VCE Chemistry Question Thread

[cosine]

Could someone explain to me how a nucleotide is formed...I can't remember (for example) which carbon in a base joins to the sugar molecule etc. Is there a way to figure out where one molecule joins to another?

The phosphate group of one nucleotide will always bind to the third carbon of the polynucleotide strand. The phosphate groups always joins the third carbon of the sugar base of the adjacent nucleotide. In chemistry terms, the oxygen in the phosphate group binds with the hydroxyl group of the third carbon of the sugar base, and hence a condensation reaction occurs and water is released.




You see how the first (from the left) nucleotide has a phosphate group protruding out? That does not bind with anything because it is the starting point of the DNA strand. The labels P and S stand for Phosphate group and Sugar base. Look at the sugar base (S) of the first nucleotide, the carbons start from where the nitrogenous base is attached, so in this case where you see the bond with cytosine and the sugar base, that is the first carbon. Now every 'corner' of the pentose sugar has one carbon attached to it. So count down from the first carbon until the third carbon or 'corner'. You see how at this third carbon that the phosphate group of the adjacent nucleotide is bonded? That's how it works! And if you continue to look downwards, the phosphate group of the third nucleotide is bonded, covalently, to the third carbon of the second nucleotide.

This rule is exempted for the first and last nucleotides, as they 'end' the nucleic acid, otherwise nucleic acids will never end in length!

[sunshine98]

Yes, however -3005 - (-3018) = +13. Intuitively, solid-->gas requires an input of energy.

I like your thinking, but unfortunately I think the sign of your answer is incorrect. Using the 'standard' way of working this out, we keep the first equation the same, and reverse the second equation to get:

P4(s) + 5O2(g) ---> P4O10(s); Delta H = -3005kJ/mol (Equation 1)
P4O10(s) --> P4(g) + 5O2(g) ; Delta H = +3018kJ/mol (Reversed Equation 2)

Then if we 'add' the two equations together (or alternatively, consider performing the first reaction to get some P4O10(s), then perform the second reaction to change that P4O10(s) to give P4(g) + 5O2(g)), we get P4(s) + 5O2(g) ---> P4(g) + 5O2(g); Delta H = +13kJ/mol. As 5O2(g) appears on both sides, this means we've effectively used a certain amount of O2(g) to make the exact same amount of O2(g) - so this would have the same enthalpy and as you've mentioned, can be disregarded. Hence, we end up with P4(s) ---> P4(g); Delta H = +13kJ/mol.

In some sense, you can 'subtract' equations from each other, as reversing an equation turns it into its 'negative', and adding the negative of something is like subtracting the original 'something'. In this case, we 'added' the negative of Equation 2, to Equation 1. This would be the same as Equation 1 - Equation 2, which again gives you the net enthalpy change of +13kJ/mol.

I suppose one final way to look at it, would be to draw an energy profile of the two (original) reactions on the same axes. Because the products of the two reactions are exactly the same, you can put one level for P4O10(s). Now, P4(s) + 5O2(g) will be 3005kJ/mol above this level (note the reaction is exothermic, so the enthalpy of the product is lower than that of the reactants), and P4(g) + 5O2(g) will be 3018kJ/mol above this level. Hence, the P4(s) + 5O2(g) level is 13kJ/mol below the P4(g) + 5O2(g) level. As 5O2(g) makes the same enthalpy contribution to both levels, we can state that the hypothetical P4(s) level will be 13kJ/mol below the P4(g) level. Hence, if we were to draw a reaction profile of P4(s) --> P4(g), we would have the product 13kJ/mol above the reactants, and hence delta H would be +13kJ/mol.

Thanks guys 

[Orb]

Sorz for being a complete chem noob,

but:
with equilibrium reactions, how do you identify what reactions are most 'complete'? as in, if all they give you was the chem equation and the K value, how do you know how 'complete' it is?

[paper-back]

Sorz for being a complete chem noob,

but:
with equilibrium reactions, how do you identify what reactions are most 'complete'? as in, if all they give you was the chem equation and the K value, how do you know how 'complete' it is?

