Chapter 5

What are the four classes of biomolecules? What molecules are in each class?

Carbohydrates (Monosaccharide; polysaccharides), lipids (fatty acids, phospholipids, steroids, vitamins), proteins (polypeptides), nucleic acids (DNA, RNA).

What are the two types of smaller molecules that construct fats? What does the term amphipathic mean?

Glycerol and fatty acids construct fats. Glycerol is a three carbon alcohol with a hydroxyl group attached to each carbon. A fatty acid consists of a carboxyl group attached to a long hydrocarbon chain. Because of the hydrophilic nature of the carboxyl, fatty acids have two regions: a hydrophilic head and a hydrophobic tail. Therefore fatty acids are amphipathic.

What are saturated and unsaturated fatty acids?

Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds. Due to their saturation, the carbon to carbon single bonds are able to rotate, and can stack and form solids. Unsaturated fatty acids have one or more double bonds. Because of their double bonds, unsaturated fats are rigid and cannot stack like saturated fats- therefore they are liquids.

What are proteins? Why are they so important?

Proteins are chains of amino acids that function to provide structural support, storage, transport, cellular communications, movements, and defense against foreign substances. Proteins are the workhorse of the cell. The presence or absence of specific proteins determines the characteristics and functions of a cell.

What are proteins comprised of?

Proteins are comprised of C,H,N,O, and S. They are made up of polymers of different combos of 20 amino acids. These aa polymers are called polypeptides and form polypeptide chains through polypeptide bonds between amino acids.

What are the two families of nitrogenous bases?

Pyrimidines and purines are the two families of nitrogenous bases. Pyrimidines have a single six membered rings and are cytosine, thymine, and uracil. Purines have a six membered ring fused to a five membered ring and are adenine and guanine.

Where are saturated, unsaturated, and trans fats found?

Saturated fats are found in all animals, due to there natural stacking ability, a diet high in saturated fats may contribute to cardiovascular disease. Unsaturated fats are found in plants, fish, and nuts. Trans fats are produced through partial hydrogenation ( a process of converting unsaturated fats to saturated fats by adding hydrogen). Trans fats are the worst fats in terms of health. They are foreign to natural body systems, they are unsaturated fatty acids converted to trans double bonds instead of cis- causing the body to respond to them as saturated fatty acids due to their more linear structure. Trans fats raise LDL levels (bad cholesterol).

What is the most common monosaccharide? What is its formula? Draw the line and the ring structure of this monosaccharide.

The most common monosaccharide is glucose. C₆H₁₂O₆

What are the four levels of protein structure? What level must proteins have in order to function?

The primary structure of protein is the unique sequence of aa, it is a single polypeptide chain joined by polypeptide bonds. The secondary structure consists of coils and folds of the polypeptide chain and is a result of hydrogen bonds between amino groups and hydroxyl groups of aa. The two secondary structures that can be formed are the alpha helix and the beta sheet. The tertiary structure is the functional structure of proteins. All proteins have at least a tertiary structure. Tertiary structures are determined by interactions (covalent and noncovalent bonds) among various side chains. The quaternary structure is the result of multiple polypeptide chains in their tertiary structures interacting together due to covalent and noncovalent bonds between R groups.

What significance of the structure of a protein have? How is it determined?

The structure of a protein is determined by the sequence of aa, the structure of a protein determines its function.

What are aa? What are their defining characteristic factor?

aa are organic molecules that have a alpha carbon with a carboxyl group and an amino group attached. The central carbon is also attached to a side chain. The characteristics pf this side chain define the characteristics/properties of the aa.

What variations can aa have in side chain? How does this effect their behavior?

aa can have a nonpolar side chain which makes the aa more hydrophobic in contrast to the other two variations. aa can have a polar side chain with an electronegative atom attached in a functional group. The most polar and hydrophilic aa are the charged aa that have either an acid (additional carboxyl group that can then be ionized) or a base (additional amino groups that can then be ionized).

What is a condensation or dehydration reaction? Draw a dehydration reaction between two glucose molecules to form maltose.

A dehydration reaction is a reaction that bonds two monomers together through the loss of a water molecule.

What is a gene? What are nucleic acids? What is the composition of a nucleotide?

A gene is a unit of inheritance that determines the amino acid sequence of a polypeptide and thus determines all the characteristics of a cell and an organism. Nucleic acids are DNA and RNA. Nucleic acids are composed of polymers of nucleotides. A nucleotide is made up of a pentose sugar, a phosphate group, and a nitrogenous base.

