AP Biochemistry

UNIT 2 – THE CHEMISTRY OF LIFE(Chapters 2 – 5 and Chapter 8)

THEMES OF THE UNIT:THEME 1 – SCIENCE AS A PROCESS – X-ray crystallography helps scientists determine the 3D structure of proteins and nucleic acids.

THEME 2 – EVOLUTION – Chemical evolution of the young earth set the stage for the origin of live.

THEME 6 – REGULATION – In feedback inhibition, a metabolic pathway is switched off by its end product.

THEME 7 – INTERDEPENDENCE – Prokaryotes play essential roles in chemical cycling for plants and animals.

CHAPTER 2 – BASIC CHEMISTRYYOU MUST KNOW:

The three subatomic particles and their significance. The types of bonds, how they form, and their relative

strength.

We will not spend any time on this chapter. If you are not familiar with this, please check out the notes in your exam review book.

CHAPTER 3 – CHARACTERISTICS OF WATERYOU MUST KNOW:

The importance of hydrogen bonding to the properties of water.

Four unique properties of water, and how each contributes to life on Earth.

How to interpret the pH scale. The importance of buffers in biological systems.

I. The Chemical Composition of WaterYou must be able to draw the structural formula of water and bind at least 4 water molecules together with hydrogen bonds. Use proper chemical symbols not circles when you draw water.

II. The Characteristics of Water

Property of water Structural explanation

Significance for life

Ice is less dense than water

Ice takes on a more regular, tetrahedral structure so the molecules are further from each other

Life under ice

Low viscosity Small molecules Flows through very small spaces, capillaries

Liquid at room temperature

H-bonds Medium for aquatic life, inside cells

Colorless with a high transmission of visible light

Small, stable molecule, no excitable electrons

Light penetrates tissues and aquatic environments

Strong adhesive and cohesive forces

H-bonds Water can be lifted and does not pull apart easily.

Water is classified as a universal solvent because many substances can dissolve in water

H-bonds, polar, small molecules

Medium for the chemical reactions of life, main transport mediumHydrophilic and hydrophobic substances

Significant amounts of energy are required before water will change state (high heat of fusion)

H – bonds Contents of cells are unlikely to freeze.

High heat of vaporization

H-bonds Heat is lost by evaporation of water. Sweating and transpiration causes rapid cooling.

Water can absorb a lot of energy for only a small rise in temperature (high heat capacity or

H – bonds Aquatic environments are thermally stable. Organisms have stable internal temperatures when

specific heat) external temperatures fluctuate.

High surface tension Close attraction between water molecules, H – bond

Water forms droplets on surfaces and runs off.

III. Acids, Bases, pH, Buffers and IndicatorsWe will not spend any time on this section either. If you are not familiar with this, please read your review book.

CHAPTER 4 – CARBON AND THE MOLECULAR DIVERSITY OF LIFE

OBJECTIVESYOU MUST KNOW:

The properties of carbon that make it so important. The functional groups.

I. OVERVIEW Every living organism is made up of chemicals based mostly on

the element carbon. Carbon enters living organisms through plants via

photosynthesis. Other important elements in living organisms are:

o Oxygeno Hydrogeno Nitrogeno Sulfuro Phosphorous

II. CARBON COMPOUNDS AND FUNCTIONAL GROUPS: Organic compounds – molecules that contain carbon, except

carbonates, carbides, carbon dioxide and carbon monoxide. Special characteristics of carbon:

o Able to form long chains and ringso Able to bind with other carbon atoms or other atoms in an

unlimited numbero Able to form stable covalent bonds (4 of them)o Able to form double bonds and triple bonds

Molecules that contain only hydrogen and carbon are called hydrocarbons. Hydrocarbons are major components of petroleum (fossil fuel) but not particularly important in living organisms.

