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AP Bio Guided Notes

Unit 1 - Chemistry of Life

Science Skills & Common Content for this Unit: 

• Structure & function are a BIG part of this unit!  When you change the structure of a molecule, it may also change the function/make it nonfunctional.

• Water is necessary for life - and you need to know how and why. Polarity is a big concept here!

• How smaller molecules such as monomers come together to form larger molecules such as polymers.

• 4 Major Classes of Biological Macromolecules, their properties, sources, and roles in biological systems.

• Types of chemical bonds and how they lead to different interactions between atoms.
  

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Unit 1.1 - Structure of Water & Hydrogen Bonding

Atoms & Chemical Bonds (Chemistry Review)

Recall that the atom is the smallest unit of matter that still retains the properties of an element.  Atoms are composed of smaller subatomic particles: protons (H⁺), neutrons (n⁰), and electrons(e^-).  Protons and neutrons are found in an atom's atomic nucleus, while electrons rapidly move around the nucleus in a “cloud”.  Electrons are what allow atoms to form bonds with each other, either by sharing or transferring electrons between atoms.

Electrons possess varying amounts of potential energy depending on their distance from the nucleus. Electrons can be found within different “electron shells” at different distances from the nucleus. Negatively charged electrons are naturally attracted to the positively charged nucleus, so electrons that are furthest from the nucleus will have the highest potential energy. The chemical behavior of an atom depends mostly on its valence electrons or those found in the outermost shell. 

Electrons prefer to exist in pairs because it stabilizes them, so when atoms form bonds it is always the unpaired electrons that are involved.

Chemical bonds occur from the reaction between electrons of different atoms to form molecules. There are a few types of chemical bonds you need to know:

• Covalent bonds - the strongest type of bond where atoms share (“cooperate”) a pair of valence electrons. Atoms can form single (ex. H-H), double (ex. O=O), or even triple (ex. N≡N) covalent bonds.

  • Nonpolar covalent bonds - electrons are shared equally, resulting in a molecule without a charge.

  • Polar covalent bond - electrons spend more time around the more electronegative atom, resulting in a molecule that is polar (more positively charged on one end and more negatively charged on another). Ex. H₂O.

• Ionic bonds - an electron is taken from one atom and transferred completely to the other, resulting in two ions (charged atoms): anions (-) and cations (+), which are innately attracted to each other, Ex. sodium chloride.

There are also weaker chemical interactions that are not as strong as chemical bonds, but are also essential for life:

• Hydrogen bonds - occurs when a hydrogen atom is covalently bonded to a more electronegative atom, resulting in a partial positive charge that allows it to be attracted to another nearby electronegative atom. Ex. hydrogen bonds form between water molecules.

• Van der Waals interactions - occur when atoms are extremely close together where positive and negative charges have a weak attraction to each other (Ex. this is how geckos climb on walls!)

Recall that chemical reactions result in the making or breaking of chemical bonds. Reactants act as the starting material, while products are the result.

Water & Polarity

All organisms are primarily composed of water, which has important properties that make it an essential molecule for life. Water is a polar molecule meaning that it has an uneven charge distribution across it: the oxygen is partially negative (δ-), while the hydrogens are partially positive (δ+). The unique properties of water arise from its polarity and its resulting ability to form hydrogen bonds.

First, water molecules have the innate ability to easily link together with other water molecules through hydrogen bonds between the oxygen of one water molecule, and the hydrogen of another water molecule. This is known as cohesion. (they “cooperate” with each other).

Water molecules also form hydrogen bonds with other substances that are either polar or charged. This is known as adhesion. (water “adheres” to something else).

Together, cohesion and adhesion allow water to defy gravity!  Capillary action occurs when water both adheres to the wall of a narrow material and coheres with other water molecules.  An example of this is evapotranspiration in trees, where water evaporating from the leaves pulls the water up through water-conducting cells in the plant up to the top of the plant.

Surface tension is also the result of cohesion between water molecules. The hydrogen bonds between water molecules form a sort of “film” across the surface of the water, allowing it to form droplets or for certain organisms to skate along the top!

