Introduction to Biology and Biochemistry In Grade 10, you studied the three main branches of science. They are all inter-connected: Biology is the study of _________ and ___________ _____________: their ________________ (structure), _______________________ (how they function) and their _______________________ with other living things and their environment (_______________). We don’t know what “life” is, but we say something is alive if it has the following characteristics: M _____________________ (it is able to change its _______________ eg. plants grow toward the _______ ) R _____________________ (it is able to obtain _______________ from food, usually requires ______ ) S _____________________ (it is able to ____________ and _________________ to changes in its

________________________, eg. shivering when it’s cold) G _____________________ (it gets ______________ over time) R _____________________ (it is able to produce _____________________) E _____________________ (it is able to get rid of _____________ such as ________ & ____________ ) N_____________________ (it is able to utilize _________________ material from their __________ or

________________________ ) Biochemistry is the study of the __________________ and _______________________________ in living things: how they use the ___________ and ____________________ which they get from their __________ or _______________________. When these atoms and molecules are _________________ in a certain way into __________, somehow it produces __________. We will start the course with ___________ and work up. The elements (atoms) that are most common in living things, including the human body, are:

Biology

Chemistry Physics

The study of matter The study of energy

Metal or Non-metal?

Tend to Lose or Gain Electrons?

Element

Symbol Percent in Body

Recall from Grade 10 that there are two types of compounds: ___________ and ________________. Living things use __________.

1. Ionic Compounds are made up of ____________ and ___________________________. ­ metal atoms have very __________ attraction for electrons. They tend to _________ electrons to form

______________ ions and achieve a more ____________________________ arrangement ­ non-metal atoms have a _____________ attraction for electrons. They tend to ________ electrons to form

______________ ions and achieve a more ____________________________ arrangement ­ elements which are found as ________ in living things are called __________________ eg. calcium and chlorine

2. Covalent Compounds (also called “___________________”) contain only _______________________ ­ non-metal atoms have a _____________ attraction for electrons. When two or more _________________

bond, they __________ valence electrons to complete a ______________________. The _____________ of valence electrons holds the atoms _______________ and forms a ___________________ bond.

In some compounds, the atoms share ___________________________________ of electrons to be stable: The covalent compounds in living things are incredibly ________________ but most are made from only ______ non-metals: _____________, ______________, _________________, ________________, __________________ and _______________ (remember them with the mnemonic ________________ ).

a) Covalent Compounds can be Organic or Inorganic If a covalent compound contains at least one _________ or _________ bond, then it is an ‘_____________’ compound. Any compound (____________ or _________________) that does NOT contain _________ or _________ bonds is ‘____________________’.

b) Covalent Compounds can be Polar or Non-polar In grade 10, we saw that some covalent compounds ________________ well in water, while others do not. In general, molecules that contain ________, _________ or _________ bonds dissolve ________ in water, while molecules without these bonds _____________. What is special about these bonds? ­ oxygen and nitrogen attract electrons _____________________________ ­ carbon, hydrogen, phosphorus and sulfur attract electrons ___________________________ Polar Covalent Bonds When atoms with very _________________ strengths of attraction for electrons are bonded together (eg. _________, _________ or _________ ), the stronger atom pulls the bonding electrons ____________ to itself. This gives the stronger atom a _________________________ charge ( ). Because the bonding electrons are pulled slightly ___________________ the weaker atom, it gets a _______________________ charge ( ). The electrons are “__________________” or ______________ toward the ______________ atom, so the bond is “___________” and ______________________________. ­ Water is a __________ covalent molecule. Its partial charges are ________________ to the partial

charges on other ___________ molecules, allowing them to ________ and _________________. ­ Polar covalent compounds are ________________ to water. They are __________________ (water

loving). Non-polar Covalent Compounds When atoms with very _______________ strengths of attraction for electrons are bonded together (eg. _________, _________, _________ etc.), they share the bonded electrons approximately ___________ so the electrons are found in the ____________ between the bonding atoms. The bonding electrons are _____ “_________________” (_______ shifted toward either atom) so the bond is “____________________” and has ________________________________.

­ Water molecules are __________ and strongly attracted to other __________ molecules. Non-polar molecules are _________________ so water is ________ attracted to them. Water does ____________ with or __________________ non-polar compounds.

