Water Properties, Structure, and Polarity. PDF

# 1.1 - Water Water is an inorganic molecule that provides no calories or nutrients. It is tasteless, odorless and nearly colorless-yet is essential to every living organism on Earth. Water is the most abundant molecule in cells, accounting for 70% or more of the mass of a cell. ## Structure of W...

# 1.1 - Water Water is an inorganic molecule that provides no calories or nutrients. It is tasteless, odorless and nearly colorless-yet is essential to every living organism on Earth. Water is the most abundant molecule in cells, accounting for 70% or more of the mass of a cell. ## Structure of Water A water molecule is a bent molecule with 1 oxygen atom covalently bonded to 2 hydrogen atoms. Bent means the molecule is: - angular - 95.84 pm **Note:** There is a diagram showing the bent molecule, an oxygen atom bonded to two hydrogen atoms at an angle. This diagram is important as it is used later in the document to show the structure of water. Covalently bonded means the electrons are shared by the different atoms. However, the Oxygen atom pulls on the electrons more strongly than the hydrogen atoms. Electrons have a negative charge. Because oxygen pulls the electrons more strongly, oxygen has a partial negative charge. That leaves hydrogen with a partial positive charge. ## By definition, this makes water a polar molecule. A polar molecule is a molecule that is a molecule that is negatively charged on one end and positively charged on the other. **Note**: The diagram shows a water molecule with the oxygen side marked with a negative sign, and the two hydrogen sides marked with a positive sign. ## Hydrogen Bonds Because water is polar, it forms hydrogen bonds. **Note**: The diagram shows a water molecule. It also shows hydrogen bonds, represented by dotted lines, between the water molecule and other water molecules. The oxygen atom forms a hydrogen bond with the hydrogen atom of a different water molecule. The partial positive charges of one water molecule are attached to the partial negative charges of another water molecule. This force of attraction is called a hydrogen bond. **CAREFUL!** Hydrogen bonds are forces between water molecules, not within them. # Why are Hydrogen Bonds a Big Deal? Water and methane are both small molecules with similar molecular masses. Water is polar, and can form hydrogen bonds. Methane is nonpolar, and cannot form hydrogen bonds. Because of this difference, they have immensely different physical properties. ## BIG IDEA: The Structure of a molecule determines its Physical properties. Hydrogen bonds account for all of the unique properties of water including: * **Cohesion** Cohesion is the force of attraction between like water molecules (ex. two water molecules) Water has cohesive forces because of hydrogen bonds. Because of cohesion, water beads together and has a very high surface tension. This allows for water striders and other insects to walk on water. * **Adhesion** Adhesion is the force of attraction between unlike molecules (ex. a molecule on a gecko toe and a glass molecule or a water molecule and a glass molecule). This is why water forms a meniscus on a glass tube and why certain animals can walk on surfaces upside down. Because water is polar, it is attracted to other polar molecules. # Water's Density Anomaly When water freezes, the water molecules form a lattice of stable hydrogen bonds. In this lattice, the water molecules are spaced further apart than they are in liquid form. As a result, water is one of the few substances that is more dense as a liquid than as a solid. Therefore ice floats, allowing creatures to survive under the ice when water starts to freeze. ## Hydrophilic vs. Hydrophobic Because water is so important and abundant in life, substances can be classified by whether they do or do not dissolve in water. * **Polar** or **Charged** substances are chemically attracted to water. Therefore they dissolve easily in water. These substances are considered **hydrophilic**. - hydro = water - philic = loving **Examples**: Salt, sugar * **Nonpolar** substances are not chemically attracted to water. Therefore they do not dissolve easily in water. These substances are considered **hydrophobic**. - hydro = water - phobic = fearing Because they are corralled by the bonds of the surrounding water molecules, nonpolar substances tend to clump together in water. **Examples**: oil, soap, $CO_2$ This is why most biological molecules are hydrophilic and therefore can be easily dissolved in water to wherever they are needed. # Living Systems depend on the properties of water that result in polarity and hydrogen bonding. # 1.2 - Biological Macromolecules *Molecular Biology* explains living processes in terms of the chemical substances involved. Every biological process can be reduced to the **structure** and the **functions** of individual molecules. By better understanding the **interactions** of these molecules, we can better understand the process as a whole. Molecular biology has allowed for enormous advances in scientific understanding, medical research, and biotechnology. It is still a field of science