Bioc lec 5 Flashcards
What is Chargaff’s rule regarding the composition of DNA?
In all cellular DNA, the number of adenosine residues equals the number of thymidine residues, and the number of guanosine residues equals the number of cytosine residues.
Which scientists used X-ray crystallography to study the secondary structure of DNA?
Rosalind Franklin and Maurice Wilkins.
Why is it difficult to form well-ordered crystals of DNA for high-resolution X-ray diffraction?
Forming well-ordered DNA crystals is hard because DNA molecules are very long and often break into fragments during isolation. These fragments don’t align well enough to create clear patterns in high-resolution X-ray diffraction.
What key discovery was made through Rosalind Franklin’s X-ray diffraction studies of DNA?
Franklin’s studies, including “Photo 51,” revealed that DNA molecules are helical and have two periodicities along the long axis.
What are the two periodicities of DNA revealed by Franklin’s X-ray diffraction studies?
A primary periodicity of 3.4 Å and a secondary periodicity of 34 Å along the long axis.
What structure is formed by two helical DNA chains?
They wind around a single axis, forming a right-handed double helix.
Where is the sugar-phosphate backbone located in the DNA double helix?
The hydrophilic sugar-phosphate backbone is on the outside of the helix, facing the surrounding water
How are the bases oriented inside the DNA double helix?
The hydrophobic bases are stacked inside the double helix, perpendicular to the helix axis.
How are bases paired within the DNA double helix?
Each base of one strand is paired in the same plane with a complementary base of the other strand: adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).
What is the orientation of the two strands in the DNA double helix?
The two strands are antiparallel, meaning their 3’ to 5’ phosphodiester bonds run in opposite directions.
What is the spacing between vertically stacked base pairs in the DNA helix?
The base pairs are 3.4 Å apart.
How many base pairs are present in each turn of the DNA helix, and what is the length of one turn?
Each turn of the helix contains 10 base pairs, measuring 34 Å in length.
What is the diameter of the DNA double helix?
The diameter of the double helix is 20 Å, which equals 2 nm.
What is the essential feature of the Watson-Crick model of DNA?
Self-complementarity.
How does self-complementarity function in DNA replication?
It allows each pre-existing strand of a double helix to serve as a template for synthesizing new daughter strands.
What biological processes does self-complementarity help explain?
It explains mitosis, meiosis, heredity, and genetics.
How does self-complementarity contribute to DNA repair?
It provides a mechanism, in principle, for the cell to repair damaged DNA by using the complementary strand as a template.
What type of bonds hold Watson-Crick base pairs together in DNA?
Sets of hydrogen bonds.
How many hydrogen bonds form between cytosine (C) and guanine (G)?
Three hydrogen bonds (GC 3).
How many hydrogen bonds form between adenine (A) and thymine (T)?
Two hydrogen bonds (AT 2).
What does a higher GC-to-AT ratio indicate about DNA stability?
A higher GC-to-AT ratio makes it more difficult to separate the two DNA strands, as GC pairs have stronger bonding.
How are the two strands of the double helix coiled around each other?
They are plectonemically coiled, meaning they are wrapped around each other.
How can the two strands of the double helix be separated?
The strands can only be separated by unwinding from an end.
What is supercoiling in DNA?
Supercoiling occurs when the double helix undergoes additional twisting, resulting in very compact structures.
What are the two grooves present in double-helical DNA?
The major groove and the minor groove.
Why do major and minor grooves form in DNA?
The glycosidic bonds of a base pair are at an angle, creating a large angle (major groove) and a small angle (minor groove).
What causes the formation of a major and minor groove as the double helix winds?
The two strands winding around each other create a wider gap (major groove) on one side and a narrower gap (minor groove) on the opposite side of the helix.
What lines the major and minor grooves in DNA?
Potential hydrogen-bond donors and acceptors from the bases line each groove, enabling specific interactions with proteins.
Why are major grooves more accessible to proteins?
The larger size of the major grooves makes them more accessible for interactions with proteins that recognize specific DNA sequences.
How does the secondary structure of DNA relate to its sequence?
This is because the two kinds of base pairs have very similar
shapes and properties.
What is the primary force that stabilizes the double helix by hiding hydrophobic bases?
