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Proteins and Enzymes

What macromolecules are present in a cell? Carbohydrates, Lipids, Proteins, and Nucleic Acids
Each class exhibits unique emergent properties. Emergent properties are properties that are found

in the macromolecule chains that are not found in the individual molecule. Three of the four classes

of macromolecules (excluding lipids) form polymers. The repeating units and building blocks of

polymers are monomers.

Carbohydrates: serve as both fuel for the cells and building material. Sugars range from three

to seven carbons in length. Triose, pentose, and hexose sugars are the most common. The spatial

arrangement and position around an asymmetric carbon give 2 sugars completely different tastes and

properties.

Simplest carbohydrate: Monosaccharides

● Glucose is a monosaccharide and an aldose sugar

● Fructose: is a structural isomer of glucose and a ketose sugar

● Glucose is required for cellular respiration

● Sugar molecules have carbon skeletons which can fuse with amino acids and fatty acids

● Glucose that is not immediately utilized by the cell can be used to become a polysaccharide

Disaccharides: Double sugars which consist of 2 monosaccharides joined by a covalent bond

● Joined by a glycosidic linkage

● Glycosidic linkages are covalent bonds formed between 2 monosaccharides by a dehydration

reaction

Polysaccharides:

● Formed by thousands of monosaccharides that are joined by glycosidic linkages

● Can be in the form of storage polysaccharides

● Storage polysaccharides in plants are starches (a polymer of glucose molecules) and are
contained in plastids. The plant can synthesize starch to stockpile extra glucose.
● Potatoes, grains, wheat, corn, and rice are good sources of starch

● Glucose monomers are joined together by C1 to C4 linkages

Stored Polysaccharides:

● Animals and humans store a branched polymer of glucose called glycogen

● Glycogen is present in muscle and liver cells and hydrolyzed when demand for sugar increases

● Glycogen storages deplete within a day unless replenished with food

● The body needs sugars for fuel and that is why low carbohydrate diets are inadvisable

Structural Polysaccharides:

● Cellulose is a starch in the beta configuration. The beta configuration of cellulose makes it so

that every other beta glucose monomer is upside down with respect to its neighbors

● Starch is in the alpha configuration. The molecules are in a straight configuration each glucose

monomer has the same orientation

Critical Thinking:

1: A dehydration reaction joins 2 molecules to form maltose. The formula for glucose is C6H12O6.

What is the formula for maltose? C12H22O

2: What would happen if a cow were given antibiotics that killed all the prokaryotes in its

stomach?

The cow would not be able to absorb the nutrients from the cellulose in its rumen. It would become

severely malnourished. The rumen bacteria are responsible for breaking down the high fiber diet of the

cow into usable molecules. If these essential bacteria were killed the cow would lose weight and would

greatly suffer from the lack of nutrients.

Lipids consist of Fats, Phospholipids, and Steroids

Fats: The hydrocarbon chains of fats are similar in form to benzene molecules and equally rich in

energy
● Fats are not polymers

● They are made up of smaller molecules (glycerol and fatty acids)

● Fats have carboxyl tail and a hydrocarbon chain

● Hydrocarbon bonds are hydrophobic

● Fats do not mix with water. Water molecules hydrogen bond to one another excluding the fats

● Three fatty acid molecules join to a glycerol by an ester linkage which is a bond between a

hydroxyl (-OH) group and a carboxyl group

● Triacylglycerol: three fatty acids attached to a glycerol

What makes fatty acids different from one another?

● Length, number of double bonds, locations of double bonds

Saturated Fats:

● Saturated with hydrogen

● Derived from animals

● Solid at room temperature

● Cause of heart disease

Unsaturated Fats:

● Oils at room temperature due to having kinks in their hydrocarbon chain

● These kinks prevent the monomers from binding tightly to each other

● Examples include: olive oil and cod liver oil

● Double bonded carbons result in having less hydrogen

Trans Fats:

● Trans Fats are unsaturated fats that have been converted to saturated fats by adding hydrogen

● Trans Fats contain trans double bonds. Ex: Peanut butter and margarine

● Trans Fats are even more harmful to one’s health than saturated fats

Phospholipids:
● Make up cell membranes

● Opposite ends of the phospholipid exhibit different behaviors

● The hydrocarbon hydrophobic tail and the hydrophilic phosphate group head

● The hydrophilic head has an affinity to water and the bilayers shield the hydrophobic portions

from contact with water

Steroids:

● hormones and cholesterol are steroids

● vertebrate sex hormones are steroids produced from cholesterol

● cholesterol is needed in moderate to low amounts

Proteins: proteins are versatile and are the most structurally sophisticated molecules known.