­ Non-polar covalent compounds are _______________________ to water. They are __________________ (water fearing).

Water and Hydrogen Bonds Nitrogen to hydrogen bonds and oxygen to hydrogen bonds are ____________________. The ____ & ____ regions on _______________________ attract the ____ & ____ regions on ______________ molecule. This attraction is quite strong – so strong that the attraction between molecules with __________ or _________ bonds is called “______________________________” even though it is not as strong as a true ______________ bond. Hydrogen “bonding” is especially significant between ___________ molecules, creating significant _________ _____________.

Water: The Universal Solvent ___________________ dissolves at least a tiny bit in water, but __________ and ___________ compounds dissolve very __________ because of their _______________. When ionic compounds dissolve, the ______ and ______ regions on water are attracted to the _________________ on the _________. Water molecules ________________ the ions, ______________ them and making them available to __________. For example, NaCℓ separates into: ________ & ________ Chemical Bonds and Energy Storage When two __________________ atoms are joined together to form either ___________ or _______________ covalent bonds, energy can be “____________” as _______________________________ energy in the bond. When covalent bonds are _____________, the chemical energy that was stored in the bond is _____________ and this energy can be used by living things to do ___________. This is how chemical energy in __________ and other _________ is used to provide energy for __________________ and other activities of living things.

O H H

O H H

H H O

H H O

A water strider supported on the surface of water, held up by hydrogen bonding between water molecules.

O H

H

O H H

O H

H O

H H

O H

H

O H H

O H

H

O

H H

Homework: 1. Understand the distinctions between the following terms then classify the compounds below as: a) ionic or covalent (it is covalent if it contains only ________________ atoms, no ______________) b) organic or inorganic (it is organic if it has at least one _________ or __________ bond) c) polar or non-polar (it is polar if it has at least one __________ , _________ or __________bond) d) hydrophilic or hydrophobic (it is hydrophilic if it is ____________, see #3 above, or ___________)

2. Study the compounds drawn below. Circle ALL of the compounds that WILL dissolve well in water.

3. Draw what a K1+ ion and a I1– ion look like when potassium iodide (KI) dissolves in water. 4. Read pages 8 to 10 in your text book, then answer the following questions: a) Name 3 small molecules that are “critical to life” and state their relationship to the process of cellular

respiration (include the chemical equation for cellular respiration). b) State 3 functions of water in living organisms. c) What are five (5) unique properties of water that are essential for life as we know it? Read p. 8 carefully!!

a) _______________

b) _______________

c) _______________

d) _______________

a) _______________

b) _______________

c) _______________

d) _______________

a) _______________

b) _______________

c) _______________

d) _______________

N O O O

a) _______________

b) _______________

c) _______________

d) _______________

O

C N N H

H

H

H

adenine (part of DNA)

glucose ethanol

lime urea

benzene a

Macromolecules

Many molecules that are important in biology are small (or __________), for example: ______, ______, _____ and ______________. However, other biological molecules are very large (or ___________) so they are called _____________________________. They are made by chemically bonding together many smaller molecules called _______________. There are four main types of macromolecules that make up all living things: _______________________, ______________, _________________ and __________________________.

1. Carbohydrates are organic molecules containing the elements ____________, ________________ and ___________ in a ______________________ ratio. This ________ is the origin of the name carbohydrate: C – H2O

a) __________________________ are single, ____________ sugar molecules

­ these are the _______________ that make up all carbohydrates ­ the names of sugars all end in _______ ­ they contain ____ to ____ carbon atoms ­ the ___________ bonds make sugars ____________ so they dissolve

well in ____________ (are water ______________ or _______________________) ­ the _______ and ________ bonds make them __________________ molecules for storing _________ eg. ribose (in ________) is a five carbon sugar: _______________ eg. ________________, ______________ and _______________ (in _________) are six carbon sugars

with the same chemical formula __________________, but the atoms are bonded differently

b) ____________________________ are formed when ____ monosaccharide subunits are bonded together eg. glucose + glucose = ___________________ glucose + fructose = ___________________ glucose + galactose = ___________________ c) ____________________________ are formed when ___________ monosaccharide subunits (usually

_______________, represented by one in the diagrams below) are chemically bonded together ­ may form in long ____________ or they may be highly ________________

a sucrose molecule

glucose + fructose

eg..

