Copyright © Houghton Mifflin Company. All rights reserved.16a–1 EXAM 2 RESULTS High score = 106 (...

EXAM 2 RESULTS

High score = 106 ( Nine students scored 100 or above!!!)

Median = 74

Average = 72

IMPORTANT NOTICE

The third hour exam will be given on

FRIDAY, March 2nd, 2007

More corrections to the text:

Question 15.65: The correct answer is “False”

Question 14.73: Ignore this question; it is not properly formulated.

Thanks to G. Bradds

News from Space

Astronomers have found more than 130 different organic compounds in outer space (detected from their spectra).

The latest finding is of large amounts of acetone and its close relative 1,3-dihdroxyacetone (DHA).

O O || || CH3-C-CH3 CH2OH-C-CH2OH

Acetone DHA

Acetone is used as a nail polish remover.DHA is used as an active ingredient in sunless tanning lotion.

Reference: C. Liu, “Cosmic Cosmetics”, Natural History, Feb. 2006, p. 58-59.

Chapter Sixteen

Proteins

￭ Proteins are the most abundant substances in animal cells (other than water). They account for almost 50% of a typical cell’s dry mass.

￭ The presence of nitrogen sets proteins apart from lipids and carbohydrates, which contain very little nitrogen.

￭ A typical human cell has roughly 1 million proteins of about 9000 different varieties. The human body has about 100,000 different types of proteins.

￭ What is a protein? It is a polymer (a biopolymer) inwhich the monomer units are amino acids. Thus, amino acids are the building blocks of all proteins.

About Proteins …

Amino Acids: The Building Blocks of Proteins

An alpha-amino acid is an organic compound that contains both an amino group and a carboxylic acid group attached to the alpha carbon atom.

H2N CO2H

alpha carbon atom

side chain

The R group is the side chain which defines theamino acid.

For example …………..

The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity.

The 20 Standard Amino Acids, Grouped According

to Side-Chain Polarity. (cont’d)

The 20 Standard Amino Acids, Grouped According

to Side-Chain Polarity. (cont’d)

￭ Twenty different “standard amino acids” are foundnormally in proteins (see Table 16.1). They are classifiedinto four groups:

￭ Nonpolar amino acids contain a nonpolar side chain; e.g. Gly, Ala, Val, Leu, Ile, Pro, Phe, and Met.

￭ Polar neutral amino acids contain a polar neutral side chain; e.g. Ser, Cys, Thr, Asn, Gln, Tyr, and Trp.

￭ Polar acidic amino acids contain an acidic side chain; e.g. Asp, Glu. Have a negative charge at physiological pH.

￭ Polar basic amino acids contain a basic side chain; e.g.His, Lys, Arg. Have a positive charge at physiological pH.

Protein details …

Protein Structure and Function: An Overview

￭ Proteins are polymers of amino acids. ￭ Each amino acid in a protein contains an amino group, -NH2, a carboxyl group, -COOH, and an R group, all bonded to the central carbon atom. The R group may be a hydrocarbon or it may contain a functional group.

Amino Acids

20 amino acid types are used by nature to build all peptides in living organisms presented in the table

￭ All but one of the natural amino acids differ only in the identity of the R group or side chain.

￭ The remaining amino acid (proline) is a five- membered secondary amine.

￭ Each amino acid has a three letter shorthand code--for example, Ala (alanine), Gly (glycine), Pro (proline).

￭ The 20 amino acids present in proteins are classified as neutral, acidic, or basic depending on the nature of the side chain.

￭ The 15 neutral amino acids are divided into two groups – polar and nonpolar on the basis of the nature of their side chain.

￭ The sequence of amino acids in a protein and the chemical nature of their side chains allow proteins to do their function.

￭ Intermolecular forces are of central importance in determining the shapes and functions of proteins.

￭ In biochemistry, noncovalent forces refer to all interactions other than covalent bonding.

