Ms. SastryAP Biology
Leigh High School
Unit 1 – Chemistry of Life;
After reading through the text book and attending class lectures you should be able to answer these questions:
Chapter 1 AP Themes Objectives:
1)List the AP Themes and explain what they are.
Chapter 2 Objectives:
1)Name the levels intp which life can be organized.
2)Name the important elements that make up life.
3)Name some important trace elements and state why they are needed in living beings.
4)Define Atomic Number, Atomic Weight, Isotopes
5)How are isotopes useful in carbon dating?
6)What are covalent bonds? Give an example. Are they weak or strong bonds?
7)What are polar covalent bonds? Draw the polar bonds in water molecules.
8) What are hydrogen bonds? Are they weak or strong bonds? Draw the hydrogen bonds between water molecules.
9)What are ionic bonds?
10)Why is the shape of a molecule important for its function?
11)What is chemical equilibrium – why is it important in living systems?
Chapter 3 -Water - Objectives:
1)How much of your cell is made up of water?
2)What is the single most important chemical property of water that makes it behave in incredibly versatile ways?
3)What is cohesion and when does this property of water become useful in living organisms?
4)What is adhesion and when does this property of water become useful in living organisms?
5)What is surface tension and when does this property of water become useful?
6)How does the density of liquid water compare with its solid form – ice? When does this property of water become useful?
7)How does the high specific heat of water and the high heat of vaporization become useful properties in living systems?
8)Why is water considered a universal solvent?
9)What happens when water dissociates?
10) A pH of 0 to 6 is , while a pH of 8 to 14 is increasingly
11)A difference of 1 pH unit is representative of a difference oftimes in concentration of the acid or base.
12) How is pH important in humans?
Chapter 4 – Carbon - Objectives:
1)What is the Abiotic Synthesis Theory for the origin of lfe?
2)What is Stanley Miller’s evidence for the Abiotic Synthesis Theory? Why is this theory questioned today?
3)What types of bond does carbon make with surrounding atoms?
4)Illustrate the following with examples - Carbon compounds are highly varied due to differences in:
a) Length of carbon skeleton
b) Arrangement of atoms around the carbon atoms
c) Functional groups
5)What are Isomers? What are the 3 kinds of Isomers?
6)What are Structural Isomers – give an example.
7)What are Geometric Isomers? Give an example. What is one important characteristic to look for before you decide if a CARBON compound is a geometric isomer?
8)What are Enantiomers? Give an example.
9)What are functional groups?
10)Identify the chemical structure of the following functional groups:
a)Hydroxyl/Alcohol
b)Carbonyl – both types namely aldehyde and ketone
c)Carboxyl acid
d)Sulfhydryl
e)Amino
f)Phosphate
Practice: Go to and practice identifying functional groups. Unless you can identify these funtional groups by sight and name, you will be lost in the next chapter …..
Assignment: Chapter 4 - Functional Groups Hunt + Biomolecules Online Review
Chapter 5 Macrmolecules - Objectives:
1)What are macromolecules?
2)What are the 4 important types of macromolecules?
3)What are monomers and polymers?
4)What reaction makes polymers from monomers? Describe the process.
5)Give an example of an anabolic (building polymers) reaction.
6)What reaction makes monomers from polymers? Describe the process.
7)Give an example of an catabolic (breaking down polymers) reaction.
8)The common biochemical name for sugars is :
9)The monomer of sugars is called:. Give examples.
10) The polymer of sugars is called:. Give examples.
11)What is a disacharride? Give some examples and sources of these sugars.
12) Sugars end with the letters:
13) What is the difference between a ketose and an aldose? What type of macromolecule are they?
14) Identify the number of carbon atoms in the Hexose sugar – glucose and the Pentose sugar – Ribose. Why is ribose an important sugar to remember?
15) How many forms can glucose take chemically?
16)What reaction makes disacharrides from monosacharrides?
17)What is a glycosidic linkage? In ht macromolecule can you see this?
18)What are the 2 types of polysacharrides? Give examples of each in plant and animals.
