Biochemistry

Introduction in Biochemistry

Chapter 1What is BiochemistryBiochemistry: Greek : Bios =life

It is branch of science deals with study of chemical basis of life

That means chemistry of living matters at cellular and molecular level in living beings

BiochemistryBiochemistry is a special branch of organic chemistry that deals with matter inside the living cell called Protoplasm.

Protoplasm is an enormously complex mixture of organic compounds where high levels of chemical activity occur. What is Life Made of?Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation.

All students of life must have a fundamental understanding of organic chemistry and biochemistry.Organic ChemistryOrganic chemistry is the study of Carbon compounds.Organic compounds are compounds composed primarily of a Carbon skeleton.All living things are composed of organic compounds.Organic VS. inorganic compoundsOrganic compound : contain carbon (C) and hydrogen ( H ).

Inorganic compounds: rarely contain carbon.Organic VS. inorganicOrganic compound: typically larger molecules due to carbons bonding capabilities.

Inorganic compound: usually smaller than organic compounds.Organic VS. inorganic Organic compound: some dissolve in water.nonelectrolytesMost dissolve in organic liquids

Inorganic : usually dissociate in water electrolytes.

Organic VS. inorganic Organic compound: carbohydrateProteinsLipidsNucleic acids

Organic ChemistryWhat makes Carbon Special? Why is Carbon so different from all the other elements on the periodic table?

The answer derives from the ability of Carbon atoms to bond together to form long chains and rings.Organic Chemistry

Organic Chemistry

Carbon can covalently bond with up to four other atoms.Carbon can form diverse compounds, from simple to complex.

Methane with 1 Carbon atomDNA with tens of Billions of Carbon atomsBiochemistryHow much biochemistry do you need to know for this course?1. You need to know the structure of organic molecules important to major biological processes.

2. You will be expected to learn the basic biochemical processes of major cell functions, such as photosynthesis, respiration, and protein synthesis.Primary Organic CompoundsCarbohydratesLipidsProteinsNucleic Acids

You are expected to learn the structure and functions of these organic compounds:Polymers and MonomersEach of these types of molecules are polymers that are assembled from single units called monomers.Each type of macromolecule is an assemblage of a different type of monomer.

MonomersMacromoleculeCarbohydrates

Lipids

ProteinsNucleic acidsMonomerMonosaccharide

Hydrocarbon chains

Amino acids

Nucleotides

How do monomers form polymers?In condensation reactions (also called dehydration synthesis), a molecule of water is removed from two monomers as they are connected together.

.HydrolysisIn a reaction opposite to condensation, a water molecule can be added (along with the use of an enzyme) to split a polymer in two.

CarbohydratesCarbohydrates are made of carbon, hydrogen, and oxygen atoms, always in a ratio of 1:2:1. Carbohydrates are the key source of energy used by living things.The building blocks of carbohydrates are sugars, such as glucose and fructose. CarbohydratesWhat do the roots mono-, di-, oligo-, and poly mean?Each of these roots can be added to the word saccharide to describe the type of carbohydrate you have.

How do two monosaccharides combine to make a polysaccharide?

Polysaccharides

LipidsLipids are molecules that consist of long hydrocarbon chains. Attaching the three chains together is usually a glycerol molecule. Lipids are non polar.

Saturated vs. Unsaturated Fat

ProteinsProteins are building blocks of structures called amino acids. Proteins are what your DNA codes to make . A peptide bond forms between amino acids by dehydration synthesis.Levels of Protein Structure

Protein StructureLevelPrimarySecondary

TertiaryQuaternaryDescriptionThe amino acid sequenceHelices and Sheets

Disulfide bridgesMultiple polypeptides connectCellular Metabolism31Cellular metabolism refers to all of the chemical processes that occur inside living cells.Pathway: a series of biochemical reactions.In general, we can classify metabolic reactions into two broad groups:

(1) those in which molecules are broken down to provide the energy needed by cells (Catabolism)

(2) those that synthesize the compounds needed by cells both simple and complex (anabolism). Anabolism: the pathways by which biomolecules are synthsized (use ATP energy to build larger molecules from smaller building blocks). Catabolism:the biochemical pathways that are involved in generating energy by breaking down large nutrient molecules into smaller molecules with the concurrent production of energy

Comparison of catabolic and anabolic pathways

The food we eat consists of many types of compounds, carbohydrates, lipids, and proteins. All of them can serve as fuel, and we derive our energy from them.

A biochemical pathway is a series of consecutive biochemical reactions.The purpose of catabolic pathways is to convert the chemical energy in foods to molecules of ATP. To convert those compounds to energy, the body uses a different pathway for each type of compound. All of these diverse pathways converge to one common catabolic pathwayEnergyEnergy can exist in two states:1- Kinetic energy energy of motion.2- Potential energy stored energy. Chemical energy potential energy stored in bonds, released when bonds are broken.Energy can be transformed form one state to another.The ultimate source of energy for most living things is the sun.

37- ATP consists of adenosine (adenine + ribose) and a triphosphate group.- The bonds between the phosphate groups are high energy bonds.A-P~P~P

Importance of ATPAMP (adenosine monophosphate) ADP (adenosine diphosphate) - The energy gained in the oxidation of food is stored in the form of ATP.The mitochondria, which possess two membranes, are the organelles in which the common catabolic pathway takes place in higher organisms. The enzymes that catalyze the common pathway are all located in these organelles

The matrix is the inner nonmembranous portion of a mitochondrion. The inner membrane is highly corrugated and folded. - These enzymes are synthesized in the cytosoltherfore, they must be imported through the two membranes.- The enzymes are located inside the inner membrane of mitochondria so,the starting materials of the reactions in the common pathway must pass through the two membranes to enter the mitochondria. Products must leave the same way- We will discuss in detail how the specific sequence of these enzymes causes the chain of events in the common catabolic pathway. Regulating Cellular RespirationRate of cellular respiration slows down when your cells have enough ATP.

Enzymes that are important early in the process have an allosteric (regulating) site that will bind to ATP.

When lots of ATP is present, it will bind to this site, changing the shape of the enzyme, halting cellular respiration.41