￭ The nonpolar side chain of proteins are described as hydrophobic – they are not attracted to water.

￭ The polar, acidic, and basic side chains are described as hydrophilic – they are attracted to water.

Essential amino acids are those which must be obtainedfrom the diet; i.e. they cannot be biosynthesized by thehuman body.

Most animal proteins, such as those obtained frommeat, fish, eggs, and milk contain all of the essentialamino acids. On the other hand, proteins from plantssuch as vegetables, grains, and legumes (peas and beans)lack one or more of the essential amino acids. Therefore,they must be eaten in complementary pairs to get all of theessential amino acids in our diet.

The Essential Amino Acids for Humans.

Handedness in Amino Acids

Mirror images of a hand do not superimpose on each other. Image of left hand on the mirror looks like the right hand – objects that have handed-ness in this manner are said to be chiral.

Molecular Handedness and Amino Acids

Amino acids are chiral.

￭ Recall: A molecule is a chiral molecule if four different atoms or groups are attached to a carbon. The carbon carrying four different groups is called a chiral carbon. Chiral molecules have no plane of symmetry. ￭ The two mirror image forms of a chiral molecule like alanine are called enantiomers or optical isomers. ￭ Enantiomers have the same connections but different spatial arrangements of their atoms.

They’re all lefties!

￭ 19 out of 20 natural amino acids are chiral – they have four different groups on the a-carbon. Only glycine is achiral. ￭ Nature uses only one isomer out of a pair of enantiomers for each amino acid to build the proteins. ￭ The naturally occurring amino acids are classified as left-handed or L-amino acids.

Designation of handedness in amino acid structures involves aligning the carbon

chain vertically and looking at the position of the -NH2 group.

Rules for designating handedness in amino acids

when drawing their structures are:

1. The CO2H group is put at the top of the structure

and the R group is put at the bottom.

2. The NH2 group is in a horizontal position. When

the NH2 group is on the left, it is the L isomer and

when the NH2 group is on the right, it is the D isomer.

an L amino acid in aFischer projectionstructural formula

Acid-Base Properties of Amino Acids

￭ Amino acids contain both an acidic group, -COOH, and a basic group, -NH2.

￭ As a result of intramolecular acid-base reactions, a proton is transferred from the –COOH group to the –NH2 group producing a dipolar ion or zwitterion that has a positive and also a negative charge and is thus electrically neutral.

OH H3N

The amino acid does not exist like this because aninternal acid-base reaction occurs within the molecule.The NH2 group is a base and it wants to accept a proton,and the COOH group is an acid and it wants to donatea proton.

zwitterion

Because they are zwitterions, amino acids have many properties that are common for salts. Such as:￭ amino acids are crystalline￭ amino acids have high

melting points￭ amino acids are somewhat water soluble.

￭ In acidic solutions (low pH), amino acid zwitterions accept a proton on their –COO- group to give –COOH and leave only the positively charged –NH3

+ group.

￭ In basic solutions (high pH), amino acid zwitterions lose a proton from their –NH3

+ group to give –NH2 and leave only the negatively charged –COO- group.

• The charge of an amino acid molecule at any given moment depends on the identity of the amino acid and the pH of the medium.

• The pH at which the net positive and negative charges are evenly balanced is the amino acid’s isoelectric point- the overall charge or net charge is zero.

OH H3N

low pH (acidic) neutral solutionhigh pH (basic)

OH H3N

COOH COOH COO

For amino acids with acidic or basic side-chains, theexistence of four ionized forms becomes possible. Consider the amino acid, glutamic acid.

low pH form

moderately lowpH form

neutral pH formhigh pH form

More corrections to the text:

Question 13.36: Ignore this question; it is not properly formulated.Thanks to A. Dalton

Question 16.29: The answer in the back of the book is incorrect. The correct answer is Ser-Ala-Cys.Thanks to R. Rea

Peptide Formation

￭ All amino acids present in a proteins are -amino acids in which the amino group is bonded to the carbon next to the carboxyl group. ￭ Two or more amino acids can join together by forming an amide bond, which is known as a peptide bond when they occur in proteins.