19)What reaction makes a polysacharride from a monosacharride?
20)What are lipids? Are they made of monomers?
21)What are some important types of lipids?
22)What are the two parts of a fat molecule? What reaction puts those two parts together to make a fat?
23)What is the difference between a saturated fat and an unsaturated fat?
24) What is a trans fat? Why is it unhealthful?
25) Should you avoid eating ALL fats? What is the function of fats in the body?
26) What are phospholipids? Where can you find them?
27)What are steroids? What is their function in the body?
28)What are proteins? Name some important proteins in the body.
29)What is the monomer in proteins? Draw the structure of a monomer with the functional groups indicated clearly.
30)What are the amino acids made of ? How many amino acids make up ALL the proteins in our body? How can so many different proteins be composed from just a few amino acids?
31)What is different in the structures of the 20 amino acids found in the body? Elaborate on how this difference is critical to the functioning of the protein they make up.
32)What is a peptide bond – draw one.
33)What is the primary structure of a protein? If there is a change in the primary structure, how will the function of the protein change?
34)What is the secondary structure of a protein? If there is a change in the seconday structure, how will the function of the protein change?
35)What is the tertiary structure of a protein? If there is a change in the tertiary structure, how will the function of the protein change?
36)What is the quarternary structure of a protein? If there is a change in the quarternary structure, how will the function of the protein change?
37)What will happen to a protein when it is heated or when an acid is added to it?
38)What is a nucleic acid – is it the same as an amino acid?
39)What is the monomer in Nucleic Acids? What are these monomers made up of?
40)What are the two important types of Nucleic Acids? Where are they found in the cell?
41)Describe the way the monomers link up to make these Nucleic Acids.
42)Name a really important nucleotide that is involved in energy transfer in cells.
Lab:
Identifying Major Macromolecules in Foods
Reading (one of the following):
The New Food Pyramid – Jan 2003 Sci. Am Article
Transgenic Livestock as Drug Factories – Jan 1997 Sci Am Article
Proteins Rule – Apr 2002 Sci Am Article
Chapter 6 Enzymes - Objectives:
1)What is Metabolism?
2)What is an anabolic reaction? Is it energy yeilding or energy consuming reaction? Give an example.
3)What is a catabolic reaction? Is it energy yeilding or energy consuming rection? Give an example.
4)Is an anabolic reaction an exergonic or endergonic reaction? Why?
5)Is an cataabolic reaction an exergonic or endergonic reaction? Why?
6)What is the energy molecule of the cell? What type of macromolecule is it?
7)How does the energy released in an catabolic reaction get harnessed and utilized in a anabolic reaction?
8)What ‘activities’ need energy inside a cell?
9)What is Activation energy?
10) What do enzymes do inside our cells?
11) What class of macromolecule do enzymes belong to?
12) Explain the following statement: Enzymes are specific and recyclable.
13) Illustrate and explain the way an enzyme works – be sure to include the following concepts: Active site, Enyme Substrate complex, Induced Fit Hypothesis, Activation Energy. What happens to the enzyme at the end of a reaction?
14) What is the overall effect of adding an enzyme on the rate/speed of a reaction?
15) How can you make this above enzyme catalyzed reaction go faster?
16) Draw graphs showing the effect of changing the following factors on the speed of an enzyme catalyzed reaction:
a)Substrate concentration
b)Temperature
c)pH
17) What is feedback inhibition – illustrate with an example.
18) Complete the following table:
Factor / Effect on Enzyme Catalyzed reaction / Biochemical Reason For This Effect / Is there a limit to this effect? What is it? / ExampleSubstrate concentration
Temperature
pH
Cofactors/coenzymes
Factor / Effect on Enzyme Catalyzed reaction / Biochemical Reason For This Effect / Is there a limit to this effect? What is it? / Example
Salt
Competitive Inhibitor
Noncompetitive Inhibitor
Allosteric Activator
Lab:
Enzymes
Stronger Proof That Trans Fats Are Bad
(Science News Article - April 2004)
Edna Francisco
WHERE FAT'S AT. People encounter trans fats when they eat baked and fried foods. A new study examining body fat adds weight to evidence that trans fats are associated with heart problems.
