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Presentation on theme: "BIOCHEMISTRY NOTES UNIT 2"— Presentation transcript:


2 The Key to remember about BIOCHEMISTRY is:
It is the Chemistry of the Living World! All organisms use the same basic chemical organic compounds to live their lives. Biochemistry is not about the cells or the organisms; it's about the smallest parts of those organisms, the Compounds and Molecules and then looking at the smallest parts of the compounds: the Monomers which are the building blocks. It's also about the chemical processes that occur to create these Organic Compounds; the Organic Compounds are also called the Polymers.

3 The cycles that repeat over and over are the chemical processes that allow living creatures to survive on Earth. It could be the constant process of photosynthesis in plants that creates sugars or the building of complex proteins in the cells of your body which is protein synthesis. In each of these cycles, molecules are produced or broken down. It's one big network of activities where each part relies on all of the other parts in order to function.

4 But First, We need to understand Basic Chemistry
Matter Matter occupies space and has mass. It can exist as a solid, liquid, or gas. Atom is made up of 3 subatomic particles Protons (+) The protons and neutrons are found in the nucleus of the Neutrons (neutral) - atom. Electrons (-) They orbit the nucleus in clouds. The # of protons is always equal to the number of electrons in every element. Elements Elements are substances made up of only one type of atom. There are 92 naturally occurring elements.. The rest are synthetic!!! The following elements make up 96% of living organisms: Carbon, Hydrogen, Oxygen, Nitrogen. (C, H, O, N)

5 Why is Carbon so important?
All living organisms contain Carbon. How does a scientist determine how old a fossil is? Carbon Dating Carbon is a very unique element!! It must always form 4 bonds at one time!!! It always makes up the Backbone of the molecule in organic compounds. Carbon will do this by forming a Chain or a Ring to make the backbone of the molecule!!

6 Types of Chemical Bonds:
Atomic Mass Number (is the # of protons + neutrons) (the # of protons is = to the # of electrons) Atomic Number (is the # of protons) Types of Chemical Bonds: Covalent Bonds: Covalent bonds form when atoms share electrons. All Organic Compounds form through covalent bonds. Look at the example in the book! Types of Covalent Bonds: Polar Bonds---there is a slight unequal charge which causes a constant attraction; ex: H2O Hydrogen Bonds-a partial positive charge develops on the hydrogen due to unequal sharing of electrons. The partial positive charge on the hydrogen atom will be attracted to atoms with a negative charge.

7 Ionic Bonding Ions Isotopes there is a transfer of electrons
(1 element loses an electron and 1 element gains an electron) Ions are formed Look at the example in the book!! Inorganic Compounds form through Ionic Bonds. Ex: salt, pepper, etc. Ions an element with a charge; if it has a (+), then it has lost and electron; if it has a (-) charge, then it has gained an electron. K+ has lost an electron O- has gained an electron Isotopes are variations of an element because they have different #’s of neutrons. They are identified by their atomic mass #. Look at the examples in the book of Carbon 12, 13, & 14!!!

8 Water Water covers approximately 71% of the Earth's surface.
Living things are made up of 70-90% water. In nature, water is a solvent for many kinds of chemical reactions. A solvent is what you dissolve a solute in. ex: sugar is (the solute) that is dissolved in water (the solvent) when you make koolaid!!! Water is a polar molecule because the oxygen atom is negative and the hydrogen atoms are positive, resulting in an unequal sharing of electrons (2H+ to O- in H2O ) As a result, water forms Hydrogen Bonds with other water molecules.

9 Water Properties Cohesion Adhesion (water bonding to water)
Molecules of the same type are attracted to each other. Ex: surface tension (water bonding to water) Adhesion Molecules of different types Ex: meniscus (water bonding to glass)

10 Acids and Bases pH measures the concentration of H+ in a solution to determine if it is an acid or a base. H+ are called hydroxyls and OH- are called hydroxides. Acids (0-6) produce H+ The smaller the #, the stronger the acid. Bases (8-14) produce OH- The larger the #, the stronger the base. (7) is neutral-ex; water, milk, human blood Acids are acidic and Bases are alkaline. Buffers are substances that weaken the pH of an acid or base. Ex: Tums or Rolaids

11 Quick Quiz Time What are the subatomic particles of an atom?
How many naturally occurring elements are there? What 4 elements make up 96% of living matter? How do the carbons bond together when making the backbone? What is atomic mass #? What is an ion? What does this mean Na+? What is an example of adhesion? What is an example of cohesion? What does pH measure?