What is a hydrolysis reaction? Draw the hydrolysis of maltose.

A hydrolysis reaction is a reaction that disassembles polymers through the addition of a water molecule.

What is a polymer? What is a monomers? What are the monomer and polymer groups for the four classes of macromolecules?

A polymer is a long molecule consisting of many similar building blocks; these building blocks are called monomers. Carbohydrates consist of monosaccharides (simple sugars) to form polysaccharides. Lipids consist of fatty acids that join to form fats, lipids, and membranes. Proteins consist of amino acids joined to form proteins. Nucleic acids consist of nucleotides joined to form nucleic acids.

What is ATP composed of?

ATP is a nucleotide and is Adenine triphosphate. ATP is made up of adenine, ribose, and 3 phosphate groups.

How do all aa behave in aqueous environments?

All aa are hydrophilic to some extent due to the ionization of their hydroxyl (neg charge) and amino groups (pos charge).

What do carbs serve as? What are they composed of?

Carbs are the most abundant organic compounds on earth and serve as fuel and building material. Carbs are made up of C, H, and O in a 1:2:1 ratio respectively. The simplest are monosaccharides (simple sugars) and the carb macromolecules are polysaccharides. When monosaccharides are joined; they are linked by a covalent bond referred to as a glycosidic linkage. The position of this glycosidic linkage and the monomers it is composed of determine the structure and function of the polymer.

What are carotenoids and steroids?

Carotenoids and steroids are classes of lipids with very different structures than the other lipids. Both use units of isoprene as building blocks. Carotenoids function to trap light energy; beta carotene (the precursor to vitamin a) is an important pigment in photosynthesis. Carotenoids are responsible for the pigments in many foods. Steroids function as signaling molecules; they are made up of multiple carbon rings and are important components of membrane (cholesterol). Steroids act as messengers (sex hormones) in the form of hormones.

What are chaperonins? What role do they play in the formation of functional protein structures?

Chaperonins are protein molecule that assist in the proper folding of other proteins. The aa in chaperonins interact with the polypeptide bonds in the protein to help it form its functional structure.

What is the molecular formula of ribose? What is its line and ring structures? What makes this carb different than other carbs?

C₅H₁₀O₆. Ribose is a building block of DNA and RNA. It is the only carb that is a component of nucleic acids.

What are the main distinctions between DNA and RNA?

DNA and RNA both have the same nucleotide components, however their sugars differ. DNA has no oxygen attached to its 2' carbon, making the sugar deoxyribose. RNA has an oxygen attached to that 2' carbon, making the sugar ribose. Due to this difference, the lack of the oxygen allow DNA to form a double helix and is therefore more stable than RNA. Also, RNA does not posses the nitrogenous base thymine and instead has uracil. Likewise, DNA has thymine and no uracil.

What is denaturation?

Denaturation is the disruption of chemical bonds in tertiary or quaternary structures and result in changes in protein shape as well as loss of protein function/biological activity. Change in temperature as well as changes in pH can cause a protein to become denatured. Once a protein is denatured it can (as is the case with humans) usually undergo renaturization once the conditions return to normal, and resume functioning as usual.

What are enzymes? How do they function?

Enzymes are a proteins that at as a catalyst to speed up chemical reactions. They can preform their functions repeatedly and carry out the processes of life. Enzymes work as a base to which certain monosaccharides can link to (key and lock) and form a polysaccharide. This can speed up the otherwise slow process of dehydration and hydrolysis reactions. The ending 'ase' usually identifies a protein as an enzyme.

What is the difference between an alpha monosaccharide unit and a beta monosaccharide unit? How do they differ when they are joined?

In an alpha monosaccharide unit, the C₂ hydroxyl group is below the ring plane. In a beta monosaccharide unit, the C₂ hydroxyl group is above the plane. Due to the placement of hydroxyl groups, a linkage of alpha monomers forms branched macromolecules that are not uniform. A linkage of beta monomers is uniform, and forms straight chains that are stackable. The monosaccharide units in this chain alternate in orientation.

What about the direction of each nucleotide chains differs in DNA?

In the double helix, the two backbone run in opposite 5' to 3' directions and are referred to as antiparallel.

Which class of molecules do not form polymers?

Lipids

What are lipids?

