Unit 2

Chemistry in Living Systems

Unit 2.1 Chemical Bonds and reactions

• atom
• element
• ion
• molecule
• compound
• chemical reaction
• catalyst
• enzyme

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Draw or type 2 things you already know about today’s topic:

An atom is the smallest unit that retains the property of an element.

There are three particles within an atom

Proton- positively charged, weighs one unit and is found in the nucleus

Neutron- neutral, weighs one mass unit and is found in the nucleus

Electron- negatively charged, “weightless” found orbiting the nucleus

The atomic number is the number of protons that an atom has. The number of protons defines the element.

Valence electrons

• Electrons in the outermost level, or shell, are called valence electrons.
• Atoms tend to combine with each other such that eight electrons will be in the valence shell. When atoms combine, a force called a chemical bond holds them together. (Octet rule)
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Chemical bonds are the electrons pairing with electrons .

Bonds are NOT associated with protons or neutrons!!

The acronym CHONPS describes the 6 most common elements found in life

WHich of the following are not among the most common six elements in life forms

• CHEMICAL BONDS -Chemical bonds form between groups of atoms because most atoms become stable when they have eight electrons in the valence shell

Valence electrons

Chemical bonds are formed between

Two MAIN types of chemical bonds:

• Covalent
• Ionic

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Two subtypes of covalent bonds are

• Hydrogen bonds
• Polar bond

Types of bonds-

• Covalent- sharing valence electrons forms a covalent bond.

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Types of bonds-�

• Ionic bond- when one atom “steals” an electron from another atom- leaving a charge that makes each one “magnetic”(and both are happier atoms)

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Molecule- two or more atoms held together by a covalent bond

Compound- two or more elements held together by a covalent bond

Compounds- substances composed of atoms of two or more elements

Covalent bonds

• POLARITY – some covalent bonds may have charges that are not distributed equally. Molecules with partial charges on opposite ends are said to be polar

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�Covalent bonds

• Hydrogen Bond- when a hydrogen is bound to a highly electronegative atom, there is a slight positive charge on the hydrogen. This makes the molecule POLAR. It is called hydrogen bonding when hydrogen is involved

A covalent bond

An ionic bond

A hydrogen bond is an intermolecular force that is associated with

Properties of Hydrogen Bonds

High specific heat- this means it takes a lot of energy to raise or lower the temperature.

Cohesion- water molecules stick to themselves

Adhesion- water molecules stick to other surfaces

Adhesion is

Cohesion is

Water forming drops or beads is

When water and mercury are placed in glass tubes, the water (in the right tube) adheres to the sides of the tube. The mercury (in the left tube) forms a rounded surface at the top of the liquid. Which of these substances has greater cohesion than adhesion? Explain your answer.

Water as a solvent

Like dissolves like

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Think of an example where two things can not dissolve each other

pH

• pH is a measure of how acidic or basic a solution is.
• Each one-point increase in pH represents a 10-fold decrease in hydronium ion(H+) concentration. (logarithmic scale)
• Pure water has a pH of 7. Acidic solutions have a pH below 7, and basic solutions have a pH above 7.
• The pH of solutions in living things must be stable. For a stable pH to be maintained, the solutions in living things contain buffers.

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Each .1 increase in pH is a ___ increase in acidity or alkalinity

WHich do you think is more dangerous? An acid or a base?

WHich do you think is more dangerous? An acid or a base?

Acids Acids Bases

The pH scale is measuring

• A buffer is a substance that reacts to prevent pH changes in a solution.

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An acid has more

A base has more

In one minute, �write the most important thing from today’s �lesson.�

�Chemical Reactions

• A physical change occurs when only the form or shape of the matter changes.
• A chemical change occurs when a substance changes into a different substance.
• A chemical reaction changes a substance into a different substance by breaking the existing bonds and FORMING NEW CHEMICAL BONDS!!! It does not change the identity of the elements!!!!!

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�Chemical Reactions

Matter is neither created nor destroyed in any change. This observation is called the law of conservation of mass. Every change in matter requires a change in energy.

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Energy may change from one form to another, but the total amount of energy does not change. This observation is called the law of conservation of energy.

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• CHEMICAL REACTIONS -Chemical reactions can only occur when the activation energy is available and the correct atoms are aligned.

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Chemical equilibrium

Irreversible chemical reaction proceeds in one direction until one reactant is completely consumed.

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Think of an irreversible chemical reaction...