Functional groups (parts of organic molecules that are mostly involved in chemical reactions that behave consistently in various compounds and determine the chemical characteristics of those compounds):

CHAPTER 5 – THE STRUCTURE AND FUNCTION OF MACROMOLECULES

OBJECTIVE QUESTIONS:YOU MUST KNOW:

The role of dehydration synthesis in the formation of organic compounds and hydrolysis in the digestion of organic compounds.

How to recognize the four biologically important organic compounds (carbohydrates, lipids, proteins, nucleic acids) by their structural formulas.

The cellular functions of all four organic compounds. The four structural levels that proteins can go through to

reach their final shape (conformation) and the denaturing impact that heat and pH can have on protein structure.

I. OVERVIEW: A new level of hierarchy is reached when small molecules and

atoms combine to form very large molecules – macromolecules.

The architecture (structure) of these molecules helps to determine their function (how they work). – Theme of Biology

The four major groups of macromolecule that are common in living organisms are:

a. Nucleic acidsb. Carbohydratesc. Lipidsd. Proteins

II. MACROMOLECULES ARE BUILT FROM MONOMERS Three of the four groups of macromolecules (nucleic acids,

carbohydrates, proteins) are chains of smaller units called monomers. When these chains combine, they form polymers – a long molecule consisting of many similar or identical building blocks linked together by covalent bonds.

Some of the monomers have other functions. Example: some amino acids are neurotransmitters or hormones, some nucleic acids carry electrons, protons or high energy bonds.

Condensation (dehydration) reaction – the chemical reaction that connects monomers by covalent bonds to form polymers, while water is released.

M – OH + H – M – M – M – OH → H2O + M – M – M- M – OH

Hydrolysis – Chemical reaction, in which polymers are disassembled into their monomers. Water is inserted into the reactants to get the products.

H2O + M – M – M- M – OH → M – OH + H – M – M – M – OH With the help of these reactions, a few monomers can give rise

to a huge number of polymers within each individual and among species.

http://www.tvdsb.on.ca/westmin/science/sbioac/biochem/condense.htm

III. CARBOHYDRATES Include both sugars and the polymers of sugars. They are

molecules that contain carbon, hydrogen and oxygen

A. Monosaccharides The simplest form of carbohydrates are monosaccharides

(CH2O), the most important representatives of monosaccharides

are glucose (C6H12O6)

Important functional groups in sugars are carbonyl group, hydroxyl group.

Monosaccharides can be very diverse for three reasons:o Location of the carbonyl group can be at the end of the

chain (aldose) or not at the end of the chain (ketose)o Number of carbon atoms can vary (hexose, pentose, triose)o Spatial arrangement of the parts of asymmetric carbon

atoms Glucose as well as most monosaccharides form ring structures Monosaccharides are generally used as sources of energy during

cellular respiration. If they are not immediately used than they are stored as polysaccharides or disaccharides

B. Dissacharides: Molecules that consists of two monosaccharides joined by

glycosidic linkage (a covalent bond formed between two monosaccharides by dehydration reaction)

Most important representatives are:o Maltose (two glucose) – ingredients of beer makingo Sucrose (glucose + fructose) – table sugaro Lactose (glucose + galactose) – found in milk.

C. Polysaccharides: Macromolecules of a few hundred to a few thousand

monosaccharides joined by a glycosidic linkage Most important representatives and their functions:

o Starch – a storage polysaccharide of plants that consists entirely of glucose molecules that join by a 1-4 carbon linkage by two α-glucose molecules. The molecule is helical. Two subgroups of starches are amylose and amylopectin.

o Glycogen – a storage polysaccharide of animals that is like amylopectin but more branched. In higher animals it is mostly stored in the liver and the muscles.

o Cellulose – a structural polysaccharide that is the major component of plant cell walls. A polymer of glucose molecules but in this case the OH group on the first carbon has a β orientation. This orientation results in long fiber-like molecules that are very though. Enzymes in humans cannot digest cellulose but can digest starch. Digestion of cellulose in animals is frequently helped by microbes.

o Chitin – structural polysaccharide that is found in arthropods shells (exoskeletons) and in many fungi.

