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Chemistry of Life Chapter 2-5, 8
CHAPTER 2 A lot of this should be amazingly easy review of chemistry from last year!
Basics of Chemistry Matter Element vs. Compound Trace elements Isotopes Life Requires about 25 chemical elements
ATOMS AND MOLECULES Atomic structure determines the behavior of an element Atoms combine by chemical bonding to form molecules Weak chemical bonds play important roles in the chemistry of life A molecules biological function is related to its shape Chemical reactions make and break chemical bonds
Fig 2-3. The effect of nitrogen deficiency in corn. In this controlled experiment, the plants on the left are growing in soil that was fertilized with compounds containing nitrogen, an essential element. The soil on the right is deficient in nitrogen. If the poorly nourished crop growing in this deficient soil is harvested, it will yield less food--and less nutritious food-- than the crop on the left. Click image to enlarge What happens when a living thing is lacks an essential element?
Fig 2-4. Goiter. The enlarged thyroid gland of this Malaysian woman is due to an iodine deficiency. Click image to enlarge
Radioactive Isotopes A PET scanner detects the energy released in these collisions and maps as "hot spots" the regions of an organ that are most chemically active at the time. The color of the image varies with the amount of the isotope present in an area. In this image the bright yellow color identifies cancerous bone tissue in the patients spine and at the bottom of one shoulder blade.
Energy and Electrons Electrons in different shells, more energy to move out, less to fall back down. Electron arrangement determines how elements act Covalent vs. ionic bonds Electronegativity Polar vs. non polar bonds
Living things depend on Weak bonds Hydrogen bonds- polar molecules Van der Waals- non polar molecules
Structure determines function This should sound familiar!!!!! In cells, most chemical reactions are determined by the shapes of the molecules
Matter cannot be created or destroyed… All chemical reactions are balanced! # reactants = # products 6H 2 O + 6CO 2 + light C 6 H 12 O 6 + 6O 2
Review Questions from book Element:_____::tissue: _______ A. atom, organism B. compound, organ C. molecule, cell D. atom, organ E. compound, organelle
The atomic number of S = 16. When it combines with H it forms a covalent bonded molecule called Hydrogen Sulfide. The molecular formula for hydrogen sulfide is _____
Which of these statements is true of all anionic atoms? A. the atom has more e- than p+ B. the atom has more p+ than e- C. the atom has fewer protons than does a neutral atom of the same element D. the atom has more N than p+ E. the net charge is -1
What 4 chemical elements are most abundant in living matter?
Which arrangement of electrons represents the 18 O isotope? A. 6p, 8N, 6e B. 8p, 10N, 8e C. 9p, 9N, 9e D. 7p, 2N, 9e E. 10p, 8N, 10e
CHAPTER 3 The importance of water!!!!! A small molecule that breaks just about every chemical law of small molecules!!!
The Key is Polarity! Cohesion Adhesion High surface tension High specific heat High heat of vaporization Density decreases when solid
Energy measurements in chemistry Kinetic vs potential energy Heat- the quantity of kinetic energy due to molecular motion Temperature- the intensity of heat due to average kinetic energy of molecules
A swimmer in cold ocean water, like the English Channel, has a higher temperature than the water, but the water has more heat because there is so much of it.
Calories vs. calories 1 cal = amount of heat energy needed to raise the temp of 1g water 1°C 1 Cal = 1 kcal = 1000 cal = the amount of energy needed to raise the temp of 1kg water 1°C
Nearly Universal Solvent Even large molecules can dissolve in water if there are enough polar regions Hydration shell Why do smaller solutes dissolve faster?