The hydrophobic effect, which buries the hydrophobic bases in the core of the helix.
What type of bonding contributes to the stabilization of the double helix through base pair interactions?
Hydrogen bonding between base pairs.
What non-covalent interaction helps stabilize the double helix by stacking the bases?
Van der Waals interactions through base stacking.
What is the central dogma of molecular biology?
DNA is transcribed into RNA, and RNA is translated into protein.
What is transcription?
Transcription is the process of making an RNA copy of a DNA sequence.
What is translation?
Translation is the process of using RNA to build a protein.
What type of bonds hold the phosphate groups in ATP together?
Phosphoanhydride bonds.
What happens when phosphoanhydride bonds in ATP are broken?
Breaking these bonds releases a large amount of energy.
What are the components of an ATP molecule?
A base (adenine), a sugar (ribose), and three phosphate groups labeled alpha (α), beta (β), and gamma (γ).
Is ATP a store of chemical energy?
No, ATP is not a store of chemical energy; it links catabolism and anabolism.
How is ATP synthesized in cells?
Cells break down nutrients (catabolism) and use the free energy to synthesize ATP from ADP.
How rapidly does ATP turnover in cells?
ATP is broken down and synthesized very rapidly, with a lifetime of seconds to minutes.
What is the free energy change (ΔGnotprime) for the hydrolysis of ATP?
The free energy change is large and negative, approximately -30.5 kJ/mol under standard conditions.
How does the ΔG of hydrolysis for ATP compare to other bonds?
G for ATP hydrolysis (~-50 kJ/mol) is much greater than for amides, esters, and phosphoesters (~15–20 kJ/mol).
Where do energy-releasing and energy-requiring processes involving ATP occur?
At the phosphate groups of ATP.
What happens to the electrostatic repulsion in ATP during hydrolysis?
Hydrolysis releases the electrostatic repulsion among the negative charges in ATP.
Why does the inorganic phosphate (Pi) produced in ATP hydrolysis have greater stability than ATP?
The inorganic phosphate has greater resonance stabilization than ATP.
What is the formula for calculating the free energy change (ΔG°’)?
ΔG°’ = Free energy of products - Free energy of reactants.
How many high-energy bonds are present in ATP?
ATP contains two high-energy bonds, which are phosphoanhydride linkages.
Which bond in ATP is broken during hydrolysis?
The bond between the gamma (γ) and beta (β) phosphates is broken during hydrolysis.
What type of reaction occurs during the hydrolysis of ATP?
A nucleophilic attack on the gamma phosphate occurs during ATP hydrolysis.
What are the products of ATP hydrolysis?
The products are ADP (adenosine diphosphate) and inorganic phosphate (Pi).
How much energy is released during the hydrolysis of ATP?
Approximately 30 kJ of energy is released during ATP hydrolysis.
What happens during the hydrolysis of the alpha-beta linkage in ATP?
A nucleophilic attack on the alpha phosphate occurs, resulting in the breakdown of ATP to AMP and pyrophosphate (PPi).
What are the products of hydrolyzing the alpha-beta linkage in ATP?
The products are AMP (adenosine monophosphate) and pyrophosphate (PPi).
What happens to pyrophosphate (PPi) in the cell?
Pyrophosphate (PPi) is immediately hydrolyzed by the enzyme pyrophosphatase, producing two moles of inorganic phosphate (Pi).
: How does the hydrolysis of ATP to AMP + PPi compare to the hydrolysis of ATP to ADP + Pi?
The hydrolysis of ATP to AMP + PPi releases twice as much energy as the hydrolysis of ATP to ADP + Pi, because it breaks both phosphoanhydride bonds in ATP.
Why does the hydrolysis of ATP to AMP + PPi release more energy than ATP to ADP + Pi?
The hydrolysis of ATP to AMP + PPi breaks two phosphoanhydride bonds, while ATP to ADP + Pi only breaks one, leading to more free energy being released.
What is the result of the hydrolysis of ATP?
ATP is hydrolyzed into ADP (adenosine diphosphate) and inorganic phosphate (Pi).
What is the free energy change (ΔG) for the hydrolysis of ATP?
The hydrolysis of ATP has a negative ΔG, meaning it releases energy, making it an exergonic reaction.
