Unit 2- Biochemistry

Question 1

What is the structure of water molecules? What type of bond forms water molecules?

Answer 1

Water molecules are made up of one oxygen atom and two hydrogen atoms joined by covalent bonds.

Question 2

Why are water molecules polar?

Answer 2

Water molecules are polar because the oxygen atom is more electronegative than the hydrogen atoms (meaning that the electrons are more attracted towards the oxygen atom). This causes the hydrogen atoms to take on a slight positive charge (positive dipole) and the oxygen atom to take on a slight negative charge (negative dipole).

Question 3

What is hydrogen bonding and why does it occur?

Answer 3

Hydrogen bonds are weak, short-lived bonds resulting from the electrostatic attraction between water molecules. Hydrogen bonding occurs due to the polarity of water molecules. Weak hydrogen bonds from between the positive end of the molecule (hydrogen atoms) and the negative end of the molecule (oxygen atoms).

Question 4

What are hydrophilic and hydrophobic substances? What are some examples?

Answer 4

Hydrophilic substances are “water-loving”. Examples include polar and charged compounds which are attracted to water, form hydrogen bonds and dissolve.

In contrast, hydrophobic substances are “water-hating”. Examples include fats and oils.

Question 5

What are some properties of water and how are hydrogen bonds responsible for these properties.

Answer 5

1. Being liquid rather than gas at room temperature. Hydrogen bonds allow water to be condensed enough at room temperature to remain at liquid state.
2. Having high specific heat capacity. It requires more energy to heat water due to the weak bonds that exist between molecules.
3. Having high heat of vaporization. It requires more energy to heat water to the point of vaporization.
4. Serving as a powerful solvent of polar molecules.
5. Adhesion and Cohesion. Hydrogen bonds cause water molecules to be stick together.
6. Hydrophobic exclusion.
7. Ice floats. This is because the solid form of water is less dense than the liquid form (due to hydrogen bonding).

Question 6

What are adhesion and cohesion?

Answer 6

Cohesion is the attraction between like molecules, while adhesion is the attraction between non-like molecules.

Question 7

How do the properties of water help living organisms?

Answer 7

1. Adhesive Properties- Helps blood circulate through blood vessels.
2. Cohesive Properties- Permits water to be pulled up from the roots to the stems in plants.
3. Thermal Properties- It requires lots of heat to evaporate water, therefore, you lose heat when your sweat evaporates, keeping you cool.
4. Solvent Properties- Allows the blood to easily transport water soluble substances.

Question 8

Which compounds are transported in the blood plasma throughout the body?

Answer 8

• Glucose (polar molecule)
• Amino Acids (positively and negatively charged, however, not all amino acids can be transported in the blood)
• Fats (Despite being non polar, they are transported in their own structures called lipoproteins in the blood)
• Cholesterol (Also non polar and requires transport lipoproteins)
• Oxygen (Non polar, but small enough to be dissolved in water to a limited extent)
• Sodium Chloride (ionic compound)

Question 9

What are the similarities and differences between water and methane?

Answer 9

Water and Methane are comparable in terms of weight, size and valence structure. However, due to water’s polarity, water requires far more energy to melt, boil or evaporate and water has a higher specific heat capacity.

Question 10

What are carbohydrates?

Answer 10

Carbohydrates are organic compounds with a certain number of carbon atoms and a certain number of water molecules. Carbohydrates are the most abundant category of molecule in living things by number and include sugars, starches, cellulose and chitin.

Question 11

What are the monomers of carbohydrates?

Answer 11

The monomers of carbohydrates are monosaccharides (one unit sugars). These cannot be further broken down via hydrolysis. Two monosaccharides form a disaccharide and more than two monosaccharides form polysaccharides.

Question 12

What are the bonds that form carbohydrates? What is the reaction that takes place to form carbohydrates?
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Answer 12

Monosaccharides are joined via glycosidic linkages. These bonds form between the hydroxyl functional group on the monosaccharides. This reaction (condensation) produces water.

