Chapter 1 Introduction: Themes in the Study of Life
What are Themes? General principles or ideas that occur over and over. In the new AP curriculum, the themes are “the Big Ideas”.
The 4 Big Ideas: E2 – I2 1. Evolution 2. Energy 3. Information 4. Interactions
The Big Ideas – E2 - I2 1. Evolution – the process of evolution drives the diversity and unity of life. 2. Energy – biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 3. Information – living systems store, retrieve, transmit and respond to information essential to life processes. 4. Interactions – biological systems interact and these systems and their interactions possess complex properties.
Why Big Ideas? We will see the Big Ideas at various times throughout the course. The Big Ideas will be the “connectors” between the content of the course.
Scientific Method Steps 1. Identify the problem. 2. What is already known? 3. Formulate a hypothesis. 4. Conduct an experiment changing one variable at a time. (Why?) 5. Collect data. Have replicates. (Why?) 6.Compare data to hypothesis. Does the data support the hypothesis? 7. Conclusions and new hypothesis
Comment Nothing is ever proven in science. – Can only be disproven Experiments either support or fail to support a particular hypothesis. Disproving a hypothesis is as important as supporting it. We will learn about the 7 Science Practices in Lab.
Chapter Summary Big Ideas can provide a common framework for learning Biology. What are the characteristics of Life? How does Science work? Evolution’s role in the study of Biology.
QUESTIONS FROM CHAPTER 2 and/or 3? Questions I have for you: 1. Why would weak bonds between molecules be important in the biological world? a. brief contact is important for chemical signaling in the brain b. Hydrogen bonding in DNA c. Van der Waals Interactions (may occur in proteins) d. Lock and key fit of biological molecules aids in the formation of weak bonds. e. DNA replication f. Gecko climbing a wall I am assuming you remember and know the basic chemistry information from this chapter. If you need more information or practice with this information, let me know.
2. What does it mean that water has a high specific heat and how is this biologically significant? (think adaptive value) a. water will change its temperature less when it absorbs or loses a given amount of heat. b. large bodies of water keep temp. fluctuations on land and in water within limits that permit life c. organisms are made primarily of water, this enables them to resist changes in their own temp, than if they were made of a liquid with a lower specific heat. 3. What is the difference between hydrophilic and hydrophobic?
Examples of Macroelements: C HOPKNS CaFe Mg NaCl
QUESTIONS FROM CHAPTER 4? I.Introduction to Organic Compounds and Their Polymers A. Carbon 1. Organic molecules – compounds made by cells and contain 2 or more carbon atoms. 2. 6 electrons…four covalent bonds 3. Hydrocarbons…compounds composed of only carbon and hydrogen 4. Carbon skeleton…chain of carbon atoms in organic molecules a. may include double bonds b. vary in length, may be straight, branched, or arranged in rings c. hydrophobic compounds because bonds between carbon and hydrogen are nonpolar
6. Isomers…compounds with the same molecular formula, different structures and therefore different properties. a. Structural Isomers…differ in covalent arrangement of atoms b. Geometric isomers…same covalent arrangement, differ in spatial arrangement c. Enantiomers or Stereoisomers...molecules that are mirror images Structural Isomers
B. Functional Groups (pg. 64-65 in book) 1. LEARN to understand properties of organic compounds 2. Attached to carbon skeleton, usually involved in reactions a. Some are attached to the end Hydroxyl group ( -OH) molecules containing this group are called alcohols Amino group (--NH 2 ) molecules containing this group are called amines. b. Some include a carbon atom of the skeleton Carbonyl group (-C=O) If carbon is at end of skeleton the compound is called an aldehyde. If carbon if within the chain it is called a ketone. Carboxyl group (-COOH) Compounds in this group are called carboxylic acids
3. Nonpolar functional groups a. Sulfhydryl (-SH) Compounds with this group are called “thiols” Help to stabilize structure of protein. b. Phosphate (PO 4 ) Anion. Function is the transfer of energy between molecules (ATP) C. General terms (this is where chapter 5 starts) 1. Macromolecules 2. Polymer 3. Monomer 4. Dehydration Synthesis (condensation reaction) 5. Hydrolysis
For each Macromolecule know the following: Elements it contains Monomer units and structures Examples Uses or roles
II. Carbohydrates A. Monosaccharides 1. Molecular formula CH 2 O 2. Classifying a sugar a. hydroxyl group attached to each carbon except for one b. the one carbon is bonded to an oxygen to form a carbonyl group (aldose or a ketose depending on location) B. Dissacharides 1. “glycosidic linkage” bonds two monosaccharides 2. Sucrose (gl + fr), Maltose (gl + gl), Lactose (gl + ga)
C. Oligosaccharides 1. 2 - 10 joined simple sugars. 2. Used in cell membranes. D. Polysaccharides 1. polymers of a few hundred to a few thousand monosaccharides linked together by dehydration 2. Storage molecules a. starch b. glycogen 3. building material for protective structures a. Cellulose b. Chitin c. Pectin
III. Lipids A. Fat or triglyceride 1. nonpolar 2. made of 1 glycerol and 3 fatty acids a. glycerol is an alcohol b. fatty acid is a carboxyl group on a hydrocarbon chain 3. Unsaturated vs. Saturated 4. energy storage B. Phospholipids 1. major component of cell membrane (2007 essay ques) 2. structurally similar to fats, but contain phosphorus and have 2 fatty acids instead of 3
Phospholipids have a hydrophobic tail, but a hydrophilic head. Self-assembles into bilayers, an important part of cell membranes.