Other important properties of water involve its ability to regulate temperature! Water has a high specific heat, meaning it is able to absorb a high amount of heat before changing temperature. This makes it an excellent medium for living things, as it is slow to change temperature.  This also means that water can absorb and store a large amount of energy from the sun, cooling the nearby area during the day, and then releasing that heat at night. This also allows organisms (which are made of water!) to resist rapidly changing temperatures.

For the same reasons water has a high specific heat, it also has a high heat of vaporization, which means it can absorb a lot of heat before it evaporates. Evaporative cooling is used by many organisms to regulate their body temperature.  As the water evaporates from a surface, it “takes” the heat with it. For example: Evapotranspiration can cool the leaves of plants, sweating and panting can cool down certain animals, and evaporation from large bodies of water helps to keep the temperature stable.

Water is also one of the few substances that is less dense as a solid than as a liquid.  This allows ice to float - this is important because it ensures that bodies of water do not freeze completely. Instead, the ice can float on the top and actually help to insulate or trap heat, beneath the surface.

Finally, water is the universal solvent for living things, called this because of its ability to dissolve a large number of different substances. Recall that a solution is a mixture of a solute (substance being dissolved) and a solvent (substance doing the dissolving). Aqueous solutions contain water as the solvent.  The polar regions of water molecules are able to associate with molecules that have an opposing charge, breaking molecules apart and surrounding them in spheres of water called hydration shells. 

Substances that are either ionic or polar can be dissolved in water because they are hydrophilic (water-loving). This allows water to be used by living things to transport substances, as well as acting as a medium for metabolic reactions within an organism. Some substances, however, cannot be dissolved in water because they are either nonionic or nonpolar, and are known as hydrophobic (water-fearing). Examples of hydrophobic molecules include fats and oils.

Most chemical reactions carried out by organisms involve solutes dissolved in water. To measure the concentration of molecules within a solution of water, we use the unit of measurement mole (mol). The number of moles of solute per liter of solution is known as molarity. Many of the experiments we do in this course will involve a substance with a specific molar concentration.

Lastly, let’s talk about pH! This stands for the “power of hydrogen” and represents the concentration of hydrogen ions (H⁺) in an aqueous solution. It is expressed in a logarithmic scale, meaning that each step on the scale increases by a power of 10. The scale we look at ranges from 0-14.

• 0 is the most acidic and will have a greater concentration of H+ ions than OH- ions.

• 7 is neutral - this is where water lies with an equal concentration of H+ and OH- ions.

• 14 is the most basic/alkaline and will have a greater concentration of OH- ions than H+ ions.

That was a lot!  Be sure to go back later and record any notes you feel necessary, as well as take the Unit 1.1 Practice Quiz on AP Classroom! If you’re a little confused, give some of the videos a watch.

Unit 1.2 - Elements of Life

Carbon & Essential Elements of Life

Living organisms are made up of chemicals primarily composed of carbon. Carbon is unique because it is able to form large, complex molecules with other elements.  Carbon has 4 valence electrons and is thus able to form 4 covalent bonds. As a general rule, an organic compound is any compound that contains carbon and is found in living things. Some of the other important elements found in living things include hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHNOPS!)

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In all living organisms, there are four main classes of large, organic molecules.  These are known as biological macromolecules because of their size and complexity.  These macromolecules are: carbohydrates, lipids, proteins, and nucleic acids.

While all four macromolecules contain carbon, hydrogen, and oxygen, nitrogen is found only in proteins and nucleic acids, sulfur only in proteins, and phosphorus only in nucleic acids and specific lipids called phospholipids.

Because of carbon’s 4 valence electrons, it is great at forming chains of carbons and hydrogens.  Hydrocarbons are organic molecules consisting of ONLY hydrogens and carbons and form a framework for the macromolecules.  Below are some examples.

Other important chemical groups make up the macromolecules and can impact their function, hence why they are called functional groups. The seven most common functional groups are see below.

Unit 1.3 - Introduction to Biological Macromolecules

Building & Breaking Macromolecules

Three of the four types of macromolecules, carbohydrates, proteins, and nucleic acids, are formed into large, chain-like structures called polymers (poly = many).  As polymers, they consist of many smaller, repeating subunits called monomers (mono = one). You can think of it similarly to a set of Lego blocks.  A monomer is like a single block, while a polymer is a large structure you have built out of many of the same types of blocks.