They also vary extensively in structure

Proteins are:

● instrumental in speeding up chemical reactions (enzymes), provide structural support, storage,

transport, cellular communication, movement, and for defense against foreign substances

Enzymes are proteins which catalyze reactions

● Enzymes speeds up chemical reactions without being consumed by the reaction

Amino acids can join through a dehydration reaction. The resulting covalent bond is called a peptide

bond.

● Amino acids have an N Terminus and a C Terminus. The N terminus is the amino terminus and

the C terminus is the carboxyl terminus hence the name amino acid

● A polypeptide is not the equivalent of a protein, even if the protein is comprised of only one

polypeptide. The polypeptide must be twisted, folded, and coiled into a molecule of a unique

shape in order to become a protein

Primary Protein Structure: consists of a sequence which is ordered like letters in a very long word.
The sequence is determined by genetic information. Ex: Transthyretin. The primary protein structure

has covalent bonds and is therefore not sensitive to temperature of pH changes


Secondary Protein Structure: Hydrogen bonds form between repeating constituents of the

polypeptide backbone. The oxygen and nitrogen are electronegative. Individually the hydrogen bonds

are weak but together (over the long region of the polypeptide chain) they can support the protein’s

shape

Alpha helix: Hydrogen bonding between every 4th amino acid. Ex: Hair incorporates alpha helix

secondary structure

Beta Helix: A spider’s web contains strong silk proteins. The large quantity of hydrogen bonds makes

the spider’s web fiber stronger than a steel strand of the same weight. The shape is maintained despite

wind, rain, and insect’s touch while still maintaining its strength

Tertiary Protein Structure: 4 types of bonds mediate tertiary interactions: hydrogen bonds, ionic

interactions, and disulfide bonds

Quaternary Protein Structure: The same bonds exist in tertiary and quaternary protein structures

except in quaternary structures the bond exists between atoms in different polypeptide chains while

in tertiary structures the bonds are between atoms in the same polypeptide chain

A folded protein exists at a lower energy level than an unfolded protein (can be made to unfold in vitro

such as in a test tube) You can denature a protein by greatly raising the temperature. Proteins can go

through denaturing and renaturing process indefinitely. If the denaturant is removed, the protein will

spontaneously renature (exceptions are proteins that require chaperones)

Nucleic Acid: Form the genetic material and are proteins that are primarily responsible for biological

functions. DNA is a repository of genetic information. Nucleic acids are polymers of nucleotide

monomers which are linked by phosphodiester linkages (covalent attachments)

There are 2 types of Nucleic Acids: DNA and RNA

There are 2 classes of nitrogenous bases:


Purines: Adenine and Guanine

Pyrimidines: Cytosine, Thymine, and Uracil (exclusive to RNA)

An ester linkages is an oxygen bonded to 2 other atoms as such: x - O - x

The molecule has directionality. The N-Terminus is different from the C-Prime end (The 5’ end is

different from the 3’ end) The 5’ end has a free phosphate group (free meaning that it is not attached to

any other nucleotides) which is attacked to the 5’ carbon

At the 3’ end the free Hydroxyl (OH) group is attached to the 3’ Carbon

Compare and Contrast DNA and RNA

DNA:

● Nucleotides: G C A T

● Double Stranded

● Direction of first strange is anti parallel (or opposite in direction) to the second strange

● Ex: 5’ A T G C A T G C A 3’ Must be a DNA strand due to the presence of Thymine

RNA:

● GCAU

● Single stranded

Phosphodiester backbone: includes everything except for the nitrogenous

Can also be called the sugar phosphate backbone

What are the biological functions of Nucleotides and Nucleic Acids?