12 Now we start the ORGANIC COMPOUNDS!!

13 ORGANIC COMPOUNDS Carbohydrates Lipids Proteins Nucleic Acids

14 Elements in Organic Compounds
The compounds of life all contain: Carbon Hydrogen Oxygen Some also contain: Nitrogen Phosphorus trace elements – like sulfur

15 CARBO/HYDRATES Carbon/water(H2O) ELEMENTS: C, H, O RATIO: : 2 : 1

16 Carbohydrate is a fancy way of saying "SUGAR."
Carbohydrates supply our main source of energy & it is a quick energy!!! Carbohydrates can be very small or very large molecules. Why is a carbohydrate an organic compound? A carbohydrate is called an organic compound because it contains carbon. What are they used for? Sugars provide living things with energy. They may be stored to use later or they may help make up the structure of an exoskeleton on an insect or a crustacean. They are also be found in the cell walls of fungi or plants cells.

17 What does Sugar make you Think of?
But Not all Sugars Are Sweet!!!

18 Scientists also use the word saccharide to describe sugars.
If there is only one sugar molecule, it is called a monosaccharide. If there are two, it is a disaccharide. If there are more than two, it is a polysaccharide. You get the idea???

19 What about the simplest of sugars?
Monosaccharides are the monomers of carbohydrates and they have no taste!!! What about the simplest of sugars? A sugar called glucose is the most important monosaccharide on the Earth. Glucose is created by Photosynthesis in Plants and is used in Cellular Respiration to make ATP. Disaccharides are double sugars and they are made up of 2 monomers (2 monosaccharides). They have the sweet taste!!! When you think of table sugar, like the type of sugar in candy or the type you put in tea, it is actually a disaccharide. This sugar is made of glucose and another monosaccharide called fructose.

20 1st Level of Carbohydrates
FUNCTION: SUPPLY QUICK ENERGY Monomers = Monosaccharides (No taste-they are not sweet!!) These are the simple sugars. Glucose-blood Galactose-milk Fructose-fruit Chemical Formula— C6H12O6 The Chemical Formula tells you how many atoms of each type of element are in the molecule.

21 Molecular Formula for Glucose
The molecular formula shows you the location of each atom in the molecule!!

22 C6H12O6: one formula, three sugars
How are they different? What makes them different from each other is the arrangement of the H & O atoms in location to the C atoms in their Molecular Formula!! Glucose Galactose

23 2 Monomers = Disaccharides (Sweet!!) These are the Double Sugars.
Sucrose-sugar cane (table sugar) Maltose-fruits & vegetables Lactose-milk What is the chemical formula? C12H22O11 HOW?????? What is missing???? The difference between the disaccharides is the same as the monosaccharides—the locations of the elements!!

24 Dehydration Synthesis
(loss of H2O) (to make or build) This is Anabolic Metabolism. (building a molecule) C6H12O6 + C6H12O C12H22O H2O

25 How are disaccharides & polysaccharides made?
This is the molecular formula for Maltose.

26 Molecular Formula for Sucrose

27 Hydrolysis (add H2O) (to split) This is Catabolic Metabolism.
(breaking down a molecule) C12H22O H2O C6H12O C6H12O6

28 Polysaccharides Polymer of Carbs
(Starches) They are called Complex Sugars and are made up of many, many sugars. When several carbohydrates combine, it is called a Polysaccharide ("poly" means many). Hundreds of sugars can be combined in a chain. These chains are also known as starches. You can find starches in foods such as pasta, bread, and potatoes. They are very good sources of energy for your body. Whole grain wheat starches from wheat grains are healthier for you to digest—they have fewer monosaccharides to break down during hydrolysis than complex starches like those found in white bread!!!!

29 Starches are Polysaccharides
They no longer taste sweet!! They are flavorful!!!!

30 Storage Forms of Polysaccharides
Glycogen-storage form of starch in animals Cellulose-storage form of starch in plant cell walls Chitin-storage form of starch in the cells walls of fungi & the exoskeletons of insects & crustaceans

31 GLYCOGEN Glycogen-this is the main way that animals store glucose. It is readily converted to glucose as needed by the body to satisfy its energy needs. After 48 hrs, if it hasn’t been used as energy, it is converted into fat.