IV. LIPIDS: These compounds are all hydrophobic and have little or no

affinity to water. They contain very few oxygen molecules but have long chains of

hydrocarbons. Their form and function varies greatly in each subgroup:

o Fatso Phospholipidso Steroids

A. FATS:

These molecules are not polymers but large molecules that are assembled from simpler units of 1 glycerol and 3 fatty acid molecules by dehydration synthesis:

Important functional groups are hydroxyl and carboxyl groups. But the long CH2 chains make the fats hydrophobic

Fats vary in length and number of carbon atoms in the carbon chain. They also can have varying number of double bonds. This results in two types of fats:

o Saturated fats – don’t have any double bonds in the carbon chain. These fats are mostly animal originated, harder and mostly solid on room temperature.

o Unsaturated fats – they have one or more (polyunsaturated) double bonds in the carbon chain. These fats are mostly plant originated, liquid on room temperature.

Health issues. Biological function of fats:

o Fats are important energy storage molecules. 1 g of fat stores more than 2x as much energy as 1 g of polysaccharide.

o Adipose tissue (fat storage cells) also cushions vital organs and provides thermal insulation.

B. PHOSPHOLIPIDS: Structure: similar to fats but one of the fatty acids are replaced

by a phosphate group:

Because of the negative charge of the phosphate group, phospholipids are polar and can be linked to other polar molecules. Phospholipids form bilayers in water to shield their hydrophobic portions:

Biological function of phospholipids: Their bilayers are the basis of the cell membrane structure that separates every cell from its environment.

C. STEROIDS: Lipids that have a characteristic carbon skeleton of four fused

rings:

Because of their multiple nonpolar rings, sterols are usually fat soluble and insoluble in water.

The most common sterol is cholesterol. Biological function of cholesterol:

o Cholesterol is a common component of cell membranes that give the membrane more rigidity

o Many hormones including sex hormones are steroidso Vitamin D is also made of sterol derivatives

IV. PROTEINS: As the main structural components of all living organisms they

account for 50 % of the total dry mass of cells. Their functions are very diverse:

Proteins’ diverse functions are supported by a very strictly determined hierarchical arrangement of protein structure.

A. AMINO ACIDS AND THE PRIMARY PROTEIN STRUCTURE: All proteins are constructed from the same 20 different amino

acids. Amino acids are smaller organic molecules that have both

carboxyl and amino functional groups:

The 20 amino acids are all different in the R group. The polarity and other characteristics of this group will determine the 3 dimensional structure of the protein that is formed from amino acids:

Amino acids bind to each other by peptide bonds and form long chains of polypeptides. This process is a type of condensation reaction:

The first protein that had its amino acid order determined was insulin. Since than the science of proteomics determined many more protein structures.

B. SECONDARY PROTEIN STRUCTURE: The repeated folding of the polypeptide chain and fixing this

folding by hydrogen bonds is called the secondary structure of a protein.

This structure is fixed by hydrogen bonds between the oxygen and nitrogen atoms and the hydrogen atoms of the main backbone of the polypeptide chain.

The secondary structure can take two different shapes:o - helix: a delicate coil that is fixed with a hydrogen bond

between every fourth amino acid. -helix provides flexibility to proteins.

o pleated sheet: two or more regions of polypeptide chains lying side by side and connected by hydrogen bonds. - sheet provides strength to proteins

C. Tertiary Structure: Multiple sets of various secondary structures add up to the

tertiary structure of a protein. This structure constructs the protein’s three dimensional shape and determines important sites that are necessary for the normal functioning of the protein.

The tertiary structure is fixed by various bonds of the side chains of the amino acids. Potential bonds include covalent bond, ionic bond, hydrogen bond, hydrophobic interactions, and van der Waals interactions, disulfide bridges.