2. Lipids are a diverse group of organic molecules containing _____, _____ and only a little ______ ­ they have no ________ bonds so they are _________________ and ____________ dissolve well in water ­ they have many _______ and _______ bonds so they are excellent ________________________ molecules

a) __________________________ (________ and _______) are the most abundant types of lipids

­ subunits are one molecule of ________________ and three molecules of ___________________

­ the ____________ of carbon atoms and absence or presence of _________ double bonds in the fatty acids change the type of fat

­ if a fatty acid has no _________ it is ___________________ (has the _______________ number of ________________ atoms). Saturated

fatty acids have ______________ carbon chains.

­ if a fatty acid has one ________ it is _________________________. The C = C double bond removes _______________________ atoms and introduces a ________ or “________” in the fatty acid chain.

­ if a fatty acid has many ________ it is ________________________. Each C = C double bond removes _____________________ atoms and makes a _________ in the fatty acid, so they are very _________

a.1) Saturated Fats ­ if a triglyceride contains _______________ saturated fatty acids, it is called

a __________________ fat ­ saturated fatty acids have _____________ carbon chains so they

____________ nicely and pack together ____________ making saturated fats ___________ at room temperature

­ the fat from _____________________ animals is usually _____________, for example: pig fat (_______), beef fat (___________) and milk fat (____________).

a.2) Unsaturated Fats (_________) ­ if a triglyceride contains _______________ unsaturated fatty acids, it is

called an ___________________ fat ­ unsaturated fatty acids have many _________ so they ____________ line

up and pack together tightly making unsaturated fats ____________ at room temperature (_______)

­ the fat from _____________________ animals and ___________ is usually _____________________, for example: _______ oil, _________ oil and _______ oil.

Lipids (cont.) b) ________________________ are similar to triglyceride

molecules except that one of the __________________ is replaced by a _______________ group

­ the _________ and _________ bonds are ___________ so they are attracted to ___________ (___________________ or “______________________”)

­ the _________ bonds in the fatty acid chains are __________________ so they _________ water (____________________ or “___________________”)

­ it is this “_____________________” that enables phospholipids to form ______________________, as we will see later.

c) ______________ (sterols) are lipids with _________ structures ­ they include ___________________ and many ________________

such as ________________ and _____________________ 3. Proteins are the most _____________ macromolecules and contain _____,

_____, _____ and _____. There are over ___________ proteins in the human body ­ they have ________ and _________ bonds so they are _______________ ­ proteins subunits are called ______________________. There are _____ different types of amino acids,

____ of which can not be ______________ by the human body so they are called ________________ amino acids and must be provided in the _________.

Amino acids can be ______________ together in an ______________ number of combinations. _________ (in ________) basically tell the cell the __________ in which to put the amino acids to make long chains called ___________________ (the bond that holds amino acids together is called a ____________ bond). The polypeptide is then ____________ and ______________ into its _____ shape to form the functional ________.

the “general” amino acid glycine alanine cysteine

H

H C C N

H O

R O H

• • • • • •

H

H C C N

H O

C O H • • • •

• • • • • •

H

H H • • • • H

H C C N

H O

H O H

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• • • •

H

H C C N

H O

C O H

• • • • • •

– H H –

S – H The 3-D shape of

• • • •

The 3D shape of a protein is maintained, in part, by _____________________ between the _______________ ( _______________) of adjacent amino acids. If the ________________________ between R groups are ____________, the protein ____________ and loses its correct ____________. This _________________ the protein so it can no longer perform its ____________. Proteins can be denatured by:

a) extreme ______________________, especially high ________; for example, cooking egg whites b) extreme changes in _____ (______________); for example, _______________ foods to preserve them c) harsh ______________; for example, using ________________ to straighten hair

Different types of proteins perform many functions in the body, including: a) ________________ proteins provide _____________ and _____________ (eg. ____________ in bone and

teeth, _____________ in hair and nails) b) ______________ that ____________ and _________________ chemical reactions (eg. ____________ to

break down ___________ (fats), ________________ to break down _____________ (a disaccharide) c) ________________ proteins that ___________ specific substances through the body (eg. ______________

carries ______________ in the blood) d) polypeptide _________________ that send ________________ to control ________________ in the body