Question 13

What are the functional groups? What are the atoms/ elements in each functional group?
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Answer 13

The functional groups include:

• Carbonyl (Carbon double bonded to Oxygen)
• Hydroxyl (Hydrogen bonded to Oxygen)
• Carboxyl (Carbon bonded to OH and doubled bonded to oxygen)
• Amino (NH2)
• Phosphate (PO4)

Question 14

What are some examples of monosaccharides?
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Answer 14

Monosaccharides:

• Glucose (found in most disaccharides and polysaccharides)
• Ribose
• Galactose
• Fructose

Question 15

What is the chemical structure of carbohydrates?
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Answer 15

Carbohydrates are composed of a chain of carbon with a carbonyl group (which disappears once the chain forms a ring). Each carbon atom has H and OH on either side, which results in the molecule being polar and therefore, hydrophilic and soluble and water.

Question 16

What are considered sugars?

Answer 16

Both monosaccharides and disaccharides are considered sugars.

Question 17

How are monosaccharides categorized?
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Answer 17

Monosaccharides are either classified as aldose (aldehyde sugar) or ketose (ketone sugar) based on where the carbonyl group is located. If the carbonyl group is located on a terminal carbon, it is a aldehyde sugar and if the carbonyl group is attached to a carbon atom with two carbon atoms on either side, it forms a ketone sugar.
(External carbon-aldose, internal carbon, ketose)

Question 18

What are isomers?
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Answer 18

Isomers are molecules with a slightly different configuration of atoms, but with the same chemical formula. Isomers also have different properties. Glucose, galactose, and fructose are all isomers.

Question 19

What are some examples of polysaccharides? Describe each example's functions.
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Answer 19

Polysaccharides:

• Cellulose (Structural carbohydrate, main component in the plant cell wall, fortified by hydrogen bonds, beta 1-4 linkages)
• Glycogen (Storage carbohydrate, stores energy in the human body in the liver, extensively branched)
• Starch (Storage carbohydrate, stores energy in plants, an example would be the chloroplast)
• Chitin (Structural carbohydrate, found in the exoskeleton of fungi and arthropods)

Question 20

What are the different forms of sugars and how are they different?
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Answer 20

Sugars may be connected via alpha bonds or beta bonds. Alpha bonds occur when the hydroxyl group on carbon 1 is located “below” the ring (on the opposite side from CH2OH). Beta bonds occur when the hydroxyl group is “above” the ring (on the same side as CH2OH)..

Question 21

What is an example of a disaccharide?
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Answer 21

Maltose

Question 22

What are the functions of carbohydrates?

Answer 22

• Direct supply of energy
• Energy storage (glycogen for animals, starch for plants)
• Structural Materials

Question 23

What makes up starch? What kinds of bonds form starch polymers? How does this differ from cellulose polymers?

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Answer 23

Starch is a mixture of amylopectin and amylose. Alpha bonds form starch polymers (since the hydroxyl group is located on the opposite side from the CH2OH molecule). In other words, it’s right side up. This contrasts cellulose, since in cellulose, every second monosaccharide is upside down, forming beta bonds.

Question 24

What are Lipids?

Answer 24

Lipids are substances that are soluble in organic solvents, but insoluble in water. They are composed of carbon, oxygen, hydrogen and sometimes, phosphate. There is also a different ratio of hydrogen to oxygen than carbohydrates (the number of hydrogen atoms is always more than double the number of oxygen atoms).

Question 25

What is the chemical structure of lipids? (triglycerides) What type of reaction is this and between which molecules does it occur? What type of bond is this?

Answer 25

Triglycerides are composed of a glycerol molecule () bonded with three fatty acid chains. A condensation reaction occurs between the hydroxyl group of the glycerol and the hydroxyl group on the fatty acids. These form ester bonds.

Question 26

What are the functions of lipids?