How does the hydrolysis of ATP drive energetically unfavorable reactions?
Although ATP hydrolysis itself has a negative ΔG, some reactions require an input of energy to get started. ATP hydrolysis provides that energy, driving unfavorable reactions by coupling them with favorable ones.
What does ATP = ADP + Pi mean?
The equation ATP → ADP + Pi represents the breakdown of ATP into ADP (Adenosine Diphosphate) and an inorganic phosphate (Pi).
What chemical mechanism allows ATP hydrolysis to drive reactions forward?
ATP hydrolysis drives reactions forward by coupling energy-releasing ATP breakdown to energy-requiring processes, such as the synthesis of biomolecules.
Give an example of a reaction driven by ATP hydrolysis.
The synthesis of glutamine by glutamine synthetase.
How does the cell drive the synthesis of glutamine forward?
The reaction is coupled to ATP hydrolysis, where ATP is converted to ADP and Pi (ATP → ADP + Pi).
What is the first step in the mechanism of glutamine synthetase?
ATP reacts with glutamate to produce a covalent intermediate, a mixed anhydride of phosphate and glutamate.
What is the second step in the mechanism of glutamine synthetase?
Ammonia (NH₃) acts as a nucleophile and reacts with the electrophilic carbonyl carbon atom of the intermediate, displacing Pi as the leaving group.
How does ATP provide energy to drive reactions forward?
ATP provides energy not by simple hydrolysis but through group transfer.
What makes ATP chemically versatile?
ATP’s phosphate group can participate in a variety of chemical reactions with common organic functional groups.
Besides transferring a phosphoryl group, what other groups can ATP transfer?
ATP can transfer a pyrophosphoryl (PPi) group or an adenylate (AMP) moiety.
What role does ATP’s group transfer capability play in biochemical reactions?
Group transfer from ATP helps to drive reactions forward by modifying substrates or enzyme amino acid residues.
What are the 5 high energy compounds (highest to lowest
- Phosphoenol pyruvate,
- 1,3-biphosphoglycerate,
- creatine phosphate
- Acetyl-CoA,
- ATP
What are the two low energy compounds (highest to lowest)
- Glucose 6 - Phosphate
- Pi (no energy)
How is metabolism divided?
Metabolism is divided into two halves: catabolism and anabolism.
What is catabolism?
Catabolism is the breakdown of large molecules and foodstuffs into simpler products.
What is anabolism?
Anabolism is the process of building up larger and more complex molecules from simple precursors.
What are the main inputs and outputs for catabolism?
In:Carbohydrates, fats, and proteins.
Out:CO₂, H₂O, and NH₃
What energy-related molecules are involved in catabolism?
Catabolism produces ATP and reduced cofactors while consuming ADP and oxidized cofactors.
What are the main inputs and outputs of anabolism?
In: Amino acids, sugars, and fatty acids.
Out: Proteins, lipids, and nucleic acids
What energy-related molecules are involved in anabolism?
Anabolism consumes ATP and reduced cofactors while producing ADP and oxidized cofactors.
What happens to carbon skeletons in catabolic pathways?
The carbon skeletons of most sugars, fats, and amino acids are converted into a single, centrally-important metabolite called acetyl coenzyme A (acetyl CoA).
(converge into acetyl coA)
What is the role of acetyl CoA in metabolism?
Acetyl CoA serves as a precursor for building fatty acids, steroids, components of proteins, and nucleic acids.
What happens in anabolic pathways?
Anabolic pathways diverge, meaning they use common precursors to build a variety of complex molecules.(diverge into complex molecules)
What can acetyl CoA be used to build?
Acetyl CoA can be used to build fatty acids, steroids, and components of proteins and nucleic acids.
What is a metabolic pathway?
A metabolic pathway is a series of enzyme-catalyzed reactions that converts a precursor (A) into a product (E) through intermediates known as metabolites.
What happens at each step of a metabolic pathway?
Each step involves a small, specific chemical change, such as the removal, addition, or transfer of an atom or functional group. When all steps are strung together, the pathway achieves a transformation that may not be obvious from individual steps.
Why are metabolic pathways considered irreversible?
They contain at least one reaction that is thermodynamically very favorable, making the pathway essentially irreversible.