Scientists have warned us that eating lots of trans fats, a common component in a variety of fatty foods, can lead to heart problems. A recent study has strengthened the caution, as researchers have investigated these fats in the bodies of first-heart-attack patients.
Whenever food manufacturers transform vegetable oils into solids—via a process called hydrogenation—trans fats are created. For the sake of texture and preservation, trans fats show up in most margarines, shortening, and foods cooked with partially hydrogenated oils. Different types of trans fats also occur naturally in dairy foods and some meats, but they tend to have health.
Trans fats have raised concern for decades, as research has increasingly suggested a causal link between the hydrogenated fats and heart problems. Just as saturated fats and cholesterol do, trans fats raise people's concentrations of artery-clogging low-density lipoprotein (LDL) cholesterol. In addition, trans fats have been known to lower high-density lipoprotein (HDL) cholesterol, the beneficial cholesterol.
Both trans fats and other fats are blamed, in part, for more than 500,000 heart disease deaths in the United States each year, according to the U.S. Food and Drug Administration. Many studies, however, suggest that the adverse effects of trans fats are worse than those of saturated fats, says Walter C. Willett, an epidemiologist from the Harvard School of Public Health. Adding to this argument is a new study looking at people's body fat.
Trans in fat
From 1995 to 1997, scientists from the Commonwealth Scientific and Industrial Research Organization (CSIRO) in Adelaide, South Australia, acquired dietary information as well as fat biopsy samples from 79 people. Each had just had a first heart attack. The researchers obtained similar information and biopsy samples from 167 residents of Adelaide without heart problems. The researchers inquired specifically about the participants' type and amount of fat intake. The heart patients and healthy individuals were also matched for age, gender, and socioeconomic background.
Analysis revealed that trans fats from both animal and vegetable sources were significantly more abundant in the fat tissues of heart attack patients than in the healthy volunteers. The finding supports the idea that trans fats increase the risk of heart disease. "It doesn't necessarily absolutely confirm cause and effect, but it's certainly very damning evidence," says study coauthor Manny Noakes.
Moreover, trans fats are "possibly worse" for the heart than saturated fats are, Noakes adds, as the relationship of abundant trans fats with heart risk remained even after the scientists statistically accounted for the effect of saturated fats in the participants' diets. The findings appear in the April Journal of Nutrition.
Noakes says that the significance of her team's findings stems from their measurement of trans fats in body fat, which correlates with a relatively long-term record of trans fat intake. Earlier studies based on blood-fat data and other observations about people with heart disease linked cardiovascular disease with trans fat consumption. The older data and the stronger CSIRO study together are "sufficiently strong to make a recommendation to reduce the level of trans fat in the food supply," says Noakes.
Disappearing act
Indeed, trans fats' adverse effects on people's health have prompted a few countries to urge consumers away from trans fat-rich foods. Last year, Denmark became the first country to announce that it would ban hydrogenated fats, says Noakes. The United States has since requested food manufacturers to label quantities of hydrogenated trans fat in most foods ( Australia also plans trans fat labeling of foods so people at risk of heart disease, type 2 diabetes, and other conditions can avoid excessive consumption of trans fats.
During the CSIRO study, major margarine producers in Australia voluntarily and coincidentally replaced trans fats in their products with small amounts of saturated fats. Margarine had been the primary vegetable source of trans fats and had accounted for between 36 and 64 percent of the country's total trans fat intake.
The removal of trans fats from the product during the study gave Noakes' team an opportunity to assess how quickly trans fats clear from body fat. The data show that the body clears such fats "unexpectedly" rapidly in people with and without heart disease, Noakes says. The concentration of trans fats in the body fat of people who continued to eat margarine dropped by some 20 percent within a few months.
What happened to the trans fats? "As we change our diet, the nature of our [body] fat changes too," because it's constantly being used for energy, Noakes explains.
