Lecture 3: Water and carbon, the secrets of life

Lecture 3: Water and carbon, the secrets of life

In this lecture Heat, temperature and energy The four emergent properties of water Acids and bases Carbon skeletons Hydrocarbons Isomers

First, a little aside about heat and energy Energy: the ability to do work Two main categories of energy: potential energy and kinetic energy Energy cannot be created nor destroyed 2 nd law of thermodynamics it can only be converted To transform one type of energy into another, you must input even more energy!

Potential energy is energy that is not doing anything right now, but has the stored energy to be able to do it in the future Kinetic energy is the energy in movement right now Chemical potential energy is the energy stored in chemical bonds Radiant energy is in the form of electromagnetic radiation (light, UV, gamma rays) Gravitational potential energy is the ability of something to fall due to gravity Thermal energy is in the form of molecules vibrating

Tracing energy transformations Sunlight Ancient ferns Oil/Gas Cars Kinetic solar energy in photons CO 2 + H 2 O + photons Potential chemical energy in the bonds of glucose Potential chemical energy in the bonds of oil Kinetic energy in the car tires moving C 6 H 12 O 6 C 8 H 12 CO 2 + H 2 O Photosynthesis Chemical reaction using the kinetic energy in photons to create potential chemical energy Heat and pressure Chemical reaction using earth s heat and pressure to convert the chemical energy of glucose into the chemical energy of oil Spark plug Combustion reaction using electricity to convert the chemical energy of oil into the kinetic energy of moving tires

A little bit about heat and temperature Heat is a measure of the total amount of kinetic energy due to molecular motion Temperature measures the intensity of heat due to the average kinetic energy of molecules A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1 C The calories on food packages are actually kilocalories (kcal), where 1 kcal = 1,000 cal

Water is crucial to life on Earth!! Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 70 95% water The abundance of water is the main reason the Earth is habitable

Why water? Four properties of water: Water is a versatile solvent Water sticks to itself (cohesion) Water moderates temperature Water expands upon freezing

Water s secret: Hydrogen bonding All of water s properties come from the fact that it: Is polar Can hydrogen bond because of its polarity

Water is a versatile solvent In chemistry, like dissolves like Water is a polar molecule Polar molecules can dissolve other polar molecules Most molecules in biology are polar enough that water can solvate them

A protein solvated by water

A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution The solute is the substance that is dissolved An aqueous solution is one in which water is the solvent Most biochemical reactions occur in water Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution

Water and cohesion Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Surface tension is a measure of how hard it is to break the surface of a liquid Surface tension is related to cohesion

Cohesion allows plants to drink

Water and temperature moderation Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat with only a slight change in its own temperature The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC The specific heat of water is 1 cal/g/ºc Water resists changing its temperature because of its high specific heat

Water s high specific heat can be traced to hydrogen bonding Heat is absorbed when hydrogen bonds break (thermal energy converted to chemical energy) Heat is released when hydrogen bonds form (chemical potential energy converted into thermal energy) The high specific heat of water minimizes temperature fluctuations to within limits that permit life

Figure 3.5 Santa Barbara 73 70s ( F) 80s 90s 100s Los Angeles (Airport) 75 Burbank 90 Pacific Ocean 68 San Diego 72 Santa Ana 84 San Bernardino 100 Riverside 96 Palm Springs 106 40 miles

Water and freezing Water s hydrogen bonding forces it to create orderly, angular bonds when it freezes These bonds force the water molecules further apart than they are when liquid Ice floats in liquid water because it is less dense fewer water molecules/cm 3 Water reaches its greatest density at 4 C If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth

Ice: stable hydrogen bonds Shrimp?? Liquid water: transient hydrogen bonds

A hydrophilic substance is one that has an affinity for water A hydrophilic molecule has lots of polar regions A hydrophobic substance is one that does not have an affinity for water A hydrophobic molecule has lots of nonpolar regions (A colloid is a stable suspension of fine particles in a liquid) Hydrophilic and hydrophobic are IMPORTANT VOCABULARY WORDS!!!!