(eg. ____________ is a small protein which tells cells to absorb _____________ from the ___________) e) _________________ are proteins that help us fight ___________________ (eg. ______________________

in breast milk) 4. Nucleic Acids are enormous macromolecules that make up the

_____________________________. ­ DNA _____________ the cell’s genetic information (________)

in the ________________ ­ RNA is a __________ of _________ of the DNA with the

information to the cell needs in order to make _______________ DNA and RNA are made of subunits called ___________________. In turn, a nucleotide is made of a __________ (deoxyribose in DNA and ribose in RNA), a ________________ group and a __________-containing _________. There are five nitrogen bases: A ______________________ C _____________________ T ______________________ G _____________________ U ______________________ (replaces T in RNA)

Summary:

MACROMOLECULES Carbohydrates Lipids Proteins Nucleic Acids Monosaccharides Triglycerides DNA RNA Disaccharides Phospholipids Polysaccharides Steroids

Questions on Carbohydrates (class notes and info on pages 10 -12 ) 1. What three elements (types of atoms) make up all carbohydrates? What is the usual ratio of these elements? 2. Name 3 common monosaccharides found in food. 3. State the main function of monosaccharides. (See Figure 1.8) 4. Name 2 common disaccharides and state the monosaccharides they contain. 5. How are starch and glycogen the same? In what two ways do they differ? 6. Describe the structure and function of cellulose. Why are humans unable to use cellulose for energy? Questions on Lipids (class notes and info on page 12) 1. What are the three main types of lipids? 2. Explain why triglycerides are non-polar. 3. Explain the difference between a fat and a fatty acid. 4. It is generally believed that unsaturated fats are healthier for humans. Explain the difference between saturated and unsaturated

fats (oils). 5. What is unique about phospholipids? 6. What are five functions of lipids in our bodies? Questions on Proteins (class notes and info on pages 14 -16) 1. What element is found in protein that is not found in carbohydrates or lipids? 2. Why are some amino acids considered “essential”? 3. How is the molecular structure of all amino acids the same? How do they differ? 4. Are amino acids polar or non-polar? Explain why. 5. Explain why amino acids are capable of hydrogen bonding. 6. Explain the difference between a polypeptide and a protein. 7. Explain why some proteins are soluble in water while others are not. Questions on Nucleic Acids (class notes and info on page 17) 1. In what way are DNA and RNA the same? In what two (2) ways do they differ? 2. The subunits of nucleic acids are called nucleotides. What three components make up a nucleotide? Summary Question: 1. Use the information in this note along with additional information from your textbook to complete a chart which summarizes the

following information about the four main macromolecules (polysaccharides, triglycerides, proteins and nucleic acids): a) Examples of this type of macromolecule b) The type of subunits that make up the macromolecule c) Functions of this macromolecule

Metabolism: Chemical Reactions in Living Things

All of the ______________________________ that take place in ____________ things are collectively referred to as “_____________________”. Metabolism can be sub-divided into two types of chemical reactions: ____________________ and _________________________. 1. Anabolism: anabolic reactions “__________________” or _________ small, simple molecules into

____________, more _______________ molecules. The joining of small molecules is called _________________________. Anabolic reactions ___________________________ for the formation of ___________________________.

eg. many glucose subunits are combined to make a large molecule of _____________: eg. amino acid subunits are combined to make large ___________________ or _____________ molecules:

eg. glycerol and three fatty acids are combined to make a _______________________ molecule

The anabolic reactions that join small _______________ molecules into a large ______________________ produce one molecule of ___________ for every subunit they connect. Because water is ________________ by these reactions, they are called ________________________________________ reactions or simply _____________________ reactions, as well as __________________________ reactions.

2. Catabolism: catabolic reactions “____________________” or ________________ large, complex molecules into _______________, ________________ molecules. Catabolic reactions _____________ ____________ when chemical bonds are ________________.

eg. glycogen is broken down into _______________ molecules, releasing _______________

+ +

+ +

+ +

eg. a ____________________ or ______________ is broken down into amino acids, releasing ___________

eg. a _______________________ is broken down into three _______________________ and one molecule of ________________, releasing __________ The _________________ reactions that ___________ large macromolecules into their _______________ require one molecule of _____________ for each ______________ that is taken off. These reactions are called “____________________” reactions (to “_________________________________”).

