Week 3 (needs friday prelecture content)

Question 1

What do different base sequences result in?

Answer 1

Difference genes and thus proteins.

Question 2

If a 5’ end has a 5’ carbon at it’s end, what does a 3’ end have?

Answer 2

A 3’ carbon.
5’ end ends in a phosphate group and 3’ in a hydroxyl group.

Question 3

How do DNA strands run?

Answer 3

Antiparallel.

Question 4

How do we find the orientation?

Answer 4

Using the ends (5’ and 3’).

Question 5

What does a RNA look like?

Answer 5

It has irrelgular twists from H-bonds within the RNA molecule.

Question 6

What does the mRNA sequence determine?

Answer 6

The shape of the protein, which is necessary for function.
Sometimes an RNA can be what is transcribed and made.

Question 7

What is the strand opposite of the template strand called?

Answer 7

The sense strand. It is basically the same sequence as the RNA.

Question 8

What is the structure of DNA?

Answer 8

A sugar phosphate backbone with nitrogenous bases ATCG. Each strand has a 5’ end and a 3’ end. - these primes refer to polarity.

Question 9

For polysaccharides, what is an example of a monomer, polymer, and the type of linkage?

Answer 9

Glucose - starch, glycogen, cellulose - glycosidic linkage.

Question 10

For nucleic acids, what is an example of a monomer, polymer, and the type of linkage?

Answer 10

Nucleotides - DNA/RNA/Oligonucleotides (a short polymer ~ 10-50 nucleotides) - phosphodiester linkage.

Question 11

What is the name of the linkage that joins nucleotides to the nucleic acid?

Answer 11

Phosphodiester linkage.

Question 12

What does one monomer of DNA include?

Answer 12

1 sugar and 1 phosphate, includes RNA & DNA. Nitrogenous base (?).

Question 13

What are the size differences between A, T, G, C, and U?

Answer 13

C, T, U are smaller chemical structures, while G and A are larger.

Question 14

Why is the 5’ end called the 5’ end?

Answer 14

Because the carbon at the end/coming off the ring is connected to a phosphate group.
For 3’, it is connectedto a hydroxyl group.

Question 15

Why is the direction of the DNA strands important?

Answer 15

Enzymes that make nucleic acids only work in one direction. (5’ to 3’)

Question 16

You can have a purine base x a purine (big) base, and pyrimidine x pyrimidine (small)? Yes or no.

Answer 16

No. Only Purine x Pyrimidine.

Question 17

What type of bond is between bases in DNA?

Answer 17

Hydrogen bond.

Question 18

DNA is … handed?

Answer 18

Right handed.

Question 19

Explain DNA replication.

Answer 19

The double stranded DNA is unwound, and each strand is used as a templatre to form daughter molecules depending on what is complimentary. (only works because of redundency). Polymerase enzyme can only add to the 3’ end.

Question 20

What is the central dogma?

Answer 20

DNA is transcribed to RNA that is transported to the cytoplasm and then translated into given protein.

Question 21

What type of structure does RNA have?

Answer 21

A 3D structure as the RNA folds in on itseld - it only has one backbone/

Question 22

What is genetic material?

Answer 22

Molecules that carry on genetic info to offspring.

Question 23

What is the Hershey-Chase experiment?

Answer 23

The Hershey-Chase experiment, conducted in 1952, definitively demonstrated that DNA, not protein, is the genetic material passed from viruses to bacteria, using bacteriophages (viruses that infect bacteria) and radioactive labeling techniques.
(refer to Week 3 lecture 1 prelecture content)

Question 24

What percentage of genome has protein encoding sequence?

Answer 24

1-2% of the DNA.

Question 25

Name some types of proteins/uses.

Answer 25

Enzymes, defensive proteins, storage (eg. storing amino acids for embryos to use), transport proteins, etc.

Question 26

What percentage of dry mass in most cells do proteins account for?

Answer 26

More than 50%.

Question 27

What is the monomer of the macromolecule Protein (polypeptide)?

Answer 27

Amino acids that connect with a peptide bond.

Question 28

What do Amino acids generally contain?

Answer 28

An amino group, carboxyl group, and an R-group (side chain).

Question 29

What is the primary structure of a protein?

Answer 29

The original polypeptide sequence of amino acids.

Question 30

What is the secondary structure of a protein?

Answer 30

α helix or β pleated sheet, both of which depend on the Amino acid sequence.

Question 31

What is the tertiary structure of a protein?

Answer 31

Entire 3D shape of polypeptide. Can make up a part of a whole protein or be the whole protein.

Question 32

What is the quartinary structure of a protein?

Answer 32

Several polypeptide chains together to make one functioning protein.