While different types of macromolecules are composed of different types of monomers, the mechanisms by which they are built and broken are all similar.  The reactions are facilitated by enzymes, which are almost universally a type of protein, and water.  Enzymes are essential because they help to speed up chemical reactions by lowering the required activation energy for the reaction. The two types of chemical reactions to either form or break down polymers are:

Dehydration synthesis (literally “lose water to combine”) - Two monomers are bonded together, one losing an -OH and the other losing an -H, which allows a covalent bond to form between them.  This loss of the -H and -OH forms a water molecule.

Hydrolysis (literally “water break”) - Two monomers are broken apart by adding water at the covalent bond between them, attaching an -OH to one monomer and an -H to another.

Unit 1.4 - Properties of Biological Macromolecules

Unit 1.5 - Structure & Function of Biological Macromolecules

Structure & Function of Carbohydrates

Carbohydrates are composed of monomers called monosaccharides (literally “one sugar”). There are many different types of monosaccharides that can join together to form more complex carbohydrates or be used on their own. Disaccharides (“two sugar”) consist of two monosaccharides, while polysaccharides (“many sugar”) consist of many monosaccharides bonded together.  The covalent bonds that form between monosaccharides are known as glycosidic linkages.

As a rule, carbohydrates all follow the same ratio of C:H:O.  This ratio is 1:2:1, for example, glucose is C₆H₁₂O₆.  Carbohydrates can be found in either linear or ring forms but can be easily recognized by this ratio.

Carbohydrate functions include energy extraction, energy storage, and as a structural material. Ultimately, their structure will determine their function. (you’re going to be hearing this a lot!)

A few examples of carbohydrates include the following:

Glucose is great for energy transfer because is it stable, soluble in water, and has high potential energy that can be oxidized to form ATP.  Lactose is a milk sugar that can be broken down by the enzyme lactase, found in mammals, but as we age most mammals lose the ability to produce lactase and develop lactose intolerance!

Glycogen and starch are both made of long chains of glucose monosaccharides and are great for storing away energy for quick use at a later time.  Vertebrate animals store glycogen in their livers and muscles for quick access, and plants tend to store starch in their chloroplasts as well as in their roots, tubers, and seeds. (yum!)

Cellulose and chitin are polysaccharides that are both used for structural support. Cellulose, often called insoluble fiber, helps make up plant cell walls. While most animals cannot digest cellulose, many ruminants such as cows and sheep contain bacteria in their gut that help them to break it down. This is why they can digest grass, but you can’t!  Chitin is another structural polysaccharide that is used in anthropods to build their exoskeletons, and in fungi to build their cell walls. It is similar to cellulose with some slightly differences, and is digestible by most animals.

Structure & Function of Lipids

Lipids are unique macromolecules that do not have true monomers or polymers, but all share a common trait - they are hydrophobic and do not mix well with water.  Some lipids do have polar regions, the the majority of the molecule is nonpolar. 

The lipids we will focus on are fats & waxes, phospholipids, and steroids.

Fats are made up of a glycerol molecule and three fatty acid molecules, together known as a triglyceride. Fatty acids are made up of long chains of carbon and hydrogen (hydrocarbon!), and because of this, they can store an abundance of energy. While fats contain over twice the amount of energy per gram than carbohydrates, they are more difficult to break down than carbs, making them better for long-term energy storage.

Fats can be found in two main forms: saturated and unsaturated. 

• Saturated fatty acids have no double bonds, and are “saturated” with hydrogens along their carbon chain. This allows them to pack closely together, and thus saturated fats tend to be solid at room temperature.  Most animal fats are saturated, such as butter and lard.

• Unsaturated fatty acids have one or more double bonds in their carbon chain, forming small “kinks” that allow them to bend. This keeps the fat molecules further apart from each other, and thus unsaturated fats tend to be liquid at room temperature. Most plant fats and fish fats are unsaturated, such as vegetable and fish oils.

