Unit 3: Lecture 13

How many strands are synthesized in DNA replication?

Two strands b/c of DNA's antiparallel nature (leading and lagging strand)

What is the leading strand?

The strand that is continuously created by DNA polymerase III b/c it is following behind the replication fork (where helicase is located)

What is the lagging strand?

\-The strand that requires constant "priming"

\-grows backward

How does priming work in a lagging strand?

Every time DNA helicase unfolds a segment of DNA an RNA primer is placed onto the lagging strand where DNA polymerase III will add nucleotides until it runs into another primer

What are the fragments temporarily created on the lagging strand called?

Okazaki fragments

What is the role of DNA polymerase I?

Removes the RNA primer and replaces it with DNA

What is the role of DNA ligase?

Seals the gap between Okazaki fragments (forms phosphodiester bonds)

How many replication forks are there at the origin of replication?

2 replication forks

What happens to the end of the strands if it is not long enough to synthesize (min. 5 nucleotides long)?

Telomeres are added to protect the ends

What are telomeres?

Special nucleotide sequences at the end of eukaryotic chromosomes created by an enzyme

What is telomerase?

Contains an RNA template to help synthesize the complementary DNA sequence. Human telomere composed of TTAGGG repeats

What happens to telomeres with age?

Telomeres shorten (helps determine age)

Do all adult cells continue extending their telomeres?

No, when some reach a critical length, they stop proliferating

What might shorter telomeres do?

Protect cell from cancerous growth by limiting the number of cell divisions; cancer cells exploit this b/c elongating a telomere of a healthy cell can create cancer cells

What is the error rate of DNA replication?

1 error per 100,000 bp ; Actual error rate: 1 error per 10,000,000,000 bp

Why is the actual error rate of DNA replication so low?

1. Proofreading
2. Mismatch/ Nucleotide excision repair

Define nuclease.

Enzyme that cuts out and replaces damaged stretches of DNA

Why must sequence changes be fixed?

Sequence changes may become permanent and can be passed onto the next generation; the mutation can potentially become a tumor

Are all changes (mutations) bad?

No, many are the source of genetic variation upon which natural selection operates

What will happen when DNA polymerase III places a mismatched base?

It will notice the mistake and correct it or the NER (nucleotide excision repair) pathway will notice and correct it; the mistake must be fixed before division (otherwise a mutation will occur)

What are thymine dimers?

Two thymines next to each other connected w/ a double covalent bond when exposed to UV light making it unable to bind w/ Adenine in the other strands due to lack of available electrons

What is the most common energy currency of the cell?

ATP

What are the energy storing molecules needed for cellular respiration?

ATP, NADPH, NADH (NAD+), FADH (FAD+), FADH2

What does ATP do?

Supplies most of the immediate energy that drives metabolism in living things

What does ATP do when converted to ADP?

Releases energy

How do cells release the energy?

ATP hydrolysis: ATP + H2O -\> Pi + ADP

What is Pi?

Inorganic phosphate (free unbound phosphate group)

How does ATP hydrolysis release energy?

By transferring its third phosphate to some other molecule, changing its shape (phosphorylation)

How quickly is ATP used compared to monosaccharides?

MS: 1-2 hours; ATP: immediately

What does cellular respiration do for ATP?

Recharge it; ADP\= 50% charged; AMP\= 0% charged

What type of organisms perform cellular respiration?

All living organisms (every living thing needs ATP)

Define cellular respiration.

The process that releases energy (slowly) by breaking down glucose and other food molecules in the presence of oxygen; exergonic reaction

What can be used as fuel for cellular respiration?

Carbohydrates, fats, proteins, and glucose (most common)

Define aerobic respiration.

Occurs in presence of oxygen

Define anaerobic respiration.

Occurs w/o presence of oxygen

Define photosynthesis.

Converts energy from the sun into sugars that store potential energy; endergonic reaction

What is the formula for cellular respiration?

C6H12O6 (glucose) + 6O2 (oxygen) -\> 6 CO2 (carbon dioxide) + 6H2O (water) + ATP (energy)

What is the formula for photosynthesis?

6 CO2 (carbon dioxide) + 6H2O (water) + light energy-\> C6H12O6 (glucose) + 6O2 (oxygen)

Where is energy stored in a molecule of glucose?

Chemical bonds

Glucose is an \_______________.

Electron donor

How are electrons passed from atoms/molecules in chemical rxns (especially in cellular respiration)?

Oxidation & reduction (always occur together) AKA redox rxns

Do electrons transfer during chem rxns release energy?

Yes, energy stored in organic molecules is released and will be used to synthesize ATP

Define oxidation.

The process of losing an electron (often a whole H atom)

Define reduction.

The process of gaining an electron (often a whole H atom)

LEO says GER.

Loses Electrons \= Oxidation; Gains Electron \= Reduction

Define reducing agent.

X loses electrons; X is oxidized by Y (becomes more positive)

Define oxidizing agent.

Y gains electrons; Y is reduced by X (becomes more negative)

What is oxygen?

A common electron acceptor (the final e- acceptor in cellular respiration); highly electronegative

Why is sugar a good molecule for cellular respiration?

Electrons can be easily taken by electron carriers (NAD+ and FAD

Electron carriers are members of the \______________________.

B vitamin family

Why is H atom taken by oxygen at the end?

Anything that is charged and free will cause a lot of damage

What is the difference between NAD+ and NADH?

NAD can easily pick up and release electrons (a carrier). Is reduced to form NADH, which contains a lot of potential energy

During cellular respiration, what happens to the potential energy stored by the electrons?

An electron loses potential energy when it is transferred to oxygen

What are the four stages of cellular respiration?

1. Glycolysis
2. Pyruvate Oxidation
3. Citric Acid Cycle
4. Oxidative Phosphorylation

What is the main form of energy produced in cellular respiration?

ATP

What is the first stage of cellular respiration?

\-"Splitting of sugar" breaks down glucose into two molecules of pyruvate

\-occurs in the cytoplasm and has two major phases: energy investment phase (energy spent) and energy payoff phase

What occurs in the energy investment phase?

Glucose is phosphorylated to Glucose 6-phosphate faster by the enzyme hexokinase ("kinase"- phosphorylate something); requires ATP

What is the input and output of glycolysis per glucose?

Input: 1 Glucose, 2 NAD+, 2 ADP + 2P Output: 2 pyruvate, 2 NADH + 2H+, 2 ATP

What are the two ways to make ATP?

1. Substrate-level phosphorylation
2. Oxidative phosphorylation; difference between the two is where the phosphate comes from

Explain the first way to make ATP.

Substrate-level phosphorylation: an enzyme transfers a phosphate group from an organic substrate onto ADP, forming ATP

Explain the second way to make ATP.

Oxidative phosphorylation: the generation of ATP is driven by the flow of electrons. ADP + Pi, forming ATP

Where does pyruvate oxidation take place?

Mitochondrial matrix

What are the inputs and outputs of pyruvate oxidation?

Inputs: 2 CoA, 2 Pyruvate, 2 NAD+ Outputs: 2 Acetyl CoA, 2 CO2 (exhaled out), 2 NADH

Is any ATP made by pyruvate oxidation?

No