Chemical equilibrium

A reversible chemical reaction proceeds to an equilibrium point. The reaction does not stop but proceeds in both directions at equal rates so that the net amounts do not change.

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Think of a reversible chemical reaction...

Activation energy

A reactant is a substance that is changed in a chemical reaction.

A product is a new substance that is formed.

The activation energy of a reaction is the minimum kinetic energy required to start a chemical reaction. Even if enough energy is available, the product still may not form. The correct atoms must be brought together in the proper orientation.

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Endothermic and exothermic reactions

Endothermic reactions absorb heat from the environment

Endothermic and exothermic reactions

Exothermic reactions give heat into the environment

Catalyst- substance that increases the rate of a reaction but is not changed or consumed with the reaction. They lower the activation energy

This is a(n)

This is a(n)

This is a(n)

Enzymes act as biological catalysts. Enzymes are proteins that do something

• By assisting in necessary biochemical reactions, enzymes help organisms maintain homeostasis.

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Enzymes

• In living things, chemical reactions occur between large, complex biomolecules. Many of these reactions require large activation energies.

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• An enzyme is a molecule that increases the speed of biochemical reactions.
• Enzymes hold molecules close together and in the correct orientation. An enzyme lowers the activation energy of a reaction.
• Each enzyme has an active site, the region where the reaction takes place.
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An enzyme is a

An enzyme acts as a catalyst by doing what?

• The shape of the active site determines which reactants, or substrates, will bind to it. Each different enzyme acts only on specific substrates.
• Binding of the substrates causes the enzyme’s shape to change. This change causes some bonds in the substrates to break and new bonds to form.
• Most enzymes need a certain range of temperatures and pH.

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Enzymes are like a lock and key. This model is true in many areas of biology.

This prevents haphazard reactions.

When a substrate fits into the active site, the enzyme molds around it to tighten the fit. This is called the induced fit model (think of sticking your finger into a chinese finger lock)

Because enzymes are proteins, they work best in a certain temperature and pH range.

Changes in temperature and pH can decrease the effectiveness of the enzyme because it becomes denatured (the hydrogen bonds are no longer holding it into it “lock” shape

Catalase experiment

In one minute, �write the most important thing from today’s �lesson.�

Unit 2.2

Exploration 1- Properties of carbon

Exploration 2- Structure and function of carbon based molecules

Exploration 3- chemical energy

Exploration 4 Cell membrane

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Vocab unit 2.2

• polymer
• hydrocarbon
• carbohydrate
• phospholipid
• protein
• amino acid
• ATP
• cell membrane

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Carbon is the foundation of biomolecules (and therefore life) because it can form single, double or triple bonds- carbon rings often have floating bonds

4 types of biomolecules

Carbohydrates

Proteins

Nucleic acids

Lipids

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Biomolecules are polymers. Polymers are made up of repeating subunits called monomers

Proteins are polymers made of amino acids

Nucleic acids are polymers made of nucleotides

Carbohydrates are made of saccharides

Lipids are repeating subunits of carbon chains

Which of these are true?

• Polymers are linked together to form monomers
• Monomers are linked together to form polymers
• Both a and b can be true depending upon the molecule in question

WHat is the building block for nucleic acids?

What is the building block to proteins

WHat is the building block for carbohydrates?

What is the building block for enzymes?

Polymers can be made through dehydration synthesis

What is removed during dehydration synthesis?

Isomers have the same chemical formula, but the atoms and bonds are rearranged. This gives them different properties

In one minute, �write the most important thing from today’s �lesson.�

Carbohydrates

• CARBOHYDRATES - Carbohydrates are molecules made of sugars. A sugar contains carbon, hydrogen, and oxygen in a ratio of 1:2:1.
• Carbohydrates are a major source of energy
• Chitin and cellulose are complex carbohydrates that provide support.
• Chitin is found in the shells of insects and the cell walls of mushrooms.
• Cellulose is found in the cell walls of plants.

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Lipids

• LIPIDS - Lipids are another class of biomolecules, which includes fats, phospholipids, steroids, and waxes.
• Lipids consist of chains of carbon atoms bonded to each other and to hydrogen atoms. This structure makes lipids repel water.
• The main purpose of fats is to store energy. Fats can store energy even more efficiently than carbohydrates.
• The cell’s boundary(cell membrane) is made of phospholipids. The structure of cell membranes depends on how this molecule interacts with water.