The K value usually tells you how complete a reaction is
A greater K value suggests there is a greater concentration of products than reactants, suggesting that the reaction is mostly complete

I think in the Heinemann chemistry book, they state:
If the K value is greater than 10^4, then the reaction has gone to the product side, hence it's mostly complete
If the K value is less than 10^-4, then the reaction has mostly gone to the reactant side, hence it's mostly not-complete

[bavelzzz]

The phosphate group of one nucleotide will always bind to the third carbon of the polynucleotide strand. The phosphate groups always joins the third carbon of the sugar base of the adjacent nucleotide. In chemistry terms, the oxygen in the phosphate group binds with the hydroxyl group of the third carbon of the sugar base, and hence a condensation reaction occurs and water is released.


(Image removed from quote.)

You see how the first (from the left) nucleotide has a phosphate group protruding out? That does not bind with anything because it is the starting point of the DNA strand. The labels P and S stand for Phosphate group and Sugar base. Look at the sugar base (S) of the first nucleotide, the carbons start from where the nitrogenous base is attached, so in this case where you see the bond with cytosine and the sugar base, that is the first carbon. Now every 'corner' of the pentose sugar has one carbon attached to it. So count down from the first carbon until the third carbon or 'corner'. You see how at this third carbon that the phosphate group of the adjacent nucleotide is bonded? That's how it works! And if you continue to look downwards, the phosphate group of the third nucleotide is bonded, covalently, to the third carbon of the second nucleotide.

This rule is exempted for the first and last nucleotides, as they 'end' the nucleic acid, otherwise nucleic acids will never end in length!

Thank you, that really helped Also, how would you figure out how the nitrogenous bases join to each other? Where do the hydrogen bonds form and between which functional groups do they form?

[Orb]

The K value usually tells you how complete a reaction is
A greater K value suggests there is a greater concentration of products than reactants, suggesting that the reaction is mostly complete

I think in the Heinemann chemistry book, they state:
If the K value is greater than 10^4, then the reaction has gone to the product side, hence it's mostly complete
If the K value is less than 10^-4, then the reaction has mostly gone to the reactant side, hence it's mostly not-complete

ahh cheers <3

[lzxnl]

The K value usually tells you how complete a reaction is
A greater K value suggests there is a greater concentration of products than reactants, suggesting that the reaction is mostly complete

I think in the Heinemann chemistry book, they state:
If the K value is greater than 10^4, then the reaction has gone to the product side, hence it's mostly complete
If the K value is less than 10^-4, then the reaction has mostly gone to the reactant side, hence it's mostly not-complete

I wouldn't even say 10^-4. It depends on the reaction; HSO4- has a Ka of 0.01 and if you do calculations you'll find that 1 M HSO4- is about 10% dissociated only. That counts as mostly incomplete to me.

[cosine]

Thank you, that really helped Also, how would you figure out how the nitrogenous bases join to each other? Where do the hydrogen bonds form and between which functional groups do they form?

The nitrogenous bases join to each other via hydrogen bonds, so you should know the G paris with C and T pairs with A. So if we have a nucleotide with a nitrogenous base G, the ONLY nucleotide that the G can bond with, through the hydrogen bond, is if the parallel nucleotide has a nitrogenous base C. Same goes with T, it can ONLY form a hydrogen bond with a nucleotide with base nitrogenous base A.

You should also know that G and A are derived from purines, that is, they are doubled-ringed. Whereas T and C are pyrimidines, that is, they are single-ringed. Three hydrogen bonds form between G - C and only two hydrogen bonds form between T - A. Why? Due to the structure and location of the elements that are responsible for the hydrogen bonds on the nucleotides, don't think you need to know much more about that!

[cosine]

I have a few questions about energy:

1). I understand that exothermic reactions have a net loss of enthalpy, and that endothermic have a net gain of energy. But what is meant by, the activation energy is the energy required to break the bonds of the reactants?