that is relatively young. What an exciting thing to be a part of! ## Organic Compounds Life on Earth is based on **carbon**. Most elements can only form a few bonds. Carbon is special because it can form $4$ covalent bonds. Carbon can form **single**, **double** or **triple** bonds, and it can bond with a wide variety of different elements. This allows for a huge diversity of compounds that can be created with carbon. Molecules that contain carbon are called **organic** molecules. **Note**: There are diagrams showing the structure of different organic molecules, including glucose, dopamine, testosterone, DNA, caffeine, alanine, heroin, and fatty acids. # How to Read Molecular Drawings **Where are the carbons? ** Draw an arrow pointing to each carbon below. **Note**: Here, there is a diagram of a molecule, including the carbon atoms. **How many carbons do caffeine, glucose, and alanine each have?** There are 6 carbons in each. # Life is based on 4 Main Classes of organic molecules: ## The Biological Macromolecules ### Carbohydrates * **Uses**: energy, short term energy storage, structure, cell to cell recognition Usually made of carbon, hydrogen, and oxygen in the ratio $C_n(H_2O)_m$. **Examples**: **sugar**, **starch**, **cellulose** **Note**: There are diagrams showing the structure of glucose, starch, and fructose molecules. ### Lipids * **Uses**: long term energy storage, cell membranes, signaling Made of carbon, hydrogen, and oxygen. Largely hydrophobic. **Examples**: **fats**, **steroids**, **waxes** **Note**: There are diagrams showing the structure of a triglyceride, a cholesterol molecule, and a steroid hormone (estradiol). ### Proteins * **Uses**: catalyzing chemical reactions, signaling, transport, structure Primarily made of carbon, hydrogen, oxygen, and nitrogen. Incredibly diverse class of molecules. **Note**: There are diagrams illustrating the structure of a protein, the primary, secondary, tertiary, and quaternary structure of a protein. ### Nucleic Acids * **Uses**: store and transmit genetic information Made of carbon, hypoten, oxygen, nitrogen, and phosphorus. The **most important** macromolecule. **Examples**: **Ribonucleic acid (RNA)** and **deoxyribonucleic acid (DNA)**. **Note**: There are diagrams showing the structure of a DNA nucleotide and an RNA nucleotide. ## Monomers and Polymers Each class of macromolecule has its own set of **monomers**. * A **monomer** is a molecule that can **bond** to other molecules to form a **polymer**. * A **polymer** is a larger molecule made of many monomers. # Dehydration Synthesis Reaction Macromolecules are **built** from monomers via dehydration synthesis reactions (also called condensation reactions). **Note**: There is a diagram showing how two molecules are bonded together by removing a water molecule. It's called a dehydration synthesis reaction because it **makes** the polymer bond by **removing this water molecule**. **Draw the product of a dehydration synthesis reaction,** showing the two molecules bonded together and the water molecule that was removed. # Hydrolysis Reaction Macromolecules are **broken down** into monomers via hydrolysis reactions. **Note**: There is a diagram showing how the bond between two molecules is broken by adding a water molecule. It's called a hydrolysis reaction because it **breaks** the polymer bond by **adding this water molecule**. **Draw the product of a hydrolysis reaction**, showing the two separate molecules and the water molecule that was added. **Each class of biological macromolecule has different properties and is used for different purposes.** # 1.3 - Carbohydrates Carbohydrates are the most abundant carbohydrate biological molecule in the biosphere. Carbohydrates serve a variety of purposes, but the most common are: **energy**, **short term energy storage**, and **structure**. Carbohydrates are made out of simple sugars and are generally categorized based on length. * **Monosaccharides** * **Disaccharides** * **Oligosaccharides** * **Polysaccharides** ## Monosaccharides Monosaccharides are the building blocks (**monomers**) of all carbohydrates. **What do these monosaccharides have in common?** **Note**: There are diagrams showing the structure of different monosaccharides, including glucose, fructose, galactose, deoxyribose, and ribose. They are all **polygons**. ## Disaccharides **Monosaccharides** can be joined together by a **dehydration reaction** to form a **disaccharide**. **Note**: There is a diagram showing this reaction, with two monosaccharide subunits bonding together to form a disaccharide. **Complete the reaction shown. The products are incomplete.** ## Examples of Disaccharides * **Sucrose:** common table sugar. Plants produce it naturally and humans refine it into table sugar. The average American consumes $17$ teaspoons of added sugar per day. * **Lactose:** makes up 2-8% of cow's milk by mass. Formed from glucose and galactose subunits. 