IB Biology SL - U2, Part 1

Metabolism, Water, Carbohydrates, Lipids, & Proteins

What is the theory of vitalism?

What is the theory of vitalism?

That living organisms were composed solely of organic chemicals that could only be produced in living organisms, because a “vital force” was needed.

Note: No ‘vital force’ has been discovered and a better answer to the question of what makes living organisms from non-living matter is natural selection

What is molecular biology?

A science that aims to explain living processes in terms of the chemical substances involved.

What was urea?

An organic compound discovered in human urine that helped falsify the theory of vitalism, but it didn’t disprove it completely. It falsified the theory partially, because a chemist was able to synthesize it without a “vital force”

Define metabolism

The web of all the enzyme-catalysed reactions in a cell or organism.

Note: Most metabolic pathways happen in chain reactions, but some happen in cycles

Define anabolism, & say a type of anabolic reaction.

Anabolism is the synthesis of complex molecules from simpler molecules; where monomers create polymers (macromolecules)

Ex. Condensation reactions where water is produced

Define catabolism & say a type of catabolic reaction.

Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Ex. Hydrolysis where water molecules are split

What are water molecules (charge wise)?

Polar

• They have dipoles and are therefore dipolar

What is a hydrogen bond?

An intermolecular bond between the positive pole of one water molecule and the negative pole of another. For water evaporation, H bonds between one and another water molecule must be broken. Heat energy is used to do this, explaining the use of sweat as a coolant - evaporation of water from sweat removes heat from body. (Latent Heat of vaporization)

Compare the thermal properties of water and methane based on their H bonds, on the basis of melting point, specific heat capacity, latent heat of vaporization, and boiling point.

If a substance is attractive to water and forms intermolecular bonds with water, what is it in terms of solubility?

Water-soluble, or hydrophilic

What kinds of compounds are hydrophilic?

Ionic compounds and substances with polar molecules.

• Many hydrophilic substances dissolve in water because their ions or molecules are more attracted to water than each other

What does it mean if a substance is hydrophic?

Not that it is repelled by water, but instead if a substance is hydrophobic that means that water molecules are more strongly attracted to each other than to the non-polar molecules of hydrophobic substances. They're insoluble in water.

What are the unique properties of water (nonthermal)?

• Cohesion

• Adhesion

• Thermal (but already explained)

• Solvent

Explain cohesion in terms of H bonding and dipolarity? Give an example benefit to living organisms.

Water molecules cohere (stick to each other) because of the H bonds that form between them.

• Strong pulling forces can be exerted for water to get to the tops of the tallest trees through the xylem

Explain adhesion in terms of H bonding and dipolarity? Give an example benefit to living organisms.

The dipolarity of water molecules make them adhere to surfaces that are polar and therefore hydrophilic.

• Adhesive forces between water and cellulose in cell walls in the leaf cause water to be drawn out of xylems, keeping the cell walls moist and able to act as a gas exchange surface

Explain solvent in terms of H bonding and dipolarity? Give an example benefit to living organisms.

Many substances dissolve in water due to its polarity including those composed of ions or polar molecules

• Most chemical reactions take place with all substances dissolved in water, so water is a medium for many metabolic reactions

Describe condensation reactions thoroughly.

Two molecules are joined to form a larger molecule plus a molecule of water. Anabolic reactions are condensation reactions. A single sub-unit (monomer), can be added to another to create a dimer. A longer chain of monomers = polymer.

Give an explained example of a condensation reaction.

Ex. Two amino acids can be joined together to form a dipeptide by condensation reaction. Further chaining together creates a polypeptide. The new bond formed to link amino acids together is a peptide bond.

Describe hydrolysis reactions thoroughly.

The reverse of condensation reactions. In hydrolysis, a large molecule is broken down into smaller molecules, using up water. Water molecules are split into H and OH groups. Hydrolysis = water splitting. The H & OH are needed to make new bonds after hydrolysis. Hydrolysis=Catabolism.

Give an explained example of hydrolysis reaction.

Polypeptides+water → dipeptides or amino acids

Polysaccharides+water → disaccharides or monosaccharides

Glycerides+water → fatty acids + glycerol

What are the monomers, dimers, and polymers of;

• Carbohydrates

• Fats

• Proteins

Monomers:

• Monosaccharide

• Fatty Acid

• Glycerol

• Amino Acid

Dimer:

• Disaccharide

• Dipeptide

Polymer:

• Polysaccharide

• Triglyceride

• Polypeptide

Name all the monosaccharides.

Glucose

Fructose

Galactose

What is the alpha d ribose acronym.

Under

Under

Over

Under

(In reference to the OHs, going right to left)

What is the beta d ribose acronym.

Over

Under

Over

Under

(In reference to OHs, going right to left)

What are the two versions of ribose and glucose?

Right handed vs. left handed versions

D-Ribose & D-Glucose = right handed, but living organisms can only use the right handed versions.

Imagine the structure of Alpha-D-Glucose. If you know it, mark this flashcard as right, if not, then don’t.

What are the possible combinations of monosaccharides to create disaccharides?