Question 33

What will a tiny difference in the DNA code do?

Answer 33

It has the chance to effect the shape and thus the function.

Question 34

How important is structure?

Answer 34

It is basically everything, whether it is physical structure, an enzyme, or an antibody.

Question 35

What determines the shape of a protein?

Answer 35

The amino acid sequence.

Question 36

What determines the function of a protein?

Answer 36

The structure.

Question 37

Types of structural models?

Answer 37

Space-filling model, Ribbon model, Wire-frame model. *solid or simple shape can be used if details aren't needed.

Question 38

Is the structure of a protein permanent?

Answer 38

No. Most of the chemical interactions holding the structure together are not strong. They are highly susceptible to pH, salt concentrations, and high temperatures.

Question 39

What happens when a protein is given conditions heavily outside of its optimal?

Answer 39

The shape will unravel - denature.

Question 40

What does it mean if a protein is denatured?

Answer 40

The protein is biologically inactive - its 3D shape is lost.

Question 41

What happens if you undo external changes to a denatured protein?

Answer 41

The protein may be able to renature.

Question 42

What is an enzyme?

Answer 42

A catalyst that assists a chemical reaction where it begins with a specific molecule(s) and ends with a product(s). It can be breaking things down or binding things together.

Question 43

What is a metabolic pathway?

Answer 43

Several enzyme reactions, where each step is catalysed by a specific enzyme/

Question 44

What is Gibb's Free Eneregy?

Answer 44

ΔG. The energy available to do 'work' in a cell.

Question 45

What is based on ΔG?

Answer 45

Whether a process is spontaneous or non-spontaneous.

Question 46

What is important about the speed of a spontaneous reaction?

Answer 46

They can be both fast and slow, but enzymes increase the reaction speed.

Question 47

What type of reaction is a spontaneous reaction?

Answer 47

An exergonic reaction as energy is released and ΔG is negative.

Question 48

What type of reaction is a non-spontaneous reaction?

Answer 48

An endergonic reaction as energy needs to be taken in (energy in product has more than reactant), ΔG is positive.

Question 49

What can the released energy in an exergonic reaction be used for?

Answer 49

The energy can be repurposed and used in non-spontaneous reactions.

Question 50

What do enzymes do in a reaction?

Answer 50

Enzumes come in as there is often a hump of energy required called the activation energy that enzymes can reduce.

Question 51

What are 3 types of work in a cell? (that ATP is used for)

Answer 51

Chemical work: pushing endergonic reactions. Transport work: pumping substances against concentration gradients. Mechanical work: eg. muscle cell contractions.

Question 52

How important is ATP?

Answer 52

Everything in the cell is making or using ATP.

Question 53

Where is ATP known from?

Answer 53

RNA - it is composed of ribose, adenine, and 3 phosphate groups.

Question 54

What is ATP known as?

Answer 54

Energy currency.

Question 55

How much Gibb's free energy does ATP have?

Answer 55

Very high amounts.

Question 56

What happens when a phosphate in ATP is hydrolised and removed?

Answer 56

It is very exergonic and thus releases a lot of energy, becoming ADP.

Question 57

Where does the energy change in ATP -> ADP come from?

Answer 57

The chemical chjange of state to lower free energy, not the phosphate bonds.

Question 58

How can ADP return to being ATP?

Answer 58

It can be phosphorylated based on energy released by other exergonic/catabolic reactions in the cell.

Question 59

What is an Enzyme?

Answer 59

A subset of proteins that catalyses reactions. It is a catalyst that is a chemical eagent that speeds up a reaction without beign consumed.

Question 60

How does Enzyme naming work?

Answer 60

Names end in 'ase'.

Question 61

How important is the shape to Enzyme?

Answer 61

Enzymes need to perfectly match with its substrate shape, eg bringing 2 reactants close together, lowering the activation energy?

Question 62

Do enzymes affect ΔG?

Answer 62

No, they only speed up the reaction.

Question 63

What are the steps for an enzyme in a cell?

Answer 63

1. Substrate enters the active site. 2. Substrates are held in active site by weak interactions. 3. Active site lowers activation energy. 4. Substrates become products. 5. Products are released. 6. Active site is ready for new substances.

Question 64

What is it called when a substrate binds to an enzyme?

Answer 64

It is called an enzyme-substrate complex.

Question 65

How well do enzymes and substrates match?

Answer 65

They usually match 1-1 as the reaction catalysed is very specific.

Question 66

What is important to maintian enzyme structure?

Answer 66

Optimal temperatures and pHs.

Question 67

What are the two types of inhibitors?

Answer 67

Competitive (binds to the active site), non-competitive (binds elsewhere and changes the shape of the enzyme).