Set 3 - Organic Molecules of Life - Bio 100

What is an organic molecule?

An organic molecule is a molecule containing carbon.

Technically, they are molecules with a backbone of carbon and hydrogen (so carbon dioxide would not be considered organic), but for our purposes, we will just say the carbon-containing molecules are organic.

What are the four important groups of organic biological molecules we studied in class?

~ Carbohydrates

~ Proteins

~ Nucleic Acids (DNA and RNA)

~ Lipids

Which of the four major organic biomolecules is/are hydrophilic (polar), meaning they dissolve well in water?

Which is/are hydrophobic (nonpolar), meaning they do not dissolve well in water?

Carbohydrates, Proteins and Nucleic Acids are all hydrophilic (polar).

Lipids are hydrophobic (nonpolar)

Which of the four organic biomolecules is/are capable of forming large polymers, which are long strings of repeating units of single molecular units (monomers)?

Which one(s) only exist in single molecule form (as stand-alone molecules)?

Carbohydrates, Proteins and Nucleic Acids are all capable of forming polymers from individual monomer units.

Lipids are stand-alone molecules; they do not form polymers (although fats and phospholipids do have individual parts that connect to form the final molecule).

What does the word, "monomer" mean?

What does the word, "polymer" mean?

mono = one or single

poly = many

mer = part or unit

So monomer = single part (or single unit) and polymer = many parts (or many units)

Linking monomers together to form a dimer (or a polymer) is done by _______ (adding/removing) a molecule of __________ from the two molecules.

This process is called _____________.

This is a(n) _____________ (catabolic/anabolic) reaction.

Linking monomers together to form a dimer (or a polymer) is done by removing a molecule of water from the two molecules.

This process is called dehydration synthesis.

This is an anabolic reaction.

Digesting a polymer into monomers (or removing a single monomer from a larger macromolecule) is done by _________ (adding/removing) a molecule of __________ to the two molecules.

This process is called _____________.

This is a(n) _____________ (catabolic/anabolic) reaction.

Digesting a polymer into monomers (or removing a single monomer from a larger macromolecule) is done by adding a molecule of water to the two molecules.

This process is called hydrolysis.

This is an catabolic reaction.

How many molecules of water would need to be removed to synthesize a molecule of 4 repeating units? (a tetramer)

3 water molecules

Monomers for carbohydrates are called __________.

monosaccharides

What is the chemical formula of a monosaccharide?

(CH2O)n where n = 3-8

The most common monosaccharide, glucose, has what chemical formula?

There are actually a couple of other monosaccharides with this chemical formula. How can that be?

Name two that we looked at.

C6H12O6 is the chemical formula for glucose.

It is also the chemical formula for fructose and galactose!

This can occur by using the same atoms and rearranging them differently around the carbon backbone.

What is the main function of monosaccharides, particularly glucose?

very rapid source of fuel

Do monosaccharides have to be digested before they are absorbed into your bloodstream?

No, monosaccharides do not require digestion - they can be immediately absorbed into the bloodstream and it only takes about 10 minutes to feel "effect".

Besides being an immediate source of fuel, what other function do monosaccharides have?

Monosaccharides can be used to synthesize other important nutrients such as amino acids and fatty acids (we can also convert other monosaccharide to glucose).

Two monosaccharides bonded together is called a _____________.

Provide three examples that we studied in class.

disaccharide

maltose, lactose, and sucrose

If you link two glucose molecules together through dehydration synthesis, you end up with the disaccharide, ___________. This disaccharide is found in milkshakes and beer.

maltose

The sugar found in mammalian milk is a disaccharide comprised of glucose and galactose. What is it called?

lactose

In order to digest lactose into glucose and galactose fast enough to absorb it into your bloodstream, you need a molecule called a(n) ___________.

The name of the molecule in this specific case is called ___________.

enzyme

lactase

Those individuals who do not make lactase are lactose ____________. What happens to the lactose that they consume?

intolerant

When lactose intolerant individuals consume lactose, it is NOT digested into monosaccharides, and is NOT absorbed into the bloodstream by the digestive system. It therefore continues to travel within the digestive system to the colon, where it is broken down by bacteria that live there. It is eventually pooped out, and does not provide the individual with any nutrition.