The structure of vegetable oil Oil molecules are hydrophobic because they have mostly nonpolar bonds

Acids, bases, and life An acid is any substance that increases the H + concentration of a solution, or reduces the OH - concentration Another definition: acids accept electron pairs A base is any substance that reduces the H + concentration of a solution, or increases the OH - concentration Bases donate electron pairs H+ means hydrogen ion, a hydrogen minus its electron H+ is therefore just a single proton! H+ is interchangeable with proton

The ph scale The ph scale goes from 1-14 Acidic solutions have ph values less than 7 Basic solutions have ph values greater than 7 Pure water has a value of 7 Most biological fluids have ph values in the range of 6 to 8 Stomach acid is at ph 2 Humans can t tolerate large changes in ph, but some plants and bacteria can!

Buffers The internal ph of most living cells must remain close to ph 7 Buffers are substances that minimize changes in concentrations of H + and OH in a solution Most buffers consist of an acid-base pair that reversibly combines with H +

Increasingly Basic [H + ] < [OH ] Increasingly Acidic [H + ] > [OH ] Figure 3.10 ph Scale 0 1 Battery acid H + H+ H + H + OH OH H + H + H + H + Acidic solution OH OH H + H + OH OH OH H + H + H+ Neutral solution OH OH OH H + OH OH OH H + OH Basic solution Neutral [H + ] = [OH ] 2 3 4 5 6 7 8 9 10 11 12 13 14 Gastric juice, lemon juice Vinegar, wine, cola Tomato juice Beer Black coffee Rainwater Urine Saliva Pure water Human blood, tears Seawater Inside of small intestine Milk of magnesia Household ammonia Household bleach Oven cleaner

Acidification: A Threat to Water Quality Human activities such as burning fossil fuels threaten water quality CO 2 is the main product of fossil fuel combustion About 25% of human-generated CO 2 is absorbed by the oceans CO 2 dissolved in sea water forms carbonic acid; this process is called ocean acidification

Figure 3.11 CO 2 CO 2 + H 2 O H 2 CO 3 H 2 CO 3 H + + HCO 3 H + + CO 3 2 HCO 3 CO 3 2 + Ca 2+ CaCO 3

Figure 3.12 As seawater acidifies, H + ions combine with carbonate ions to produce bicarbonate Carbonate is required for calcification (production of calcium carbonate) by many marine organisms, including reef-building corals

The burning of fossil fuels is also a major source of sulfur oxides and nitrogen oxides These compounds react with water in the air to form strong acids that fall in rain or snow Acid precipitation is rain, fog, or snow with a ph lower than 5.2 Acid precipitation damages life in lakes and streams and changes soil chemistry on land

Vocabulary Hydrophilic, hydrophobic Potential energy, kinetic energy Buffer Acid, base Heat, temperature Calorie, kilocalorie Astrobiology

Carbon: the backbone of life Living things are composed largely of carbon Proteins, DNA, and carbohydrates all use carbon as their base Organic chemistry (o-chem) is the study of the chemistry of carbon An organic molecule contains carbon Most organic molecules have hydrogen as well as carbon

The chemistry of carbon Carbon has four valence electrons, and so can have up to four bonds Carbon can have single bonds, double bonds, etc. Carbon s ability to have four bonds lets it create large, complex molecules The four bonds have very exact angles and positions Carbon most frequently bonds with hydrogen, nitrogen, oxygen, and itself

Missing four of the eight electrons it needs to be happy

Figure 4.3 Name and Comment Molecular Formula Structural Formula Ball-and- Stick Model Space-Filling Model (a) Methane CH 4 (b) Ethane C 2 H 6 (c) Ethene (ethylene) C 2 H 4

Figure 4.5 (a) Length (c) Double bond position Ethane Propane 1-Butene 2-Butene (b) Branching (d) Presence of rings Butane 2-Methylpropane (isobutane) Cyclohexane Benzene

Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats and oil have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy Gasoline is a hydrocarbon

Figure 4.6 Hydrocarbons in human fat Nucleus Fat droplets 10 m (a) Part of a human adipose cell (b) A fat molecule