￭ A dipeptide results when two amino acids combine together by forming a peptide bond using the amino group of one amino acid and a carboxyl group of another amino acid. (This is a condensation reaction; it splits our a water molecule.)

￭ A tripeptide results when three amino acids combine together by forming two peptide bonds, and so on. Any number of amino acids can link together and form a linear chain-like polymer – i.e. a polypeptide.

Naming a dipeptide (or polypeptide):

￭ Start from the N-terminal end - that is, the end with the amino group sticking out. Then start naming the amino acids:

H O H H + | || | |H3N--C---C---N---C---COO- | | H CH3

This is Gly Ala

Chemical Portraits:Biochemically Important Small Peptides

Aspartame (Asp-Phe)

• Note first that this is not a “pure” dipeptide, since the carboxyl group has been esterified with a methyl group.

• Aspartame is 180 times as sweet as sucrose.

• Only the L-L form is sweet; the L-D, D-L, and D-D forms are bitter.

• Sold as Nutrasweet and Equal. It has no bitter aftertaste, unlike some other sweeteners..

Levels of Protein Structure

Primary: The sequence of amino acids

Secondary: How the chain is folded in space (alpha helix, beta pleated sheet)

Tertiary: The folds of the folds; how the secondary structures are arranged in space

Quaternary: The joining of subunits; many proteins are clumps of three or four subunits

Primary Structure of Proteins

The sequence of amino acids in the chain

Insulin

• Insulin is a hormone that regulates blood glucose levels.

• Insulin contains a single strand of 51 amino acids; it’s primary a.a. sequence was first determined in 1953 by Frederick Sanger. It took 8 years to work this out, and Sanger received a Nobel Prize for his work.

• Today amino acid sequences can be relatively easily determined using automatic machines.

• Understand that many proteins have more than one strand; the strands are usually linked by disulfide (-S-S-) bonds.

The primary structure of human myoglobin.

Myoglobin is a string of 153 amino acids.

The actual three-dimensional structure

is not shown here.

Secondary Structure of Proteins

How the chain is configured in space

Four representations of the alpha-helix protein structure.

(a) Arrangement of the protein backbone. (b) Backbone arrangement with hydrogen-bonding shown. (c) Backbone atomic detail shown. (d) Top view of an alpha-helix showing that amino acid side chains (R groups) point away from the long axis of the helix.

Two representations of the beta-pleated sheet protein structure. (a) A representation emphasizing the hydrogen bonds between protein chains. (b) A representation emphasizing the pleats and the location of the R groups.

The secondary structure of a single protein often shows areas of -helix and -pleated sheet configurations, as well as areas of random coiling.

Tertiary Structure of Proteins

How the secondary structures are twisted in space

Human insulin, a small two-chain protein, has both intra-chain and inter-chain disulfide bonds as part of its tertiary structure.

Types of Noncovalent R group interactions that contribute to the tertiary structures of proteins: (a) electrostatic interaction, (b) hydrogen bond, and (c) hydrophobic interaction.

A schematic diagram showing the tertiary structure of the single-chain protein myoglobin.

Quarternary Structure of Proteins

Two or more subunits are brought togetherto form a complex

A schematic diagram showing the tertiary and quaternary structure of the oxygen-carrying protein hemoglobin (four subunits, each with a heme group).

Protein Classification and Functions

Types of Conjugated Proteins (proteins bonded to other things)

Proteins can be combined with other types of compounds, to form heme proteins,

lipoproteins, metalloproteins, etc.

Chemistry at a glance:Protein Structure

Two Major Protein Types: Fibrous and Globular Proteins.