D. Quaternary structure: When two or more polypeptide chains aggregate into one

functional macromolecule, the quaternary structure of the protein is formed. Ex. Collagen is formed from 3 long helical polypeptide chains. This protein is found in the connective tissue of animals and gives the tissue stability and resistance. Hemoglobin is an other complex protein that is formed from 4 polypeptide chains. It is a protein that is necessary to carry oxygen in the red blood cells.

A simple change in the primary structure of a protein can affect the protein’s entire conformation and function. A good example is sickle cell disease.

Watch: http://www.pbs.org/wgbh/evolution/library/01/2/quicktime/l_012_02.html on malaria and sickle cell anemia relationship

Protein conformation is mostly determined by the type and order of amino acids in the protein molecule, however, there are other factors that influence it, such as: temperature, pH, salt concentration. If these factors are not ideal, denaturation of proteins can take place. Denaturation is the loss or change of the native conformation of the protein that makes the protein temporarily or permanently inactive. Denaturation usually

breaks the bonds that form to keep up the protein’s tertiary structure.

V. NUCLEIC ACIDS: The primary structure of proteins is determined by the sequence

of genetic code in the genes. The biochemical representative of genes are nucleic acids.

There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

DNA is a very unique molecule because it is able to provide directions for its own replication and for the replication of RNA as well, and through RNA it controls protein synthesis.

Each chromosome in the nucleus of cells contains one single DNA molecule with thousands of genes. These chromosomes are passed on from one generation to the next during cell division.

We can summarize the flow of genetic information as DNA → RNA → protein. This route is universal in every living organisms,

among nonliving only some viruses break this order and can form DNA from RNA.

A. The Structure of Nucleotides: Nucleic acids are polymers that are made up of monomers called

nucleotides by condensation Nucleotides are also complex and form from three parts:

a. Nitrogenous basesb. Pentose (five-carbon sugar)c. Phosphate group

The unit without the phosphate group is called a nucleoside Each nitrogenous base can be either a purine base (two attached

carbon rings) or a pyrimidine base (one carbon ring). Purine bases can be adenine (A) or guanine (G), while pyrimidine bases can be cytosine (C), thymine (T) or uracil (U):

Thymine is only found in DNA, while uracil is found only in RNA. Pentose is also different in DNA and RNA. DNA has deoxyribose

while RNA has ribose:

The numbering of the carbon atoms of the pentose determine where the phosphate and the nitrogenous base binds. When nucleotides form:

B. Nucleotide polymers: Nucleotides are linked together to form a polynucleotide chain

by forming a type of covalent bond called phosphodiester linkages between the –OH group of the 3’ carbon of the pentose

and the phosphate group of the other nucleotide on the 5’ carbon. This repeated pattern forms the sugar-phosphate backbone of the nucleic acid

The RNA molecule is made up of one single chain.

The DNA double helix was discovered by Watson and Crick in the 1950’s. In this double helix the sugar-phosphate backbone runs antiparallel. The sugar-phosphate backbones are on the outside, while the nitrogenous bases turn inside and tie the two chains together by hydrogen bonding. Most DNA molecules are very long, with thousands or millions of bases.

Only certain bases in the double helix are compatible with each other – base pairing rule. Adenine always binds with thymine while cytosine binds with guanine.

With this sequence of nucleotides, DNA is a perfect molecule to store genetic information and inherit it from one generation to the next.

CHAPTER 8 – AN INTRODUCTION TO METABOLISMOBJECTIVES

Metabolism, Energy, and Life1. Explain the role of catabolic and anabolic pathways in cellular respiration.2. Distinguish between kinetic and potential energy.3. Explain why an organism is considered an open system.4. Explain why highly ordered living organisms do not violate the second law of thermodynamics.5. Write and define each component of the equation for free-energy change.6. Distinguish between exergonic and endergonic reactions in terms of free energy change.7. Explain why metabolic disequilibrium is one of the defining features of life.8. List the three main kinds of cellular work. Explain in general terms how cells obtain the energy to do cellular work.9. Describe the structure of ATP and identify the major class of macromolecules to which ATP belongs.10. Explain how ATP performs cellular work.