32 Glycogen storage form of a polysaccharide in animals
In animals, the storage form is called glycogen. It forms a branched structure.

33 CELLULOSE Cellulose-it is found in the cell walls of plant cells.
It is used to support and protect plants. It gives plant cells shape and rigidity!!! You know that shirt you're wearing? If it is made of cotton, that's cellulose, too!

34 Cellulose storage polysaccharide in plants

35 CHITIN It is found in the shells of crustaceans (crabs, lobsters, crawfish, etc.) and the exoskeletons of insects. It is similar in some ways to the structure of cellulose but has a far different use. The shells are solid, protective structures that need to be molted (left behind) when the crustacean needs to grow. It is very inflexible and is very resistant to damage. While a plant may burn, it takes very high temperatures to hurt the shell of a crab.

36 Quick Quiz Time What are the monomers of carbs?
What elements make up carbs? Name the 3 monosaccharides. Name the 3 disaccharides. Which type is sweet? Name the 3 storage polysaccharides. How are polysaccharides made? Do you need to study?

37 This is the end of your CARBOHYDRATE notes!!!

38 LIPIDS MONOMERS: Glycerol—backbone ELEMENTS: C, H, O
Fatty Acid Chains--attached to the glycerol ELEMENTS: C, H, O FUNCTIONS OF LIPIDS: Stores Energy Provides Insulation Protects Cell Membranes

39 Types of LIPIDS Fats Oils Waxes Steroids (FOWS)

40 Lipids When you think of fats, you should know that they are lipids.
Lipids are also used to make steroids and waxes. So your ear wax is a lipid, too!

41 FATS & OILS It connects the fatty acid chains together. TRIGLYCERIDES:
Fat is also known as a triglyceride. It is a molecule made up of glycerol that is connected to 3 fatty acids chains: Glycerol is the backbone of all fats: It is made up of a three-carbon chain. It connects the fatty acid chains together. A Fatty Acid Chain is a long chain of carbon atoms with H and O atoms attached to it. Reminder—Each Carbon has to form 4 bonds!!!


2 TYPES OF FATS: Saturated fats have no double bonds between the carbons in the fatty acid chain. There are only single bonds between the carbons. Unsaturated fats have 1 or more double bonds between the carbons in the fatty acid chains. Unsaturated fats are Oils. A double bond forms when 2 electrons are shared or exchanged in a bond. They are much stronger than single bonds!

Saturated fatty acids : have no double bonds between the carbons. Monounsaturated fatty acids: have one double bond. Polyunsaturated fatty acids: have multiple double bonds through the carbon chain.

45 Fats have a lot of energy stored up in their molecular bonds.
That's why the human body stores fat as the main energy source! When your body needs extra fuel, your body breaks down fat to get the energy it needs. Think about it; when you exercise, your body burns fat and uses energy to do this!! Where 1 molecule of sugar only gives a small amount of energy (quick energy), a fat molecule gives off many times more!!!

46 SATURATED FATS UNSATURATED FATS *Solid @ room temperature
*Come from Animals *Unhealthy Lard or shortening in a can (Crisco or Wesson is the brand name for shortening or oil. It is not a type of fat or oil!!!) *They only have single bonds between the carbons so there are more H+ atoms attached to the carbons in the chain!!! Draw the correct # of H+ that would be attached to the carbon chain. C-C-C-C-C room temperature *Come from Plants *Healthier Oil in a bottle>> Types: (Canola,Olive,Corn,Peanut,Veg) *They have double bonds between the carbons so there are less H+ attached to the carbons in the chain!!! Draw the correct # of H+ that would be attached to the carbon chain. C=C=C=C=C

47 Lard Oil

48 SATURATED FATS: UNSATURATED FATS: The excess amount of H+ in
saturated fats contribute to Heart Disease! They cause plaque to build up in the arteries which results in high blood pressure!! High blood pressure is known as the Silent Killer because often; the symptoms are unnoticed. This is why it is important for adults to check their blood pressure regularly!!! UNSATURATED FATS: Unsaturated fats are healthier because there are less H+ found in the fat, so they do not contribute to plaque building up in arteries!!!! There are certain types of these fats that are essential for your body to stay healthy!! So understand that your body has to have a certain percentage of fat!! Not all fats are bad for you! Your cells must have certain types of these fats in order to function!!!

