Bio Chp 2 Molecular Biology

Question 1

What is the chief concern of Molecular Biology?

Answer 1

It is the study of the interactions between the various systems of a cell. For example, the interaction between DNA, RNA, and protein biosynthesis. It answers questions like how these interactions are regulated and how they proceed. It is concerned with the genesis and function of the molecules at work.

Question 2

What is another what to discuss the study of Molecular biology?

Answer 2

Possible answer: It is the study of the molecular underpinnings of the processes of transcription, translation, replication, and cell function.

Question 3

What is the central dogma of molecular biology?

Answer 3

The central dogma of molecular biology deals with the transfer of sequence information in a cell from DNA to RNA to Protein. Simply put, “DNA makes RNA makes Protein.” However, this is indeed an over simplification. All cells are believed to have the general flow of sequence information: DNA -> RNA -> Protein. And some special cases have been observed to demonstrate the flow of information from RNA -> DNA, RNA -> RNA, and DNA -> Protein. However, it is believed and not observed yet that there is any flow of information from protein -> protein, dna, rna.

Question 4

Where in the cell does transcription take place?

Answer 4

The nucleus

Question 5

Around what are chromosomes wrapped?

Answer 5

Histones

Question 6

What molecule grabs onto DNA and encodes it into RNA in the transcription process?

Answer 6

RNA polymerase

Question 7

To what end does RNA polymerase add nucleotides when encoding RNA from DNA?

Answer 7

The 3’ end.

Question 8

How does DNA replication occur? DNA->DNA

Answer 8

A complex of proteins called helicase unwind DNA, then use DNA polymerase and its associated proteins to replicate the master template.

Question 9

What is the term used for molecules that aide RNA polymerase in transcription?

Answer 9

transcription factors

Question 10

What is the difference between translation in eukaryotic and prokaryotic cells?

Answer 10

Eukaryotic cells have a nucleus. So translation takes place outside of the nucleus at the ribosomes. Prokaryotic cells have no such cellular boundaries and as such transcription and translation ‘happen next to each other.’

Question 11

How is mRNA read by the ribosome?

Answer 11

It is read in triplets of base pairs called codons.

Question 12

What is the start codon for reading mRNA?

Answer 12

AUG

Question 13

For what amino acid does the start codon of mRNA code? Is this the only amino acid that the start codon codes for?

Answer 13

methionine; yes

Question 14

With some exceptions, how many nucleic acids code for an amino acid?

Answer 14

3

Question 15

Does THE genetic code exist? Are there exceptions

Answer 15

In fact, it can be said that THE genetic code exists. Because the vast majority of genes are encoded by the same code. What does this mean? This means the relationship between what codons map to what amino acids is roughly constant between organisms. However, we know, for example that mitochondria and chloroplasts use different genetic codes.

Question 16

What do we call the transfer of information from RNA to DNA?

Answer 16

reverse transcription

Question 17

What enzyme mediates reverse transcription?

Answer 17

reverse transcriptase

Question 18

What is an example of a biological agent responsible for reverse transcription?

Answer 18

Retroviruses cause reverse transcription. An example of such a virus is HIV.

Question 19

What is a retrotransposon?

Answer 19

This is a chunk of DNA, that transcripts into mRNA, which then via reverse transcriptase (like a retrovirus) is inserted back into the DNA at a different location in the DNA resulting in multiple copies and possibly mutation. This is a relatively stable form of mutation because the transposon can always be read into and will insert itself back into the genome– so called ‘jumping genes.’

Question 20

What is a telomere?

Answer 20

It is a repetitive region of nucleotides at the end of each chromatid. Its function is to prevent the fusion of chromatids, and to protect the chromatid from deterioration.

Question 21

Why are telomeres needed?

Answer 21

During DNA replication, the response enzymes cannot read to the very end of the chromosome. So during duplication a chromosome is shortened. So the telomere provides a discardable buffer at the end of the chromosome, so that no genetic information is lost.

Question 22

What enzyme replenishes telomeres? Why is it needed?

Answer 22

telomerase reverse transcriptase. It is needed because after each replication the telomere is shortened.

Question 23

What is the primary way that viruses copy into each other?

