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CLEMSON / Genetics / GEN 3000 / What is griffith?

What is griffith?

What is griffith?

Description

School: Clemson University
Department: Genetics
Course: Fundamental Genetics
Professor: Kate tsai
Term: Fall 2015
Tags: Genetics
Cost: 50
Name: GEN 3000 Study Guide Exam 3
Description: This study guide covers all of chapters 9-11. This is based off of the study guide Dr. Tsai has posted. This does not include chapter 12, since we have not finished this chapter just yet. I will be upl
Uploaded: 03/07/2016
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Key Terms Imporant People Key Ideas


What is griffith?



11

Study Guide Exam 3: Chapters 9-12 

Chapter 9:  

1. Important People:

a. Griffith: Proposed the Transforming Principle 

i. Transforming Principle: early name for DNA. At the time of this  

proposed concept, they did not know that DNA is what held the genetic  

information. However, they knew that something could transform one type  of bacterial into another.  

b. Avery, MacLeod, and McCarty: isolated the transforming bacteria. Determined  that DNA is the “Transforming Principle” in bacteria. 

i. The experiment: Destroyed each component of bacteria that could be the  Transforming Principle (RNA, DNA, and proteins) to determine which  


What is transforming principle?



component was the one that is transforming the bacteria. They destroyed  

one of the components and left the others alone. If they type of bacteria  

doesn’t change when the component was destroyed, then this would be the  Transforming Principle. They conducted this experiment with a strand of  pneumonia. (Explained again and more in depth below in the Key Ideas

section.)  

c. Hershey and Chase: conducted tests to determine the Transforming Principle in  viruses, (proteins or DNA).  

i. The experiment: Resulted in them determining that DNA is the  

Transforming Principle in viruses. They conducted their experiment with a  T2 Bacteriophage and E. coli. They used radioactive labeling to determine  which one is the Transforming Principle. (Explained again and more in  


What is viral neutralization?



Don't forget about the age old question of What is low viscosity?

depth below in the Key Ideas section.)  If you want to learn more check out What is foreign markets?

d. Chargaff: isolated DNA and determined the base pairing of DNA, called this  Chargaff’s Rule. Disproved the previous belief of Tetranucleotide Theory.  i. Chargaff’s Rule: Adenine bonds with Thymine. Guanine bonds with  Cytosine by discovering different amounts of these base pairings.  We also discuss several other topics like What are teratogens?

ii. Tetranucleotide Theory: DNA has four bases that are in a fixed sequence  (base pairing) and of equal amounts.  

e. Watson and Crick (Wilkins and Franklin): Franklin used X-rays to take  photographs of DNA, a process called crystallography. The photo she took was  then given to Watson and Crick (by her boss Wilkins). This was the missing piece  in Watson and Crick’s work. They were then able to build the first model of  DNA. 

2. Key Ideas:

a. Nucleic Acids: Can be DNA or RNA  

i. Nucleotide: this is the basic component of DNA.  

1. Consists of: consists of a sugar, phosphate, and a base.  

2. For DNA: the sugar is deoxyribose; the bases are adenine,  Don't forget about the age old question of What are the two ways o2 is transported in blood?

thymine, guanine, and cytosine  

3. For RNA: the sugar is ribose; the bases are adenine, uracil  

(replaces thymine), guanine, and cytosine.  

ii. Purine: a nitrogenous base that has two rings and is bigger in size.  

1. Consists of: adenine and guanine.

iii. Pyrimidine: a nitrogenous base that only has a single ring and is smaller  in size.

1. Consists of: Cytosine, Thymine/Uracil

iv. Nucleotide Components: consists of a sugar, phosphate group, and a  base.

