Exam 5

Question 1

Initiator proteins and Helicase

Answer 1

The initial proteins in T-A regions that bind to DNA so helicase can also bind and break the hydrogen bonds between two nucleotides.

Question 2

Primase

Answer 2

Adds RNA primers as a starting point for new strands of DNA

Question 3

Single strand binding proteins

Answer 3

Holds single strands of DNA apart to prevent the DNA from rebinding to each other.

Question 4

Sliding clamp

Answer 4

Assists in holding polymerase III to the template strand of DNA

Question 5

Clamp Loader

Answer 5

Loads the sliding clamp onto DNA template strands and connects the polymerase III of the lagging and leading strands together

Question 6

Polymerase III

Answer 6

Bonds new nucleotides forming new phosphodiester bonds with the free hydroxyl group of growing strands of new DNA.

Question 7

Polymerase I

Answer 7

Removes the RNA primers that assisted in DNA replication and adds DNA nucleotides, creating phosphodiester bonds

Question 8

Ligase

Answer 8

Forms new phosphodiester bonds where new nucleotides have been placed (gaps where primer was removed, sections in circular DNA where the lagging and leading strands connect, etc).

Question 9

Explain the fundamental principles of base pairing in DNA replication

Answer 9

One purine is bonded with one pyrimidine and the nucleotide placed should match the correct number of hydrogen bonds possible. For example, A-T can create two hydrogen bonds and C-G as they can create three hydrogen bonds. Adenine and guanine are purines and cytosine, thymine and uracil are pyrimidines

Question 10

Identify and describe the origin of replication and the formation of replication forks including how the replication process proceeds bidirectionally from the origin, leading to the synthesis of leading and lagging strands.

Distinguish between the synthesis of the leading and lagging strands during DNA replication

Answer 10

The origin of replication is a region thick of thymine nucleotides bonded to adenine as they contain only two hydrogen bonds and are easier to break apart. As this section of DNA is broken apart by helicase, a small bubble forms and single stranded binding proteins hold individual strands apart to prevent rebinding. This allows helicases to continue unzipping and breaking the hydrogen bonds of DNA in two different directions. This allows forms two replication forks in each direction of the original bubble. The strands that form, the leading strands, oriented 5’ to 3’ ends, are ones that are replicated continuously with polymerase III. The lagging strands, oriented 3’ to 5’, are replicated in discontinuous jumps with polymerase III as the enzyme can only add new nucleotides to existing free hydroxyl groups on the 3’ end.

Question 11

Outer membrane of the mitochondrion

Answer 11

A membrane that contains large porins or transport channels

Pyruvate enters the mitochondria through porins

Question 12

Intermembrane space of the mitochondrion

Answer 12

The space between the two membranes that contains enzymes capable of phosphorylation

Question 13

Inner membrane of the mitochondrion

Answer 13

Numerous cristae folds that contain proteins for oxidative phosphorylation (ETC, ATPase) as well as transport proteins

Pyruvate is transported through the membrane by mitochondrial pyruvate carrier

Question 14

Matrix of the mitochondrion

Answer 14

The space that contains highly concentrated mixture of 100’s of enzymes required for oxidation of pyruvate and fatty acids of the CAC

Pyruvate is converted into fatty acids and acetyl CoA with pyruvate hydrogenase

Citric Acid Cycle occurs here

Question 15

Understand the citric acid cycle’s role in cellular metabolism, including its major inputs and outputs.

Answer 15

Requires two acetyl CoA

Provides 6 NAHD, 2 GTP, 4 CO2 and 2 FADH

Question 16

Master the mechanics of the electron transport chain, recognizing its critical role in cellular respiration as it facilitates the transfer of electrons to generate a proton gradient

Answer 16

Electron carriers such as FADH2 and NAHD provide electrons to the electron transport chain, a series of protein complexes in the inner mitochondrial membrane. This charges the membrane as protons (H+ ions) are pumped into the intermembrane space, creating a proton gradient. At the end of the electron transport chain, an electron bonds with a proton and oxygen to form H2O.

