Biology 172 Exam #2 University of Michigan

What are the three energy molecules in the cell?

Glucose, NADH, ATP

Reaction for ATP

ATP + H20 ---> ADP + P

What is phosphorylation?

The addition of a phosphate group

What bonds have high free energy? Low free energy?

High free energy= nonpolar and low free energy= polar

What is an important source of chemical potential energy?

Electrons

What electrons have the most potential energy?

The ones farthest from the nucleus

What does OIL RIG mean?

Oxidation is losing and reduction is gaining

What are photoautotrophs)?

They use carbon from CO2 to create energy/feed themselves

What are heterochemotrophs?

They use carbon from organic compounds to create energy/feed themselves

What is the central atom in heterotroph metabolism?

Glucose

What are the three steps of cellular respiration?

Glycolysis, Citric Acid Cycle, and Electron Transport Chain

Describe the first phase of glycolysis (energy investment phase)

Glucose comes into the cell and has two phosphate groups added to it (high energy). The enzyme that adds the second phosphate to create fructose 1-6, bisphosphate is called phosphofructokinase. Two ATP created

What are the key energy carrying molecules?

NAD+ and FAD (electron carriers)

What is the reduced form of NAD+?

NADH and H+ (reduced form) have high energy

What happens with the enzymatic pathway in glycolysis?

ATP is the end result of the pathway, and goes back to the beginning to inhibit phosphofructokinase.

How does ATP regulate phosphofructosekinase?

Phosphofructosekinase is inhibited by large amounts of ATP because it has an active site and regulatory site which both bind ATP (allosteric inhibitor) and when there are high amounts of ATP it binds to the regulatory site and slows things down because the cell has more energy than it needs and glucose doesn't need to be broken down.

Describe phase 2 of glycolysis:

6 carbon molcules are cleaved into two 3 carbon molecules (glyceraldehyde 3-phosphate) no ATP created but no ATP consumed either

Describe phase 3 of glycolysis (energy payoff phase):

The two glyceraldehyde 3-phosphates enter this step and through enzyematic reactions two ATP are produced and 1 NADH

What is substrate level phosphorylation?

Enzyme mediated reaction that binds to the substrates (ADP and glyceraldehyde 3-phosphate) and has a hydrolysis reaction take place to generate ATP.

Net products of glycolysis:

2- ATP, pyruvate, NADH

What is anaerobic?

Process happening in the absence of Oxygen.

What does the Citric Acid Cycle do?

Extracts energy from pyruvate.

Where does the Citric Acid Cycle occur?

In prokaryotes-cytosol and in eukaryotes-mitochondrial matrix

Describe Pyruvate processing:

Pyruvate enters the mitochondria and coenzyme A(derived from Vitamin B) is attached which converts pyruvate to acetyl CoA and CO2 is released

Describe the Citric Acid Cycle:

Acetyl CoA enters from the break down of pyruvate and produces 8NADH+H+, 2FADH2, 6CO2 and 2ATP (for two molecules of pyruvate)

Describe The Electron Transport Chain (aka Oxidative Phosphorylation):

The ETC uses a proton gradient to produce ATP. FADH2 donates electrons to complex II and NADH donates its electrons to Complex I. The electrons are moved down the chain and proton move from inside to the inner membrane space. O2 is the final acceptor of the electrons (forms water) The protons then move back down the electrochemical gradient into the membrane via ATP synthase which creates ATP (approx. 28 ATP per glucose)

Where is the ETC?

Inner membrane of the mitochondria (cristae)

What is fermentation?

When oxygen isn't available, instead of pyruvate going on to the Citric Acid Cycle, it becomes an electron acceptor in fermentation where it accepts electrons from NADH which needs to be oxidized (NAD+) so it can return to glycolysis and lactic acid forms.

What is the photosynthesis equation?

6CO2 + 6H2O + light -----> C6H12O6 + 6O2 (CO2 is reduced and H2O is oxidized)

Where does photosynthesis take place?

In the chloroplasts

Where do the light reactions take place?

In the thylakoid membrane

Describe relationship between genes, chromosomes, proteins, and DNA:

DNA is what makes up chromosomes and chromosomes are composed of smaller units called genes which code for proteins

Describe Griffith's experiment:

It involved the transformation of Streptococcus and it's two forms, pathogenic and non. There were two colonies, smooth (capsule around them) and rough (no capsule). When S cells were injected, the mouse died, when R cells injected mouse lives. S cells were heat killed then injected and the mouse lived. When the heat killed S cells were mixed with the R cells and injected, the mouse died and living S cells were found in the blood. Proved that dead S bacteria had strains to transform R bacteria into S. Evidence that DNA is the genetic material.