Why do individuals with lactose intolerance have terrible digestive problems when they eat large amounts of food containing lactose?

Since the lactose cannot be absorbed by our bloodstream, it remains intact until it gets to our colon where we have tons of bacteria that CAN digest the lactose. The by-products of this digestion cause gas, bloating, diarrhea and other digestive issues. Sad.

Is table sugar a monosaccharide, disaccharide or polysaccharide? What is its official name?

Table sugar is a disaccharide called sucrose (it contains glucose and fructose).

If you are feeling light-headed because are blood sugar is low, which is better to consume, glucose, table sugar, or a polymer of glucose to get fuel as QUICKLY as possible to your cells?

You would want to consume a source of pure glucose (hard candy, for example) because it does not require digestion and can be IMMEDIATELY absorbed into the bloodstream to supply fuel to your cells. Table sugar is a disaccharide, which would take a little longer to get into your bloodstream (it must be digested first), and a polymer of glucose would also take some time because you would need to digest individual glucose monomers off the polymer to get absorption.

Carbohydrates that contain only one monosaccharide or a couple of monosaccharides linked together are called ________ sugars, while carbohydrates that contain many monosaccharides linked together are called ________ sugars. These are also known as ____________.

simple, complex, polysaccharides

There are four important polysaccharides that we encounter in biology, each of which is a polymer made of one monosaccharide. Which monosaccharide? _________ What are the names of these four polysaccharides?

glucose

starch, glycogen, cellulose, and chitin

Both plants and animals store a polymer of glucose as fuel for later usage. These polymers can be broken down by hydrolysis, releasing monosaccharides for a more sustained level of fuel. What is the polysaccharide used by plants for fuel storage? What is the polysaccharide used by animals for fuel storage? Can we fully digest these molecules?

Plants store excess glucose as a polysaccharide called starch.

Animals store excess glucose as a polysaccharide called glycogen.

Yes, we can fully digest these two molecules!

Which two organs/tissues do we store most of our glycogen?

The liver - we store glycogen in the liver so that when our blood glucose goes too low, the liver can break down the glycogen to glucose and send the glucose to the bloodstream for the entire body.

The muscles - we also store glycogen in our muscles because our muscles need energy to contract. The muscles break down the glycogen to glucose to provide the energy to contract, but it doesn't release the glucose to the bloodstream - it keeps it for itself (selfish muscles!)

Polysaccharides often play a structural role in certain organisms. Which polysaccharide is the main component of cell walls in plants? ____________

cellulose

Plants have rigid cell walls surrounding their cell membranes. Do animal cells also have cell walls?

Besides protection, what is the benefit of having a cell wall in plant cells? (think water)

Animal cells do not have cell walls surrounding their cell membranes, like plant cells.

The benefit of a cell wall is that it allows the plant to take up a lot of water without exploding. Animal cells will explode when put in pure water.

Note: Fungi and bacteria have cell walls, but their walls are made of a different polysaccharide. I will NOT ask you this on an exam!

Can humans digest cellulose? Why or why not? What is the enzyme that digests cellulose called?

No, humans cannot digest cellulose because we do not produce the enzyme required to digest it.

The enzyme that digests cellulose is called cellulase.

Which types of organisms can digest cellulose? Why are they able to do so?

Herbivores like cows, horses, sheep, goats can digest cellulose, and termites! They are able to digest it because they have bacteria in their guts that produce the enzyme that digests cellulose! These animals do NOT make cellulase themselves (they rely on the bacteria).

The general term for a relationship or interaction between two different organisms living close together is ______________.

symbiosis

In which type of symbiosis do both the "visitor" and "host" benefit?

mutualism

In which type of symbiosis do we see the "visitor" benefiting and the "host" not affected either negatively or positively (and sometimes does not even know the visitor is there)?

commensalism

In which type of symbiosis do we see the "visitor" benefiting and the "host" being harmed?

parasitism

Which type of symbiosis, mutualism, commensalism, or parasitism is occurring with the cow and the bacteria that lived inside it and digests its cellulose? Why?