1. Bases: A, T/U, G, C

2. Sugar: deoxyribose or ribose (for DNA or RNA respectively) 3. Phosphate group: gives the negative charge. Consists of a  

phosphate surrounded by oxygen.

a. Monophosphate: is when a single phosphate group is  

attached to a sugar

b. Phosphodiester Bonds: the bond between a phosphate  

group and a sugar of different nucleotides. Very strong  

bond

b. Transforming Principle: A concept that Griffith proposed.

i. Griffith’s experiment:

1. Used a strain of bacteria that causes pneumonia. A virulent strain  has a smooth coat (the lethal strain). An avirulent strain has a  If you want to learn more check out How does history as a social process involve people in three distinct capacities?

rough/lack of coat (the nonlethal strain).

2. Griffith noticed that if a mouse gets injected with a lethal smooth  strain that has be heat killed, the mouse does not die.

3. Griffith also noticed that if a mouse gets injected with a mixture of  lethal smooth strain and nonlethal rough strain, the mouse dies.

4. Why? He proposed that something in the mixture “transforms” the  rough strain into a smooth strain, which is what causes the mouse  to die. He called this the Transforming Principle. However, he did  not know what was doing the transformation. We also discuss several other topics like What are the 5 primary tastes?

ii. Avery, Macleod, and McCarty’s experiment: Wanted to determine the  Transforming Principle of bacteria.

1. They used the same strains of pneumonia that Griffith used (the  smooth lethal strain and the rough nonlethal strain)

2. Took the filtrate of the lethal smooth strains (they knew that  

something within this filtrate is the Transforming Principle) and  

destroyed individual components in separate experiments to  

determine what was doing the transformation. (The components  

were DNA, RNA, and proteins.)

3. In the first experiment, they destroyed RNA within the filtrate  through the use of RNase. They then put this filtrate in with the  

nonlethal rough strain. This resulted in a mixture that they then  

injected into a mouse to see if the mouse would live or die. The  

mouse died, meaning that the rough strain transformed into the  

smooth lethal strain. RNA is NOT the Transformation Principle.

4. In the second experiment, they destroyed proteins within the  filtrate through the use of protease. They then put this filtrate in  

with the nonlethal rough strain. This resulted in a mixture that they

then injected into a mouse to see if the mouse would live or die.  The mouse died, meaning that the rough strain transformed into the  smooth lethal strain. The proteins are NOT the Transformation  Principle.

5. In the third experiment, they destroyed DNA within the filtrate  though the use of DNase. They then put this filtrate in with the  nonlethal rough strain. This resulted in a mixture that they then  injected into a mouse to see if the mouse would live or die. The  

mouse lived, meaning that the rough strain did not transform into  the smooth lethal strain. DNA IS the Transformation Principle. 6. Conclusion: When DNA was destroyed, the filtrate of smooth  lethal strain did not transform the nonlethal rough strain. Resulting  in the mouse living. This means that the DNA is what “transforms”  the rough strain, therefore, it is the Transformation Principle. 7. Issues with this study: though the data backed up this claim,  many people did not want to believe DNA could be the  

Transforming Principle. This is due to the belief that DNA was not  complex enough to be the Transforming Principle. The team had to  replicate the experiment many times to get people to believe the  data.

iii. Hershey and Chase: Wanted to determine the Transforming Principle of  viruses.

1. Knows that something happens within a cell to allow for  replication of a virus to take place when a virus infects a cell.  Proteins or DNA is what causes this “transformation.”

2. Proteins have sulfur in them and DNA has phosphorus in it. 3. Took the virus and labeled the sulfur/phosphorus of the  

proteins/DNA as radioactive. Allowed for the viruses to infect an  unlabeled nonradioactive E. coli cell. The virus multiplied and then  it was blended, and then placed in a centrifuge. The heavy portion  will sink to the bottom while the lighter portion will go on top.

a. For protein/sulfur: the radioactivity was on top within the  protein coats and not in the phage that was produced.

b. For DNA/phosphorous: the radioactivity was on the  

bottom within the phage that was reproduced and not on  

tope with the coats.