C. Waxes 1. one fatty acid linked to an alcohol a. more hydrophobic than fats D. Glycolipid 1. 3 rd carbon in glycerol is bonded to a short carbohydrate chain 2. hydrophilic in cell membrane E. Steroid 1. carbon skeleton is bent to form 4 fused rings (3 six sided rings and 1 five sided ring) 2. Cholesterol is an example 3. female and male sex hormones 4. anabolic steroids (variant of testosterone)
Question ? Which has more energy, a kg of fat or a kg of starch? Fat - there are more C-H bonds which provide more energy per mass.
IV. Proteins A. Essential to structures and activities of life 1. From Greek word proteios 2. Monomer is amino acid 3. Seven different classes of proteins a. Structural b. Contractile c. Storage d. Defensive e. Transport f. Signal g. Enzymes
B. Made from 20 kinds of amino acids 1. Basic structure 2. R group determines the properties of each amino acid C. Amino acids linked by “peptide bonds” 1. Dehydration synthesis 2. Carboxyl group carbon bonds to the amino group nitrogen of the neighboring amino acid = peptide bond 3. Chain of amino acids = “polypeptide chain” 4. A protein consists of one or more polypeptide chains folded and coiled into a specific conformation D. Shape determines its function E. Denaturation = polypeptide chain unravels, losing shape and thus function
F. There are 4 levels of structure that go into determining the shape of a protein 1. Primary Structure – amino acid sequence a. this is what determines the 3-D conformation 2. Secondary Structure – coils and folds made by polypeptide chain a. coils caused by hydrogen bonds at regular intervals along the polypeptide backbone b. Alpha helix – coil held together by H-bonding between every 4th amino acid. c. Pleated Sheet – two regions of the polypeptide chain lie parallel to each other.
3.Tertiary structure – the overall, 3-D shape of the polypeptide a. most are described as “globular” or “fibrous” b. results from the interactions between the R groups c. Hydrophobic interaction – type of bonding that causes the tertiary structure d. Disulfide bridges – strong covalent bonds that reinforce the protein conformation. Form when two cysteine monomers are close together. 4. Quaternary Structure – overall structure that results from the aggregation of these polypeptide subunits. a. not all proteins have this structure (only ones with two or more polypeptide chains. b. Collagen and Hemoglobin are examples that have this structure
F. How does a protein know how to fold? 1. Chaperone proteins – molecules that function as temporary braces in assisting the folding of other proteins. G. Linus Pauling Tertiary Structure Quarternary Structure
Chaperone Protein (aka “chaperonins”) A chaperon protein found in E. coli Provides a “shelter” for the folding polypeptide
V. Nucleic Acids A. Information rich polymers of nucleotides 1. holds recipe to make proteins 2. DNA and RNA 3. a gene codes for one protein (sequence of amino acids) 4. Monomer is a nucleotide (nucleoside monophosphate) a. a 5-carbon sugar (ribose or deoxyribose) b. phosphate group (attached to the 5 th carbon) c. nitrogen base (two families – pyrimidines and purines) Pyrimidines (Cytosine, Thymine, Uracil) Purines (Guanine, Adenine)
5. DNA is double helix, while RNA is single stranded 6. Phosphodiester linkage creates the phosphate sugar backbone 7. Watson and Crick – Cambridge 1953