As you can see from the examples above, anabolic and catabolic reactions are often the _____________ of each other: eg Photosynthesis combines ____________ and __________________________, making ____________

and storing energy from the ________ in high energy __________ and __________ bonds. Glucose stores a lot of chemical energy so it is an _______________________ molecule.

eg. Cellular respiration breaks down _____________ into ____________ and _____________________, releasing the stored chemical _____________. This energy can be used by __________ to _________ and drive other __________________.

Energy Storage Molecules Anabolic reactions _____________ energy in order to form new __________. This energy is provided by an ________________________ molecule. There are many different energy storage molecules, but one of the most important is _____________________________________ (______). It is very similar to the nucleotide ________________ (___). (Recall: the nucleotides _________________ are the subunits used to make the ____________________________ such as ________).

+ +

High energy bonds

+ Energy Released ~ ~ ~

As its name suggests, ATP has __________________________ groups. They are ___________ to each other, all in a row. The bond between the ___________________ phosphate groups stores a great deal of _____________, so ATP is an “____________________” molecule. When a cell needs energy for an ________________ reaction or to do __________, the bond between the last two phosphate groups is ______________, __________________ the chemical energy. The remaining molecule has only two phosphate groups, so it is called ________________________________________ (________). It is a “___________-______________” molecule. When energy becomes available from the ________ (in plants) or from __________, this energy can be used to bond the third phosphate __________________ the _________ molecule, recreating ________. This allows the cell to _____________________ until it is needed. Energy storage molecules _______________ back and forth between their __________________________ form (________) and their _______________ ________________ form (_______). Homework Questions: 1. Define or explain each of the following terms in

your own words: a) metabolism b) anabolism c) catabolism d) condensation reactions e) dehydration synthesis reactions f) hydrolysis reactions g) chemical energy h) energy storage molecules

2. Study the diagram to the right.

a) Explain why anabolism and catabolism are “complementary” processes.

b) How does the ATP/ADP cycle tie these two processes together?

3. Explain why some chemical reactions release

energy and some require (absorb) energy. 4. Regarding the reaction for photosynthesis: a) Why is glucose considered to be an

“energy-rich” molecule? b) What is the original source of the chemical

energy stored in the glucose molecule? 5. Classify the following reactions as either

anabolic or catabolic: a) hydrolysis of starch b) hydrolysis of triglycerides c) condensation of amino acids d) dehydration synthesis of glucose e) synthesis of ATP

6. a) Distinguish clearly between ATP and ADP. b) Explain how the ATP molecule stores chemical energy. c) When a cell is short of energy, ADP can lose a phosphate to form AMP (adenosine monophosphate). Is this an anabolic or

catabolic reaction? d) How are ATP and glucose similar? 7. Testosterone is an “anabolic steroid hormone”. From your knowledge of the word “anabolic”, predict the effect of testosterone

on muscle.

Enzymes

Animation: http://highered.mheducation.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

Homework Questions: 1. Define: enzyme, active site, substrate enzyme-substrate complex. 2. What type of macromolecules are enzymes? 3. Explain what is meant by “denaturing” an enzyme. The diagram to the right may

help. 4. List three different conditions that may denature an enzyme. 5. Enzyme action is often described as being a “lock and key” model. Explain why

this is an appropriate description. 6. If a cell’s metabolism includes 184 different chemical reactions, how many

different types of enzymes will this cell have? 7. Enzymes are named for the substrate they act on or the action they perform.

Enzyme names end in “ase”. For example, the enzyme that breaks down lactose (the sugar in milk) is called “lactase”. Predict the name of the enzyme that breaks down each of the following substrates:

a) sucrose is broken down by the enzyme __________________ into _____________ and _______________ b) the starch called “amylose” is broken down by the enzyme ______________________ into ________________ c) maltose is broken down by the enzyme __________________ into ___________________

d) the polysaccharide “cellulose” is broken down by the enzyme ______________________ into ___________________ (do humans have this enzyme?)

Catabolic reaction: one substrate is broken down into smaller molecules. Energy is released.

Energy is released. It is captured by an energy storage molecule.

Anabolic reaction: two substrates are combined into one larger molecule. Energy is required (absorbed).

Energy is required. It is provided by an energy storage molecule.

Enzyme can be used again.

Enzyme can be used again.

enzyme denatured

substrate fits into active site

substrate no longer fits into active site