chap 5 campbell structure and function of macromolecules

Chap 5 Campbell

Structure and Function of Macromolecules

Condensation Reaction

Hydrolysis

The subunit for carbohydrates is sugar (sacharride)

Carbons could be straight chained or

cyclical

• Starch is a storage polysaccharide composed entirely of glucose monomers.– Most monomers are joined by 1-4 linkages between

the glucose molecules.– One unbranched form of starch, amylose, forms a

helix.– Branched forms, like amylopectin, are more complex.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 5.6a

• Plants store starch within plastids, including chloroplasts.

• Plants can store surplus glucose in starch and withdraw it when needed for energy or carbon.

• Animals that feed on plants, especially parts rich in starch, can also access this starch to support their own metabolism.


• Animals also store glucose in a polysaccharide called glycogen.

• Glycogen is highly branched, like amylopectin.• Humans and other vertebrates store glycogen in the liver

and muscles but only have about a one day supply.


Insert Fig. 5.6b - glycogenFig. 5.6b

• While polysaccharides can be built from a variety of monosaccharides, glucose is the primary monomer used in polysaccharides.

• One key difference among polysaccharides develops from 2 possible ring structure of glucose.– These two ring forms differ in whether the hydroxyl

group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the ring plane.


Fig. 5.7a


Fig. 5.7

• Starch is a polysaccharide of alpha glucose monomers.

• Structural polysaccharides form strong building materials.

• Cellulose is a major component of the tough wall of plant cells.– Cellulose is also a polymer of glucose monomers, but

using beta rings.


Fig. 5.7c


Fig. 5.8

• The enzymes that digest starch cannot hydrolyze the beta linkages in cellulose.– Cellulose in our food passes through the digestive

tract and is eliminated in feces as “insoluble fiber”.– As it travels through the digestive tract, it abrades the

intestinal walls and stimulates the secretion of mucus.

• Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes.

• Many eukaryotic herbivores, like cows and termites, have symbiotic relationships with cellulolytic microbes, allowing them access to this rich source of energy.


This Tiny Crustacean Menace Could Fuel the World By Clay Dillow Posted 03.09.2010 at 2:58 pm 11 Comments Gribbles via BBC

They don't exactly look like the saviors of our energy economy, but that's exactly what some researchers think they could be. Gribbles -- tiny crustacean pests with a knack for digesting wood -- have long been considered a marine parasite for the destruction they cause to wooden hulls and piers. But the enzymes gribbles use in to break wood fibers down into sugars could make them the next biofuels breakthrough.Essentially, gribbles are blessed with a digestive process unparalleled (to our knowledge) by other wood-consuming insects and animals. Their digestive enzymes can break down woody cellulose and even lignin -- the normally indigestible part of woody plants -- creating sugars that are more or less ideal for fermenting into alcohol-based fuels.

A biofuel factory based on the gribble's digestive biology could yield energy-dense sugars for biofuel production in an efficient manner. But of course there's a give-and-take in the equation that involves feeding woody plant materials -- like trees -- into the process as fuel. But by pushing forward with more efficient means to convert woody cellulose into fuels -- and perhaps by engineering woodier trees -- we reduce the amount of organic matter we need to feed in to get the combustible stuff out. The gribble -- thorn in the side of harbormasters, plague of the age of sail -- might just be good for something after all.

Chiton forms the exoskeleton of arthropods such as insects

and also the cell walls of fungi


• Glycerol consists of a three carbon skeleton with a hydroxyl group attached to each.

• A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long.

Fig. 5.10a

Fat = 1 glycerol + 3 fatty acids

• The many nonpolar C-H bonds in the long hydrocarbon skeleton make fats hydrophobic.

• The C-H bonds store a lot of energy.

• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol.

Fig. 5.10b

Unsaturated fatty acids are liquid at room temperature

Hydrogenating them makes them saturated

Saturated fatty acids are solid at room temp

• The three fatty acids in a fat can be the same or different.

• Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds.– If there are no

carbon-carbon double bonds, then the molecule is a saturated fatty acid - a hydrogen at every possible position.


Fig. 5.11a

– If there are one or more carbon-carbon double bonds, then the molecule is an unsaturated fatty acid - formed by the removal of hydrogen atoms from the carbon skeleton.