Protein Hydrolysis and Denaturation

Protein denaturation involves loss of the protein’s three-dimensional structure. Complete loss of such structure produces a random-coil protein strand.

Selected Physical and Chemical Denaturing Agents (just examples; not for memorizing)

Enzymes(Biological Catalysts)

The active site of an enzyme is usually a crevice-like region formed as the result of the protein’s secondary and tertiary structural characteristics.

The lock-and-key model for enzyme activity. Only a substrate whose shape and chemical nature are complementary to those of the active site can interact with the enzyme.

The induced-fit model for enzyme activity. The enzyme active site, although not exactly complementary in shape to that of the substrate, is flexible enough that it can adapt to the shape of the substrate.

A schematic diagram representing how amino acid R group interactions can bind a substrate to an enzyme

active site.

Factors That Affect Enzyme Activity

Effect of temperature on the rate of an enzymatic reaction.

Effect of pH on an enzyme’s activity.

A graph showing how the reaction rate changes with change in substrate concentration at constant enzyme concentration. The reaction rate remains constant above a certain substrate concentration because the enzyme is saturated.

A graph showing the change in reaction rate with change in enzyme concentration for an enzymatic reaction. Temperature, pH, and substrate concentration are constant.

Extremophiles

These are creatures (usually bacteria) that live under extreme conditions (e.g., high or low temperatures, high or low pH, or very salty conditions)

￭ Often their enzymes have special properties, special structures. They may resist denaturation at high temperatures or low pH. ￭ Scientists can gather such creatures (for example, from hot springs in Yellowstone Park) and try to find out how they can tolerate the extreme conditions. ￭ Example: Procter & Gamble wanted an enzyme for its laundry detergents that could continue to break down grease at high temperatures.

Turnover Numbers for Selected Enzymes.

Turnover number is the maximum number of substratemolecules that a single enzyme molecule can cause to

react per second.

Chemistry at a glance:enzyme activity

Some enzymes are inducible

￭ “ Inducible” means that cells produce more of the enzyme when they find more of its substrate present.

￭ The point is that it takes energy and effort to make enzymes, so the body doesn’t want to produce enzymes if they are not needed.

￭ Alcohol hydrogenase is an example.

￭ Enzyme induction involves a complex process of recognition and feedback loops.

Primary Protein Structure

The primary structure of a proteins is its sequence of amino acids connected by peptide bonds. The backbone of a protein is its chain of peptide bonds, and the amino acid side chains are connected to this backbone at the carbons.

By convention, peptides and proteins are always written with the amino terminal amino acid (N-terminal) on the left and the carboxyl-terminal amino acid (C-terminal) on the right.

Shape-Determining Interactions in Proteins

￭ The essential activity of each protein depends on its polypeptide chain being held in a particular shape by the interactions of the atoms in the side chains. ￭ The kinds of interaction that determine the shapes of protein molecules are shown in Fig 18.4.

Fig 18.4 Interactions that determine protein shapeFig 18.4 Interactions that determine protein shape

Protein shape-determining interactions are:

• Hydrogen bonds between neighboring backbone segments.

• Ionic attractions between charged side chain groups (salt bridges).

• Hydrophobic interactions between side chain groups.

• Covalent disulfide (sulfur-sulfur) bonds.

Secondary Protein Structure

• Secondary structure of a protein is the arrangement of the polypeptide backbone in space. The secondary structure includes two kinds of repeating patterns: -helix and -sheet.

• Hydrogen bonds between backbone atoms are responsible for both of these secondary structures.

Alpha-Helix: A single protein chain coiled in a spiral with a right-handed (clockwise) twist.

Beta-Sheet: The polypeptide chain is held in place by hydrogen bonds between pairs of peptide units along neighboring backbone segments.

Fibrous and Globular proteins

•Fibrous protein: Tough and insoluble protein in which the chains form long fibers or sheets. The Secondary structure is responsible for the shape of fibrous proteins. Wool, hair, and finger nails are made of fibrous proteins.