1. Provide Energy to drive endergonic processes (such as ATP hydrolysis)

2. Some RNAs are enzymes and regulators of gene expression

3. DNA (and RNA in some viruses) acts as the genetic material

4. Necessary functions of genetic material

5. Must account for the characteristics of an organism

6. Must be precisely copied and passed onto offspring


Hydrogen bonds form between complementary base pairs

What class of organic macromolecule is most directly responsible for the characteristics of an

organism? Proteins. However proteins do not get passed onto offspring. DNA gets expressed. DNA is

what gets packaged into the sperm and egg cells

How do nucleic acids account for an organisms characteristics? Proteins acts as enzymes

ATP: ATP has the nitrogenous base adenosine and three phosphates. The terminal phosphate acts as a

high energy bond which can be cleaved and hydrolyzed to release energy

The DNA sequence determines the amino acid sequence. The DNA sequence also determines the

protein sequence. DNA is transcribed by transcription and becomes an RNA sequence and is then

translated through the process of translation into an amino acid

The double stranded DNA molecule has complementary base pairs. One is the coding strand or the

non-template strand which represents the code created by the RNA except with uracils in place of

the thymines. The other strand is the template strand which acts as a template for the synthesis of the

RNA template strand. RNA that is transcribed is complementary to the template strand. Within a long

strange of dsDNA (chromosome) there are many transcription units.

DNA and RNA are universal across different species. Insulin for example can be made for diabetics by

grinding up pig pancreas then purifying it for use in humans.

Each segment of the DNA is called a gene.

Nucleotide language must be converted into an amino acid sequences

Transcription is an anabolic process

RNA polymerase (makes an RNA polymer)

Each set of three bases is called a codon

4 different RNA bases must account for 20 different amino acids in a polypeptide chain

There are a total of 64 possible codons. 61 code for 20 amino acids and three codons code for
termination of the polypeptide chain (stop codons)
There are more combinations than amino acids. Amino acids that are represented by more than one

codon are known as degenerates. AUG is a start codon (most codons begin with this) Leucine is very

degenerate because it has six different codons. Three different amino acids signal the end of the nucleic

acid chain sequence (stop codons)

What is a condensation reaction?

● Monomers are connected in a condensation reaction

● The monomers are connected in a specific condensation reaction called a dehydration reaction

● This reaction is called a dehydration reaction because water is lost in the process and a new

bond is formed

● The water molecule is lost from the (-H) and (-OH) group

● This reaction can be repeated as monomers are added to the chain linking themselves

● The dehydration reaction is propelled by enzymes

What is hydrolysis?

Hydrolysis is a process by which polymers can disassemble into monomers

through hydrolysis (hydrolysis is the opposite of dehydration)

● Hydro is a prefix meaning: water

● Lysis is a suffix meaning breaking down

● Ex: A good example of hydrolysis is the reaction that occurs within our own bodies as we

digest food. Food is made up of large polymers. The nutrients from these large molecules

are unable to pass into our cells unless they are broken down into smaller and more simple

monomers. In the digestive tract, enzymes attack the polymers to speed up hydrolysis. Finally,

the nutrients pass into the bloodstream, and permeate into all of the body’s cells.

● The cycle continues when cells use dehydration reactions to assemble the polymers into new
polymers which fit the needs of the cells of the body.
● Proteins are made up of 20 amino acids in chains that are hundred of amino acids in length.

Concept Check:

1) How many molecules of water are needed to completely hydrolyze a polymer that is ten monomers

in length? Nine molecules of water are needed to hydrolyze a polymer that is ten monomers in length

2) Suppose you eat a serving of green beans. What reactions must your body undergo for the amino

acid polymers in the protein of the green beans to be converted into proteins and nutrients in your

body? The polymers in the green beans must first undergo hydrolysis. The enzyme within the digestive

track must attack the polymers to speed up hydrolysis. The monomers can then be distributed into the

body cells.