4. Conclusion: DNA is what makes the next generation of viruses,  therefore, it contains genetic material (it is the Transformation  Principle).

iv. Eukaryotic Evidence: this was done to support that DNA contains the  genetic information.

1. Was indirect evidence

2. UV light causes mutations in heredity, meaning it can change  heredity components.

3. Whatever is absorbing the UV light at a certain wavelength is what  is being mutated (is what contains the genetic information).

4. Nucleic acids and proteins both absorb UV light, but nucleic acid  absorbs UV light at the same wavelength that UV light causes  

genetic mutations.

5. Conclusion: DNA contains genetic information/is the  

Transforming Principle.

c. Chargaff’s Rule: Chargaff established that Adenine binds with Thymine and  Cytosine binds with Guanine. He also disproved the Tetranucleotide Theory. i. Looked at the ratios of nitrogenous bases of different organisms. Noticed a  1:1 ratio between bases in E. coli.

ii. Noticed that this ratio changed as the organism changes.

1. Conclusion: Tetranucleotide Theory cannot be true, since the ratio  of the bases is not constant in all organisms.

iii. Noticed a common ratio between Adenine to Thymine and Guanine to  Cytosine.

1. Conclusion: This means that for every Adenine there is a Thymine  and for every Cytosine there is a Guanine. Therefore: A bonds with  T and G bonds with C.

d. Franklin/Wilkins and Watson/Crick: with the research of both people, the first  model of DNA was created.

i. Franklin’s photograph showed the required width that DNA would have to  be.

ii. Watson and Crick then used pyrimidine and purines to determine what  pairing is being down to reach this required width.

1. Paired a pyrimidine with a pyrimidine and resulted in the DNA not  being thick enough.

2. Paired a purine with a purine and resulted in DNA being too thick. 3. Paired a purine with a pyrimidine and resulted in DNA being the  right width.

4. Remember: Chargaff’s Rule states that A bonds with T (Purine  bonds with Pyrimidine) and G bonds with C (Purine bonds with a  Pyrimidine)

iii. Conclusion: they were able to find out the way DNA is structured and  built the first model, their model is based on B-form DNA. (Discussed  down below). Also, they proved that Chargaff’s Rule is correct.

iv. Alpha Helix: the “backbone” (proteins and sugar) wraps around the  nitrogenous bases, does not twist.

e. DNA Characteristics:

i. Bonds of DNA:

1. Phosphodiester Bonds: the bond between a phosphate group and  a sugar of different nucleotides on a DNA strand. This is a very  

strong bond that makes up the “backbone” of DNA.

a. These are hydrophilic bonds, meaning that they are water  

loving. So they will wrap around the bases bonds, since  

these are hydrophobic.

2. Base Pairing Bonds: the bonds formed between base pairs are  hydrogen bonds. These are weak bonds that are hydrophobic,  meaning water fearing.

a. Cytosine and Guanine: cytosine and guanine bond  

together forming 3 hydrogen bonds.

b. Thymine and Adenine: thymine and adenine bond  

together forming 2 hydrogen bonds.

c. The C-G Bond is stronger than the T-A Bond!

i. This is due to the greater amount of hydrogen bonds  

in C-G.

ii. Directionality of DNA: DNA is antiparallel

1. Antiparallel: this means that the strands run parallel to each other  but in opposite directions.

2. DNA is read from 5’ to 3’

a. So, one strand is going 5’ to 3’ while the antiparallel strand  is going 3’ to 5’. However, DNA is still read in the 5’ to 3’  

direction (more on this subject in a later chapter).

3. Re-association: DNA wants to re-associate, meaning that when  one strand is by itself, it wants to pair its bases back up.

a. Reassociation Kinetics: How quickly can DNA renature? i. Double stranded DNA is denatured through heat,  

causing the strands to separate and become single  

stranded DNA

1. Breakage of the hydrogen bonds between  

base pairs, the phosphodiester bonds remain  

intact, meaning the that backbone does not  

break. This results into a single stranded  

DNA

ii. Single stranded DNA is allowed to cool, causing the  

DNA to want to renature into double stranded  

DNA.