Answer 26

Lipids store energy (they can store double the amount of energy per gram as carbs), provide components for cell membranes (phospholipids- lipids with two fatty acid chains and one phosphate group), provide insulation against the cold, protect internal organs by acting as a cushion, act as hormones, conduct nerve impulses and store certain fat soluble vitamins (A, D, E and K).

Question 27

What is the structure of fatty acids (AKA carboxylic acids)?

Answer 27

Fatty acids are composed of a chain of carbon with hydrogens bonded to each carbon atom and a carboxyl group on a terminal carbon. This carboxyl group makes it acidic.

Question 28

How are triglycerides formed?

Answer 28

Triglycerides are formed via condensation reaction, forming ester bonds.

Question 29

What are the types of fats?

Answer 29

The types of fats are fats and oils, fats being solid at room temperature and oil being liquid.

Question 30

Why are lipids non polar?

Answer 30

Lipids are non polar due to the fatty acid chains. The fatty acids are composed of a hydrophobic region and a hydrophilic region. The more carbons you add to the chain, the less soluble the molecule will be in water because the hydrophobic region grows.

Question 31

What is the difference between saturated fatty acids, unsaturated fatty acids, and trans fatty acids?

Answer 31

Saturated Fatty Acids (Bad);
- The molecule has as many hydrogen atoms as possible

Unsaturated Fatty Acids (Good):

• The molecule does not have the maximum amount of hydrogen atoms and therefore, some of the carbon atoms in the chain form double bonds.
• Unsaturated fatty acids can be either cis or trans isomers

Cis/Trans Unsaturated Fatty Acids:

• In Cis isomers, the two hydrogen atoms are attached to the same side of the two carbon atoms (Good).
• In Trans isomers, the two hydrogen atoms are attached to opposite sides of the two carbon atoms (Bad).

Question 32

What are proteins? What are some specific examples (that IB wants you to know) and provide a brief description.

Answer 32

Proteins are large molecules that consist of one or more long chains of amino acids. Proteins usually fall under one of two categories (functional or structural). Some examples include:

• Rhodopsin (functional, found in the retina, pigment containing protein involved in signalling)
• Rubisco (functional, involved in photosynthesis)
• Insulin (functional, regulates blood glucose levels)
• Collagen (stuctural, located in the skin and connective tissue)
• Spider SIlk (structural)

Question 33

What are the monomers of proteins? How many types are there?

Answer 33

Amino Acids. There are 20 different types of amino acids (that are involved in coding for polypeptides).

Question 34

What is the chemical structure of amino acids (what functional groups are present)?

Answer 34

Amino acids are composed of a central carbon atom bonded to an animo group (NH2), a hydrogen atom, a carboxyl group and a side variable chain (R). This R group creates more functionality since it can change based on the required function of the protein.

Question 35

How can you tell if an amino acid is polar?

Answer 35

We must look at side chains to determine polarity (side chains are the variable group). If there are polar compounds on the end of the side chains, the amino acids are polar/ hydrophilic. If there are non polar side chains, the amino acids are non polar/ hydrophobic.

Question 36

How are polypeptides (chains of amino acids) formed? What reaction takes place? What are the bonds called?

Answer 36

Polypeptides are formed via a condensation reaction and amino acids will always react, end to end (carboxyl group to amino group). These are known as peptide bonds.

Question 37

Are polypeptide chains polar?

Answer 37

Yes, polypeptide chains are polar because one end also has the carboxyl group (C-terminus), while the other contains a amino group (N-terminus).

Question 38

What are the levels of protein structure?

Answer 38

Level 1 (Primary Structure)

• This consists of sequences of amino acids
• All proteins have a primary structure

Level 2 (Secondary Structure)

• This consists of the folds and coils held together by hydrdogen bonds between the polypeptide chains
• All proteins have a secondary structure
• The most common secondary structures are the alpha helix and the pleated sheet.