– Saturated fatty acids are straight chains, but unsaturated fatty acids have a kink wherever there is a double bond.


Fig. 5.11b

• Fats with saturated fatty acids are saturated fats.– Most animal fats are saturated.– Saturated fat are solid at room temperature.– A diet rich in saturated fats may contribute to

cardiovascular disease (atherosclerosis) through plaque deposits.

• Fats with unsaturated fatty acids are unsaturated fats.– Plant and fish fats, known as oils, are liquid are room

temperature.• The kinks provided by the double bonds prevent the

molecules from packing tightly together.


Trans-double bonds straighten the fatty acid chain and make them act like saturated fats

What is trans fat, how does it get into our food, and what are its effects on human health?

Traditionally, animal fats like butter and lard (saturated fats) were used as spreads and for baking. Vegetable oils (unsaturated fats) were cheaper, but as liquids they were not a suitable alternative. Unsaturated fats have a structure with kinks; these kinks result in a liquid state at room temperature. In the early 20th century, a chemical process called hydrogenation was developed that converts vegetable oils into saturated, more solid fats (margarine and vegetable shortening). When it was discovered that eating saturated fats increases the risk for coronary heart disease, the food industry turned to partial hydrogenation. This process lowerd the content of saturated fat in vegetable shortening and margarine, but also dramatically increased the amount of a certain kind of fat - trans fat - in our diets. While suppliers praised processed vegetable oils as healthy unsaturated and cholesterol-free substitutes for animal fats, there is now strong evidence that introducing trans-fatty acids into our diets does more harm than good.

The Skinny On Trans Fat It's found almost everywhere, but even a small amount of trans fat can drive up cholesterol levels, says a nutrition expert at Tufts University. Boston [08.15.02] -- Found in over 42,000 food products and considered more potent than saturated fat, trans fat is difficult to avoid. While the average American consumes close to 5 grams of the substance a day, researchers say even one gram--which can drive up LDL cholesterol levels--is too much in a healthy diet. To help better educate consumers, nutrition experts including Tufts' Alice Lichtenstein are working on new ways to inform the public about the dangers of trans fat and ways to avoid it."Anything above zero will increase the LDL cholesterol levels," Lichtenstein, a nutritional biochemist at Tufts University and a member of the National Academy of Sciences, told the San Jose Mercury News. "If you double the trans intake, you [nearly] double the rise in LDL cholesterol. So the recommendation is to minimize it."

http://hnrc.tufts.edu/scientists/people/lichtenstein.php

• The major function of fats is energy storage.– A gram of fat stores more than twice as much energy

as a gram of a polysaccharide.– Plants use starch for energy storage when mobility is

not a concern but use oils when dispersal and packing is important, as in seeds.

– Humans and other mammals store fats as long-term energy reserves in adipose cells.

• Fat also functions to cushion vital organs.

• A layer of fats can also function as insulation.– This subcutaneous layer is especially thick in whales,

seals, and most other marine mammals.


Hydrophobic tails

Steroids are lipids characterized by four fused rings

Examples are cholesterol, testosterone and estrogen

• Cholesterol, an important steroid, is a component in animal cell membranes.

• Cholesterol is also the precursor from which all other steroids are synthesized.– Many of these other steroids are hormones, including

the vertebrate sex hormones.

• While cholesterol is clearly an essential molecule, high levels of cholesterol in the blood may contribute to cardiovascular disease.


• Amino acids consist of four components attached

to a central carbon, the alpha carbon.

• These components include a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain).– Differences in R groups

produce the 20 different amino acids.

1. A polypeptide is a polymer of amino acids connected in a specific sequence


R groups determine the type of amino acid

Amino group

Acid group

Peptide bonds form forming a polypeptide

• A functional proteins consists of one or more polypeptides that have been precisely twisted, folded, and coiled into a unique shape.

• It is the order of amino acids that determines what the three-dimensional conformation will be.

2. A protein’s function depends on its specific conformation


Fig. 5.17

• The primary structure of a protein is its unique sequence of amino acids.– Lysozyme, an enzyme

that attacks bacteria, consists on a polypeptide chain of 129 amino acids.

– The precise primary structure of a protein is determined by inherited genetic information.