2). "When the new bonds in the products are formed, energy is released" I don't understand this statement, it is telling us how bonds of the reactants break, and energy is used up for that, I understand that part because that's the activation energy, but then it says that when the new bonds of the products are formed/forming, energy is being released. Does this only apply for exothermic reactions? I thought when new bonds of endothermic reactions absorb energy from the surroundings?

Cheers xD

[sunshine98]

I have a few questions about energy:

1). I understand that exothermic reactions have a net loss of enthalpy, and that endothermic have a net gain of energy. But what is meant by, the activation energy is the energy required to break the bonds of the reactants?

2). "When the new bonds in the products are formed, energy is released" I don't understand this statement, it is telling us how bonds of the reactants break, and energy is used up for that, I understand that part because that's the activation energy, but then it says that when the new bonds of the products are formed/forming, energy is being released. Does this only apply for exothermic reactions? I thought when new bonds of endothermic reactions absorb energy from the surroundings?

Cheers xD

Two things are happening in all reactions regardless of endothermic or exothermic
1-bonds in reactants are broken. Needs energy.
2- then (after reactants collide according to collision theory) bonds for the products are formed. Releases energy.
So activation energy refers to the energy needed to break the bonds (or in other terms the energy needed in step 1 above). Bonds will not just break they need energy to break them. That's why you need light energy in the light dependent phase of photosynthesis(bit of bio ). But the energy cant just be any random amount it needs to be the sufficient amount to break the bonds in the reactants. Hence , activation energy.

for question 2 - remember energy is released regardless of the reaction being exothermic or endothermic, but where I think your getting a bit confused is :
- in endothermic reactions:  the net energy absorbed (to break bonds ) is greater than the amount released (when bonds are formed)
- in exothermic reactions: the net energy released (when bonds are formed in products ) is greater than the amount absorbed (to break bonds)

Hope this helps 

[cosine]

Two things are happening in all reactions regardless of endothermic or exothermic
1-bonds in reactants are broken. Needs energy.
2- then (after reactants collide according to collision theory) bonds for the products are formed. Releases energy.
So activation energy refers to the energy needed to break the bonds (or in other terms the energy needed in step 1 above). Bonds will not just break they need energy to break them. That's why you need light energy in the light dependent phase of photosynthesis(bit of bio ). But the energy cant just be any random amount it needs to be the sufficient amount to break the bonds in the reactants. Hence , activation energy.

for question 2 - remember energy is released regardless of the reaction being exothermic or endothermic, but where I think your getting a bit confused is :
- in endothermic reactions:  the net energy absorbed (to break bonds ) is greater than the amount released (when bonds are formed)
- in exothermic reactions: the net energy released (when bonds are formed in products ) is greater than the amount absorbed (to break bonds)

Hope this helps 

Doesn't enthalpy refer to the chemical energy stored within the bonds of the reactants and products, and not the energy require to break them? o.O

do you mean to say that:
endothermic reactions: the net energy stored in the products is greater than the net energy that was in the reactants
exothermic reactions: the net energy stored in the products is less than the net energy that was in the reactants

[grannysmith]

Doesn't enthalpy refer to the chemical energy stored within the bonds of the reactants and products, and not the energy require to break them? o.O

do you mean to say that:
endothermic reactions: the net energy stored in the products is greater than the net energy that was in the reactants
exothermic reactions: the net energy stored in the products is less than the net energy that was in the reactants

If I'm not mistaken, enthalpy refers to the total internal energy of a system e.g. a chemical reaction, which includes both potential (e.g. chemical bonds) and kinetic (e.g. I guess you could say heat) energy. In an exothermic reaction, enthalpy is negative because the potential energy of the products is lower than that of the reactants. There's a release of heat energy - where does this come from? It comes from the difference in potential energies of the products/reactants. I may be wrong.

When we talk about endothermic/exothermic, as the names suggest, we are referring to the heat energy released/absorbed by the participant molecules.