Phospholipids are a unique type of lipid responsible for the structure of cell membranes. Phospholipids are composed of two fatty acids connected to a glycerol with an added phosphate group.  This unusual structure leads to phospholipids being something called amphipathic; both polar AND nonpolar!  The “head” of a phospholipid is polar, while the “tail” is nonpolar. The two ends thus exhibit different behavior around water, with the heads being hydrophilic and the tails being hydrophobic. Because of this, when added to water, phospholipids will actually self-assemble into a phospholipid bilayer! This will be especially important in later units when learning about the cell.

Steroids are a type of lipid characterized by their four-ringed carbon skeleton. Steroids are important structure and signaling molecules. Cholesterol is a steroid found in cell membranes and is also the precursor molecule to make steroid hormones such as testosterone and estrogen.

Structure & Function of Proteins

Proteins are the most diverse of the four macromolecules, and are necessary for an incredibly wide range of functions!  Different proteins account for over 55% of the dry mass (without water) of a cell; you are made primarily of proteins! Protein functions include some of the following:

• Speeding up (catalyzing) chemical reactions as enzymes.

• Defense/protection, such as antibodies and antimicrobial proteins.

• Storage of amino acids and minerals, such as casein or ferritin.

• Transport of substances, such as hemoglobin in blood or protein channels in cell membranes.

• Hormones to signal actions between cells, such as insulin and glucagon.

• Receptors to respond to stimuli, such as receptor proteins.

• Movement, such as actin and myosin proteins in muscle cells.

• Structure/support, such as keratin in hair or collagen in skin.

These are just a few examples of what proteins can do! You have 10s of thousands of different types of proteins in your body, all performing different but specific functions!

Because of function of proteins is so vast, the structure must also be incredibly diverse. Amino acids are the monomers of proteins.  Amino acids are bonded together through dehydration synthesis by peptide bonds.  Two amino acids are a dipeptide, while 3 or more are known as polymers called polypeptides.  Proteins are any biologically functional molecule made up of one or more polypeptide chains in a 3-dimensional structure. Currently, the largest identified protein is known as Titin, and is between 27,000 and 35,000 amino acids long!

There are 20 essential amino acids that are used to build every protein in different amounts and combinations.  All amino acids have a common structure:

• A central carbon (α) in the middle

• An amino group

• A carboxyl group

What makes each of the 20 different is their variable R-group aka side chain. Each amino acid has an R-group with different chemical properties, including: polar, nonpolar, acidic/negatively charged, and basic/positively charged. The properties of these R-groups are important in how the final structure of the protein ultimately forms. Amino acids can be drawn with R-groups above or below the central carbon, so don’t let that confuse you!

Below is a table of the 20 essential amino acids.  Note their different R-groups/side chains, as well as their full names, the 3-letter abbreviation, and the 1-letter abbreviations used to identify them. You do NOT have to memorize these, but you do need to understand that the different properties of amino acids are important in the final structure of a protein.

Protein Structure & Folding

The unique nature of proteins results from their unique 3D structure.  A polypeptide is NOT a functional protein until it has folded into its functional shape! Chains of amino acids twist and fold into a molecule with a shape that allows it to perform its function.  The R-groups of the amino acids are what influence HOW the protein will fold into its functional form. It’s kind of like the difference between a loose ball of yarn and a fully knitted sweater - you can’t really wear a ball of yarn (at least not in a functional wait), instead, you have to knit and fold it into a form that you can use.  The key takeaway is that a protein’s structure determines its function. Proteins need to be able to interact with other molecules of precise shapes in order to perform their functions.

So what are the the different levels of protein structure? All proteins share at least the first three levels of structure: primary, secondary, and tertiary. A fourth level, quaternary, can occur when two or more polypeptide chains are involved in forming the protein.

So, what happens if a protein structure changes? Protein structure can change at any level.  Even a slight change of amino acids at the primary level can ultimately influence how the protein folds, which will influence whether or not it can function. 

An example of this is Sickle Cell Disease, which is caused by a single change of a glutamate for a valine in a hemoglobin β subunit.  Glutamate is polar, while Valine is nonpolar.  This change at the primary level changes how the polypeptide chain folds at the tertiary level, changing the shape of the hemoglobin and ultimately changing the shape of the red blood cells that contain it. Remember, structure determines function.