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Hydrophobic-fear of water

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Hydrophilic- love of water

Hydrophobic and Hydrophilic

Coulrophobia -? pedophile?

pediatrician

Lipids

Phospholipds contain a glycerol, rwo fatty acids and a phosphate group. These are the major components of cell membranes

Phospholipids are the main component of

Hydrophobic means something

Hydrophilic means something

A surfactant means something

Lipids

Waxes- solid at room temperature and hydrophobic

Lipids

STeroids- fused ring structure- important for cell membrane, hormones (both adrenal and sexual). Cholesterol (a steroid fat) can be made from the body by all cells but more frequently by the liver.

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Why would this be important to know if you have high cholesterol?

Saturated vs unsaturated

Connect to your own life:

What’s something interesting you learned today?

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Can you relate this to something in your own life? �(How is it similar, different, or helpful �to events in your life?)

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Proteins

• PROTEINS -Proteins are chains of amino acids that twist and fold into certain shapes that determine what the proteins do. Proteins may be involved in structure, support, movement, communication, transportation, and carrying out chemical reactions.

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• A protein is a molecule made up of amino acids, building blocks that link to form proteins.
• Every amino acid has an amino group and a carboxyl group.
• Amino acids can form links called peptide bonds between two amino acids
• The side group gives an amino acid its unique properties.
• Twenty different amino acids are found in proteins.

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For each type of protein, there are different levels of structure

• amino acids are arranged in a specific order, the protein’s primary structure. 1
• The interactions of the various side groups may form coils and folds, the protein’s secondary structure. 2
• The overall shape of a single chain of amino acids is the protein’s tertiary structure. 3
• The quaternary structure is the overall shape that results from combining the chains to form proteins. 4

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The R group gives each amino acid its properties

The carboxyl end of one amino acid binds to the amine group of the next amino acid. This synthesis removes a water molecule (remember from earlier that this is a common way to join monomers)

Nucleic Acids

• NUCLEIC ACIDS - A nucleic acid is a long chain of nucleotide units.
• A nucleotide is a molecule made up of three parts: a sugar, a base, and a phosphate group.

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• Nucleotides of deoxyribonucleic acid, or DNA, contain the sugar deoxyribose. DNA molecules act as “instructions” for the processes of an organism’s life
• Nucleotides of ribonucleic acid, or RNA, contain the sugar ribose. RNA also interacts with DNA to help decode the information.
• Adenosine triphosphate, or ATP, is a nucleotide that has three phosphate groups and supplies energy to cells. Energy is released in the reaction that breaks off the third phosphate group.

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Cell respiration

Cell respiration is not “breathing”

It is the use of glucose to create ATP.

ATP is then used to do anything in the cell (homeostasis, growth, digestion, reroduction, defense, movement)

Energy is stored in the high energy phosphate bonds of ATP. This then turns to ADP when the phosphate bond is broken -letting off energy in the process

Cell membrane

The cell membrane is composed of a phopholipid bilayer. This allows the hydrophobic tails to be near the hydrophobic tails of another phospholipid

MEMBRANE PROTEINS-

• Cell-surface markers -act like a name tag. A unique chain of sugars acts as a marker to identify each type of cell. These sugars (carbohydrates) are attached to the cell surface by proteins called glycoproteins. Glycoproteins help cells work together.

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MEMBRANE PROTEINS-

• Receptor proteins -enable a cell to sense its surroundings by binding to certain substances outside the cell. When this happens, it causes changes inside the cell.

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MEMBRANE PROTEINS-

• Transport proteins -Many substances that the cell needs cannot pass through the lipid bilayer. Transport proteins aid the movement of these substances into and out of the cell.

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MEMBRANE PROTEINS-

• Enzymes- allow reactions to take place- can break a larger molecule into 2 smaller molecules

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TRANSPORT ACROSS THE MEMBRANE-

• There are 2 types of transport-

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• Passive- does not require energy
• Active- requires energy to happen

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TRANSPORT ACROSS THE MEMBRANE-passive

• PASSIVE TRANSPORT-In passive transport, substances cross the cell membrane down  their concentration gradient. No energy is required for this. Passive transport includes
• �SIMPLE DIFFUSION- Small, nonpolar molecules can pass directly through the lipid bilayer. This type of movement is called simple diffusion. Oxygen moves down its concentration gradient into the cell. Carbon dioxide diffuses out of the cell. Also,natural steroid hormones, which are nonpolar and fat soluble, can also diffuse across the lipid bilayer.
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TRANSPORT ACROSS THE MEMBRANE-passive