This is an example of mutualism, where both organisms are benefiting. The cow benefits because it can now get nutrition from grass, which is mostly cellulose, due to harboring the bacteria that digests the cellulose for the cow. The bacteria benefits because it doesn't have to hunt for food (the cow consumes the grass for the bacteria), and the bacteria is protected in the nice, cozy, warm stomach of the cow. :-)

If you want to include more fiber in your diet, you would want to eat more:

A) meat

B) plant-based food

C) fish

D) dairy products

e) eggs

plant-based food (more cellulose in the plant cell walls that is not digested)

What specific group of organisms (Phylum) have both jointed feet and an exoskeleton?

Arthropods, have jointed feet and also an exoskeleton.

The Arthropods include insects, arachnids (like spiders and ticks) and crustaceans (like lobsters, crabs and shrimp)

The exoskeleton of arthropods is made of a polysaccharide called ________. Can we digest this polysaccharide? Why or why not?

chitin

No, we cannot digest chitin because we do not have an enzyme to facilitate its digestion.

Of the four types of biological molecules we are examining (carbohydrates, proteins, nucleic acids, and lipids), which of the four are the "workhorses" of the cell? In other words, which group of molecules do most of the work in our cells?

proteins

What type of protein catalyzes, or speeds up, chemical reactions? These molecules are usually _________ (not very/highly) specific for the reaction they catalyze.

enzymes

Enzymes are usually highly specific for the reaction they catalyze.

Enzymes have a 3-dimensional "pocket" within their structure where the reactant molecule (also known as a substrate) binds. This pocket is called the ______________.

active site

What are the monomers (building blocks) that make up proteins called?

amino acids

How many amino acids are there (that are put in our proteins)?

20

All amino acids look exactly the same except for their _____________

side chain (symbolized with "R")

The central carbon of an amino acid will attach to four parts: a hydrogen, the side chain, a(n) ________ group, and a(n) ________ group. What do these two groups look like?

amino group and a carboxyl group

The amino group contains a nitrogen with two or 3 hydrogens attached, depending on the pH (NH2 or NH3+), and the carboxyl group contains a carbon with a double bond to oxygen, and a bond to oxygen and hydrogen, or just oxygen, depending on the pH (OH or O-)

A side chain that consists of all carbon and hydrogen would be a ____________ (polar/nonpolar) side chain. This would make this side chain __________ (hydrophobic/hydrophilic).

nonpolar

This would make this side chain hydrophobic.

This is because carbon and hydrogen always form nonpolar bonds with each other because they have very close electronegativity values.

Which amino acids are negatively charged at pH 7?

Which amino acids are positively charged at pH 7?

At pH 7, aspartic acid and glutamic acid are negatively charged.

At pH 7, lysine, arginine, and histidine are positively charged.

What would be the overall charge of the following peptide at pH 7?

Glycine-Aspartic Acid-Leucine-Proline-Lysine-Serine-Cysteine-Arginine

+1

aspartic acid provides -1 charge, lysine and arginine each provide +1 charge, and the amino terminus (NH3+) and carboxyl terminus (COO-) cancel out.

The bond that is formed between two amino acids is called a _________ bond. This bond forms through the _________ of water, also known as ____________.

peptide

removal

dehydration synthesis

The function of every protein is different. This function is dependent on the protein's overall _________.

shape

Proteins come in two general types of shapes: __________ proteins and ___________ proteins.

globular (kind of "blob"-like), fibrous (string, or rope-like)

What is the primary structure of a protein?

It's the linear amino acid sequence of a protein (one amino acid written after another, in order).

What actually determines the primary structure of a protein

The specific sequence of nucleotides in a gene determines the primary structure of the protein the gene is coding for.