Enzymes are Catalytic Proteins11. Describe the function of enzymes in biological systems.12. Explain why an investment of activation energy is necessary to initiate a spontaneous reaction.13. Explain how enzyme structure determines enzyme specificity.14. Explain the induced-fit model of enzyme function.15. Describe the mechanisms by which enzymes lower activation energy.16. Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction.17. Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity.

The Control of Metabolism18. Explain how metabolic pathways are regulated.19. Explain how the location of enzymes in a cell may help order metabolism.

I. OVERVIEW: The process of cellular respiration drives the cells to obtain

energy by breaking down organic molecules. This energy is used to perform various functions such as the transport of

solutes, contraction of muscles, building up the cell’s own biomolecules.

II. METABOLISM AND THE LAWS OF THERMODYNAMICS Metabolism is the totality of an organism’s all chemical

reactions. These chemical reactions are organized into metabolic pathways

that begin with a specific molecule that will be altered in a series of specific steps that result in a certain product. Each step has its specific enzyme.

Enzymes are proteins that will regulate these metabolic pathways at every step.

Some metabolic pathways release energy while breaking down complex organic molecules into simpler ones – catabolic processes

Anabolic processes – chemical reactions that consume energy to build complex molecules from simpler ones.

Bioenergetics – the study of how organisms manage their energy sources.

III. FORMS OF ENERGY: Energy – the capacity to cause change. Virtually all the energy for living things comes from the sun and

is captured by electrons. Kinetic energy – the energy that is associated with the relative

motion of objects Potential energy – energy that matter possesses because of its

location or structure. Chemical energy is a type of potential energy that is available for release in a chemical reaction. Generally, complex organic molecules are high in energy that can be released during catabolic processes. The released energy is used to fuel life processes.

During energy studies, scientists use the expression “system” to denote the matter under study. Living organisms are considered “open systems” because they interact with their surroundings and exchange energy with them.

Whether a chemical reaction will take place spontaneously or not is determined by the amount of available energy. The energy in a system available for doing work under conditions of constant temperature and pressure is called free energy. If energy is not available it needs to be obtained from an outside source (First Law of Thermodynamics – Law of Conservation of Energy).

The Second Law of Thermodynamics states that in the universe as a whole the total amount of free energy is declining – heat is not useful as a new energy source. With the decreasing free energy, entropy is increasing in spontaneous processes. (Entropy is the measurement of disorder or randomness).

The net charge in free energy that accompanies a reaction determines whether a reaction is spontaneous or not (DG = Gf – Gi). If the reaction results in products with less free energy, the reaction is spontaneous. These reactions are said to be exothermic or exergonic (DG is negative). If the reaction requires the input of energy the reaction is said to be endothermic or endergonic (DG is positive). Energy changes in living organisms tend to take place spontaneously in the direction that results in a decrease in usable energy.

NEXT USE: http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookATP.html

IV. THE ROLE OF ATP MOLECULES The cell does three main kinds of work:

o Mechanical work (beating of cilia, contraction of muscle cells, movement of chromosomes)

o Transport work (pumping substances across the cell membrane, carrying respiratory gases)

o Chemical work (forming polymers from monomers) Cells use energy coupling (pairing endergonic processes with

exergonic ones) to fuel all energy requiring processes. Adenosine triphosphate (ATP) plays a key role in these

energy coupling reactions as a mediator. The structure of ATP: an adenine + ribose + three phosphate

groups join together by dehydration synthesis. The phosphate groups of the molecule can be broken down by

hydrolysis. When the terminal phosphate breaks down ADP (adenosine diphosphate) is produced. This reaction releases 7.3 kcal of energy per mole of ATP because of the lower free energy level of the ADP molecules.