Answer 23

RNA-> RNA replication

Question 24

What enzyme catalyzes RNA-> RNA replication?

Answer 24

RNA-dependent RNA polymerase aka RNA replicase.

Question 25

What can modify gene expression without altering the genes themselves?

Answer 25

DNA Methylation and other similar modifications

Question 26

What do we a call a change in gene expression that is not caused by a change in genotype AND is heritable? What is an example?

Answer 26

epigenetic ; DNA methylation

Question 27

If there is a change in gene expression that is not caused by genetic mutation but IS NOT heritable, what do we call it?

Answer 27

somatic epitype

Question 28

Besides DNA methylation, what is one other mechanism of epigenetic/somatic epitype genetic modification?

Answer 28

Chromatin modifications

Question 29

What is a prion?

Answer 29

It is a proteinaceous infectious agent.

Question 30

How is a prion theorized to work?

Answer 30

It is a misfolded protein that stimulates other proteins of its kind to change conformation. Since conformation is everything for pteoins. It makes sense that such prions could adversely affect and organizes health

Question 31

Why are prions not a violation of the central dogma of molecular biology?

Answer 31

While they change the conformation of sister proteins, they do not change its primary structure or thereby 'recode' the protein itself.

Question 32

What is the heterodimer model?

Answer 32

It explains how prions replicate in a protein-only manner. In this model, PrP^Sc (the infectious conformation of the common protein PrP^c) binds to PrP^c and catalyzes its conversion into PrP^Sc. Then the two PrP^Sc molecules go forth and repeat the process. The problem with this model is that it requires PrP^Sc to be an extraordinarily effective catalyst because its spontaneous appearance must be incredibly rare to agree with observations.

Question 33

What is the fibril model of prions?

Answer 33

This model assumes that PrP^Sc exists only as fibrils. And that the fibril ends bind to PrP^C and convert it to PrP^Sc. However, this would suggest a linear growth of the PrP^Sc. So in addition, there must be breakage of the fibrils in order to agree with the observed exponential growth of PrP^Sc.

Question 34

What is the RNA world hypothesis?

Answer 34

This hypothesis suggests that RNA based life predated the current DNA based life. Thus, RNA provided the genetic material, the structural and catalytic molecules rather than dividing them between DNA and proteins as is today.

Question 35

What can RNA do that DNA cannot and how does that relate to pre-cellular life?

Answer 35

In addition to storing genetic information, RNA can also catalyze reactions as an enzyme. Therefore, it may have been able to support life before the cell as in any chemical soup it could act as both information storage and metabolism.

Question 36

What are ribo-enzymes? Is there an example of a ribozyme in present day cells?

Answer 36

In general, terms it is an RNA molecule that is capable of catalyzing certain biochemical reactions analogous to the action of protein enzymes. Examples of ribozymes include hammerhead ribozyme, VS ribozyme, and the hairpain ribozyme. In fact, in the laboratory ribozymes capable of catalyzing their own synthesis under very specific conditions have been created. An example of RNA polymerase ribozyme. One example of ribozymes in present day cells is the functional part of the ribosome. It is composed of tertiary structural motifs that are often coordinated to metal ions such as Mg2+ as cofactors.

Question 37

What are riboswitches?

Answer 37

This is a regulatory segment of mRNA that binds to a small molecule. This binding causes a change in the production of the proteins encoded by the mRNA. This means then that the mRNA is sensitive to concentrations of small molecules in the environment and can adapt its protein synthesis accordingly. This is a novel function of RNA beyond protein synthesis, catalysis, and binding to other RNA and protein molecules.

Question 38

What would a RNA world require?

Answer 38

A) prebiotic/abiotic synthesis of RNA monomers AND their activiation B) assembly of the monors into oligomers that are further elongated associated with metal ions as catalysts C) the ligation (or linkage) or additional monomers or oligomers. Catalytic activity from RNA requires at least 20-30 nucleobase fragments and often more than 100) D) These longer RNA polymers are self-catalyzing-- that is they synthesis their own reproduction. E) Once there are a critical number of RNA molecules and catalytic RNAs (ribozymes!) then they can sustain their own replication in a 'prebiotic' environment.

