Biology 30Unit 1Biochemistry

What are we? If we take a piece of skin, hair or any other piece of us and

break it down we will eventually end up with Atoms. If we did our whole body we would have the following %'s.

  Oxygen 65 (by mass) Carbon 18.5 Hydrogen 9.5 Nitrogen 3.3 Calcium 1.5 Phosphorus 1.0 K,S,Cl,Na,Mg 1.2 Fe,I trace

All things we are made of are from these and their combinations. When these elements join together they have different properties than when separate.

Ex. Table salt (NaCl) is a white crystal composed of Na and Cl

Na is a white metal and Cl is greenish-yellow gas.

Organic compounds Nearly 99% of the human body is made

of 6 elements. Carbon is one of the six. Carbon is nearly in every compound of the body except water. Things made of Carbon and hydrogen are called organic compounds. Other elements may be included.

Ex. C6H12O6, CH4, CH3COOH

Inorganic Compounds are those not containing carbon and

hydrogen. CO2 and H2O are inorganic.

Compound formation and destruction.

When atoms or molecules join they join by chemical bonds. This is the attraction between outer electrons of different atoms. There are two major types of bonds:

Covalent This is when one atom shares its electrons with one or

many other elements. An equal sharing is called Covalent Bonds.

When two or more elements join together they usually release energy to form a bond. When the compound is separated energy is usually required to break the bond. The amount released to form is equal to the amount required to break the bond.

When energy is released in a reaction it is said to be Exothermic. If energy is required for a reaction to occur it is said to be Endothermic.

Covalent

Single, Double and Triple bonds Double bonds are stronger and the

elements are closer together. Triple bonds are even stronger and closer.

Ionic Bonds The electrons from atoms are not shared but

removed from one and placed on another. This leaves the affected atoms as ions. One positive and one negative.

Ex. NaCl

Ionic bonds usually split very easy in water were as water doesn't affect covalent bonds.

Ionic bonding

Chemical reactions and equations in the body

Respiration

Protein formation

Lipid Formation

Special cases of bonding-H bonding

Often when a molecular bond is formed ends of the molecule are charged or slightly charged. If there is enough attraction a new bond can form. This bond is especially strong when between H and one of N, O or F. These are called H-bonds. They add strength to the molecule and increase melting and boiling points to a large degree.

H-Bonding

Special cases of bonding- polymerization

The hooking together or many smaller molecules to make very large structures. Individual molecules are called monomers two monomers are called dimers three monomers are called trimers Many monomers are called polymers

Our body makes and breaks up polymers all the time. Examples of polymers are: Carbohydrates, Proteins, lipids nucleic acids.

Other Polymers Polymers do not only exist in Biology.

Synthetic polymers include the production of nylon, rayon, Teflon, polyethylene (plastic).

Many of these are not biodegradable because natural occurring organisms don't have the ability to decompose the bonds.

Carbohydrates These are made of Carbon, Hydrogen

and oxygen. The proportion of hydrogen atoms to oxygen is two to one. Sugars are only made in plants and some simple one celled organisms. The carbohydrates come in different levels.

Carbohydrates-simple sugars

These are 5 or 6 carbon sugars. C6H12O6. - They are also called

monosaccharides - Examples include glucose,

fructose and galactose

Carbohydrates- double sugars

Also called disaccharides formed when two simple sugars join C12H22O11

One H2O is released when this occurs. (Dehydration synthesis)

Examples include sucrose (table sugar) and lactose

Lactose

Carbohydrates-Polysaccharides

Many sugar molecules join together Starch and cellulose are examples Starch is less complex than cellulose and it may have

chains of dozens to thousands of sugar strands. Cellulose is responsible for the support of plants rather

than bones. Only herbivore animals have the ability to break cellulose

down into a usable form. All we get out of the cellulose is the minerals which are in the water which is stores.

Another example of a polysaccharide is chitin. This is so tough that it forms the protective shell of insects and crustaceans.

Cellulose

Carbohydrates and animals For carbohydrates to be used they all

have to be broken down into simple sugars, to do this water is required to be added. This process is called Hydrolysis.

Animals cannot make sugar but they can make starch. Animal starch is called glycogen and it is produced in the liver and stored in the liver and muscles.

Lipids Lipids are the fats, waxes and oils. They are not soluble in water. Fats or lipids are made from three fatty

acids joining with a glycerol molecule. Three water molecules are released when this occurs.

They are usually formed for food storage

Lipids (continued)

Many types of fatty acids exist. The simple ones are strings of hydrocarbons. When this reaction takes place all available carbon bonds are shared with other molecules. This is said to be saturated. If some double bonds exist in the fatty acid when it joins it is said to be unsaturated. If it really complex and many double bonds exist the fatty acid is referred to as polyunsaturated.