Question 17

ATP synthesis based off the ETC

Answer 17

Protons were pumped out of the mitochondrial matrix and into the intermembrane space by the electron transport chain which created an electrochemical gradient. Hydrogens in the intermembrane space want to move down their chemical gradients and inter the matrix.

This movement is couple with the ATP synthase protein which uses this flow of hydrogens to power the motor of ATPase. This provides the energy to phosphorylate ADP to ATP as conformation changes are made to ADP with the center shaft rotation of ATP synthase. ATP is made in the matrix.

Question 18

Elucidate the mechanism by which ATP synthase harnesses the proton gradient established by the electron transport chain to synthesize ATP, emphasizing the enzyme’s role in converting electrochemical energy into the cellular energy currency.

Answer 18

H+ ions or protons flow from high to low gradients through the rotor subunit (F0) of ATP synthase in the inner membrane to the matrix. This charges the motor and allows the center shaft (F1) of the protein to rotate. ADP and inorganic phosphate bind to the enzyme causing conformational changes bringing them closer that allow them to be phosphorylated, creating ATP. As a result ATP synthase converts electrochemical energy from the chemical gradient in the form of ions into chemical energy, or ATP.

Question 19

Articulate the quantity of ATP produced from a single glucose molecule through the stages of cellular respiration, detailing the contributions of glycolysis, the citric acid cycle, the electron transport chain, and chemiosmosis to the overall energy yield.

Answer 19

Glycolysis: 2 ATP, 2 NADH (3 ATP)

Pyruvate Oxidation: 2 NADH (5 ATP)

Citric Acid Cycle: 6 NADH (15 ATP), 2 FADH2 (3 ATP), 2 GTP (2 ATP)

Question 20

nitrogenous bases

Answer 20

molecules that contain nitrogen and have the chemical properties of a base that are the building blocks for RNA and DNA nucleotides

they are categorized into either purines (two ring structures) or pyrimidines (one ring structure

Question 21

pentose sugars

Answer 21

five-carbon ringed sugars with either two hydroxyl groups (ribose) or one hydroxyl group (deoxyribose) that forms the sugar background of DNA.

Question 22

phosphate groups

Answer 22

act as the building blocks for the backbone of the molecule, connecting the sugar molecules of each nucleotide together (sugar-phosphate backbone)

Question 23

phosphodiester bonds

Answer 23

covalent bonds that form the backbone of DNA and RNA (pentose to phosphate)

Question 24

N-glycosidic bond

Answer 24

the bond between a nitrogenous base and a sugar molecule

Question 25

Explain the process of DNA packaging in eukaryotic cells, detailing how histones organize DNA into nucleosomes during interphase and condense it further into chromosomes for mitotic division

Answer 25

Histones are small, positively charged proteins that attract negatively charged backbones of DNA. Eight histones form an octamer, or nucleosome core, that curl DNA around the octamer. This forms the chromatin chain that appears as if the DNA wraps are beads on a long strand of DNA.

The DNA histones keep folding, creating chromatin fibers that loop around and condense further, eventually forming a mitotic chromosome with a centromere in the middle.

Question 26

Connect your learning to cancer biology

Answer 26

In cancer, injured cells do not experience apoptosis but continue through cell division, propagating erroneous cells.

Mutations occur at the DNA level in which a cell may change protein structure or function based on mutations caused.

Question 27

Three types of mutations

Answer 27

Silent
Nonsense
Missense

Question 28

Silent mutations

Answer 28

DNA mutation effects RNA but the correct amino acid is still formed (typically, 3rd litter is affected)

Question 29

Nonsense mutation

Answer 29

The change in DNA structure results in the STOP codon and the sequence is shorter than intended so the protein is not fully made (UAG)

Question 30

Missense mutation

Answer 30

An amino acid is still synthesized but it is the incorrect one causing altered structures.

Conserved: amino acid created has similar properties to the original

Non-conserved: amino acid created does not have similar properties to original