What is the secondary structure of a protein? What are the two types of secondary structure called, and what type of interaction between atoms causes this secondary structure to form?

Secondary structure is regular, patterned folding of a protein due to interaction between the backbone atoms of the polypeptide.

The two types of secondary structure are the alpha helix and the beta pleated sheet. The backbone atoms of the polypeptide interact through hydrogen bonding (oxygen of the former carboxyl group (it is now a carbonyl group) and hydrogen of the amino group in the peptide backbone).

What is the tertiary structure of a protein?

Tertiary structure is the irregular, non-patterned folding that ultimately provides a protein with its overall shape. It is due to the interaction of the atoms in the side chains of amino acids that come close together when the protein is folding.

What are four types of interactions that can form to create this tertiary structure? (Don't have to include Van der Waals, but that's another one)

Hydrogen bonding between side chains that have polar oxygen, nitrogen and hydrogen atoms.

Ionic bonding between positively and negatively charged amino acid side chains.

Hydrophobic interactions between nonpolar amino acid side chains.

Disulfide bonds between two cysteines that are close together as a protein undergoes folding under specific conditions.

Of the four types of side chain interactions that can occurs, which is the strongest? Which is/are covalent?

The strongest interaction is the disulfide bond, and it is the ONLY interaction of the four types that is covalent. In fact, a disulfide bond, like other covalent bonds (like peptide bonds), is not broken when you boil a protein!

Under what conditions can a disulfide bond form?

A disulfide bond can form if two cysteine side chains come close together under conditions that are oxidizing (there is either a lot of oxygen to accept the two hydrogens/electrons from the two cysteines, or other molecules that are electron acceptors). This is required so that the two cysteines can each donate a hydrogen (with its electron) to the electron acceptor which will allow a new covalent bond to form between the sulfur atoms of the cysteines.

Would the following amino acid side chains likely interact when close to each other in a folded protein? If so, what type of interaction would most likely occur between them? If not, why not?

-CH2-OH (Serine) and -CH2-C6H4-OH (Tyrosine)

(Look up structures if you want - I would give you them on an exam)

Yes, they would likely interact.

They would most likely interact by forming a hydrogen bond through the hydroxyl groups found at the end of each.

Would the following amino acid side chains likely interact when close to each other in a folded protein? If so, what type of interaction would most likely occur between them? If not, why not?

-CH2-COO- (that's negatively charged) and -CH2CH2CH2CH2NH3+

(Aspartic Acid) (Lysine)

(Look up structures if you want - I would give you them on an exam)

Yes, they would likely interact.

They would most likely interact by forming an ionic bond between the negatively charged oxygen on Aspartic Acid and the positively charged nitrogen on the Lysine.

Would the following amino acid side chains likely interact when close to each other in a folded protein? If so, what type of interaction would most likely occur between them? If not, why not?

-CH3 (Alanine) and -CH(CH3)2 (Valine)

(Look up structures if you want - I would give you them on an exam)

Yes, they would likely interact.

Both of these side chains are hydrocarbon, so very nonpolar. That means they would both like to get away from water and likely be buried in the folded protein. They would be attracted to each other through hydrophobic interactions (which we talked about), which occurs due to trying to get away from water, and the force that would keep these side chains attracted to each other would be Van der Waals forces (which we did NOT discuss, so just know hydrophobic interactions). Please note that the forces that keep nonpolar amino acid side chains interacting with each other are NOT covalent (and they are relatively weak).

Would the following amino acid side chains likely interact when close to each other in a folded protein? If so, what type of interaction would most likely occur between them? If not, why not?

-CH(CH₃)CH₂CH₃ (Isoleucine) and −CH2CONH2 (Asparagine)

(Look up structures if you want - I would give you them on an exam)

NO, these two amino acid side chains would NOT likely interact as is very nonpolar and all hydrocarbon (isoleucine), and the other is rather polar, with both oxygen ad nitrogen present (asparagine). They hate each other. :-)

What is the quaternary structure of a protein? What types of interactions result in quaternary structure? Do all proteins contain quaternary structure?