Another way that proteins can change structure is through denaturation. This process can occur because of changes in the environment that the protein is in, causing it to change shape and become inactive/nonfunctional.  This change in the environment breaks the bonds at the secondary and tertiary structure of the protein, causing it to unfold. Some environmental changes that can cause denaturation include: changes in pH, salinity (salt), temperature, or even water.  Most proteins cannot return to their functional shape after denaturing, but some can renature themselves depending on the environment. An example of a denatured protein is the protein in an egg when you cook it!

Wow, that’s a lot! Proteins are complex and incredible molecules. Below are just a few examples of some cool protein structures.

Unit 1.6 - Nucleic Acids

We’re going to talk about nucleic acids in their own section.  Nucleic acids are important macromolecules that store, transmit, and express hereditary information. There are two major types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid.  Nucleic acids are actually responsible for “coding” for the primary structure of proteins through sections in the DNA known as genes.  You can think of nucleic acids as forming the recipes for making the wide variety of proteins in living organisms.

DNA and RNA are essential for living things to be able to perform the process known as protein synthesis, where cells use the molecular codes found in DNA to build proteins the necessary proteins for life.  The overall process of using DNA to code for proteins is known as gene expression because if a gene is being “read” to make a protein, it is being “expressed”. The flow of this process of gene expression is DNA → RNA → Protein, and is often called “the central dogma of molecular biology”.

Nucleic acids are also essential for living things to be able to pass on their genetic information (their “recipes”) to the next generation. DNA can be replicated into exact copies and passed on when cells divide.

Nucleic acids are composed of monomers called nucleotides. The general components of each nucleotide are: a 5-carbon sugar, a nitrogenous base, and a phosphate group. Nucleotides have specific ends to them, and when they are bonded together it is in linear chains that follow a certain direction.  Covalent bonds called phosphodiester bonds are formed between the 5’ phosphate of one nucleotide and the 3’ end of the sugar of another.  Make note of the numbers in the diagrams below.

As a chain of nucleotides builds, it creates something known as a “sugar-phosphate backbone”.

While the phosphate group between nucleotides is the same, there are some differences between the sugars and nitrogenous bases.

The 5-carbon sugars of nucleotides come in two varieties: 

• Deoxyribose - the sugar found in nucleotides that compose DNA.

• Ribose -the sugar found in nucleotides that compose RNA.

The nitrogenous bases on nucleotides also come in two major varieties, each with different members: 

• Pyrimidines - Single ring of carbon and nitrogen atoms. The 3 types of pyrimidines are cytosine (C), thymine (T), and uracil (U).

• Purines - Double ring of carbon and nitrogen atoms. The 2 types of purines are adenine (A) and guanine (G)

Note that the nitrogenous base thymine (T) is only found in nucleotides that compose DNA, while the nitrogenous base uracil (U) is only found in nucleotides that compose RNA.  This is important!

One more thing that is important to understand is the major structural difference between DNA and RNA: RNA consists of a single strand of nucleotides, while DNA is made from two separate strands of nucleotides, running in opposite directions. These two opposite strands are bonded tougher by hydrogen bonds and form a structure known as a double-helix.

Recall that nucleotides have specific directionality along the molecule, a 5’ end and a 3’ end.  When two strands of DNA form their double helix, they are running in opposite directions.  This is known as running antiparallel.

When the two strands form hydrogen bonds, they are forming them at their nitrogenous bases.  Only certain nitrogenous bases are molecularly compatible with each other, also known as complementary:

• Adenine (A) bonds with Thymine (T) - remember that APPLES go in TREES.

• Cytosine (C) bonds with Guanine (G) - remember that CARS go in GARAGES.

Later we will discuss how Uracil (U) in RNA is involved, but for now, focus on these.

We will come back to nucleic acids and other macromolecules in greater detail later in the year, so don’t feel like you need to go any deeper than this for now. Note that p.72 in your book has a great review diagram for the 4 macromolecules. Great work!