I have a few questions about energy:

1). I understand that exothermic reactions have a net loss of enthalpy, and that endothermic have a net gain of energy. But what is meant by, the activation energy is the energy required to break the bonds of the reactants?

2). "When the new bonds in the products are formed, energy is released" I don't understand this statement, it is telling us how bonds of the reactants break, and energy is used up for that, I understand that part because that's the activation energy, but then it says that when the new bonds of the products are formed/forming, energy is being released. Does this only apply for exothermic reactions? I thought when new bonds of endothermic reactions absorb energy from the surroundings?

Cheers xD

1. I suppose the reason why we say endothermic/exothermic reactions involve a net gain/loss of energy is because the activation energy itself requires a net input of energy. For any chemical reaction to take place, bonds have to be broken. Subsequently, new bonds can be formed or they can remain broken. Depends on the reaction.

2. This may not be entirely accurate, but think of it this way. The formation of a bond releases energy because it causes the participants to be at a more stable state. Breaking a bond requires energy because it's the reverse process - the participants of the reaction are made to be less stable. However, if the amount of heat energy released during bond formation is greater than the amount of heat energy absorbed (from the surroundings) during bond breakage, then the reaction is exothermic. The converse is true for endothermic reactions.

So in essence, bond formation always releases energy and bond breakage always absorbs energy. But the 'exchange' of heat energy varies depending on the reaction, and gives rise to whether it is exothermic/endothermic. That's also why activation energy is always positive, because energy input is necessary for bonds to be broken.

[cosine]

If I'm not mistaken, enthalpy refers to the total internal energy of a system e.g. a chemical reaction, which includes both potential (e.g. chemical bonds) and kinetic (e.g. I guess you could say heat) energy. In an exothermic reaction, enthalpy is negative because the potential energy of the products is lower than that of the reactants. There's a release of heat energy - where does this come from? It comes from the difference in potential energies of the products/reactants. I may be wrong.

When we talk about endothermic/exothermic, as the names suggest, we are referring to the heat energy released/absorbed by the participant molecules.

1. I suppose the reason why we say endothermic/exothermic reactions involve a net gain/loss of energy is because the activation energy itself requires a net input of energy. For any chemical reaction to take place, bonds have to be broken. Subsequently, new bonds can be formed or they can remain broken. Depends on the reaction.

2. This may not be entirely accurate, but think of it this way. The formation of a bond releases energy because it causes the participants to be at a more stable state. Breaking a bond requires energy because it's the reverse process - the participants of the reaction are made to be less stable. However, if the amount of heat energy released during bond formation is greater than the amount of heat energy absorbed (from the surroundings) during bond breakage, then the reaction is exothermic. The converse is true for endothermic reactions.

So in essence, bond formation always releases energy and bond breakage always absorbs energy. But the 'exchange' of heat energy varies depending on the reaction, and gives rise to whether it is exothermic/endothermic. That's also why activation energy is always positive, because energy input is necessary for bonds to be broken.

I still don't get it...

I don't understand how forming a bond releases energy.
Isn't chemical energy the energy that is stored in the bonds of the reactants? I always thought that if the chemical energy in the reactants, when the bonds are broken, is less than the chemical energy stored in the bonds of the products, then it's an endothermic reaction because more energy has been absorbed from the surroundings..

So confused o.O

[grannysmith]

I still don't get it...

I don't understand how forming a bond releases energy.
Isn't chemical energy the energy that is stored in the bonds of the reactants? I always thought that if the chemical energy in the reactants, when the bonds are broken, is less than the chemical energy stored in the bonds of the products, then it's an endothermic reaction because more energy has been absorbed from the surroundings..

So confused o.O

It's a fundamental rule that bond formation releases energy and bond breakage absorbs energy. Yes, chemical energy is the energy stored within the bonds of the reactants, as well as the products. You're exactly right - additionally however, the gain/release of energy is in the form of heat.

[Sundal]

When figuring out K or concentration fraction values, does the concentration of substances always have to be in molarity?

Thanks.