Quaternary structure is the interaction of multiple polypeptides to form a multi-subunit protein. The interactions between polypeptides can be through hydrogen bonding, ionic bonding, hydrophobic interactions and/or disulfide bonds.

No, not all proteins contain quaternary structure. In fact, most do not.

If a protein does not fold properly, will it be functional? What do we call a protein that is either unfolded or malfolded?

No, proteins that do not fold properly are not functional. When a protein is unfolded or malfolded we say it is a denatured protein.

When a protein denatures, it will generally expose certain types of amino acids that were normally buried in the folded protein. What types of side chains do these newly exposed amino acids contain? (i.e. polar uncharged, polar charged, or nonpolar)

As a protein unfolds and becomes denatured, nonpolar amino acids that were normally buried (to get away from the aqueous solvent) become exposed to water, which makes them VERY unhappy.

As these amino acid sides chains in an unfolded protein become exposed to water, what do they do?

The exposed nonpolar side chains hate water, so they will tend to aggregate with other exposed nonpolar amino acids by forming hydrophobic interactions. These aggregations tend to form precipitates.

Who received the Nobel Prize for his work in determining that the all of the information required for a protein to fold into its 3-D shape is found in the amino acid sequence? [The primary structure (amino acid sequence) of a protein determines its tertiary structure (overall shape)]

Christian Anfinsen

What protein did Anfinsen use in his work on the mechanism of protein folding? Why didn't this protein easily denature when it was boiled?

RNase

The protein didn't easily denature because aside from being small, it has four disulfide bonds that are resistant to boiling, keeping the protein stable.

In order to denature RNase, you have to add a reversible denaturing agent (a chemical that can be removed) AND what else?

A reducing agent to reduce the four disulfide bonds.

If a protein becomes unfolded by some sort of stress to the cell (like higher than normal temperatures, radiation or oxidative stress), a group of proteins called _________________ can often assist in the refolding of the denatured protein.

Chaperones (or chaperonins)

DNA and RNA are polymers called ____________.

nucleic acids

The monomers for nucleic acids are called ___________.

nucleotides

What are the three parts of a nucleotide? Which of the three parts gives the nucleotide its variety (the "flavor")?

Every nucleotide has a:

~ 5-carbon sugar

~ phosphate group

~ nitrogenous base

The nitrogenous base is where the nucleotide gets its variety, as there are four possible bases in DNA, and four possible bases in RNA.

What is the name of the 5-carbon sugar that DNA uses?

deoxyribose

What are the names of the four nitrogenous bases that DNA uses?

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

What is the shape of DNA?

DNA exists as two polynucleotide strands wrapped around each other in a double helix.

What is the name of the covalent bond that connects individual nucleotides in a single polynucleotide strand of DNA or RNA?

Phosphodiester bond

If you are give the sequence of one of the strands of DNA, can you predict the sequence of the other strand? Why or why not?

Yes, you can predict the other strand's sequence because there are specific base-pairing rules.

For example, if one strand has an "A", on the opposite strand you will find a "T", and vice versa.

The base-pairing rules are:

A-T

C-G

The two strands of a double helix connect to each other through weak bonds between the complementary bases on each strand. What type of weak bonds connect the two strands?

hydrogen bonds

When DNA replicates, we start with one parent DNA molecule and end up with two identical daughter molecules that replace the parent. Briefly describe how this occurs.

The parent DNA molecule is unwound and each strand acts as a template for new DNA synthesis. Then the appropriate nucleotide, one-by-one, is added to the growing polynucleotide chain of the new strand. An enzyme knows which nucleotide to use because it is guided by the opposite strand template and the base-pairing rules.

Ribonucleic acid (RNA) is a molecule that is similar to DNA. What is the 5-carbon sugar used by RNA?

ribose

RNA uses four specific nitrogenous bases, three of which are the same ones used by DNA. What are the four, and which of the four is different from that used in DNA?