Question 39

What is ligation?

Answer 39

The joining of two DNA strands or other molecules by a phosphate ester linkage.

Question 40

What is phylogeny?

Answer 40

The study of the evolution of a group of organisms as opposed to a single organism, for example, what/when was their common ancestor, for how long have they diverged, what was the divergence?

Question 41

How long ago did the first life appear on Earth?

Answer 41

4 billion years

Question 42

For how long since life appeared on Earth was all life single-cell microorganisms?

Answer 42

3 billion years

Question 43

What are the dominant forms of single celled life?

Answer 43

archaea and bacteria

Question 44

What is endosymbiosis?

Answer 44

The process by which any organism lies within the body or cells of another organism. Some endosymbioses are obligatory in the sense that either the host or endiosymbiont will die without the other. The most common example of endosymbiosis is mitochondria or chloroplasts without which human or plant cells could not survive.

Question 45

What is the second great evolutionary divergence?

Answer 45

The divergence between bacteria and archaea

Question 46

What are the differences between bacteria and archaea?

Answer 46

Initially archaea were simply classified as bacteria. However, this lack of distinction is obsolete. Archaea possess genes and metabolic pathways that more closely resemble those of eukaryotes than bacteria. In particular, the enzymes they employ in transcription and translation are more like eukaryotes than bacteria. In addition, there cell membranes rely on ether lipids. And in constrast to eukaryotes, archaea use a greater diversity of energy sources using not only organic compounds, but metal ions, hydrogen gas, and sunlight. The sequencing of ribosomal DNA was the maintain experimental method used to discover a strong distinction between archaea and bacteria. Methanogens in the human gut are an example of archaea.

Question 47

What is a hydrogenosome?

Answer 47

It is another membrane bound organelle of a cell similar to mitochondria that was likely absorbed through endosymbiosis. It produces energy under oxygen-deficient conditions and releases H2 in the process. Roughly speaking, the hydrogenosome breaks down pyruvate ultimately into ATP.

Question 48

What is morphology?

Answer 48

It is the study of the shape/geometry in this case cells.

Question 49

To what morphology does coccus correspond?

Answer 49

Spherical geometries

Question 50

To what morphology does bacillus correspond?

Answer 50

round-ended cylinders

Question 51

To what morphology does spirochetes correspond?

Answer 51

helically twisted cylinders

Question 52

In terms of morphologies, what does the prefix diplos mean?

Answer 52

It will mean taking two bacteria and combining them either two coccus, two bacillus, possibly two spirochetes.

Question 53

In terms of morphologies, what does the prefix tetrads mean?

Answer 53

From the greek, it will be four units of bacteria.

Question 54

In terms of morphologies, what does the prefix staphylos mean?

Answer 54

It means an aggregate of bacteria forming a triangularly shaped structure.

Question 55

In terms of morphologies, what does the prefix streptos mean?

Answer 55

It will be a linear combination of bacteria.

Question 56

In terms of morphologies, what does the prefix palizadas mean?

Answer 56

For bacillus, it means roughly a stacking of the bacteria making parallel their long axes.

Question 57

In terms of morphologies, what does the prefer sarcina mean?

Answer 57

It's a three dimensional two stack of tetrads.

Question 58

Do bacterial have membrane-bound organelles in their cytoplasm?

Answer 58

In general, no

Question 59

What kinds of structural complexity do bacteria have?

Answer 59

They have a prokaryotic cytoskeleton and specific localization of proteins resulting in so-called 'bacterial hyperstructures'

Question 60

Describe the encapsulation of a bacteria

Answer 60

In contract to animal eukaryotes, bacteria have a cell wall and a cell membrane. Some bacteria have two cell membranes.

Question 61

What is the difference between Gram positive and Gram negative bacteria?

Answer 61

Experimentally, the difference is that in the staining procedure is that Gram-Negative bacteria do not retain the crystal violet dye used to treat the bacteria. This is because Gram Negative bacteria so not have a thick Peptidogylcan outer layer in which the violet dye gets caught and cannot be washed away. Instead, they have a much less penetrable cell wall. We say that the peptidoglycan layer of the Gram Negative bacteria is single layered whereas the Gram Positive bacteria has a multilayered peptidoglycan layer.

