Chapter 5 - The Structure and Function of Macromolecules Notes and FRQ

In a DNA double helix, a region along one DNA strand has this sequence of nitrogenous bases: 5'-T A G G C C T-3' Write the complementary strand. Indicate the 5' and 3' ends of the new strand

3'-A T C C G G A-5'

What is a glycosidic linkage?

A glycoside linkage is a covalent bond formed between two monosaccharides by a dehydration reaction

What molecules make up the rungs?

Base pairs joined by hydrogen bonding

_________________________ serve as fuel and building material. They include both _______________ and their __________________________

Carbohydrates serve as fuel and building material They include both sugars and their polymers

The large molecules of all living things fall into just four main classes. Name them.

Carbohydrates, Lipids, Proteins, Nucleic Acids

What are Monosaccharides?

Monosaccharides -Are the simplest sugars -Can be used for fuel -Can be converted into other organic molecules -Can be combined into polymers -May be linear -Can form rings

Name two saturated fats and Unsaturated fats

Saturated fats : lard, butter, or most animal fats Un Saturated fats : olive oil, cod liver oil or most plant or fish fats

Chaperone proteins or chaperonins assist in the proper folding of proteins. Annotate this figure to explain the process

slide 76 From Left to Right: 1. An unfolded polypeptide enters the cylinder from one end. 2. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. 3. The cap comes off, and the properly folded protein is released

The components of a nucleic acid are a sugar, a nitrogenous base, and a phosphate group. Label each on the figure below.

slide 82

You may recall that early in this chapter we looked at the numbering system for the carbons of a sugar. Label the end of the strand on the left side of the figure below that has the number 5 sugar 5' and the other end of the chain 3'.

slide 82

What is a polymer? A monomer?

- A polymer Is a long molecule consisting of many similar building blocks called monomers - A monomer is a smaller molecule that serves as the building blocks of polymers.

Protein Conformation and Function

- A protein's specific conformation determines how it functions - Two models of protein conformation A ribbon model and A space-filling model

Nucleotide polymers

- Are made up of nucleotides linked by the-OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next - The sequence of bases along a nucleotide polymer is unique for each gene

The DNA Double Helix

- Cellular DNA molecules have two polynucleotides that spiral around an imaginary axis -Form a double helix the DNA double helix consists of two antiparallel nucleotide strands - The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion (A with T only, and C with G only) - Molecular comparisons help biologists sort out the evolutionary connections among species

The Diversity of Polymers

- Each class of polymer is formed from a specific set of monomers - Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers - An immense variety of polymers can be built from a small set of monomers

What are fatty acids? Name the types of fatty acids?

- Fatty acids vary in the length and number and locations of double bonds they contain. - Types of fatty acids: - Saturated fatty acids : Have the maximum number of hydrogen atoms possible. They have no double bonds - Unsaturated fatty acids : Have one or more double bonds

What are lipids?

- Lipids are a diverse group of hydrophobic molecules -Are the one class of large biological molecules that do not consist of polymers

Monomers are connected in what type of reaction? What occurs in this reaction?

- Monomers form larger molecules by condensation reactions called dehydration reactions - During a dehydration reaction, two monomer molecules are covalently bonded to each other, with the loss of a water molecule. In this reaction, each monomer contributes part of the water molecule that is released during the reaction. This reaction is repeated as monomers are added to the chain one by one, making a polymer.

The Protein-Folding Problem

- Most proteins probably go through several intermediate states on their way to a stable conformation - Chaperonins are protein molecules that assist in the proper folding of other proteins - X-ray crystallography is used to determine a protein's three-dimensional structure

The Structure of Nucleic Acids

- Nucleic acids exist as polymers called polynucleotides - Each polynucleotide consists of monomers called nucleotides

What is the role of Nucleic acids? What are the types of nucleic acids?