Hydrophilic + Hydrophobic Molecules Why is this important for the stability and function of cells? POLAR VS NONPOLAR A hydrophilic molecule is ____ A hydrophobic molecule is ____
pH Cells and molecules require specific pH conditions to function correctly Buffers are vital Acid precipitation can affect ecosystems
Calculation of pH pH= -log [H+] pH decreases as [H+] increases Example:
Review Questions from Book For 2 bodies of matter in contact, heat always flows from A. the body with greater heat to the one with less heat B. the body of higher temp. to the body of lower temp. C. the denser body to the less dense body D. the body with more water to the one with less water E. the larger body to the smaller body
Which of the following is a hydrophobic material? A. paper B. table salt C. wax D. sugar E. pasta
Why is it unlikely that 2 neighboring water molecules would be arranged like this?
CHAPTER 4 Carbon and the Molecular Diversity of Life ORGANIC CHEM !!!
Functional Groups The components of organic molecules that are most commonly involved in chemical reactions Specific combinations of elements that are tacked on to a molecule Each has its own specific properties, and they react the same way EVERY TIME
Important Info about functional groups Are the functional groups hydrophilic or hydrophobic? Why would this make a difference in how the molecule works within a cell?
Hydroxyl Group Compounds containing hydroxyl groups are called _________. Is the hydroxyl group polar or nonpolar?
Carbonyl Group AldehydeKeytone
Carboxyl Group All compounds containing the carboxyl group are called ________. Carboxyl groups act as a(n) ______.
Amino Group All compounds that contain an amino group are called _________. Amino groups act as a(n) ________.
Sulfhydryl Group All compounds containing the sulfhydryl group are called _______. The sulfhydryl group is important for which type of molecules?
Phosphate Group What function is the phosphate group commonly used for in living things? Think ATP!!!
Review Questions Hydroxyl: _____::_____: Aldehyde A. carbonyl, ketone B. oxygen, carbon C. alcohol, carbonyl D. amine, carboxyl E. alcohol, ketone
Which of the following hydrocarbons has a double bond in its carbon skeleton? A. C 3 H 8 B. C 2 H 6 C. CH 4 D. C 2 H 4 E. C 2 H 2
Gasoline is a fossil fuel that is made mostly of ___. A. aldehydes B. amino acids C. alcohols D. hydrocarbons E. thiols
These molecules are… A. structural isomers B. geometric isomers C. enantiomers D. isotopes
Which functional group is NOT present in this molecule? A. carboxyl B. sulfhydryl C. hydroxyl D. amino
Which functional group is most likely to be responsible for a molecule acting like a base? A. hydroxyl B. carbonyl C. carboxyl D. amino E. phosphate
Which of the following would produce a carbonyl group? A. replace the hydroxyl of a carboxyl group with hydrogen B. add a thiol to a phosphate C. add a hydroxyl to a phosphate D. replace the N of an amine with an oxygen E. add a sulfhydryl to a carbonyl
Why is this molecule called an amino acid?
What is the chemical similarity between gasoline and fats?
X Files based Thought Question Some scientists believe that elsewhere in the universe there may be life forms that are based on silicon, in place of carbon. WHY is this logical? (regardless of whether or not it is true)
CHAPTER 5 THE STRUCTURE AND FUNCTION OF MACROMOLECULES This is why we care about organic chemistry!
Terminology Macromolecules- 100,000+ daltons Polymers- made of many smaller pieces Monomers- the smaller repeating units
How to Make a Polymer Dehydration Reaction aka Condensation Reation
How to Break a Polymer Hydrolysis
Proteins Monomers are called ______________ There are ______ different types. A complete protein can be 100s of monomers long!!
Carbohydrates MonosaccharidesDisaccharides What functional groups are present in carbohydrates ? Glycosidic linkage
More Classification of Carbs! AldoseKetose
How to Make Sucrose The reaction is called a ________.
More Carbs!!! Polysaccharides 100s-1000s of monosaccharides long Glycogen- animal liver, muscle cells
Starch-chain of glucose in plants Glycogen- chain of glucose in animals Cellulose- cell walls in plants
Lipids Made by dehydration reactions No affinity for water FATS Made from glycerol and fatty acids Saturated vs. unsaturated
Triacylglycerol A type of fat
Phospholipids Glycerol with 2 fatty acid chains Cell membranes!