1. The DNA wants to snap back together (re

associate)

iii. The time it takes for DNA to renature into double  

stranded DNA is measured to determine bases  

within the DNA

iv. Since there are 2 hydrogen bonds between A-T,  

then these bonds can be broken faster/easier than G

C, since these bases have 3 hydrogen bonds.  

1. The time it takes for A-T bonds to break is  

shorter and can be done at a lower temp.  

than G-C.

v. The graph that is produced from DNA being  

denatured to being renatured will have three gradual  

decreasing bumps.

1. First bump: is highly repetitive, meaning it  

will have a lot of copies of a base, therefore,  

the renature of this segment can be done  

quickly.

a. Why? Since it is highly repetitive,  

then there are a lot of areas that will  

match this, it doesn’t have to be an  

exact copy.

2. Second bump: moderately repetitive,  

meaning it will have repeats, but not as  

much as the first one. Can be still renatured  

quickly, but not as quick.

a. Why? Same as above, but the reason  

for it being slower is due to needing  

close to exact copies.

3. Third bump: unique, meaning that it only  

has one copy (no repeats). This takes time to  

be renatured.

a. Why? There is only one copy that  

will match with it.

4. DNA Structure Types:

a. B-form DNA: The DNA structure that Watson and Crick  made a model for.

i. Exists in the presence of water.

ii. Most stable of the DNAs under physiological  

conditions

iii. Alpha helix (right-handed)

1. Wrapping motion, not twisting

iv. The DNA that you commonly think of

v. Most important

b. A-form DNA: Located outside of the cell.

i. When the environment changes, the DNA structure  can modify.

ii. Shorter/wider than B-form

iii. Alpha helix (right-handed)

iv. Most likely does not exist in nature

c. Z-form DNA: dramatically changed structure

i. Found inside the cell

ii. Left handed helix

iii. Zig-zag backbone

iv. Sites of active genes can make Z-DNA

1. Regions of B-DNA can change to Z-form.

2. There are two theories behind this:

a. Protein binding to DNA puts tension  

on the outside, Z-form releases some  

of this pressure

b. B-form changes to Z-form to let a  

protein attach

f. Central Dogma: the general flow of information within a cell

i.ii. Generally, the above depiction is the flow of information from within a  cell.

iii. It starts with DNA, where it can be replicated or transcribed. Once  

transcribed it goes to being RNA, where it is translated and creates a  

protein.

Chapter 11: Chromosome Structure and Organization 

1. Key Topics:

a. DNA within Prokaryotes: This DNA is DNA without free ends (circular),  allowing for this DNA to be supercoiled to take up less space.

i. Overrotate: the DNA adds two extra turns within the DNA itself.

1. Results in a Positive Supercoil: look at the way the overlapping is  

in the depiction of the positive supercoil.

2.  

ii. Underrotate: The DNA takes away two turns within the DNA itself.

1. Results in a Negative Supercoil: look at the way the overlapping  

is in this depiction of negative supercoil.

2. a. Most DNA is negatively supercoiled 

iii. Twisted loops of DNA are then attached to proteins to further organize  the DNA and too keep it from tangling up

b. Chromatin of Eukaryotes:

i. Chromatin: complex of DNA and proteins in eukaryotic chromosomes.  Proteins are always interacting with DNA. During interphase, DNA is  called chromatin because of the proteins interacting with the DNA.

ii. Heterochromatin: a highly condensed chromatin. Such as an inactive X  chromosome (Barr body). Highly condensed and turned “silent/off” iii. Euchromatin: chromatin can be transcribed active or “open” chromatin 1. DNA being uses is called active/open. Certain segments of  

chromatin can be active/open even when condensed, they need to  be available to interact with proteins. This part is called  

Euchromatin.

iv. Order of Packaging:

1. DNA wraps around histones to form nucleosomes

a. Protects DNA

b. Exists in repetitions, every so many base pairs it happens

c. “Beads-on-a-string”

d. DNA between each histone is called the “linker DNA”

e. Nucleosomes are made of 4 different types of histones with  

two copies of each (8 histones total)

2. Nucleosomes coil together to form a solenoid

3. Loop domains

4. Chromatid

a. End result of DNA compaction, most condensed

5. DNA needs to be accessed even when compacted

c. Chromatin Remodeling: structure must change to allow access to DNA,  compacted DNA needs to be accessed when needed

i. Histone tails: the targets for binding to access DNA segments 1. Histones are positively charged and DNA is negatively charged 2. Acetylation: neutralizes positive charge of histones, which results  in the relaxation of histone hold.

a. DNA can be accessed

3. Methylation and Phosphorylation: increases the charge of the  histones, which tightens the hold the histones have on DNA

a. DNA is closed down and cannot be accessed.

d. Chromosome Banding: allows quick identification of chromosomes i. Is a “finger print” of chromosomes

ii. The band order for a particular chromosome in a species is the same for  every member of that species. Example: chromosome 1 in humans has the  same banding for every human

iii. Allows you to identify specific things within a chromosome, it names the  regions.

iv. Banding is the same for chromosomes of homologous pairs, allows for  matching of pairs

e. Specialized Chromosomes: Polytene Chromosome

i. Is rare. It is only seen in certain cells of certain tissues, at a certain time. ii. By studying the rare/specialized chromosomes, we can understand the  normal ones

iii. This chromosome can be seen in interphase (normal chromosomes cannot) iv. The Chromomeres are the individual lines of the Polytene

v. The puff is a region of the Polytene that is relaxed and pulled out. 1. Allows for a ton of product to be made quickly

2. High amount of gene activity (transcription) occurs here

f. Centromeres:

i. Point Centromere: a small centromere

ii. Regional Centromere: a large centromere

1. In most plants and animals

iii. CEN region: Critical regions.

1. Without this region, the centromere will not work, meaning that  spindle fibers will not attach

iv. Centromeres are very repetitive and is the same for all other chromosomes  within a species.

1. Since centromeres are relatively the same, if you try to stain one,  all get stained

g. Telomere: the caps at the ends of chromosomes to prevent unraveling i. Replication of ends can be tricky to accomplish

1. Does not occur in somatic cells, or they will be shortened until  death.

2. Single celled organisms and germ cells do not have to worry about  this

ii. Telomeres have to be lengthened to prevent death

iii. Problems:

1. Replicative enzymes cannot replicate the ends of chromosomes 2. Chromosomes would get shorter to the point of death

3. Solution: have an enzyme that replaces the ends

iv. Telomere repeats can be very big

1. TERRA: (Telomeric repeat containing RNA)

v. Telomerase: allows for elongation of telomeres

h. Repetitive Sequences:

i. Transposable sequences: “jumping” genes. Segments that can move  within a genome

ii. SINE: short interspersed element

1. Alu family: must common sine within the human genome

iii. LINE: long interspersed element

iv. Retrotransposons: RNA intermediate using reverse transcriptase

1. Exception of central dogma

v. Pseudogenes: risen through duplication, but no longer functional

Chapter 10: DNA Replication and Recombination 

1. Important People:

a. Messelson and Stahl:

i. The Experiment:

1. Placed E. coli into 15N medium and spun  

a. The 15N is heavy and the original DNA was located on the  

bottom

2. Transferred to 14N medium and allowed the DNA to replicate and  

then spun

a. All of the DNA was in the middle, due to containing 14N  

and 15N

3. Allowed for replication to occur in 14N medium again and spun

a. ½ of the DNA was in the top (where 14N would be found)  

and ½ of the DNA was in the middle.

4. Allowed for replication to occur in 14N medium again and then  

spun

5. ¾ of the DNA was in the top and ¼ of the DNA was in the middle

ii. Conclusion of experiment:

1. Semiconservative was proven correct

a.