49 SATURATED FATS The extra H+ (ions) lead to plaque buildup!!
It restricts the flow of the blood forcing the heart to pump it harder!!! This causes blockage!!!

used to coat, insulate and protect things in nature. EXAMPLES OF WAXES: Bees make wax. Your Ears make wax. Plants even have wax on the outside of their leaves to help protect them from losing water. Plants use wax to stop evaporation of water from their leaves. Succulents are plants that have a thick, waxy covering over their leaves. They are plants like a Cactus or Aloe Vera—they live in the desert. They need that protective coating to keep what little water they get.

51 STEROIDS In animals, steroids are called created with Hormones.
They are natural steroids your body makes to aid in development control chemical cycles and to work with your immune system. You more than likely have heard of steroids in the news. Many body builders and athletes have used anabolic steroids to build muscle mass. These anabolic steroids make their body add more muscle than they normally would be able to. Anabolic steroids are illegal!!! They have severe side effects!!!

They cause a violent, aggressive behavior in people known as Roid Rage!!! Side effects of using them start with irritability and then gradually result in violent behavior leading to depression which can result in suicidal tendencies!!! Never take drugs to enhance your body!!! People who use them are actually hurting their bodies!! They can't see it because it is slowly destroying their internal organs and not their muscles! When they get older, they more than likely will have kidney or liver disease!!!!


54 The steroids your body makes are natural and needed for your health!
Your body needs steroids to survive. Many of your hormones are created with steroids. Cholesterol is one of the root steroid compounds used in your body. Cholesterol is a type of glycerol!!! Why do you need glycerol?????? Too many steroids are dangerous and can eventually destroy your organs!!! Even some prescribed medicines that are steroids become dangerous when taken in high amounts for long periods of time.

55 CHOLESTROL 2 TYPES: Cholesterol is a type of steroid.
Cholesterol is also part of cell membranes. 2 TYPES: LDL—Bad You get from this type from eating fried, greasy foods!! It clogs arteries!!!! HDL---Good—You need this type!!! The HDLs carry the LDLs away from the artery walls. The LDLs stick to the artery walls and can lead to plaque build up!!! The plaque cloggs the Arteries which is directly linked to Heart Disease!!!!

56 Structure of LIPIDS inside the Cell Membrane
The structure of the lipids in the cell membrane is called a Phospholipid Bilayer. There are two layers of phospholipid molecules. The phosphate heads face out and the fatty acid chain tails meet in the middle. This is what makes each part a phospholipid it is made up of the phosphate round head and the 2 fatty acid chains attached to the head which are lipids. The phosphate heads of the phospholipids are hydrophilic meaning water loving The fatty acid chains of the phospholipids are hydrophobic meaning water fearing. The fatty acid chains face each other in the bilayer.

57 The Phospholipid Bilayer helps to control what enters and leaves the cell.
You will also find proteins floating in the Phosphoipid Bilayer as well as carbohydrate chains and cholesterol molecules that are embedded in the membrane. The Proteins transport molecules across the cell membrane The Cholesterols lubricate the phosphate heads on each side of the bilayer so that it stays flexible and they provide energy for the membrane.. The Carbohydrate Chains identify molecules when they approach the cell and determine whether they are safe to enter or not. The Cell Membrane is called the Fluid Mosaic Model because it is flexible and is patterned!!!

58 Quick Quiz Time What are the monomers of lipids?
What elements make up lipids? What are the types of lipids? Which type of fat is unhealthy? Which type of fat does not contain single bonds between the carbons? Which type of cholesterol is bad? Name 2 organisms that make waxes? Study Time!!!!!!!!!!!!!!!!!