Describe Avery, McCarty, and Macleod's experiment:

Three basic hypotheses: Transforming factor is a) protein b)RNA c)DNA. Experiment began with heat killed streptococcus cells with lipid and carb macromolecules removed. An enzyme was added to remove a different material from each of the three cells, leaving one cell with RNA and DNA another cell with DNA and protein, and the last cell with RNA and protein. The RNA/protein cell saw no transformation, proving that DNA is the transforming factor.

Describe Hershey and Chase's experiment:

Designed to determine what part of a virus (protein or nucleic acid) enables the "take over" of host cells. The genetic component of T2 virus cells injected into host cells. Proteins contained element Sulfur and DNA contains element Phosphate. Bacteria infected with either radioactive 32P or 35S. The phage were shook off and the bacteria was examined for radioactive labels inside. 32P was found inside and 35S was not. Proved DNA not proteins is passed onto offspring.

What did Watson and Crick's DNA model suggest?

Possible copying mechanism and info contained in nitrogenous base pairings.

What is replication?

The copying of a DNA strand to create the complimentary strand.

What direction does replication proceed?

5prime to 3prime

How many points of origin do bacteria have? Eukaryotes?

Bacteria= single point
Eukaryotes= multiple

What is the first step of replication?

DNA is opened, unwound, and primed.

What is responsible for opening DNA?

Helicase

What does topoisomerase do?

Relieves the tension from the untwisting forces

What do single-strand DNA binding proteins do?

SSBPs stabilize individual strands of the helix

What must happen to RNA primer?

RNA primer must be synthesized by primase

What is the overall direction of replication?

5prime ---> 3prime

How does the synthesis of the lagging strand work?

Okazaki fragments are synthesized 5prime ---> 3prime then DNA polymerase removes ribonucleotides of primer replaces them with deoxyribonucleotides then ligase closes gap in sugar-phopshate backbone

How does replication at the end work?

Telomerase works to extend the end of the strand and then the strand is primed as normal

What problem arises when telomerase doesn't work?

Premature aging

What is transcription?

RNA synthesized by a DNA template

Where does transcription take place?

In specific portions of the genes that start with TATA boxes

What do promoters do?

Direct the RNA polymerase on where to bind

Describe transcription:

RNA polymerase unwinds the DNA, and RNA polymerase adds nucleotides to the 3prime end (direction is 5 to 3) (remember A pairs with U) terminating site is reached and RNA chain is released

What is RNA processing?

RNA in eukaryotes must be processed (not in prokaryotes) addition of "cap" to 5prime and polyA "tail" to 3prime in addition to RNA splicing (removal on introns) carried out by spliceosome

What is translation?

Synthesis of a polypeptide using info from RNA

Where does translation occur?

The cytosol

What are the three types of RNA?

mRNA: the sequence of base pairs (codons) that code for amino acids
rRNA: the ribosomal structure that carries out the process of translation
tRNA:

What is the genetic code?

Relationship between nucleotide sequence and amino acid sequence

Genetic code facts:

-triplet code (series of three base pairs code for one amino acid)
-has no ambiguity
-has redundancy
-includes a specific start codon (AUG)
-includes three stop codons (UGA, UAA, UAG)
-non-overlapping
-continuous

What is the structure of tRNA?

-The 3prime end attaches to the specific amino acid the mRNA codon codes for
-The anticodon (complimentary to codon) attached at bottom loop

How is the amino acid attached to tRNA?

Aminoacyl tRNA synthase

What is the structure of the rRNA?

Composed of a large subunit and a small subunit(where the mRNA is located/read), as well as three sites for the tRNA

What are the three sites in rRNA where the tRNA enters?

-The E Site (the exit site, hold tRNA that is getting ready to exit ribosome)
-The P site (hold tRNA that is transferring its attached amino acid to the growing polypeptide chain)
-The A site (holds aminoacyl tRNA, aka holds the tRNA next in line after the one in the P site moves to the E site)

How is translation initiated?

The small subunit of rRNA is attached to the 5prime end of mRNA and when the start codon (AUG) is read the initial tRNA brings the amino acid into the large subunit and begins the chain

How is translation terminated?

A stop codon is read and the proper amino acid is brought in and the new polypeptide chain is released and the remaining components dissociate.

What is the region on mRNA that is read by ribosomes called?

The coding region

How common are errors in replication?

Very rare about 1 in 100,000

How can errors be initially caught?