Level 3 (Tertiary Structure)

• This consists of the interactions of the side chains in order to form folds and coils of a 3-dimensional shape (these may also be held together by hydrogen bonds)
• All protein have a tertiary structure

Level 4 (Quaternary Structure)

• Not all proteins have a quaternary structure (hemoglobin and rubisco have a quaternary structure)
• Aggregation of 2+ polypeptide chains to form an entire functional unit.

Question 39

What is the difference between fibrous proteins and globular proteins?

Answer 39

Fibrous proteins are usually structural, long and narrow and generally insoluble in water (ex: collagen).

Globular proteins are usually functional, circular, and soluble in water (ex: hemoglobin)

Despite the chain of amino acids being polar, the r variable, if exposed, can influence the nature of the protein. Fibrous proteins are usually insoluble in water because their hydrophobic R groups are exposed.

Question 40

What is the denaturation of proteins? What are the factors which can denature proteins?

Answer 40

The denaturation of proteins occurs when proteins lose their secondary and tertiary structures because the hydrogen bonds (or other bonds) holding the shape together are disrupted. This can occur due to temperature and pH, since proteins have an ideal temperature and pH. Denaturation results in a loss of functionality due to the change in structure.

Question 41

What are enzymes?

Answer 41

Enzymes are large polypeptides with a tertiary or quaternary structure that are catalysts. Enzymes are highly specific (one enzyme can only catalyse one type of reaction)

Question 42

What is the active site?

Answer 42

The active site is the region of recognition and the region where the substrate binds to the enzyme.

Question 43

What is the induced fit model?

Answer 43

The induced fit model says that the binding of the substrate to the enzyme active site triggers a slight change in the shape of the enzyme to better fit the substrate. This is possible because of the flexibility of the protein molecules that make up the enzyme.

Question 44

How do enzymes work?

Answer 44

Enzymes work by reducing activation energy. The enzyme does this by weakening the bonds of the substrate while it is binded and therefore, reducing the energy required for the reaction.

Question 45

What can limit enzyme activity?

Answer 45

Enzyme activity can be halted due to temperature, pH, substrate concentration and enzyme concentration.

Temperature:
Up to a certain point, increases in temperature can increase enzyme activity since increases in temperature cause more collisions. However, if the temperature is higher than optimal, the bonds holding the enzyme’s shape will break and the enzyme will cease to function.

pH:
Enzymes have optimal pH’s depending on where they must function (ex: Optimal pH of pepsin is quite low since it functions in the stomach, an acidic environment). Therefore, if the pH is greater or less than the optimal pH, enzyme activity decreases.

Concentration of Substrate:
Increasing the substrate concentration causes more chances of collision between substrate and enzyme molecules. Therefore, the rate of enzymatic reaction rises gradually. However, this increase is halted when all active sites are occupied by substrate molecules, causing enzyme activity to plateau.

Concentration of Enzyme:
Similar to concentration of substrate, except the substrate will becoming the limiting factor, instead.

Question 46

What is enzyme denaturation and what happens when this occurs?

Answer 46

Enzyme denaturation is when the enzyme changes irreversibly and cannot function as an enzyme, anymore. This can occur due to temperature, primarily, and the pH. When an enzyme is denatured, the beta sheets and alpha helices lose their form, and the protein reverts to a primary conformation. This means there is no longer a functional active site.

Question 47

What is inhibition of enzymes and what are the different types?

Answer 47

Inhibition is another factor that can affect enzyme activity.

Competitive Inhibition:
- Another molecule (not the substrate) binds to the active site of the enzyme and blocks the active site. In this case, you can still reach the maximum rate of reaction.

Non Competitive Inhibition (AKA allosteric)
- Another molecule binds to another part of the enzyme, changing its shape and preventing it from binding to the substrate. In this case, it is less likely that the enzyme will react maximum rate of reaction.

End- Product Inhibtion:
In end-product inhibition, the final product in a series of reactions inhibits an enzyme (acts as an allosteric inhibitor) from an earlier step in the sequence (usually the first step).