•Globular protein: Water soluble proteins whose chains are folded into compact, globular shape with hydrophilic groups on the outside.

Tertiary Protein Structure

￭ Tertiary Structure of a proteins: The overall three- dimensional shape that results from the folding of a protein chain. Tertiary structure depends mainly on attractions of amino acid side chains that are far apart along the same backbone. Non-covalent interactions and disulfide covalent bonds govern tertiary structure.

￭ A protein having the shape its natural shape (as it would normally appear in an organism) is known as a native protein.

Quaternary Protein Structure

Quaternary protein structure: The way in which two or more polypeptide sub-units associate to form a single three-dimensional protein unit. Non-covalent forces are responsible for quaternary structure essential to the function of proteins.

Hemoglobin, a protein with quaternary structure

Chemical Properties of Proteins

Protein hydrolysis: In protein hydrolysis, peptide bonds are hydrolyzed to yield amino acids. This is reverse of the condensation reaction employed in protein formation.

Protein denaturation: The loss of secondary, tertiary, or quaternary protein structure due to disruption of non-covalent interactions and/or disulfide bonds. (This leaves the peptide bonds and primary structure intact.)

Agents that cause denaturation

￭ Heat The weak side-chain attractions in globular proteins are easily broken by heating. Cooking meat converst some of the insoluble collagens into soluble gelatin. ￭ Mechanical agitation Most familiar example of denaturation of protein by mechanical agitation is the foaming that occurs during beating of egg whites. ￭ Detergents Very low concentration of detergents can cause denaturation by disrupting the association of hydrophobic side chains.

Agents that cause denaturation (cont.)

￭ Organic compounds Polar solvents such as acetone or ethanol can interfere with hydrogen bonding by competing for bonding sites. ￭ pH change Excess H+ or OH- ions reacts with the basic or acidic side chains in amino acid residues and disrupt salt bridges. ￭ I norganic salts Sufficiently high concentrations of ions can disrupt salt bridges.

The active site of an enzyme is usually a crevice-like region formed as the result of the protein’s secondary and tertiary structural characteristics.

Note on Drug Action

• Most drugs act by blocking enzyme active sites or the active sites of receptors on cell surfaces.

• Pharmaceutical companies employ teams of scientists to (a) determine the structures of enzymes and receptors and (b) design compounds that will fit into the active sites of a target enzyme or receptor.

• Users of statin drugs (lipitor, zocor, etc., to lower cholesterol) are advised not to eat grapefruit at the same time as they take the drugs. Compounds in grapefruit inhibit an enzyme in the small intestine that partially breaks down these medications. When this enzyme is inhibited patients who eat grapefruit get a larger dose of the drug than intended.

Individual Differences

• Many enzymes differ from one individual to another.

• As a result peoples’ reactions to different drugs and other substances can differ. Often subgroups in the population respond differently, making broad studies hard to interpret.

• Example 1: Lactose intolerance. Many individuals lose their ability to metabolize lactose (milk sugar) as adults, due to lose of the enzyme lactase.

• Example 2: According to a recent study*, people who metabolize caffeine slowly are at greater risk of heart attacks than those who metabolize caffeine quickly. The difference in metabolism is due to individual variations in the enzyme Cytochrome P450 (CYP1A2) which metabolizes caffeine.

* M. C. Cornelis et al., JAMA 295, 1135-1141 (2006)

What you absolutely must understand from Chapter 16.

• Understand that proteins are polymers made from amino acid units.

• Understand the basic structure of an amino acid: COOH |

H2N-C-H|

• Appreciate that amino acids are distinguished by their side chains (R).

• Understand that just 20 standard amino acids are typically found in nature.

• Understand that because four different groups are normally bound to the central (alpha) carbon atom, amino acids are chiral. Almost all amino acids found in nature are L-amino acids (H2N- on the left).