The quick disappearance of trans fats from fat tissue is "not surprising, but still is nice to see," says Willett. Overall, he says, the findings from the CSIRO study strengthen the argument that "trans fats should be removed from the food supply as rapidly as possible." Indeed, he finds it troubling that some of the U.S. food industry hasn't followed the lead of European food producers, who have nearly eliminated trans fats from their products. He describes hydrogenated fat as a "metabolic poison with zero nutritional value." He asks, "At what point does . . . feeding it to people without their consent become criminal?"
References:
2003. Revealing trans fats. FDA Consumer 37(Septempber-October):20-26. Available at
Clifton, P.M., J.B. Keogh, and M. Noakes. 2004. Trans fatty acids in adipose tissue and the food supply are associated with myocardial infarction. Journal of Nutrition 134(April):874-879. Abstract available at
Raloff, J. 2003. No hiding most trans fats. Science News Online (July 19). Available at
1997. Genetically engineering a healthier margarine. Science News Online (May 31). Available at
Chapter 4 - Functional Groups Hunt – Biomolecules Review
As mentioned (in class), generally “plain” hydrocarbons are not found in living cells. There are usually other groups of atoms attached somewhere on the molecule. There are certain groups of atoms that are frequently attached to the organic molecules we will be studying, and these are called functional groups. These are things like hydroxyl groups which form alcohols, carbonyl groups which form aldehydes or ketones, carboxyl groups which form carboxylic acids, and amino groups which form amines. These groups tend to act the same and have similar properties no matter where on a carbon backbone molecule they’re stuck. Additionally, a molecule may have more than one functional group and/or more than one type of functional group attached.
Go to
Complete reading all sections – focus on the sections with functional groups (concept 6) and isomers (concept 4). Take the self quiz.
Identify the functional groups in the following molecules:
Functional group:Write the Symbol Used below:
Alcohol (Hydroxyl Group)-OH
Aldehyde (Carbonyl Group)
Ketone (Carbonyl Group)
Carboxylic Acid (Carboxyl Group)
Amine (Amino Group)
Amino Acid (Amino Group + Carboxyl Group)
Phosphate group
Sulfhydrl group
Biomolecules:
ATP or Adenosine Triphosphate – The ENERGY molecule of your cells
Glucose –ring form
Also Glucose!
Aspirin
Find 5 examples of biomolecules from your text that have functional groups and draw/print them – identify the functional group/s they carry. Use chapter 5 for this activity.
Macromolecules Notes
I. Carbon skeletons
A. Isomers
1. Structural isomers - differ in the arrangement of their atoms
2. Geometric isomers - differ in the arrangement of atoms around a double bond
3. Enantiomers
a.molecules that are mirror images of each other
b cells can tell the two apart
cusually one is biologically active while the other is not
B. Polymers
1. Large molecules made by linking many individual building blocks together in long chains. Four types – carbohydrates, lipids, proteins, nucleic acids
2. The building block subunits are called monomers.
3. Subunits are linked by a reaction called dehydration synthesis and can be cleaved/broken down into monomers by a reaction called hydrolysis.
Give examples of these 2 reactions and know their biological significance
II. Carbohydrates (p. 64) - the most important energy source for cells and include sugars and their polymers
A. Nomenclature
1. Monosaccharides (Fig. 5.3) - single sugar units - note the -ose suffix in the names. Classification: Can be ketose/aldose sugar based on functional groups. Know examples of aldose sugar and ketose sugar. Number of Carbons can change. Know examples of C3, C5, C6 sugars. Can form ring structures (Fig. 5.4). Know to identify the structures of glucose, ribose, fructose – linear and ring structures by sight!
2. Disaccharides (Fig. 5.5) - formed by linking two monosaccharides by dehydration synthesis. Bond between monosaccharides = glycosidic linkage. Know the structures of sucrose, lactose, and maltose
3.Polysaccharides (Fig. 5.6)-formed by linking many sugar units together
-general examples - starch, glycogen, and cellulose are the three common polysaccharides