2. Conservative was disproven in the first generation created

2. Important Topics:

a.

3. Dispersive was disproven in the second generation created a.

a. Replication:

i. Theta Replication: occurs within circular DNA

1. Chromosome has to have an origin of replication

2. Where the chromosome starts to unwind

3. Replication bubble: the area around where the origin opens up a. The bubble expands in both directions (bidirectional)

ii. Rolling-Circle Replication: occurs within Circular DNA

1. Has to have an origin, cuts one strand and then the strand is peeled away

2. Replication occurs of the remaining strand

3. The peeled segment reforms into a circle and is replicated

4. There is no replication bubble because the strands just peel away 5. Replicated in one direction (unidirectional)

iii. Linear DNA Replication: can have multiple origins

1. Common in Eukaryotes

2. There is a lot more DNA to replicate within Eukaryotes to replicate a. More complex so the machinery is slower

3. Multiple origins can be on one chromosome

4. Multiple replication bubbles

a. Bidirectional

b. The bubbles continue to open until they meet another  

bubble

b. DNA replication requirements and steps:

i. Requirements:

1. Single Stranded DNA template

2. dNTPs: all of the nitrogenous basses

3. Triphosphate: three phosphate groups attached to a sugar molecule a. When the phosphate is cut off, there is a release of energy.  

This allows for the base to be added

ii. Replication fork: where the double strand splits into two single strands 1. DNA is only replicated from 5’ to 3’

2. DNA strands are antiparallel, therefore bases are added in opposite  directions on the strands

a. Leading Strand: continuous DNA synthesis, moves as the  

replication fork moves forward

b. Lagging Strand: discontinuous DNA synthesis, has  

fragments of DNA called Okazaki Fragments

i. These fragments are created because of how DNA  

has to be synthesized from the 5’ to 3’ direction

ii. Has to wait for the replication fork to move forward

before it can place down more bases

1.

iii. Linear and Theta replications have leading and  

lagging strands. Rolling-circle replication only has a  

leading strand

c. Mechanisms of Replication: Bacterial DNA Replication (Eukaryotic is the same  process essentially)

i. Requires initiation: needs to be able to find the origin

1. Initiator proteins: bind to origin and twists up the DNA to release tension. This allows for the Replication Bubble to open up.

ii. Unwinding: the DNA needs to be unwound

1. Helicase: unzips DNA by breaking the hydrogen bonds of base  pairs

a. Cannot initiate unwinding, moves as the replication  

bubble opens, moves with fork and causes tension

2. Single strand Bonding proteins: bind to single strand bases, this  prevents the DNA from snapping back into place

3. DNA gyrase: a type of topoisomerase, reduces the tension that  builds up as the replication fork moves, prevents the DNA from  supercoiling, located outside the replication bubble

iii. Priming:

1. DNA polymerase: responsible for DNA synthesis

a. Cannot initiate DNA synthesis requires a 3’-OH group to  be present

2. Primase: an RNA polymerase

a. A primer: that puts down the initial 3’-OH with RNA.

b. Lagging: needs primers for each segment

c. Leading: needs one primer

iv. Synthesizing: DNA polymerase can now synthesize

1. E. coli has 5 DNA polymerases:

a. DNA polymerase I: Not critical polymerase

i. Also known as Kornberg Polymerase

ii. has 5’ to 3’ activity (building DNA)

iii. has 3’ to 5’ exonuclease activity (correction of  

errors)

iv. has 5’ to 3’ exonuclease activity (removes primers)

b. DNA polymerase III: critical polymerase

i. Has 5’ to 3’ activity (building DNA)

ii. Has 3’ to 5’ exonuclease activity (correction of  

errors)

c. Holoenzyme: complex, multiple proteins come to create enzyme

i. Just know that multiple proteins come to form  

polymerase III

v. General order of replication in bacterial cells:

1. Initiator proteins

2. DNA helicase

3. Single-stranded-binding proteins

4. DNA gyrase

5. DNA primase

6. DNA polymerase III (elongates a new nucleotide strand from 3’- OH group provided by primer)

7. DNA polymerase I (removes RNA primers and replaces them  with DNA)

8. DNA ligase (joins Okazaki fragments and seals the breaks) vi. Why does replication lack mistakes?

1. DNA polymerases are choosy: they usually pick the correct  nucleotide

2. Insertion of the wrong nucleotide leads to incorrect positioning of  3’-OH and stalls polymerase

a. A type of “red flag” if not in the right place

3. Mismatch repair: fixes any errors after replication

a. Double checks after polymerase is done and fixes errors

d. Termination of DNA synthesis:

i. Occurs when two forks meet, this causes termination

ii. Sequences in some systems bind a termination protein and blocks helicase 1. The presence of the protein=the termination

e. Eukaryotic DNA Replication:

i. Overall is the same as for prokaryotes, just more complicated ii. Differences with bacterial replication:

1. Multiple replication events at the same time on the same  

chromosome

2. More polymerases: large variety of DNA polymerases

3. Nucleosome assembly makes it messy.

a. chromatin structure and how machinery gets through

4. Linear chromosomes: replication of the ends of chromosomes iii. Eukaryotic Origins: identical sequences, initiator proteins find the  origins

1. ARS: autonomously replicating sequences, enable the DNA to  replicate

iv. Licensing of DNA replication:

1. How do we know if we started replication already at an origin? a. Replication licensing factor: attaches to the origin then  

and only this one time will the initiator proteins function. A

type of pre-initiator protein

v. Unwinding: still uses single stranded DNA binding protein, but does not  have DNA gyrase (still has a topoisomerase, just not gyrase)

vi. DNA polymerase: function in replication, recombination and repair vii. Issue with Telomeres shortening:

1. Telomerase is a ribonucleoprotein: it binds to the end of  

chromosomes to add telomere

f. Replication Fork on Eukaryotes

i. If synthesis occurs on both strands at the same time, then two DNA Pol II  are required

1. Replication is a continuous process

2. As the bubble opens, replication occurs on both strands

3. Each Fork requires:

a. Helicase, single stranded DNA binding proteins, DNA  

gyrase, DNA primase, DNA polymerase

4. Two Poly III work together on one fork, they are held together a. Issue: the leading strand is in the forward direction while  

the lagging strand is in the reverse direction.

b. DNA is looped for the lagging strand so that the pol III can  

move in the same direction

Chapter 12 Study Guide: 

1. Important Topics:

a. RNA vs. DNA

i. RNA is usually single stranded

1. Can acquire shape, meaning that it can fold upon itself. You can 

see base pairing within RNA

2. Has a ribose sugar (the sugar contains two OH groups). This makes

RNA less stable than DNA

3. Ribonucleotides contain uracil instead of thymine. Uracil is still a 

pyrimidine

4. RNA can be catalytic ribozymes

a. DNA is only carrying genetic information, it is not acting 

out any jobs

Characteristic

RNA

DNA

Composed of nucleotides

Yes

Yes

Type of Sugar

Deoxyribose

Ribose

Presence of two OH groups

No

Yes

Bases

A, G, C, T

A, G, C, U

Nucleotides joined by phosphodiester bonds

Yes

Yes

Double or single stranded

Usually Double

Usually Single

Secondary Structure

Double Helix

Many Types

Stability

Stable

Easily degraded

b. Types of RNA

i. There are multiple types of RNA. We focus on rRNA, mRNA, and tRNA 1. rRNA: Ribosomal RNA.

a. Function: structural and functional components of 

ribosomes

2. mRNA: Messenger RNA

a. Function: carries genetic code for proteins

3. tRNA: Transfer RNA

a. Function: helps incorporate amino acids into polypeptide 

chain

c. Transcription: very selective process. Only bits of the genome are ever  transcribed into RNA. Needs to be able to identify which parts are to be 

transcribed

i. Requirements:

1. DNA Template (needs to be able to access the DNA)

2. Substrates to make RNA (ribonucleotide triphosphates)

a. Loses two phosphates and provides enough energy

3. Transcription machinery

ii. Directionality:

1. Transcription only occurs on one strand in one section, meaning  that there can be many sections being described in different  directions, due to it not occurring on both strands.

a. But it still occurs in the 5’ to 3’ direction while reading the  strands from 3’ to 5’

iii. Template vs. Non­template strands

1. Template Strand: this is the DNA strand that is being actively  read/transcribed

2. Non­template Strand: This is the DNA strand that is not being  read by the polymerase, the ignored strand

a. Also known as the coding strand: the coding strand will  look like the mRNA created, only difference is that where 

the coding strand has a T, the mRNA has a U.

iv. Transcriptional Unit:

1. The stretch of DNA that codes for an RNA molecule and the  sequences necessary for transcription

2. Upstream: anything to the left of the transcription site

3. Downstream: anything to the right of the transcription site 4. Key parts:

a. Promoter: DNA sequence that the machinery that does  transcription recognizes. This indicates which strand of 

DNA will be described, determines start site, and usually 

not transcribed

i. If the promoter is damaged/messed up, the gene 

is essentially useless

b. RNA coding sequence: this is the template, the area that is  to get transcribed

c. Terminator region: the spot that transcription will stop at.  Says that enough has been transcribed and can be stopped 

now.

v. RNA Polymerase: takes care of everything

1. Bacterial RNA polymerase: usually only one type of polymerase, synthesizes all classes of RNAs (mRNA, tRNA, rRNA, etc.) a. Four key subunits to CORE enzyme: do not need to 

know the four parts

b. Sigma Factor: added to core subunits=holoenzyme

i. This will initiate transcription at a promotor

ii. Different sigma factors direct initiate at different 

promotors

iii. This gives polymerase specificity, directs it to 

which genes are to be transcribed

iv. If needs to transcribe rRNA, then the sigma factor 

identifies the rRNA promotor

2. Eukaryotic RNA polymerase: multiple kinds.

a. They are the result of large multi­protein complexes

b. RNA polymerase II: pre­mRNA become mRNA

vi. Bacterial Transcription: three major stages

1. Initiation: machinery assembles on promoter, begins the synthesis of RNA. Identification of promoters

a. Promoter recognition/binding: key to determining 

frequency that a gene is transcribed

i. Downstream: positive bases

ii. Upstream: negative bases

iii. +1: first gene that is placed down

iv. ­10 (Pribnow box): mostly A and T, few H­bonds, a

good place for transcription bubble

b. Formation of Transcription Bubble

c. Generation of first bonds between ribonucleotides

d. Escape of machinery from the promoter

i. RNA polymerase does not need primers

ii. Sigma subunit will not let go of promoter

iii. CORE enzyme has to “escape” promoter by kicking

out the sigma subunit

2. Elongation: RNA polymerase reads DNA, adds ribonucleotide to  growing RNA, this makes the RNA

a. RNA Polymerase: unwinding of DNA ahead of 

transcription bubble and rewinding behind it

b. 5’ to 3’ extensions of RNA

c. DNA/RNA duplex within bubble

i. RNA that is already transcribed trails off behind the

RNA polymerase, it can fold upon itself

3. Termination: end of transcription, separation of RNA from DNA  template, the stopping of transcription

a. Rho­Independent termination: terminator will be 

transcribed. Contains inverted repeat sequences, when this 

is transcribed it halts the process, during this halt, the bonds break, freeing the mRNA

b. Rho­Dependent Termination: requires the protein Rho i. The transcribed segment trails behind the 

polymerase, Rho slides up as the transcription 

continues. When the terminator is transcribed, it 

halts the process, allowing for Rho to catch up. This

knocks off the mRNA

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