During replication DNA polymerase can proofread and check for errors made and fix them

If DNA polymerase misses an error what happens?

Errors can be recognized by other enzymes and fixed

How can DNA acquire damage?

-Spontaneously (errors in replication)
-Mutagens (x-rays, UV light, etc)

How does UV light cause DNA damage?

Thymines next to each other are damaged and cause a bulge in the DNA (thymine dimers)

What is the mismatch repair system?

Mismatch repair enzymes help remove mismatched base pairs by breaking the phosphate backbone some distance away from the error and then an eznyme comes in and removes the nucleotides and another enzyme closes the gap by resynthesizing the sequence and fixing the mismatch

What is excision repair?

Enzymes detect irregularity in DNA structure and cut the damaged strand and the nucleotides are excised. DNA polymerase fills in the gap in the 5 to 3 direction and ligase links the new and old nucleotides

What is a synonymous (silent) mutation?

A change in base pair that doesn't result in a change in the amino acid the codon codes for

What is a non synonymous (missense) mutation?

A change in base pair that causes a change in the amino acid the codon codes for

What is a nonsense mutation?

A change in base pair that results in the coding for a stop codon

What is a frameshift mutation?

The insertion or deletion of one of two nucleotides that causes a shift in the reading/coding frame (there is no longer a number of nucleotides divisible by three so there will be no way to code for all of them, example 31 nucleotides means 10 codons and one extra nucleotide that can't be read)

What are large scale mutations?

Insertion or deletion of many nucleotide base pairs

Can a change in just one amino acid make a difference?

Yes an example of this is the fact cystic fibrosis is caused when one amino acid is missing because the three nucleotides that code for it were deleted

NADH is...

The reduced form of NAD+

What are products of the light dependent reactions?

NADPH, ATP,

Where do the light reactions begin?

In Photosystem II, the electrons are excited when sunlight strikes them.

What wavelength of light does Photosystem II accept?

680 nm (this wavelength is higher energy than Photosystem I)

What wavelength of light does Photosystem I accept?

700 nm (this wavelength has lower energy than the wavelength in Photosystem II)

What portion of the light reactions is cyclic?

Photosystem I

What is the noncyclic part of the light reactions?

Photosystem II

What happens in the first part of the light reactions? (Photosystem II)

680 nm light strikes the photosystem and excites the electrons (increases their energy) which are then passed onto pheophytin which moves them down along the ETC and generates ATP very similar to how it is generated in the ETC in cellular respiration.

Where do the electrons in Photosystem II come from?

They come from the hydrolysis of water, and the electrons attached to Oxygen which is why oxygen is a product of photosynthesis

How are the protons pumped in the ETC?

From the thylakoid membrane to the thylakoid lumen

What happens in the second part of the light reactions? (Photosystem I)

700 nm light strikes the photosystem and excites the electrons which hooks up with a molecule called ferredoxin that dumps it onto the electron carrier NADPH which goes on to the Calvin Cycle

What are the three fates for excited electrons in photosynthetic pigments?

Fluorescence- photon of light hits the electron, its energy shoots way up emits a little light and goes way back down
Resonance- photon of light hits the electron and it bounces around until it hits the reaction site (this is what happens in photosynthesis)
Reduction/Oxidation- electron is excited then transfred to a new compound

What are the three types of ATP production?

Oxidative phosphorylation (happens in ETC in inner membrane of mitochondria)
Substrate level phosphorylation (happens in glycolysis in cytosol)
Photophosphorylation (happens in ETC of thylakoid membrane)

Where does the Calvin cycle take place?

The stroma of the cholroplast

What is another name for the Citric Acid Cycle?

The Krebbs Cycle

What is the first step of the Calvin cycle?

Carbon fixation- CO2 is added to the 5-carbon compound RuBP and is catalyzed by the enzyme rubisco. This requires ATP (2 ATP per cycle, 6 total because there are 3 CO2 molecules) and the end result is 3 PGA.

What is step two of the Calvin cycle?

Reduction-electrons from NADPH generate 3-carbon sugars called G3P from PGA. A total of 6 G3P are made (1 NADPH are required for each G3P, 6 G3P are made, so 6 NADPH are needed in total)

What becomes of the 6 G3P's created?

One of the G3P exits the Calvin cycle and goes on to create macromolecules (glucose, fructose, etc) and the other 5 go on to the next step of the Calvin cycle to be recycled

What is step three of the Calvin cycle?

Regeneration- RuBP is regenerated from G3P which requires 3 ATP

What does the Calvin cycle return to the light reactions?

NADP+, ADP, Pi