Isomers are compounds with the same molecular formula but different structures and properties Structural isomers have different covalent arrangements of their atoms Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Enantiomers are isomers that are mirror images of each other

Figure 4.7 (a) Structural isomers (b) Cis-trans isomers cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (c) Enantiomers CO 2 H CO 2 H H NH 2 NH 2 H CH 3 L isomer CH 3 D isomer

Enantiomers and pharmaceuticals Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Usually only one isomer is biologically active Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

Figure 4.8 Drug Condition Effective Enantiomer Ineffective Enantiomer Ibuprofen Pain; inflammation S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol

Functional Groups In the place of hydrogen, distinct chemical functional groups groups can bond carbon The properties of an organic molecule depends on the carbon skeleton and its functional groups Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties

Figure 4.UN02 The same carbon skeleton, different functional groups, very different effects Methyl group Estradiol Testosterone Hydroxyl group Carbonyl group

There are only seven main functional groups: The seven functional groups that are most important in the chemistry of life: Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group

Figure 4.9a Hydroxyl STRUCTURE (may be written HO ) Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND EXAMPLE Is polar as a result of the electrons spending more time near the electronegative oxygen atom. FUNCTIONAL PROPERTIES Ethanol Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Figure 4.9b Carbonyl STRUCTURE EXAMPLE Acetone Propanal Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). NAME OF COMPOUND FUNCTIONAL PROPERTIES

Figure 4.9c Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE Acts as an acid; can donate an H + because the covalent bond between oxygen and hydrogen is so polar: FUNCTIONAL PROPERTIES Acetic acid Nonionized Ionized Found in cells in the ionized form with a charge of 1 and called a carboxylate ion.

Figure 4.9d Amino STRUCTURE Amines NAME OF COMPOUND EXAMPLE Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms): FUNCTIONAL PROPERTIES Glycine Nonionized Ionized Found in cells in the ionized form with a charge of 1.

Figure 4.9e Sulfhydryl STRUCTURE Thiols NAME OF COMPOUND (may be written HS ) EXAMPLE Two sulfhydryl groups can react, forming a covalent bond. This cross-linking helps stabilize protein structure. FUNCTIONAL PROPERTIES Cysteine Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be permanently curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds.

Figure 4.9f Phosphate STRUCTURE Organic phosphates NAME OF COMPOUND EXAMPLE Glycerol phosphate Contributes negative charge to the molecule of which it is a part (2 when at the end of a molecule, as at left; 1 when located internally in a chain of phosphates). Molecules containing phosphate groups have the potential to react with water, releasing energy. FUNCTIONAL PROPERTIES

Figure 4.9g Methyl STRUCTURE Methylated compounds NAME OF COMPOUND EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. FUNCTIONAL PROPERTIES 5-Methyl cytidine Arrangement of methyl groups in male and female sex hormones affects their shape and function.

ATP, the (potential chemical) energy of the cell One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

A closer look at ATP High-energy phosphate bonds

ATP s chemical energy ATP is hydrolyzed to break off a phosphate functional group The potential energy stored in the chemical bond of the phosphate can be coupled to other chemical reactions This chemical energy acts as the catalyst in other biochemical reactions

The 3D shape of organic molecules The 3D shape of organic molecules determines their ultimate function A molecule s shape is determined by the positions of its atoms valence orbitals

Biological molecules and shape Biological molecules recognize and interact with each other with a specificity based on molecular shape Lock and key model A lock will only take a key of a specific shape Molecules with similar shapes can have similar biological effects

Astrobiology: The study of life on other planets Can carbon be replaced? Silicon has a similar reactivity to carbon Have difficulty forming double and triple bonds Phosphorus can also form long-chain molecules Unstable and easily break apart Can water be replaced? Liquid methane and liquid ammonia are also candidates to support life

Organic molecules on other planets Organic molecules commonly form in the dust and gas clouds that form planets Complex molecules form as functional groups bond together Ethyl formate (C2H5OCHO). n-propyl cyanide (C3H7CN

Organic molecule Enantiomer Isomer Structural Isomer Geometric isomer Functional group Hydrocarbon ATP Vocabulary

Questions??