Glucose + Glucose → Maltose+ H2O

Glucose + Galactose → Lactose + H2O

Glucose + Fructose → Sucrose + H2O

What are the three polysaccharides we have to know and understand?

Glycogen

Starch

Cellulose

What is the basic linkage between glucose subunits?

Glycosidic bonding from C1 of a glucose to C4 of the next, but some have 1,6 glycosidic bonds, which forms a branched structure (pictured)

Describe cellulose.

Unbranched polymer of Beta-D-Glucose (Over Under Over Under). The orientation of the glucose alternates (up-down-up-down and so on), which makes the polymer straight rather than curved and allows groups of cellulose to be arranged in parallel with H bonds, forming cross links (cellulose microfibrils). They’re the basis of plant cell walls.

Describe the two forms of starch.

Amylose

• Polymer of alpha-D-Glucose with all glucose subunits in the same orientation, giving the polymer a helical shape.

• Only 1,4 linkages so amylose is overall unbranched

Amylopectin

• Polymer of alpha-D-Glucose with all glucose subunits in the same orientation, giving the polymer a helical shape.

• This is branched (1,6 glycosidic bonds), but also linear with its 1,4 glycosidic bonds.

Both forms are used by plants to store glucose in an insoluble form that doesn’t cause osmotic problems.

Describe glycogen

Similar in structure to amylopectin--branched polymer of alpha-D-Glucose. There are more 1,6 linkages than in amylopectin so it’s more branched. Glycogen is used by mammals to store glucose in liver and muscle cells. As it’s insoluble, large amounts can be stored. If it was glucose it would cause water to enter the cells by osmosis and cause bursting

You can use computer programs to look at molecular structures. What is an example of one?

The most widely used molecular visualization software is JMol

Imagine hydrogen bonding in celllulose. If you think you got it right, mark it as such, if not then don’t.

Parallel arrays of cellulose strands, bonded parallel by hydrogen bonds.

What are the three main types of lipid? Describe each of the types.

1. Triglycerides

   1. Made from three fatty acids and one glycerol by condensation reactions so they have three hydrocarbon tails. Fats and oils are triglycerides.

2. Phospholipids

   1. Similar to triglycerides but only have 2 fatty acids linked to glycerol with a phosphate group instead of the third fatty acid. Phospholipids are only partly hydrophobic and form the basis of membranes.

3. Steroids

   1. They all have a similar structure of four fused rings in their molecule.

      1. Cholesterol, progesterone, estrogen and testosterone are all steroids

Triglyceride Structure on the back of this card.

Glycerol Structure on the back of this card.

Phospholipid Structure on the back of this card.

Testosterone/steroid structure on the back of this card.

Know how to draw a fatty acid. Practice on this card, and check on the back, if you still can’t then mark this flashcard as wrong in test mode.

Also make sure you know that the acidic carboxyl group is always at one end of the chains.

What are the two overarching types of fatty acids? Describe each

Saturated

• All of the carbon atoms in the chain are connected by single covalent bonds so the number of hydrogen atoms bonded to the carbons cannot be increased

Unsaturated

• Contain one or more double bonds between carbon atoms in the chain, so more hydrogen could be bonded to the carbons if a double bond was replaced by a single bond

Know how to draw an unsaturated fatty acid. Check if you’re right (mentally) on the back of this card

What are the types of unsaturated fatty acids?

Monounsaturated

Polyunsaturated

Cis unsaturated

Trans unsaturated

Describe monounsaturated and polyunsaturated fatty acids.

Monounsaturated

• only one double bond

Polyunsaturated

• two or more double bonds

Note: in the names of fatty acids, the number tells you the position of the nearest double bond to the CH3 at the end. In omega-3 fatty acids, it’s the third bond from the CH3 and in omega-6 fatty acids its the sixth from the CH3

Describe cis unsaturated and trans unsaturated fatty acids.

Cis unsaturated

• Hydrogen atoms are bonded to the carbon atoms on the same side of a double bond

Trans unsaturated

• Hydrogen atoms are bonded to carbon atoms on opposite sides of a double bond

What are the 2 main stores of energy in organisms? How are they contained in plants and humans?

Fats or oils (Lipids), and glycogen or starch (carbohydrates)

Plants

• Store lipids and starch in seeds

Humans

• Store lipids in adipose tissue (body fat)

• Stores glycogen in the liver

What is the ratio of amount of energy released per gram, lipids compared to carbohydrates?

The amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates.

Why is storing lipids more convenient than storing carbohydrates for energy?

The same amount of energy stored as a lipid as a carbohydrate, adds half as much to body mass. This is because fats form pure droplets in cells with no water associated, whereas each gram of glycogen is associated with about 2 grams of water. Basically, lipids are 6x more efficient in energy storage per gram of body mass.

Know how to calculate BMI, it’s pretty easy. In exams they either give you a big box with shaded areas and you identify where someone is, or you connect the mass and height through the BMI line with a straight line, pictured on the back.

What are the health risks of trans-fats?

There’s a positive correlation between amounts of trans fats consumed and rates of coronary heart disease (CHD). Other risk factors have been tested to see if they were the problem, but they were not. Basically trans-fats probably do cause CHD.