59 This is the end of the Lipid notes!!!


61 Functions of Proteins Transportation---Hemoglobin transports O2 & Channel proteins move molecules across the cell membrane Storage----they store amino acids to make more proteins Muscle Movement---Actin & Myosin work with muscles to contract & relax muscles Defense---Antibodies in our Immune System-they kill the Antigen (foreign invader) to help keep us well Hormonal Proteins---ex: Insulin controls blood sugar Structural Proteins---Hair, Fingernails

62 There are 20 different amino acids.
8 of them are essential. The other 12 can be synthesized by an adult body—so you have to get the 8 essential aa from eating the right foods!!! Amino acids usually end in (ine), Amino acids are used in every cell of your body and are used to make the proteins you need to survive. All organisms need proteins!!! The inability to make 1 specific type of protein can have great consequences!!!

63 Molecular Structure of an Amino Acid
R is the functional group of the amino acid. Alanine Serine

64 Dehydration Synthesis
Thousands of combinations of those 20 aa are used to make all of the proteins in your body. The amino acids bond together through Peptide Bonds. This is a type of covalent bond. 2 amino acids bonded together make a dipeptide. Many aa bonded together make a polypeptide chain. Dehydration Synthesis (Anabolic Metabolism)

65 There are 20 amino acids. Each has a different R group. The properties of the R group determine how the polypeptide will fold into its final shape.

66 Amino acids continue to bond together to make long chains and those long chains of amino acids are also called polypeptide chains. The polypeptide chain is not yet a protein…. The polypeptide chains take on a 3D shape through a 4 step process. Proteins must have their own unique 3D shape in order to function. If they lose their shape, they can no longer function!!! Some things that can cause them to lose their shape is having an incorrect temperature or pH.

67 4 Step Process to complete a Protein
1.Primary 2.Secondary 3.Tertiary 4.Quaternary

68 Primary Structure The sequence of amino acids in the polypeptide chain.

69 Secondary Structure

70 Tertiary Structure

71 Quaternary Structure of a Protein in it’s 3D Shape

72 Each type of protein needs it’s Optimum Condition:
this means what is best and needed for it to function. If it does not have it’s optimum temperature or pH, it will become Denatured which means it loses its 3D shape and it can no longer function. If it enters an environment that is too hot or cold (temp)–or— too acidic or too alkaline (pH) it will become Denatured!!! So proteins have to have their 3D shape! You know that we get some protein from the foods we eat—like beef, poultry, pork, eggs, nuts, etc.

73 Why do you think Rocky drank Raw Eggs?
We keep eggs in our refrigerators So this must mean eggs have to stay at a cold temp right?? Then this must be their optimum temp!! When we scramble, fry, or boil eggs We change their temperature right?? Then they lose their optimum temperature and become denatured So we don’t get as much protein from eggs if we eat them cooked vs drinking a raw egg…. Now, personally… No, I could not swallow a raw egg!!! Gross!!! But a lot of athletes do!!

74 All of the organic compounds have to be broken back down into monomers during digestion.
The monomers are the nutrients and the nutrients are the smallest particles!!! Molecules have to be broken down into the form of a nutrient to be absorbed back into the bloodstream So that you can get your nutrition from your diet!!!

75 PROTEIN DEFICIENCIES They are hereditary meaning you are born with them. You will learn how they are inherited in the Genetics Unit!! One example of a protein deficiency is: Sickle Cell Anemia. A person with this disorder cannot make the protein hemoglobin that transports O2 in your blood. The result is the red blood cells will become sickle shaped. Their shape cause their arteries to clog. The organs cannot function normally because there is not enough O2 getting to the organs. This causes pain!!

76 A single amino acid substitution in a protein causes sickle-cell disease.

77 Another example of a protein deficiency is Lactose Intolerance
a person with this disorder cannot make the protein lactase. Lactase is an enzyme Some proteins act as ENZYMES: Enzymes help break down molecules in digestion and act as catalysts. Someone who cannot make the enzyme lactase cannot break down the disaccharide sugar lactose back into the monosaccharides. This causes severe abdominal cramping So they cannot drink milk, eat ice cream or any food that is a dairy product unless they take a Lactaid supplement before eating. Lactaid will help some people with this disorder, but not all. Supplements are synthetic molecules that can be taken as medicine like a vitamin if our body cannot make them. Unfortunately, there aren’t that many different types of supplements available that can be taken to help with all of the different types of protein deficiencies.