- Nucleic acids store and transmit hereditary information - Genes -Are the units of inheritance -Program the amino acid sequence of polypeptides -Are made of nucleic acids - There are two types of nucleic acids -Deoxyribonucleic acid (DNA) -Ribonucleic acid (RNA) - DNA -Stores information for the synthesis of specific proteins -Directs RNA synthesis -Directs protein synthesis through RNA

Nucleotide monomers

- Nucleotide monomers are made up of nucleosides and phosphate groups

Phospholipids

- Phospholipids -Have only two fatty acids -Have a phosphate group instead of a third fatty acid - Phospholipid structure - Consists of a hydrophilic "head" and hydrophobic "tails" - The structure of phospholipids results in a bilayer arrangement found in cell membranes

Polypeptides

- Polypeptides are polymers of amino acids - A protein consists of one or more polypeptides

Four Levels of Protein Structure (just for reference), use the slide below

- Primary structure is the unique sequence of amino acids in a polypeptide - Secondary structure is the folding or coiling of the polypeptide into a repeating configuration. Includes the a helix and the b pleated sheet - Tertiary structure is the overall three-dimensional shape of a polypeptide. Results from interactions between amino acids and R groups - Quaternary structure is the overall protein structure that results from the aggregation of two or more polypeptide subunits

Sickle-cell disease

- Sickle-cell disease results from a single amino acid substitution in the protein hemoglobin

What are the building blocks of fats? Label them on this figure.

-Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids. In the figure below, the glycerol molecule is in gray, and the three fatty acids are in yellow.

Enzymes

-Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions

summarize each type of Proteins with their functions and examples

-Proteins have many roles inside the cell

What Determines Protein Conformation?

-Protien Confirmation depends on the physical and chemical conditions of the protein's environment - Denaturation is when a protein unravels and loses its native conformation

Steroids

-Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings - One steroid, cholesterol is found in cell membranes and is a precursor for some hormones

Determining the Amino Acid Sequence of a Polypeptide

-The amino acid sequences of polypeptides were first determined using chemical means -Can now be determined by automated machines

What is a trans fat? Why should you limit them in your diet?

A trans fat is an unsaturated fat with a trans double bond; the result of the process of hydrogenating vegetable oils to prevent lipids from separating out in liquid (oil) form. Trans fats should be limited in your diet because they have been found to contribute to atherosclerosis, a cardiovascular disease caused by plaque buildup within the walls of blood vessels.

For the two nucleotides of DNA below, provide the complementary base. A — C —

A-T C-G

Notice that there are five nitrogen bases. Which four are found in DNA?

Adenine, guanine, cytosine, thymine

Which four are found in RNA?

Adenine, guanine, cytosine, uracil

Lipids include fats, waxes, oils, phospholipids, and steroids. What characteristic do all lipids share?

All lipids mix poorly, if at all, with water.

Amino acids (Amino acid monomers)

Amino acids -Are organic molecules possessing both carboxyl and amino groups -Differ in their properties due to differing side chains, called R groups -20 different amino acids make up proteins -Are linked by peptide bonds

Here are the three hexose sugars. Label each of them. Notice that all sugars have the same two functional groups. Name them: C=O OH

C=O carbonyl group OH hydroxyl group

Structural Polysaccharides - Cellulose

Cellulose -Is a polymer of glucose - Has different glycosidic linkages than starch -Is a major component of the tough walls that enclose plant cells - Cellulose is difficult to digest. Cows have microbes in their stomachs to facilitate this process

Structural polysaccharide - Chitin

Chitin, another important structural polysaccharide -Is found in the exoskeleton of arthropods -Can be used as surgical thread

Some people refer to this structure as three hexagons and a doghouse. What is it?

Cholesterol, a steroid

Besides mutation, which changes the primary structure of a protein, protein structure can be changed by denaturation. Define denaturation, and give at least three ways a protein may become denatured.

Denaturation is the changing of a protein during which the protein unravels and loses its native shape because the weak chemical bonds and interactions within a protein have been destroyed. Possible examples of ways a protein may become denatured include alteration of pH, salt concentration, temperature, transfer from aqueous environment to nonpolar solvent, chemicals, and excessive heat.

