Intro Biochemistry MCELLBIX105-025 M2 Final Prep M2

The base sequence of DNA, as written by convention, is in the _______________ direction.

5' to 3' direction

_______________: A transient copy of genetic information.

RNA

What charged group(s) are present in glycine at a pH of 7?

NH3+ and COO-

Cholesterol

modulates membrane fluidity and structure.

_______________ is a simple motif of RNA structure.

stem loop

What is the complementary DNA sequence for 5′-GACTCTTGGTAT-3′?

5′-ATACCAAGAGTC-3′

What is the H+ concentration in a urine sample that has a pH of 7.2?

6.3 x 10-8 M

According to convention, ____________ is the terminus drawn on the left side of a peptide.

Amino

______________ enhance the rate of a chemical reaction without themselves being permanently altered.

Catalysts

____________: Thermodynamic force that drives hydrophobic interactions.

Entropy

____________: An amino acid that must be supplied by the diet.

Essential

____________ is a test solution used to identify reducing and nonreducing sugars.

Fehling's

Discuss whether Crick intended the Central Dogma to be a positive hypothesis describing how a process is done or a hypothesis ruling out a process.

Francis Crick asserts in his 1970 publication in Nature that the Central Dogma was intended as a negative hypothesis or how information transfer should not occur, and therefore validating how it ought to occur. Crick puts forward that the general assumption among scientists, as evidenced by initial testing was that information flowed from DNA to RNA to proteins; the Central Dogma however, he stresses is a null hypothesis stating that "once (sequential) information has passed into a protein, it cannot get out again." (Crick, 1970) In this way, the Central Dogma as Crick intended, was a way to rule out impossibilities of information flow in the cell (from proteins back to RNA or DNA, or from DNA directly to protein synthesis), to strengthen the arguments of general information flow from DNA to RNA to proteins.

Describe the three classifications of information transfers Crick proposes

Francis Crick clarified his central dogma by presenting three classifications of information transfer in his 1970 Nature publication. The first category is transfers that are general to all cells (represented by solid arrows in his diagram); these are DNA replication, DNA transcription to RNA, and RNA translation to proteins. The second category was information transfers that are specialized (such as in the case of RNA viruses), and represented by the dashed arrows, including RNA replication, RNA back translating to DNA, and DNA directly synthesizing proteins (which Crick was dubious of due to the weak evidence for). Finally, the third category was information transfers that not possible within the schema of the Central Dogma, and included any information replication or transfers from protein to RNA or DNA.

____________: The storage form of glucose in animals.

Glycogen

___________: Chiral type of amino acids found in proteins.

L-amino acids

List atoms commonly found in biological molecules that are often hydrogen-bond acceptors.

Oxygen, Nitrogen, Flourine

Which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein?

Phenylalanine

____________: This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.

Proline

What amino acids are not found in a-helices?

Proline and Glycine

The plot that allows one to investigate the likely orientation of certain amino acid pairs is called the ____________.

Ramachandran

Changes in ____________ create amyloid fibers which are insoluble and are the source of mad cow disease, and Alzheimer's, and Parkinson's diseases.

Secondary structure

high molecular weight polymers of glucose that serve as the primary storage molecule for glucose in cells

Starches

The axis of a double helix can be over-wound by a mechanism called ____________________.

Supercoiling

The overall structure of an individual protein is referred to as ____________.

Tertiary structure

Central Dogma

The Central Dogma is a biological hypothesis explaining the flow of information in the cell from our DNA to RNA to proteins. In essence of the Central Dogma describes three main information transfer processes: a. Replication of that DNA via DNA polymerase, b. transcription of DNA to RNA (messenger RNA to be specific) via RNA polymerase, and c. translation of RNA to proteins via ribosomes.

Hair can be reshaped into curls or straightened in a process called "perming". One way this is done is by treating hair with a chemical called ammonium thioglycolate, which is a reducing agent, followed by wrapping the the hair around a curler or ironed out straight by flatirons. After the hair has been reshaped it is treated with an oxidizing agent to stabilize the new shape. What amino acids are these chemical treatments affecting and how do they allow hair to be reshaped?

The amino acids that are affected by the perming process are Cystienes, which have the tendency to oxidize (loose an electron) and create thiols or sulfur bridges between neighboring cysteine amino acids. This creates rigid folding of proteins (reinforced by sulfur bridges) that are now called Cystines, and in hair (which contains keratin proteins with cysteines), this results in a certain shape such as curly or kinked or straight. When the chemical (a reducing agent) and heat are applied to the hair, this breaks the sulfur bridges and then re-oxidizes the amino acids into the desired form (i.e. the hair straightens).

Describe the relationship between fatty acid chain length, saturation, and the melting point or fluidity of fatty acids

The melting point (and therefore fluidity) of a fatty acid chain is dependent on the fatty acid chain length, and the level of unsaturation. As the level of unsaturation (as the number of double bonds in the chain increases from unsaturated to polyunsaturated), the melting point decreases. This is due to the tight stacking of chains due to van der Walls forces in saturated fats vs. the bends from double bonds making those tight interactions weaken. Therefore, a vegetable oil such as oleic acid will be fluid at room temperature, whereas a saturated (single bond chain) fatty acid will be solid until heated to it's (higher) melting temp. By a similar token, the shorter the fatty acid chain, the lower the melting point, again due to limited van der Walls interactions with shorter chain length.

The distance when two atoms no longer repulse each other yet have the strongest attraction is known as the____________ radii or contact distance.

Van der Waals

___________: Another name for dipolar ions.

Zwitterions

Replication, DNA polymerase

_______________ is the generation of two daughter double helices from a single parent double helix. The process is catalyzed by____________.

____________ is a flat polycylic molecule that is absent in prokaryotic membranes.

cholesterol

____________: Monosaccharides that differ at a single asymmetric carbon.

epimers

Electrostatic interactions between atoms with opposite electrical charges are also called ____________.

ionic bonds

____________ are proteins that bind to specific carbohydrate structures.

lectins

____________: The charge of an amino group when the pH is one pH unit below the pKa.

positive

____________: The type of structure to which α helices, β sheets, and turns are referred.

secondary structure

The configuration of most α-carbon atoms of amino acids linked in a peptide bond is:

trans

The transfer of information from DNA to RNA is called ____________.

transcription

Glycolipids

used in cell signaling, outside of cell membrane