• FACILITATED DIFFUSION- Many ions and polar molecules that are important for cell function do not diffuse easily through the nonpolar lipid bilayer. During facilitated diffusion, transport proteins help these substances diffuse through the cell membrane. Two types of transport proteins are

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TRANSPORT ACROSS THE MEMBRANE-passive

• FACILITATED DIFFUSION
• channel proteins –channel proteins, sometimes called pores, serve as tunnels through the lipid bilayer. Each channel allows the diffusion of specific substances that have the right size and charge. Ions, sugars, and amino acids can diffuse through the cell membrane through channel proteins

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TRANSPORT ACROSS THE MEMBRANE-passive

• FACILITATED DIFFUSION-
• carrier proteins- A carrier protein binds to a specific substance on one side of the cell membrane. This binding causes the protein to change shape. As the protein’s shape changes, the substance is moved across the membrane and is released on the other side.Carrier proteins transport substances that fit within their binding site.

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TRANSPORT ACROSS THE MEMBRANE-passive

• OSMOSIS-Water can diffuse across a selectively permeable membrane in a process called osmosis. Osmosis allows cells to maintain water balance as their environment changes. Remember that in osmosis, ONLY the water molecules are free to move .

OSMOSIS- movement of water through a semi-permeable membrane down the concentration gradient

TRANSPORT ACROSS THE MEMBRANE- passive - osmosis

• If the solution is hypertonic, or has a higher solute concentration than the cytoplasm does, water moves out of the cell. The cell loses water and shrinks

TRANSPORT ACROSS THE MEMBRANE- passive - osmosis

• If the solution is isotonic, or has the same solute concentration that the cytoplasm does, water diffuses into and out of the cell at equal rates. The cell stays the same size .

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TRANSPORT ACROSS THE MEMBRANE- passive - osmosis

• If the solution is hypotonic, or has a lower solute concentration than the cytoplasm does, water moves into the cell. The cell gains water and expands in size. If left unchecked, the swelling caused by a hypotonic solution could cause a cell to burst.

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TRANSPORT ACROSS THE MEMBRANE- passive - osmosis

• The rigid cell walls of plants and fungi prevent the cells of these organisms from expanding too much. In fact, many plants are healthiest in a hypotonic environment.

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TRANSPORT ACROSS THE MEMBRANE-�active transport

• ACTIVE TRANSPORT- Active transport requires energy to move substances against their concentration gradients. In order to move substances against their concentration gradients, cells must use energy. Most often, the energy needed for active transport is supplied directly or indirectly by ATP.

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TRANSPORT ACROSS THE MEMBRANE-�active transport

• Pumps- In active transport, the carrier proteins do require energy to “pump” substances against their concentration gradient.
• The sodium-potassium pump is a carrier protein that actively transports three sodium ions out of the cell and two potassium ions into the cell. This pump is one of the most important carrier proteins in animal cells. It prevents sodium ions from building up in the cell, resulting in osmosis into the cell making it burst.
• The concentration gradients of sodium ions and potassium ions also help transport other substances, such as glucose, across the cell membrane.

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TRANSPORT ACROSS THE MEMBRANE-�active transport

• The sodium-potassium pump is a carrier protein that actively transports three sodium ions out of the cell and two potassium ions into the cell. This pump is one of the most important carrier proteins in animal cells. It prevents sodium ions from building up in the cell, resulting in osmosis into the cell making it burst.
• The concentration gradients of sodium ions and potassium ions also help transport other substances, such as glucose, across the cell membrane.

TRANSPORT ACROSS THE MEMBRANE-�active transport

• Vesicles- Many substances, such as proteins and polysaccharides, are too large to be transported by carrier proteins. Instead, they cross the cell membrane in vesicles, which are membrane-bound sacs made by pinching off of the membrane.

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TRANSPORT ACROSS THE MEMBRANE-�active transport

• ENDOCYTOSIS- The movement of a large substance into a cell by means of a vesicle.

TRANSPORT ACROSS THE MEMBRANE-�active transport

• EXOCYTOSIS- The movement of material out of a cell by means of a vesicle.

• SENDING SIGNALS- Cells communicate and coordinate activity by sending chemical signals that carry information to other cells.
• A signaling cell produces a signal, often a molecule, that is detected by the target cell. Target cells have specific proteins that recognize and respond to the signal. These proteins are usually on the cell membrane (except in steroids)
• Neighboring cells can communicate through direct contact between their membranes.
• Long-distance signals are carried by hormones and nerve cells.

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