68% of the adult population worldwide are intolerant. * **Sucralose:** Accidentally created in 1976 when researchers were trying to develop a new pesticide. It's 450-650 times sweeter than sucrose ## Polysaccharides Polysaccharides are **polymers** of **monosaccharides**. They can be anywhere from ten to thousands of monosaccharides long. **Polysaccharides** are huge molecules used for **energy storage** and **structure**. **Polysaccharides** can be **linear** or **branched** **Note**: There are diagrams showing the structure of a linear polysaccharide and a branched polysaccharide. **Used for:** storing glucose in plants, storing glucose in animals, and structure in plants. ## BIG IDEA: **Structure Determines Function** The structure of carbohydrates allows them to provide **energy**, **energy storage**, and **structure**. # 1.4 - Lipids Lipids are a diverse group of **organic** compounds that are all **hydrophobic**. They are used for: * **energy storage** * **cell membranes** * **signaling** **Note**: There are diagrams showing the structure of a free fatty acid, a triglyceride, a phospholipid, and a cholesterol molecule. ## Lipids vs. Carbohydrates Lipids are better for **long term energy storage** than carbohydrates. Per gram of body mass, lipids are about **6 times** more efficient than carbohydrates for the following reasons: 1. First, lipids store **twice** as much energy per gram as carbohydrates. 2. Second, because lipids are **hydrophobic**, they are stored as **fat droplets**. In contrast, one gram of glycogen complexes with about **10 grams** of water. Because organisms must carry all of their energy storage around with them, it is very advantageous to not carry around the extra mass. While fats are better for long-term storage, they are not very useful for **immediate energy access**. It takes an organism a while to break down fatty tissue for energy. Glycogen, however, can be rapidly broken down into its glucose monomers. Lipids are also useful for other tasks. Fats are a great **insulator** and **shock absorber**. Fatty tissue below the skin and around the organs can help keep them **safe and warm**. Carbohydrates would not be able to do that as well. ## Fatty Acids Structure Many lipids are made from **fatty acid** subunits. **Note**: There is a diagram showing a fatty acid. Fatty acids are **carboxyl** attached to a long chain of carbons and hydrogens (generally 14-20). These long chains are called **chains**. Fatty acids can be: * **Saturated**: (only C-C single bonds) * **Unsaturated**: (one C=C double bond) * **Polyunsaturated**: (many C=C) **Double bonds** can be **cis** or **trans**. **Note**: There is a diagram showing two types of but-2-ene. In **cis double bonds** the hydrogens are on the **same side** of the bond. In **trans double bonds**, the hydrogens are on **opposite sides** of the bond. Because double bonds can be cis or trans, **unsaturated** fatty acids can be cis or trans. **Indicate which fatty acid is cis and which is trans**. **Note**: There are diagrams showing an elaidic acid molecule and an oleic acid molecule, indicating which is cis and which is trans. **Saturated fatty acids** are straight molecules. **Cis-fatty acids** are bent molecules. **Trans fatty acids** are straight molecules. This allows them to pack together tightly and greatly increases their **melting point**. Saturated fatty acids and **trans-fatty acids** are **solid** at room temperature. These fatty acids cannot pack tightly and therefore have a **lower melting point**. **Cis-fatty acids** are **liquid** at room temperature. ## Fatty Acids and Food You don't have to stir conventional peanut butter, but you do have to stir natural peanut butter. Why is this? **Note**: There are two pictures, one of a jar of conventional peanut butter and one of a jar of natural peanut butter. The ingredients for both are listed. **Circle the important ingredient that causes this difference.** The important ingredient is **hydrogenated vegetable oil**. Companies add hydrogens to turn the **cis-unsaturated** fatty acids found in peanuts into either **trans-unsaturated** fatty acids or **saturated** fatty acids. **Note:** There is a table showing the type of fatty acid, where it is found, and its characteristics. **Complete the table**, filling in the missing words in the Characteristics column. # Lipids are diverse and delicious. #1.5 - Nucleic Acids All life on earth **uses** nucleic acids. Nucleic acids are named after where they were first discovered - in the **nucleus** of a cell. There are two kinds of nucleic acids: * **Deoxyribonucleic Acid (DNA)** * **Ribonucleic Acid (RNA)** Nucleic acids encode, transmit, and help express **genetic information**. ## Nucleotides **Nucleotides** are the **monomers** of nucleic acids. **Note**: There is a diagram showing one nucleotide. **Label each part of the nucleotide below**. * The **pentose sugar** * The **phosphate group** * The **nitrogenous base** **Note**: Here there is a simple diagram showing the parts of a nucleotide, with the nitrogenous base represented by a rectangle, the pentose sugar represented by a pentagon and a phosphate group represented by a circle. To make a nucleic acid, **covalent bonds** are formed **between** the **phosphate group** of one nucleotide and the **pentose sugar** of the next nucleotide. The "**backbone**" of a nucleic acid consists of alternating **sugar** groups and **phosphate** groups. **Note**: There are diagrams showing the structure of a nucleoside and a nucleotide. ## DNA and RNA each have four different nitrogenous bases Nucleotides can be linked together in **any order**because the phosphate and the sugar used to make the bond are the **same** in every nucleotide. This is how nucleic acids store information - in the **sequence** of **nitrogenous bases**. The **sugar-phosphate backbone** and **sequence** ensure that the sequence is **stable** and **secure**. ## 3 Key Differences between DNA and RNA 1. The type of pentose sugar The pentose sugar is different in DNA and RNA. **Note**: There is a diagram showing the structure of deoxyribose and ribose. **Label each sugar as either deoxyribose or ribose. Label each sugar as either in DNA or RNA**. 2. The number of strands DNA is **double stranded**. RNA is **single stranded**. **Note**: There is a diagram showing the structure of DNA and RNA, and their respective nitrogenous bases. 3. The nitrogenous bases **Three** of the nitrogenous bases are the **same** but **one** is different. ## The Structure of DNA **Note**: There are diagrams showing the structure of DNA, including the double helix, the DNA ladder, and an antiparallel DNA strand. The two strands of DNA are parallel but run in **opposite directions**. Therefore we call them **antiparallel**. We define the direction of the strand by looking at the **pentose sugar**. **One strand runs 3' to 5' and the other runs 5' to 3', the two strands are held together to form a double helix.** **Label the ends of the strands 3' or 5' in the diagram of Antiparallel DNA Strands**. The strands are held together by **hydrogen bonds** between the **nitrogenous bases**. A and T (have structures that complement each other, and so they form hydrogen bonds. (In RNA A bonds with U instead). Similarly, C and G form hydrogen bonds together. This is called **Complementary Pairing**. ## Drawing DNA and RNA You should be able to draw simplified diagrams of both RNA and DNA. **Note**: There are diagrams showing the structure of RNA and DNA. **In your diagram of DNA be sure to show two antiparallel strands and the hydrogen bonds between complementary base pairs. You do not need to know how many hydrogen bonds are between the bases in DNA.** **The structure of DNA allows efficient storage of genetic information.** # 1.6 - Proteins Proteins are biological macromolecules that carry out a large number of tasks within organisms. They **replicate DNA**, **transport materials**, and do too many other things to list here. ## Building Blocks of Proteins **Amino acids** are the **monomers** of proteins. Amino acids **make** **polypeptides**. * **Label the diagram.** ## Amino Acids and Polypeptides Amino acids are the **monomers** of proteins. **Note**: There is a diagram showing the structure of a general amino acid, with its various groups labelled: amine group, variable R-group, and carboxyl group. **Amino acids are linked together by dehydration synthesis reactions.** **Note**: There is a diagram showing how two amino acids are linked together by removing a water molecule. **Draw the products.** The **bond** between two amino acids is called a **peptide bond**. ## Polypeptides are chains of amino acids. Some polypeptide chains are short. The protein **insulin** is made from one polypeptide chain of 21 amino acids and one polypeptide chain of 30 amino acids. The longest polypeptide chain discovered so far is titin, a chain of 34,350 amino acids. Titin is found in muscles. **Note**: There is diagram showing the structure of a longer chain of amino acids, a polypeptide, including the peptide bonds. There are **20** different amino acids that are used to make polypeptides. The **R-groups** of the amino acids determine the **characteristics** of the polypeptide. For example: If you make a polypeptide out of polar amino acids, then the polypeptide will be polar. The **20 different R-groups** allow for an enormous diversity of polypeptide characteristics. **Amazingy, almost all organisms build polypeptides from the same twenty amino acids.** ## Twenty amino acids can be linked together to form a nearly infinite number of polypeptides! **Proteins** are made from **polypeptides**. **Note**: There is a table listing the number of polypeptides, name of the protein, function of the protein, and a model. # MAJOR IDEA IN BIOLOGY: **Shape** determines **function** ## Protein Denaturing Protein shape is stabilized by relatively weak **bonds** within the protein. If these bonds are **broken**, then protein will **change shape**. This is known as **denaturation**. **Note**: There is a diagram showing a protein folding and becoming denatured. For example, when an egg is heated, dissolved proteins in the egg white and yolk begin to denature and solidify. The denaturing of a protein is typically **irreversible** because **new bonds** are formed during the denaturing process. This is why you can't uncook an egg. A denatured protein is **incapable** of performing its original function. **The sequence of amino acids determines the shape of a protein, and the shape determines the function.**