: tRNA

Charging up the middle: amino acid activation

Hooking up: protein synthesis:

Activation

Initiation

Elongation

Termination

Wobble hypothesis

Variation in eukaryotic cells:

Ribosomes

Initiator tRNA

Initiation

Elongation and termination

Part 6: Part Of Tens:

Ten great applications of biochemistry:

Ames test

Pregnancy testing

HIV testing

Breast cancer testing

Prenatal genetic testing

PKU screening

Genetically modified foods

Genetic engineering

Cloning

Gene-replacement therapy

Ten biochemistry careers:

Research assistant

Plant breeder

Quality control analyst

Clinical research associate

Technical writer

Biochemical development engineer

Market research analyst

Patent attorney

Pharmaceutical sales

Biostatistician

Index.