Lipids (continued)

Lipids are extremely important in the composition of biological membranes

Lipids -Steroids

These are another type of lipid. The fat molecule is made in a ring shape. One of

the best examples is cholesterol. These molecules also help in the production of membranes and in formation of hormones used to carry chemical messages in the body.

Our body naturally produces lipids. Our diet also consumes lipids. If the balance is not set, excess lipids will be stored in fat cells. These cells are located in muscles and artery walls. This can lead to blockage of tubes and heart attacks.

Lipids-Cholesterol

HDL is good and helps to prevent heart attacks. Usually in unsaturated (trans) fats.

LDL is bad cholesterol and builds up in the arteries to cause heart attacks. Higher in saturated fats.

Blood work determines the levels and gives you a ratio.

Proteins Proteins are formed by the

polymerization of amino acids. Proteins are one of the most complex

molecules and most widely used chemicals of our body.

They vary in use from structure of our hair, skin, finger nails to transmitting chemical messages such as insulin.

Proteins (continued)

Proteins also are enzymes which break down the food we eat. They aid in transport of material into and out of the cell. And they are also responsible for genetic material and its expression.

Proteins-Amino Acids

About 40 exist but only 20 are common in every cell.

Amino acids are made from C, N, H and O. When C and N join we call this a peptide

bond. A long chain of amino acids joined together would be called a polypeptide bond. 1000 amino acids joined together are common.

H bonding occurs between the H and N to strengthen the molecule.

Proteins-Enzymes

These are proteins which have the sequences which have the ability to cause large molecules to be broken down or for small molecules to be joined.

Enzymes are specific in that one enzyme can only cause one certain reaction. This reaction may take place many times. The enzyme is not used up in the reaction.

Proteins-Enzymes

Proteins-Enzymes

Sometimes other molecules assist the enzyme with the activity.

These are called coenzymes. This process is compared to and often called the Lock and Key theory.

Testing for Protein, Carbohydrates and Lipids lab

Nucleic Acids Nucleic acids are very complex, they

contain phosphate groups, sugar groups and nitrogen compounds. They combine with proteins to form Chromosomes.

DNA In 1950 Sutton and Boveri found a

nucleic acid that controlled all cell activity. It is DNA, Deoxyribose nucleic acid. DNA is larger than any compound we have came across so far. It is larger than cellulose. It has a shape that is called Double Helix or spiral.

DNA - diagram

DNA structure The vertical parts are made of sugar joined to

phosphate. The sugar is a 5C Deoxyribose. Each sugar has a

nitrogen base. This is the joining piece to the other side.

The combination of a sugar, phosphate and nitrogen base is called a nucleotide.

A DNA molecule is a double strand of nucleotides joined by their base.

Several thousand nucleotides make up a single strand

DNA –nitrogen bases

The nitrogen base is one of four types:a) Adenineb) Guaninec) Cytosined) Thymine

The bases are selective to what they join. A TOr G C No other combinations exist, however, because of

the long chain many combinations can occur. That is why no two people are the same.

Replication of DNA It can build an exact copy of itself. This

is called replication. DNA allows its cell to pass its code from

one generation to the next. In division the bond between bases

separates. These halves of DNA then attach to a

new half ladder and now we have 2 DNA.

DNA model activity Do the lab questions, diagrams and

build a model.

RNA – ribose nucleic acid DNA when it splits in half it does one of

two things: Duplicates to form an identical to itself

or transcribes, which means to form a near identical to itself. The transcription forms RNA.

RNA -continued

This is like DNA except is usually single stranded.

It also has thymine replaced with Uracil (U) which combines with adenine instead.

The R stands for Ribose instead of Deoxyribose.

RNA -roles DNA when it splits may form an RNA strand on

the opposite side instead of DNA. This strand is then released from the nucleus to

the cytoplasm. This is called mRNA (messenger RNA).

It travels to the ribosome and requires special amino acids to attach to make a new specific protein.

The specific amino acid is brought to the mRNA by another RNA called tRNA (transfer RNA).

RNA -roles DNA is critical because it produces a

certain code that the RNA must match. This RNA then selects specific amino

acids from the cytoplasm to produce a new protein we may utilize.

RNA - codons RNA comes in sets of three nucleotides.

With one of the four nitrogen bases and all their possible combinations we have 64 possible combinations that we call CODONS.

Reading a codon wheel To interpret a gene code, we break the

nitrogen bases into three’s starting from the front. We then look at the codon wheel and start from the center with the first nitrogen base. We then move to the next ring in that sector and find the next base and then repeat in the third ring. This will identify which amino acid that produces. If the wheel shows stop, that tells the cell to stop that sequence and start a new one.

Codon wheel example ATT CTA GGG GCT TGA AAT TGC

http://www.yourgenome.org/dgg/general/proteins/proteins_2.shtml