The cell directly uses the energy that is released from the ATP by transferring the phosphate group from ATP to some other molecule. The recipient of the phosphate group is then phosphorylated and becomes more reactive than the original reactant was.

ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP. The energy for building new ATP molecules comes from exergonic reactions in the cell.

V. ENZYMES Enzymes – globular proteins that act in living organisms as

catalysts. As catalysts, enzymes speed up chemical reactions by lowering the

activation energy of the reaction, without being consumed during the reaction.

The initial investment of energy for starting a reaction is known as the activation energy (EA). The activation energy can be quite high for many biological processes. Enzymes act by lowering this activation energy so the reaction can take place with less of an energy investment than before. Without enzymes these reactions would take too long or would require high heat that would denature many organic compounds.

Because enzymes are very sensitive to the reactions that they catalyze, they will determine the type and direction of chemical processes in the body.

Enzymes are specific – a particular enzyme interacts with only one type of reactant or pair of reactants – substrates (reactants of the catalyzed reaction). Enzymes with substrates form enzyme-substrate complexes, than the enzyme converts the substrate to a product. They are very efficient – one enzyme may cause thousand or even hundreds of thousands of molecules of reactants to react each second. Enzymes are highly sensitive to changes in pH, temperature and salt concentration. These characteristics depend on the enzyme’s 3D molecular conformation. This is the reason why denatured proteins lose their enzymatic characteristics.

Show: http://en.wikipedia.org/wiki/Image:GLO1_Homo_sapiens_small_fast.gif The reactive portion of the substrate molecule binds to the enzyme

by usually weak interactions at the active site and becomes temporarily bonded.

Binding energy is the energy that is released form all of the weak interactions between the enzyme and substrate. This energy is used to help substrates get together, orienting substrates in positions favoring reaction, shutting out water or inducing changes in the enzyme’s shape that pushes the substrates to a different shape as well (induced fit model).

Most metabolic processes are reversible and an enzyme can catalyze both the forward and backward processes.

Because enzymes are proteins, many environmental factors will influence their function. Most enzymes have a range of environmental factors where they are the most efficient. These are called optimal conditions. If the temperature or the pH increases or decreases from the optimum, enzymes first slow down than denature and become completely dysfunctional.

Cofactor: A nonprotein component of enzymes. If the cofactor is organic, then it is called a coenzyme. Coenzymes are relatively small molecules compared to the protein part of the enzyme. Many of the coenzymes are derived from vitamins. The coenzymes make up a part of the active site, without the coenzyme the enzyme will not function. Vitamins frequently act as coenzymes.

Enzyme activities are controlled by many ways. They frequently depend on chemicals that mask, block, alter the active sites of the enzymes:

i. Competitive inhibition: uses an inhibitor that is similar to the substrate. It binds to the enzyme’s active site but is not changed in the process and it does not allow the substrate to bind to the active site – carbon monoxide poisoning is an extreme example.

ii. Noncompetitive inhibition: depends on two kinds of binding sites on the same enzyme. The usual active site binds the substrate and another site binds the inhibitor. Most noncompetitive inhibition is called allosteric inhibition (different site, not the active site). An allosteric enzyme usually exists in two forms. One active form can bind the substrate the other, inactive form is stabilized by inhibitor molecules (negative modulators). Frequently the product is the negative modulator – feedback inhibition. In other allosteric enzymes there is more than one active site for the substrate. When the first substrate molecule binds to the enzyme it makes the remaining sites more reactive – cooperativity (amplification of the response of enzymes to substrates – one substrate makes the enzyme accept an additional substrate).

Animations:

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

http://www.lpscience.fatcow.com/jwanamaker/animations/ Enzyme%20activity.html

http://www.northland.cc.mn.us/biology/biology1111/animations/ enzyme.swf

Biochemical pathway: http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf

Feedback inhibition: http://highered.mcgraw-hill.com/olc/dl/120070/bio10.swf

THE END OF UNIT 2