Ch. 3 Chemical Basis of Information Molecules Flashcards

1
Q

What are nucleic acids?

A

Polymers of nucleotides that are linked together by phosphodiester bonds (covalent bonds).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is a nucleotide?

A

A base, a sugar, and phosphate group(s).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is a nucleoside?

A

A base and a sugar. NO phosphate group(s).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How are nucleic acids (strands) labeled?

A

They have a 5’ termini and a 3’ termini.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How are the RNA and DNA sugars different?

A

Ribonucleotides have ribose which has a 2’ OH group. Deoxyrobonucleotides have deoxyribose which has a 2’ H.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the RNA bases?

A

adenine, cytosine, guanine, and uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the DNA bases?

A

adenine, cytosine, guanine, and thymine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Could RNA have thymine and DNA have uracil?

A

Yes. It would be abnormal, but it is possible.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are polypeptides?

A

Polymers of amino acids that are linked together by peptide bonds (covalent bonds).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the structure of an amino acid?

A

There is an ɑ carbon bonded to four chemical groups… amino group, carboxyl group, hydrogen, and an R group that varies.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How does the composition of a polymer affect structure?

A

The composition (sequence) of a polymer (nucleic acids, proteins, etc.) contributes to its structure, and structure influences function.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does a polymer need to perform its fuction?

A

It must take on structure to perform its function!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What does DNA form in the cell and why?

A

DNA forms a double helix in the cell due to bond angles in the backbone.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What does DNA form out of the cell and why?

A

DNA may not form a helix because the new environment might favor different non-covalent interactions/structures.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does RNA form in the cell and why?

A

RNA typically DOESN’T exist in a double stranded form because single strands allow for H-bonding into a variety of structures, which allows for a variety of functions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What allows proteins to have various functions?

A

The variety of aa patterns, and hence folding of aa’s, gives proteins their various functions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How can monomers of nucleic acids and polypeptides be modified?

A

Monomers can be modified by small chemical groups like phosphates, methyl groups, amine groups, etc.

18
Q

What do monomer modifications do (3)?

A

These modifications can change gene expression, protein activity, and other molecular processes.

19
Q

Why are phosphodiester bonds and peptide bonds covalent and not ionic?

A

Ionic bonds in a biological system are relatively weak because of the prevalence of water.

20
Q

What are the weaker bonds/interactions involved in macromolecule structure and function (4)?

A
  • ionic bonds (“+” and “-“)
  • hydrogen bonds (O, N, and H)
  • VDWs forces
  • hydrophobic interactions
21
Q

Why are these weaker bonds able to maintain structure?

A

While they are individually weak, their strength is additive. The more bonds present, the stronger they are.

22
Q

What is steriochemistry?

A

The spacial arrangement of molecules

23
Q

What stereochemical property do biological molecules have?

A

Biological molecules are chiral, so they cannot be superimposed on their mirror image.

24
Q

Why do biological systems only use one enantiomer of a molecule?

A

Proteins are chiral, so they can only interact with one enantiomer?

25
What enantiomer of amino acids, nucleotides, and sugars are used?
L-amino acids D-nucleotides D-carbohydrates
26
What is pH?
A measure of hydronium concentration of a solution, which relates to the proton availability.
27
What can changes in pH cause?
Changes in pH can disrupt chemical structure of a molecule, leading to changes in its function!
28
How can we combat pH changes?
pH changes can buffered using compounds that accept and donate protons to keep pH stable.
29
How are cells and tissues buffered?
Cells and tissues are buffered by various compounds. (blood=bicarbonate)
30
How do most cellular chemical reactions proceed?
Reactions can proceed in either direction, but in some cases a reverse reaction is very rare.
31
How is reaction direction determined?
Reaction direction is influenced by energy. Energy release is more energetically favorable.
32
What is required for all reactions, even if they release energy?
All reactions must reach the activation energy in order for the reaction to begin.
33
What do many biological reactions require in terms of energy?
Many biological reactions require energetically unfavorable reactions to occur.
34
What are the first two laws of thermodynamics?
1. Energy is conserved, never created or destroyed. 2. All spontaneous processes take place with an increase in disorder/randomness of the system (entropy, S).
35
What is the progression of a reaction related to (2)?
It is related to free energy (G) of the reaction and to changes in the energy (ΔG).
36
What ΔG value is energetically favorable?
"﹣" ΔG values are energetically favorable, and energy is released. (Eₐ is still required!)
37
What is a catalyst?
Somethings that can lower the activation energy making a reaction more likely to occur.
38
What is an enzyme?
Enzymes reduce the activation energy needed for a reaction. They are mostly proteins, but can be ribozymes.
39
Are enzymes universal?
No. Enzymes are specific for a reaction.
40
How do energetically unfavorable reactions take place?
You can couple the reaction with one that releases energy to give the overall reaction a "﹣"ΔG ; ATP hydrolysis for example.
41
Why does ATP hydrolysis have a negative ΔG?
1. The three phosphate groups are all negatively charged which creates "﹣" repulsion 2. The phosphoanhydride bond between the 𝝲 and β phosphate is very strong 3. Breaking the bond with water causes the Pᵢ to be shot off, releasing energy
42
It is ______ and ___________ to be alive."
It is costly and expensive to be alive.