Question 62

Explain the encapsulating structure of Gram Positive bacteria.

Answer 62

These bacteria have a thick peptidogylcan layer on the outer surface that forms the wall of the bacteria. Then there is a periplasmic space. And then there is the inner cell membrane.

Question 63

Explain the encapsulating structure of Gram Negative bacteria.

Answer 63

In contrast, to Gram Positive bacteria, Gram Negative bacteria have an outer membrane consisting of lipopolysaccharide and protein. Internal to this is the periplasmic space, then the peptidogylcan layer, and then the periplasmic space, which is then followed by the internal plasma membrane of the cell. Given the thinness of the peptidoglycan layer in the periplasmic space of the Gram Negative bacteria, the violet staining dye may easily be washed away by alcohol-acetone.

Question 64

What are four methods commonly employed by antibiotics?

Answer 64

1) Inhibition of cell wall synthesis 2) Impairment of cell membrane permeability 3) Inhibition of transcription 4) Inhibition/disturbance of translation

Question 65

What are example antibiotics that inhibit cell wall synthesis?

Answer 65

Penicillins, cycloserin, cephalosporins

Question 66

What are example antibiotics that impair the permeability of cell membranes?

Answer 66

polymycin, colistin, tyrothricin

Question 67

What are example antibiotics that inhibit transcription?

Answer 67

actinomycins

Question 68

What are example antibiotics that inhibit/disturb translation?

Answer 68

Puromycin, tetracyclins, streptomycin, chloramphenicol

Question 69

What is an example of a kind of intracellular structure that a bacteria has? What is its structure?

Answer 69

Bacteria have micro-compartments. One example is a carboxysome. These are compartments surrounded by polyhedral protein shells.

Question 70

What is the function of a carboxysome?

Answer 70

It fixes carbon.

Question 71

What are flagella? What is their primary function? What is their secondary function?

Answer 71

Flagella are helical filaments that rotate like screws. Their primary function is motility in a cell. Their secondary function is as a sensor to detect chemical and temperature changes in the environment.

Question 72

What term is used to describe a single helical filament for a flagella?

Answer 72

Monotrichous

Question 73

What term is used to describe multiple flagellum at the same location on the cell membrane?

Answer 73

Lophotrichous

Question 74

What is the term used to describe flagella at opposite ends of the cell?

Answer 74

Amphitrichous

Question 75

What is the term used to described flagella that project in all directions?

Answer 75

Petritrichous

Question 76

What are phototrophs?

Answer 76

Their source of energy is sunlight

Question 77

What are lithotrophs?

Answer 77

Their source of energy is inorganic compounds.

Question 78

What are organotrophs?

Answer 78

Their source of energy is organic compounds.

Question 79

What are heterotrophs?

Answer 79

Their source of carbon is organic compounds.

Question 80

What are autotrophs?

Answer 80

Their source of carbon is carbon fixation.

Question 81

How do archaeal membranes differ from those of bacteria?

Answer 81

While bacterial membranes have inner layers composed of fatty acid chains (non-polar), archaeal membranes have isoprene chains inside. Furthermore, archaeal membranes have ether linkages whereas bacterial membranes have ester linkages. Archaeal membranes have L-glycerol moeity whereas bacterial membranes have D-glycerol moeity, but they both have phosphate groups.

Question 82

Which is more chemically resistant the ether bonds of the archaeal membrane or the ester bonds of the bacterial membrane? What does this suggest?

Answer 82

The ether bonds are more chemically resistant. This suggests that the archaeal bacteria are possibly able to survive more extreme environments.

Question 83

What is a possible advantage of the isoprene chains in archaeal membranes that typical fatty acid tails in bacterial and eukaryotic membranes do not have?

Answer 83

The isoprene chains have extensive side chains, which may prevent leakage in the case of high temperatures.

Question 84

Can you have a monolayer membrane? In what organisms? How?

Answer 84

Yes, a lipid monolayer for a membrane is possible in archaea. The archaea fuse the tails of two independent phospholipid molecules into a single molecule with two polar heads. This fusion makes the membrane more rigid and possibly more able to resist harsh environments.