Lipids are a diverse group of hydrophobic molecules that are identified by their solubility in nonpolar solvents (usually ether or chloroform) and are composed of mainly C and H as well as a few O. The most biologically important lipids are fats, phospholipids, and steroids. Lipids function as long term energy storage, help form cellular membranes, can act as insulators and lubricators, and are important hormones.

What is a macromolecule?

Macromolecules are formed by covalent bonds between monomers and include carbs, lipids, proteins, and nucleic acids. Macromolecules have specific three dimensional shapes. Different functional groups give local sites on macromolecules specific properties. They are the most abundant of the carbon-containing molecules in a living cell; of these proteins are the most abundant followed by nucleic acids.

What is the composition of a monosaccharide? Are they hydrophilic or hydrophobic? How are monosaccharides classified?

Monosaccharides have molecular formulas in multiple of CH₂O. A hydroxyl group is bonded to each C but one. The Carbon without a hydroxyl is bonded to an O (carbonyl C). Because of the polarity present, carbs are hydrophilic. Monosaccharides are classified by the location of the carbonyl group (aldose or ketone) and the number of carbons in the carbon skeleton.

Once the polymer chain is joined via dehydration is it automatically functional? What attractions form in the chain to allow this? What type of bonds/attractions hold the chain itself together?

No, polymer chains usually must bend and twist too obtain their functional conformation. The polymer chain is held together by covalent bonds; the shape is created due to hydrogen bonds between the hydroxyl groups and hydrogens, as well as disulfide bridges formed by sulfhydryl groups, and ionic compounds found on some monomers. These non-covalent bonds also allow macromolecules to bind to or interact with other molecules.

How are nucleotide chains directional?

Nucleotide chains always have a 5' end with a free phosphate group and a 3' end with a free hydroxyl group. Nucleotide sequences are therefore always read form 5' to 3'.

What covalent bond joins nucleotides to form nucleic acids?

Phophodiester linkages join nucleotides to form nucleic acids. These linkages occur between the phosphate of one nucleotide and the 3' hydroxyl group of the sugar of another nucleotide. This phosphate-sugar bonding pattern forms the sugar-phosphate backbone and nitrogenous appendages of DNA and RNA.

What are phospholipids? How do they respond to aqueous environments?

Phospholipids are the major components of all cell membranes, in a phospholipids two fatty acids are attached to a glycerol which is attached to a phosphate group. The fatty acid tails are hydrophobic while the attachments form a hydrophilic head. Thus when they encounter water, they form a bilayer- the tails congregate in the middle while the head face the water molecules. This structure of phospholipids results in the bilayer arrangement in cell membranes. Micelles are a ball of phospholipids with the tails in the center.

How do aa join?

Polypeptide bonds join aa to form polypeptide chains. These bonds form from a dehydration reaction between the hydroxyl of the carboxyl group and the amino group of two aa.

What are the storage polysaccharides of plants? ...animals? How do they differ in composition and placement? How is this energy accessed?

Starch is the storage polysaccharide of plants and consists of glucose monomers. These monomers at joined by beta linkages and are therefore rigid and can stack. The polysaccharide cellulose is a major component of the tough wall of plant cells. Plants store surplus starch as granule within chloroplasts and other plastids. Glucose is stored as amylose or amylopectin. Glycogen is the storage polysaccharide on animals. The monosaccharides are joined by alpha linkage and are therefore helical (branched). Glycogen is stored in the liver and muscle cells. The energy in the polysaccharide is assessed through the breakdown into units of glucose through hydrolysis. The enzyme that hydrolysizes amylose cannot hydrolysize glycogen due to the difference in linkages.

How does the double helix of DNA form?

The double helix of DNA forms as a result of hydrogen bonding between the bases on two different strands of DNA. The hydrogen bonds between the sugar-phosphate backbones create the coil of the double-helix. In the helix, certain nitrogenous bases only interact with certain nitrogenous bases. A pyrimidine and a purine always interact. Adenine interacts with thymine(2 H bonds),guanine interacts with cytosine (3 H bonds).

What is triacylglycerol?

Triacylglycerol is three fatty acids joined to a glycerol by as ester linkage.

When two glucose molecules undergo dehydration, what is formed? When a glucose ad a fructose molecule undergo dehydration, what is formed?

Two glucose molecules for a maltose molecule. A glucose and a fructose molecule form a sucrose molecule.

When a protein's structure changes what occurs?

When a protein's structure changes, its ability to function is affected and can result in disease and could lead to death of certain tissues.