Central dogma (history)

Question 1

define exon

Answer 1

Sequence that codes for amino acids

Question 2

Define Introns

Answer 2

Noncoding segments

Question 3

Define gene

Answer 3

A sequence of DNA from which a specific protein is derived

Question 4

Exons are separated by?

Answer 4

introns

Question 5

Where does transcription occur

Answer 5

nucleus

Question 6

What is direction of transcription?

Answer 6

mRNA is transcribed in the 5’-3’ direction

Read in the 3’-5’

Question 7

what is transcription

Answer 7

Converting the DNA sequence of a gene into messenger RNA

Question 8

what is the central dogma

Answer 8

dogma is a description of the typical information flow within a cell from DNA through RNA, into protein.
DNA - replication - transcription - RNA- translation - Protein
• Transcription is the process by which the information is transferred from one strand of the DNA to RNA by the enzyme RNA Polymerase. The DNA strand which undergoes this process consists of three parts namely promoter, structural gene, and a terminator.

Question 9

Where is the location of a promoter

Answer 9

Located upstream of a gene

Question 10

what did gregor mendel first do?

Answer 10

Gregor Mendel first formally described heredity (1865)

• Transmission of traits from one generation to the next

Question 11

why did mendel choose peas?

Answer 11

• Fast growing, easy to control pollination, the flowers have both male and female reproductive organs, no sex chromosomes, and simple inheritance. Results were ignored for years but later became the basis for working out what exactly heredity is.
self fertilize, pollinate, cross pollination

Question 12

what was dna originally called? why?

Answer 12

DNA initially called “nuclein”
• substance of unknown function isolated from nuclei
work done by Friedrich Miescher (pub. 1871)
studied white blood cells in pus (easier isolation) and found high amounts of a substance of unknown function in the nuclei of the white blood cells, called it nuclein. Later found nuclein in samon sperm

Question 13

two points of cell theory

Answer 13

1. all living things are made from cells

2. all cells come from other cells.

Question 14

what were genes called?

Answer 14

T.H. Morgan established that Mendel’s “factors” are discrete units - now called “genes” - which are found on the chromosomes

Question 15

what are chromosomes made of?

Answer 15

• Chromosomes are made of DNA and protein

Question 16

describe griffiths mice experiment - what did it show, controls, etc

Answer 16

showed there is something that can transfer traits between organisms (injecting mice with Streptococcus pneumoniae)
: 1. Proved Streptococcus smooth cells kill mice, two different forms of Streptococcus, one kills mice and one doesnt. 2. Shows that rough don’t kill mice, 3. Shows that smooth cells need to be alive to kill mice, can isolate living smooth cells from dead mice- transfer from dead S cells to live R cells- the genetic material

Question 17

what are the three properties of genetic material?

Answer 17

1. storage of information – stable in structure and content
2. capable of replication- cells must be able to pass on a copy to daughter cells
3. ability to change- info has to be adapted to new environments, but it has to bee slow and passed on mostly unchanged

Question 18

what is contained in chromosomes?

Answer 18

DNA and protein, RNA associated with transcriptionally active chromosomes im much smaller amounts. At the time of the experiments they assumed protein would be the genetic DNA as it had so much variation.

Question 19

describe avery macleod and mcarthy’s version of the mice experiment

Answer 19

Control: confirming transfer from dead S cells and living R cells, experimental were exposed to r cells with treated S cells
one treated with DNAse, one treated with RNAse and one treated with protease

Question 20

what did hershey and chases experiment use

Answer 20

used T2 phage and E.coli, instead of S. pneumoniae and mice
- bacteriophage: virus that infects bacteria- has two macro molecules DNA and protein, phage infects bacteria and inserts its genome into the bacteria hijacking all of its useful systems

Question 21

describe the process of hersheys experiment

Answer 21

Hershey and Chase

• experiment has phage that are grown on bacteria that are fed radioactive phosphorus
• and a set of phage that are grown in bacteria fed radio active sulfur
• process: radioactive phage separately exposed to fresh bacteria, given just enough time for a decent percentage of them to inject bacteria with their genomes, then run through a kitchen blender to shake off any residual loosely attached bits. Blended samples are spun down so the heavy bacteria are in one sample and the left over phage in another.
• if protein is the genetic material you should see radioactive sulfur in the bacteria and not in the remaining liquid
• if DNA is the genetic material, you should see radioactive phosphorus in the cells and the sulfur should stay in the liquid

Question 22

what elements are found in DNA?