78 ENZYMES Some types of proteins are enzymes. Enzymes end in ase.
Enzymes act as catalysts and help complex reactions occur everywhere in life. Catalyst means it speeds up the chemical reaction. Enzymes are required for all chemical reactions to take place!!! They Time, Regulate, and Speed Up All Chemical Reactions! Chemical Reactions cannot occur normally without the specific enzyme that is required for it to work!!

When you go home at night and the door is locked, can it open itself? Nope. You need a key that is just the right shape to fit in that lock. Otherwise, you're stuck in the cold. Enzymes work in a similar way as (locks and keys). Enzymes complete very specific jobs and do nothing else. They are very specific locks and the compounds called SUBSRATES they work with are the special keys. In the same way there are door keys and car keys, there are specific enzymes required for every chemical reaction to complete!

80 Lock & Key Reaction

81 Enzyme Reaction

82 Quick Quiz Time What are the monomers of proteins?
What elements make up proteins? How many essential aa are there? How is a polypeptide chain made? What shape does a protein have to have? How does an enzyme function like a lock and key?

83 This is the End of your Protein notes!!!

84 NUCLEIC ACIDS MONOMERS----Nucleotides 1. Phosphate
(Nucleotides are made up of 3 parts) 1. Phosphate 2. 5-Carbon Sugar 3. Nitrogen Base ELEMENTS------C, H, O, N, P FUNCTIONS: Controls heredity Contains the instructions to make the Proteins!

85 DNA---Deoxyribonucleic Acid RNA---Ribonucleic Acid
2 TYPES of Nucleic Acids DNA---Deoxyribonucleic Acid RNA---Ribonucleic Acid (You Must Always Be Able To Spell These Correctly!!!)

86 DNA It is the building block of life. DNA is the “THE CODE FOR LIFE”.
What does that mean?? It contains the instructions for making the proteins. The DNA makes up the chromosomes inside of the nucleus and can never leave the nucleus.

87 RNA 3 Types of RNA mRNA-messenger RNA rRNA-ribosomal RNA
tRNA-transfer RNA The proteins are made outside of the nucleus. So the mRNA reads and translates the directions for the proteins from the DNA inside of the nucleus!! The mRNA can then leave the nucleus and take the instructions for the protein to the ribosome outside of the nucleus. The ribosome contains rRNA The tRNA brings the amino acids to the ribosome to make the polypeptide chain. tRNA mRNA rRNA

88 DNA (Differences) RNA Double-stranded It cannot leave the nucleus!!!
It is found in the nucleus!!! It is known as the Double Helix  It cannot leave the nucleus!!! DNA has the instructions for making the proteins!!! 1 type of DNA (Code for Life) it contains the instructions for making the proteins and remember proteins control everything in your body!!! Single-stranded—mRNA It is found in the Nucleolus!!! It can leave the nucleus!!! mRNA takes the instructions for making the proteins to the ribosome in the cytoplasm to make proteins!!! 3 types of RNA mRNA (messenger RNA)- transcribes the directions from the DNA tRNA (transfer RNA)-brings aa to the mRNA on the ribosome to make the polypeptide chain rRNA (ribosomal RNA)-makes the ribosomes in nucleolus

89 DNA (Differences) RNA Sugar—Deoxyribose (5-carbon sugar)
Nitrogen Bases—5 Total Bases Only 4 of them are in the DNA Purines Pyrimidines (Double-ringed) (Single-ringed) A-adenine T-thymine G-guanine = C-cytosine Complimentary Base Pairing: A – T T - A G = C C = G Sugar---Ribose (5-carbon sugar) Nitrogen Bases---5 Total Bases Only 4 of them are found in the RNA Uracil replaces Thymine A-adenine U-uracil G-guanine = C-cytosine Complimentary Base Pairing: A – U U - A G = C C = G

90 PURINES PYRIMIDINES Double-ringed Bases Cytosine & Thymine
Adenine & Guanine Double-ringed Bases Cytosine & Thymine Single-ringed Bases

91 Quick Quiz Time What are the monomers of nucleic acids?
What elements make up nucleic acids? Name a difference between DNA and RNA? Why is DNA called THE CODE FOR LIFE? What are the 3 types of RNA? Name the purines. Name the pyrimidines.

92 This is the End of your BIOCHEMISTRY NOTES!!!


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