What you must know … (cont.)• Understand that there are four basic types of amino acids:

--Nonpolar amino acids

--Polar neutral amino acids

--Acidic amino acids (have an additional COOH group)

--Basic amino acids (have an additional –NH or –NH2 group)

• You should memorize the structures for six amino acids:

Glycine, Alanine, Proline, Cysteine, Aspartic acid, Lysine

The side chains are R = H, -CH3, a cycle linking the –NH group with the alpha carbon via 3 –CH2- links, -CH2-COOH, and –(CH2)4-NH2.

• Understand that amino acids take on different ionized or neutral forms at different pHs. At neutral pH amino acids exist as zwitterions: H3N+-CH-COO- Note that both the COOH and

| the –NH2 group are ionized. R

What you must know … (cont.)

• Understand that amino acids are joined together by amide (=peptide) bonds formed in condensation reactions (splitting out water). The –NH3

+ and COO- groups react to form the bond (-NH-CO-) and a water molecule (H2O) is lost.

• Appreciate that chains of amino acids are called peptides. The end with the free –NH3 group is called the N-terminal end, and the end with the –COO- group is called the C-terminal end.

• The formula for a peptide begins with the N-terminal end, and the amino acids are listed by their abbreviations, e.g., Gly-Ala-Cys.

• Appreciate that insulin is a hormone with 51 amino acids and that it was the first protein to have its amino acid sequence determined.

• Know that myoglobin is a protein with 153 amino acid residues. It has a “heme” group attached to it, and can attach molecular oxygen and transport it in muscles.

• Know the nature of the four levels of protein structure: primary, secondary, tertiary and quaternary. (Primary = aa sequence.)

• Regarding the secondary structure, understand the natures of the alpha helix and beta pleated sheet architectures. Understand that hydrogen bonds hold these structures in place.

• Regarding the tertiary structure, understand that a single protein can have regions of alpha helix, beta pleated sheets, and random coils. A single protein can also have two or more strands linked by disulfide (-S-S-) bonds (formed when two cysteines react to release H2).

• Appreciate that quaternary structure involves the clumping of two or more protein subunits through noncovalent attractions. A good example is hemoglobin, where four subunits come together, each with a heme group. Hemoglobin carries oxygen in the blood.

• Appreciate that a protein’s structure in space is crucial to its action. A protein can become denatured, and lose its crucial structure.

What you must know … (cont.)• Appreciate that there are several ways to classify proteins. One

distinction is between fibrous proteins (mainly used for structure) and globular proteins (often hormones and enzymes).

• Understand that many proteins are joined in the body with other substances. Lipoproteins (HDL and LDL) carry cholesterol. Heme proteins carry oxygen. Glycoproteins (carbohydrates with proteins) act as antibodies and in other roles.

• Appreciate that many agents, including heat and chemicals, can denature proteins (disrupt their natural structures).

• Understand that enzymes are biological catalysts. They speed up reactions without themselves being consumed. They act on “substrates” (a chemical they affect). The substrate binds to a region called the “active site” of the enzyme, either in a “lock-key” fit or by inducing a fit with the enzyme.

• Appreciate that enzymes can speed up biochemical reactions by huge amounts. (Know turnover number.)

• Appreciate how heat can affect an enzyme’s catalytic ability, and that an enzyme’s action can become saturated at high substrate concentration.

• Understand that some enzymes are inducible, i.e., cells make more of these enzymes when their substrates are present. (Example: alcohol dehydrogenase)

• Understand the types of forces that hold protein structures together (hydrogen bonds, electrostatic forces, hydrophobic forces, disulfide bonds).

To Do List

• Read chapter 16!!

• Do additional problems

• Review Lecture notes forChapter Sixteen

• Do practice test T/F

• Do practice test MC

Copyright © Houghton Mifflin Company. All rights reserved.16a–1 EXAM 2 RESULTS High score = 106 (...

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