How do ribose and deoxyribose sugars differ?

Deoxyribose sugar lacks an oxygen atom on the second carbon in the ring

What is the difference between an aldehyde sugar and a ketone sugar?

Depending on the location of the carbonyl group, a sugar is either an aldose (aldehyde sugar) or a ketose (ketone sugar). Glucose, for example, is an aldose; fructose, an isomer of glucose, is a ketose. In aldehyde sugars, the carbonyl group is at the end of the carbon skeleton, while in the ketone sugars, the carbonyl group is within the carbon skeleton.

Disaccharides

Disaccharides -Consist of two monosaccharides -Are joined by a glycosidic linkage

Here is a model of DNA, which was proposed by James Watson and Francis Crick. What is this shape called?

Double helix slide 86 for labels

Here is the abbreviated ring structure of glucose. Where are all the carbons?

Each corner represents a carbon; each carbon in this figure is labeled 1 through 6

List four important functions of fats

Energy storage, long-term food reserve in mammals, adipose tissue cushions vital organs, body insulation.

Label each of the levels of protein structure on this figure

From Left to Right: Primary, Secondary, Tertiary, Quaternary

Storage Polysaccharides Glycogen

Glycogen -Consists of glucose monomers -Is the major storage form of glucose in animals

Why can you not digest cellulose? What organisms can?

Humans cannot digest cellulose because they lack the enzyme that can hydrolyze its beta linkages. Humans do posses enzymes that digest starch by hydrolyzing its alpha linkages; however, these enzymes cannot hydrolyze the beta linkages of cellulose because of the distinctly different shapes of these two molecules.

So, as a quick review, all of the sugars in the figure above have the same chemical formula: C6H12O6. What term did you learn in Chapter 3 for compounds that have the same molecular formulas but different structural formulas?

Isomers

Define macromolecule. What are the three classes that are called macromolecules

Macromolecules -Are large molecules composed of smaller molecules -Are complex in their structures Most macromolecules are polymers, built from monomers. Three of the classes of life's organic molecules are polymers -Carbohydrates -Proteins -Nucleic acids

Let's look at carbohydrates, which include sugars and starches. First, what are the monomers of all carbohydrates?

Monosaccharides, or simple sugars

If a fat is composed of three fatty acids and one glycerol molecule, how many water molecules will be removed to form it? Again, what is this process called?

One water molecule is removed for each fatty acid joined to the glycerol, equaling three water molecules for every triacylglycerol formed. This process is called dehydration synthesis

To summarize, what are the three components of a nucleotide?

Phosphate group, sugar, nucleoside

Large molecules (polymers) are converted to monomers in what type of reaction?

Polymers are disassembled to monomers by hydrolysis, a process that is essentially the reverse of the dehydration reaction.

Polysaccharides

Polysaccharides -Are polymers of sugars -Serve many roles in organisms

What is represented by R? How many are there?

R refers to the side chains of amino acids. There are 20.

Draw a fatty acid chain that is eight carbons long and is unsaturated. Circle the element in your chain that makes it unsaturated, and explain what this means.

See page 75 of your text for the labeled figure. Unsaturated fatty acids have one or more double bond, with one fewer hydrogen atom on each doublebonded carbon. Nearly all double bonds in naturally occurring fatty acids are cis bonds, which cause a kink in the hydrocarbon chain whenever they occur.

Here is a figure that shows the structure of a phospholipid. Label the sketch to show the phosphate group, the glycerol, and the fatty acid chains. Also indicate the region that is hydrophobic and the region that is hydrophilic.

See slide 45 for solution

To summarize, a phospholipid has a glycerol attached to a phosphate group and two fatty acid chains. The head is hydrophilic, and the tail is hydrophobic. Now, sketch the phospholipid bilayer structure of a plasma membrane. Label the hydrophilc heads, hydrophobic tails, and location of water.