Answer 22

• Sugar component- carbon, hydrogen, and oxygen
• • a phosphate group (phosphorous and oxygen) and
• a base that is different for each nucleotide, all four bases have carbon, hydrogen, oxygen, and nitrogen

Question 23

what elements would be found in protein?

Answer 23

• Proteins are made of amino acids (amino group NH, a carbon skeleton, and an acid group CO)
• Cysteine and methionine also contain sulfur

Question 24

dna vs protein how do we detect radio active decay

Answer 24

dna has phosphate, protein has sulfur

Question 25

what was already known from nuclein experiments

Answer 25

• Nucleotide structure
• 4 bases, knew they were one ringed (pyrimidines) or two ringed (purines)
-Wanted to know how it was put together

Question 26

how can we remember purines vs pyrimidines

Answer 26

Mnemonic for remembering purines vs. pyrimidines: Pure Silver

• Ag = symbol for silver in the periodic table
• Adenine and guanine are the two purines
• pu = first two letters of purine

Question 27

what were chargaffs rules?

Answer 27

In all species #A=#T or #G=#C In all species sum A+G = sum C+T Species to species sum A+T/G+C differs In the same organism no matter the cell the DNA is the same. The model fits this through base pairing rules. You can also apply this e.g. if you know the amount of A=10% you can find how much C you have. You know T must also =10%. Together they make up 20% of the molecule. So 80% of the molecule is G and C or G=40% and C=40%

Question 28

what did rosalind franklin descover?

Answer 28

X-ray crystallography

• diffraction of X-rays off crystals, exposure to sensitive photographic film to see diffraction patterns
• X-ray diffraction patterns indicated DNA is a double helix

Question 29

what six things were included in watson and crick’s structure of dna?

Answer 29

1. DNA is a double helix
2. Strands run antiparallel
3. Fixed width
4. Sugar/phosphate backbone
5. Bases inside
6. Hydrogen bonding between bases for specificity

Question 30

what is the polarity of dna? where is the hydroxyl group bonded?

Answer 30

or directionality. That is, the two ends of the chain are not the same: at one end, a phosphate group is bound to the 5ʹ carbon of a deoxyribose sugar, whereas at the other end, a hydroxyl group is bonded to the 3ʹ carbon of a deoxyribose sugar

Question 31

where does poymerase add nucleotides

Answer 31

polymerase [arrow adds nucleotides to] 3’ OH of DNA polymer.

Question 32

what is a promoter?

Answer 32

The promoter is a specific sequence of the DNA that indicates where the RNA polymerase should bind, where the process of transcription should start. b

Question 33

compare and contrast DNA and RNA

Answer 33

DNA replication and RNA transcription are similar in that they both involve building a polynucleotide; have overlapping bases (A, G, C). DNA replication and RNA transcription are different in that RNA is a single strand, has U versus T, a different sugar (ribose), and adding nucleotides does not require a free OH.

Question 34

describe wobble (having one tRNA able to read multiple codons)

Answer 34

The wobble hypothesis describes how the third base in the tRNA codon (anticodon) can pair with several different mRNA bases e.g. I (Inosine) can pair C A or U. This means there are less tRNA’s needed to pickup amino acids (one to one would require 64 different tRNA’s based on a triplet code)

Question 35

is a polyribosome possible in eukaryotes?

Answer 35

Yes. The cell needs only attach multiple ribosomes to a strand of mRNA. These are most common in Bacteria that transcribe and translate simultaneously. Eukaryotes usually edit the mRNA heavily to produce different gene products. However polyribosomes or polysomes can form at the surface of the rough endoplasmic reticulum.

Question 36

what was medels hypothesis (right/3rd

Answer 36

As a third hypothesis, Mendel proposed the following: the
pairs of alleles that control a character segregate (separate) as gametes are formed; half the gametes carry one allele, and the other half carry the other allele. This hypothesis is now known as Mendel’s principle of segregation. During fertilization, fusion of the haploid maternal and paternal gametes produces a diploid nucleus called the zygote nucleus. The zygote nucleus receives one allele for the character from the male gamete and one allele for the same character from the female gamete, reuniting the pairs.

Question 37

what would radio active phosphorus do?

Answer 37

It could impact the DNA’s ability to replicate – introducing errors. These errors often manifest themselves as mutations in the DNA during DNA replication.