Adenine (A)

Guanine (G)

Cytosine (C)

Uracil (U)

Uracil is the one that differs. It replaces the Thymine (T) found in DNA. So wherever you WOULD have put a Thymine in a strand (if it was DNA), you instead put a Uracil in when you are making RNA.

DNA exists as a double-stranded molecule, wrapped in a helix. How many strands is an RNA molecule?

RNA exists as a single-stranded molecule.

How do the 5-carbon sugars differ in DNA and RNA? Where, specifically, does this difference occur?

The sugar in DNA, deoxyribose, has one LESS oxygen than the sugar in RNA, called ribose.

Specifically, the 2' carbon of deoxyribose has only hydrogen attached, while the 2' carbon of ribose has a hydrogen and an oxygen attached.

Which of the nitrogenous bases in DNA and RNA are purines? Are they single or double-ringed structures?

Which of the nitrogenous bases in DNA and RNA are pyrimidines? Are they single or double-ringed structures?

The purines are double-ringed structures, and they include Adenine and Guanine.

The pyrimidines are single-ringed structures, and they include Cytosine, Uracil (in RNA), and Thymine (in DNA).

In what location do we find DNA in a prokaryotic (bacterial) cell? In what location do we find DNA in a eukaryotic cell?

DNA is found in the cytoplasm of a prokaryotic cell!

Remember, there are NO ORGANELLES in a prokaryote!

Everything is in the cytoplasm!!

DNA is found in the nucleus of a eukaryotic cell!

The first thing that happens when a gene is expressed is that the DNA from that gene is _________ into a single-stranded copy of _________.

transcribed

RNA (specifically, mRNA)

Where in the cell does transcription occur in eukaryotes?

the nucleus

The decoding of messenger RNA (mRNA) into protein is facilitated by a huge enzyme complex called a ____________. This decoding is called _________________.

ribosome

translation

Where in the cell does this mRNA decoding take place in eukaryotes?

the cytoplasm

The ribosome is the "machine" that synthesizes proteins by adding _________ (the building blocks of proteins), one by one, to a growing polypeptide chain. The bonds it forms between these building blocks are called _________ bonds.

amino acids

peptide

How many mRNA nucleotides code for an amino acid? _______

3

When the sequence of DNA is changed in some way, we call the change a _____________.

mutation

Lipids are different from the other organic biomolecules we studied in a couple of ways. One difference is that ______ (do/do not) form polymers. Another difference is that they ______ (do/do not) dissolve in water, meaning they are ___________ molecules.

Lipids are different from the other organic biomolecules we studied in a couple of ways. One difference is that do not form polymers. Another difference is that they do not dissolve in water, meaning they are hydrophobic (nonpolar) molecules.

The three types of lipids we are studying are _________, _________, and _________.

fats, cholesterol, and phospholipids

Note: only fats will be on the first exam! Cholesterol and phospholipids will be covered on the second exam!

Fat has a number of important functions in our body (even though we hate it). What are some of the important roles of fat in our body?

~ It is a very high energy storage molecule

~ It provides insulation that protects our organs

~ It provides an insulating layer to keep up warm

Athough fat molecules do not combine together to form polymers, in order to make an individual fat molecule, dehydration synthesis has to occur using 1 ___________ molecule and 3 ___________ molecules

A fat is made using 1 glycerol molecule and 3 fatty acid molecules.

The covalent linkages between glycerol and each of the fatty acids to form a fat are called _____________ linkages.

ester

What is the difference, structurally, between a saturated fat and an unsaturated fat? What is a monounsaturated fat? A polyunsaturated fat?

Saturated Fat: No double bonds between any of the carbons in the fatty acid chains (saturated with maximum hydrogen)

Unsaturated Fat: One or more double bonds between the carbons in the fatty acid chains

Monounsaturated Fat: only one double bond between the carbons in the fatty acid chains

Polyunsaturated Fat: more than 1 double bond between the carbons in the fatty acid chains

Most saturated fats are ___________ (solid/liquid) at room temperature, while most unsaturated fats are ____________ at room temperature (solid/liquid).

saturated = solid

unsaturated = liquid