See slide 45 for solution

Study the figure. See if you can understand why some R groups are nonpolar, some polar, and others electrically charged (acidic or basic). If you were given an R group, could you place it in the correct group? Work on the R groups until you can see common elements in each category.

See slides 58 and 59

Do you remember when, in Chapter 4, we said, "Change the structure, change the function"? Explain how that principle applies to sickle-cell disease. Why is the structure changed?

Sickle-cell disease is an inherited blood disorder caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carried oxygen in red blood cells. This changes the typical three-dimensional shape of hemoglobin. Normal red blood cells are disk-shaped, but in sickle-cell disease, the abnormal hemoglobin molecules tend to crystallize, deforming some of the cells into sickle shapes. Slide 74 for pic

Storage Polysaccharides Starch

Starch -Is a polymer consisting entirely of glucose monomers -Is the major storage form of glucose in plants

Have you noticed that all the sugars end in -ose? This root word means ____________.

Sugar

What two molecules make up the "uprights"?

Sugar and phosphate

Why is the "tail" hydrophobic?

The "tails" are hydrophic (avoid water) because they are hydrcarbon. As previously discussed in chapter 4, hydrocarbons are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen

Which of the two fatty acid chains in the figure with question 31 is unsaturated? Label it. How do you know it is unsaturated?

The fatty acid chain on the right is unsaturated. We know this because of the kink in the chain, indicating a double bond

Why are many unsaturated fats liquid at room temperature?

The kinks where the cis bonds are located prevent the molecules from packing together closely enough to solidify at room temperature.

The flow of genetic information is from DNA RNA protein. Use this figure to explain the process. Label the nucleus, DNA, mRNA, ribosome, and amino acids.

The mRNA molecule interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein. The sites of protein synthesis are tiny structures called ribosomes. In a eukaryotic cell, ribosomes are in the cytoplasm, but DNA resides in the nucleus. Messenger RNA conveys genetic instructions for building proteins from nucleus to the cytoplasm

Why are the strands said to be antiparallel?

The strands are said to be antiparallel because they run in opposite 5' 3' directions from each other.

Study your sketch. Why are the tails all located in the interior?

The tails are in contact with each other and remote from water because they are hydrophobic.

Here is a molecule of starch, which shows 1-4 glycosidic linkages. Translate and explain this terminology in terms of carbon numbering

When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring. These two ring forms for glucose are called alpha and beta. In starch, all the glucose monomers are in the alpha configuration.

The root words of hydrolysis will be used many times to form other words you will learn this year. What does each root word mean? hydro - lysis -

hydro- water lysis break

Is this reaction dehydration synthesis or hydrolysis?

hydrolysis as the reaction above is breaking bonds and releasing energy

Define these terms: dipeptide polypeptide peptide bond Label each of these terms on the diagrams.

peptide bond: A covalent bond in which two amino acids are joined by a dehydration reaction. dipeptide: A polymer of two amino acids linked by a peptide bond. polypeptide: A polymer of many amino acids linked by a peptide bond. see slide 52 for labeled pic

On the figure with question 34, label the ester linkages

see 35 for solution

Enzymes are an important type of protein. They will be studied in Chapter 8. For now, use this sketch to review what you know about enzymes. Label the active site, the substrate, and the products. Show what happens to water

see slide 56 for labelled figure

Enzymes are globular proteins that exhibit at least tertiary structure. On this figure, identify and explain each interaction that folds this portion

see slide 69 Hydrophobic interaction: amino acids with hydrophobic R groups end up in clusters at the core of the protein, out of contact with water. Van der Waals interaction: transient interactions between R groups Hydrogen Bond: weak bonds between the hydrogen of one R group and the oxygen or nitrogen of another R group Disulfide Bridge: links between the sulfhydryl groups of two cysteine amino acids, sulfur to sulfur Ionic Bond: bonds between an R group that is positively charged and an R group that is negatively charged These interactions tend to fold an amino acid chain into a distinctive three-dimensional form.

What are other examples of steroids?

vertebrate sex hormones