Fig. 5.18

Fig. 5.19


• The secondary structure of a protein results from hydrogen bonds at regular intervals along the polypeptide backbone.– Typical shapes

that develop from secondary structure are coils (an alpha helix) or folds (beta pleated sheets).


Fig. 5.20

• The structural properties of silk are due to beta pleated sheets.– The presence of so many hydrogen bonds makes

each silk fiber stronger than steel.

Fig. 5.21


• Tertiary structure is determined by a variety of interactions among R groups and between R groups and the polypeptide backbone.– These interactions

include hydrogen bonds among polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups. This causes the protein to fold up into a 3D structure

Fig. 5.22

• While these three interactions are relatively weak, disulfide bridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.


Fig. 5.22

HYDROPHILLICHYDROPHILLIC

• Quarternary structure results from the aggregation of two or more polypeptide subunits.– Collagen is a fibrous protein of three polypeptides

that are supercoiled like a rope.• This provides the structural strength for their role in

connective tissue.

– Hemoglobin is a globular protein with two copies of two kinds of polypeptides.

Fig. 5.23

Fig. 5.24

Animation 5.9.5Animation 5.9.5

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How biotech is driving computingThe most super of supercomputers are folding proteins, not crunching numbers. That's because the life sciences have

overtaken physics as the source of the most challenging computing problems.

By Chris Taylor, Business 2.0 Magazine senior editor

August 31 2006: 4:32 PM EDT

SAN FRANCISCO (Business 2.0 Magazine) -- Pop quiz: What new technology has the United States and Japan engaged in the virtual equivalent of the Space Race? The surprising answer: It's biotech.

Some background, in case you haven't been keeping up with current computing news: Japanese researchers have cobbled together a $9 million supercomputer called MDGrape-3 that last month broke the petaflop barrier for the first time.

http://money.cnn.com/services/newsletters/

Prosthetic group

• A protein’s conformation can change in response to the physical and chemical conditions.

• Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein.– These forces disrupt the hydrogen bonds, ionic

bonds, and disulfide bridges that maintain the protein’s shape.

• Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell.



Fig. 5.25

• In spite of the knowledge of the three-dimensional shapes of over 10,000 proteins, it is still difficult to predict the conformation of a protein from its primary structure alone.– Most proteins appear to undergo several intermediate

stages before reaching their “mature” configuration.



Fig. 5.26

• The folding of many proteins is protected by chaperonin proteins that shield out bad influences.

• A new generation of supercomputers is being developed to generate the conformation of any protein from its amino acid sequence or even its gene sequence.– Part of the goal is to develop general principles that

govern protein folding.

• At present, scientists use X-ray crystallography to determine protein conformation. – This technique requires the formation of a crystal of

the protein being studied.– The pattern of diffraction of an X-ray by the atoms of

the crystal can be used to determine the location of the atoms and to build a computer model of its structure.



Fig. 5.27

• The sugar-phosphate backbones of the two polynucleotides are on the outside of the helix.

• Pairs of nitrogenous bases, one from each strand, connect the polynucleotide chains with hydrogen bonds.

• Most DNA molecules have thousands to millions of base pairs.


Fig. 5.30

• Genes (DNA) and their products (proteins) document the hereditary background of an organism.

• Because DNA molecules are passed from parents to offspring, siblings have greater similarity than do unrelated individuals of the same species.

• This argument can be extended to develop a molecular genealogy between species.

4. We can use DNA and proteins as tape measures of evolution


• Two species that appear to be closely-related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species.– In fact, the sequence of amino acids in hemoglobin

molecules differ by only one amino acid between humans and gorilla.

– More distantly related species have more differences.


ATP is a nucleotide used to transfer energy

DNA is used to store genetic information (heredity)

RNA is used in the synthesis of proteins

Do Lab simulation

• Go to this site:

• http://midpac.edu/~biology/Intro%20Biology/PH%20Biology%20Lab%20Simulations/bioprop/intro.html

• Do the lab simulation on Properties of Biological Molecules, then take the practice test – print out the test to turn in.

chap 5 campbell structure and function of macromolecules

Documents

benjamin cummings slide

b slide

hydrolysis slide

cyclical slide

c slide

condensation reaction

sugar sacharride slide

surplus glucose