Steroids lipids made of rings of carbon Cholesterol- In animal cell membranes Starting point for making other steriods Sex hormones are made from cholesterol
Proteins Diversity of jobs and structures Very complex structures Made of amino acids held together with peptide bonds aka polypeptide Many polypeptides folded into specific shapes= protein Made by dehydration reactions
20 different amino acids Why are they acidic?
DO NOT MEMORIZE THE INFORMATION ON THIS PAGE! The key is to know that the amino acid will behave according to the chemistry of the R group.
Structure of a Protein Primary Sequence of Amino Acids
Secondary Coils and folds of the amino acid sequence
Tertiary Irregular folds and bends created when R groups interact and attract or repel each other Hydrophobic interaction- all hydrophobic parts fold to the inside away from water Disulfide bridges help hold shape together
Quartenary Structure Final shape when all polypeptide pieces are together
Denaturation The unfolding of a protein due to environmental factors Think back to grade 10 enzyme lab What can cause this??
Chaperonins Proteins that assist to make sure the final structure is correct
Nucleic Acids DNA Characteristics RNA Characteristics
Nucleotide N Base + phosphate+ pentose Pyrimidine Purine
Watson and Cricks Idea: Double Helix Shape
Chapter 8 Introduction to Metabolism
Starting with Enzymes Reduce activation energy of a chemical reaction. Reactions will happen w/o enzymes but VERY SLOWLY IF you understand the lessons of the lab we did, you understand what you need to know of enzymes.
Induced fit Substrate attaches then enzyme changes shape to keep a better hold on it for the reaction Allosteric regulation Substrate A attaches to enzyme induced fit kicks in NEW shape opens a separate active site for another substrate
cofactors Non-protein helper molecules required for catalytic activity IF the cofactor is an organic molecule it is called a COENZYME
Inhibiting Enzyme function Competitive inhibitors- molecules that fit into the active site (or part of it) and block the chemical reaction. Solved by adding more of the enzyme for the correct substrate to attach to –Viagra and methotrexate (a chemotherapy med) work this way
Non competitive inhibitors Molecules bind to a second part of the enzyme (NOT active site) Causes conformation change in enzyme correct substrate cant attach no chemical reaction –Some Parkinsons disease meds work this way
Feedback Inhibition The end product of a metabolic pathway loops back to inhibit an enzyme earlier in the process. Causes the pathway to stop no more product made
Bioenergetics- study of how energy flows through living organisms
Energy forms Kinetic Thermal Potential Chemical Radiant
First Law Thermodynamics Energy can be transferred and transformed, but it cannot be created or destroyed Biochem application: Plants transfer radiant energy into chemical energy
Second Law Thermodynamics Every energy transfer or transformation increases the entropy of the universe. Biochem application: spontaneous reactions
Gibbs Free Energy: G The portion of a systems energy that is available to do work in a living cell. Change in free energy (ΔG) as positive or negative shows the energy of the products of a reaction –Named for Willard Gibbs (1878) but easy to remember if you know NCIS
Math you should recognize for AP Exam ΔG= ΔH – TΔS ΔG: change in free energy ΔH: change in enthalpy = total energy T: temperature in Kelvin ΔS: change in entropy ΔG= G final – G initial
Endergonic Reaction Absorbs free energy, +ΔG NOT spontaneous You should know this metabolic pathway- what is it?
Exergonic Reaction Releases free energy, -ΔG Spontaneous (does not mean FAST) The opposite pathway of the previous example is exergonic…what is it? FYI for any test in this class you should understand what this graph means!
ENERGY COUPLING REACTIONS Cells often use the free energy from an exergonic reaction to power a necessary endergonic reaction.
ATP Created by enzyme: ATP synthase Hydrolized to become ADP Word of the Day: Phosphorylation Transferring Phosphate groups from one molecule to another ADP is phosphorylated in order to create ATP.