Chemistry of Life Chapter 2-5, 8. CHAPTER 2 A lot of this should be amazingly easy review of...

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 molecule’s 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 patient’s 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

• 6H2O + 6CO2 + light C6H12O6 + 6O2

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 18O 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 it’s 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

Aldehyde Keytone

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 it’s carbon skeleton?

• A. C3H8

• B. C2H6

• C. CH4

• D. C2H4

• E. C2H2

• 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 100’s of monomers long!!

Carbohydrates

• Monosaccharides • Disaccharides

What functional groups are present in carbohydrates?

Glycosidic linkage

More Classification of Carbs!

• Aldose • Ketose

How to Make Sucrose

• The reaction is called a ________.

More Carbs!!!

• Polysaccharides 100’s-1000’s 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

• Testosterone

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

• Purine

Watson and Crick’s 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 can’t attach no chemical reaction– Some Parkinson’s 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= Gfinal – Ginitial

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.

http://www.youtube.com/watch?v=W3KxU63gcF4