What evidence gives another causal link between trans-fat consumption and CHD?

Often in patients who die from CHD, fatty deposits in the diseased arteries have been found to contain high concentrations of trans-fats, thereby forming a causal link

What are the health risks of saturated fatty acids?

There aren’t concrete health risks of saturated fatty acids. A positive correlation has been found between saturated fatty acid intake and rates of CHD, but many populations don’t fit the model. For example, the Kenyan Maasai population that have a diet that’s rich in saturated fatty acids, yet CHD is rare. It’s possible the actual cause of CHD isn’t saturated fat itself but another factor associated with its intake.

Think about the structure of an amino acid, check whether you’re right on the back of this card.

How many amino acids are there?

20

What determines the variability of amino acids?

The R group, it varies a lot. In fact, you could make over 100 amino acids in a lab with different R groups, but the theory is, organisms only use 20 amino acids. However, organisms can produce exceptions to these 20 amino acids, such as selenocysteine and pyrrolysine, but these are believed to be a product of evolution, after the original 20.

Why is the theory of there being 20 amino acids produced by organisms not falsified by the existence of exceptions?

Because they’re defined as extra variations instead of exceptions that disprove the theory.

Between what groups does a peptide bond form?

The amine group of one amino acid and the carboxyl group of the other.

Imagine the condensation reaction resulting in a peptide bond. Check if you’re right on the other side of this card.

What is a polypeptide?

An unbranched chain of amino acids

How many amino acids are usually in a polypeptide?

Usually between 50 and 2000 amino acids, but it can be up to 10,000

What are peptides?

Chains of fewer than 40 amino acids

There are a large number of possible polypeptides, considering a string of 100 amino acids, they can be arranged in so many ways; 20^100, but comparatively how many are actually made by living organisms?

A very small proportion of the possible sequences, particular sequences are usually made in very large quantities because they’re useful for organisms. Over 2 million polypeptides have been found in living organisms.

What is a protein?

Either a polypeptide, or many polypeptides linked together

What codes for the amino acid sequence of a polypeptide?

Genes

What is a proteome?

All of the proteins produced by a cell, a tissue or an organism. Whereas a genome (all of its genes) is fixed, the proteome is variable because different cells in an organisms make different proteins. What proteins a cell makes can even change over time.

What is a protein conformation?

The three dimensional structure. The polypeptides of most proteins are folded up to make a globular shape.

What determines the protein conformation?

The sequence of amino acids in a polypeptide.

Note: each time a polypeptide with a specific sequence of AAs is synthesized on a ribosome, the conformation will tend to be exactly the same. Basically, a specific polypeptide being made by a ribosome will be almost exactly the same always

How is a protein’s structure stabilized?

By the intramolecular bonds between the amino acids in the polypeptides that are brought together by the folding process (disulfide bridges)

Info card: Sodium Potassium pump

This is an example of a protein that switches reversibly between alternative conformations. It allows the Na-K pump to pick up ions from one side of the membrane (dotted rectangle) and discharge them on the other side

What is denaturation? What can cause it (that we should know)?

How a protein conformation can be damaged by substance and conditions.

• Heat & pH

How does heat cause denaturation?

Heat causes vibrations within protein molecules that break intramolecular bonds and cause the conformation to change. Heat denaturation is almost always irreversible.

An example of this is egg whites: The albumin proteins are clear, but are denatured by heat and turn white. They can’t turn back once they’re denatured into a white solid.

How does pH cause denaturation?

Each protein has an ideal or optimum pH at which its conformation is normal. If the pH is increased by adding alkali or decreased by adding acid, the conformation will initially stay the same, but denaturation will occur when the pH is too far from the optimum. This is because the pH causes the intramolecular bonds to break.

What examples of proteins do we have to know?

Rubisco

Insulin

Immunoglobulins

Rhodopsin

Collagen

Spider silk

Describe Rubisco. Describe Insulin

1. Enzyme with an active site that catalyses the photosynthesis reaction that fixes carbon dioxide from the atmosphere, providing all the carbon needed by living organisms to make sugars and other C compounds

2. Hormone that’s carried dissolved in blood and binds specifically and reversibly to insulin receptors in the membranes of body cells, causing the cells to absorb glucose and lower blood glucose concentration

Describe immunoglobulins. Describe Rhodopsin.

1. Antibodies that bind to antigens on pathogens. The immune system can produce a huge range of immunoglobulins, each with a different type of binding site, allowing specific immunity against different diseases

2. Pigment that makes the rod cells of the retina light-sensitive. It has a non-amino acid part called retinal that absorbs a photon of light, and when it happens, the rod cell sends a nerve impulse to the brain

Describe Collagen. Describe Spider silk.

1. Structural protein. It has 3 polypeptides wound together to form a rope-like conformation and it’s used in skin to prevent tearing, in bones to prevent fractures and in tendons and ligaments to give tensile strength

2. Structural protein that’s used to make webs for catching prey and lifelines on which spiders suspend themselves. It has very high tensile strength and becomes stronger when it is stretched, so resisting breakage.