Question 38

purine vs pyrimidine structure

Answer 38

these were determined by the hydrogen bonding in the bases (remember A can bond with T not C). Also see the cool clip of Watson showing how he figured this out and that the bases stacked on top of one another. Purines are A and G or two ring bases. Pyrimidines are single ringed or C and T and U in RNA

Question 39

ow does DNA fit the requirements for the hereditary molecule?

Answer 39

. Storage of information It can record information in the order of base pairs. Words to the cell occur in triplets
5 or three “letters”. The cell can read sentences in the order of the words to insert amino acids. E.g. the red dog ate the catb. Capable of replication It can copy itself and pass on the information.c. Ability to change Mutation or changes can occur in the DNA introducing variability in the sequences of genes and “junk DNA” or non-coding regions. This variability can be detrimental or beneficial.

Question 40

what did meselson and stahl discover? (full process on pg 259 of textbook)

Answer 40

strated that DNA replication is semiconservative (Figure 11.9). In their experiment, Meselson and Stahl had to be able to distinguish parental DNA molecules from newly synthe-sized DNA. To do this, they used a nonradioactive “heavy”
nitrogen isotope to tag the parental DNA. The heavy isotope, 15N, has one more neutron in its nucleus than the normal 14N isotope. Molecules containing
(denser)

Question 41

describe DNA polymerase function. what are the substrates?

Answer 41

During replication, complementary polynucleotide chains are assembled from individual deoxyribonucleotides by enzymes known as DNA polymerases. More than one kind of DNA poly-merase is required for DNA replication in all cells. Deoxyribonu-cleoside triphosphates are the substrates for the polymerization reaction catalyzed by DNA polymerases

Question 42

what are the names of the DNA nucleosides?

Answer 42

the deoxyribonucleoside triphos-phates for DNA replication are given the short names dATP, dGTP, dCTP, and dTTP, where the “d” stands for deoxyribose.

Question 43

DNA polymerase in bacteria, archaea, and eukaryote

Answer 43

DNA polymerases of bacteria, archaeans, and eukaryotes all consist of several polypeptide subunits arranged to form differ-ent domains
. The palm domain is evolutionarily related among the polymerases of bacteria, archaea, and eukaryotes
are different sequences in each of these three types of organisms.

Question 44

describe DNA polymerase extending the polymer

Answer 44

however. Instead, the template strand and the 3ʹ –OH of the new strand meet at the active site for the polymerization reaction of DNA synthesis, located in the palm domain. A nucleotide is added to the new strand when an incoming dNTP enters the active site carrying a base complementary to the template strand base positioned in the active site. By moving along the template strand, one nucleotide at a time, DNA polymerase extends the new DNA strand,

Question 45

what is the sliding dna clamp (Overall, the rate of DNA synthesis is much faster because of the sliding DNA clamp.)

Answer 45

The sliding DNA clamp is a pro-tein that encircles the DNA and binds to the rear of the DNA
polymerase in terms of the enzyme’s forward movement dur-ing replication. The function of the sliding DNA clamp is to tether the DNA polymerase to the template strand.

Question 46

what are the key molecular events of DNA replication?

Answer 46

1. The two strands of the DNA molecule unwind for replica-tion to occur.
2. DNA polymerase can add nucleotides only to an existing chain
3. The overall direction of new synthesis is in the 5ʹ  3ʹ direction, which is a direction antiparallel to that of the template strand.
4. Nucleotides enter into a newly synthesized chain according to the A–T and G–C complementary base-pairing rules.

Question 47

what would happen without DNA polymerase?

Answer 47

the DNA polymerase makes replication more efficient because, without it, the enzyme will detach from the template after only a few dozen polymerizations. But, with the clamp, many tens of thousands of polymerizations occur before the enzyme detaches.

Question 48

which domains have similar DNA replication?

Answer 48

. Archaeans and eukaryotes follow many of the same processes but with enzymes that have distinct differences from those found in bacteria. Due to evolutionary relatedness (Chapter 19), Archaea and Eukarya are more similar to each other than either one is to Bacteria.

Question 49

what is the primer?

Answer 49

If DNA polymerases can add nucleotides only to the 3ʹ end of an existing strand, how can a new strand begin when there is no existing strand in place? The answer lies in a short chain a few nucleotides long called a primer, which is made of RNA instead of DNA (Figure 11.13). The primer is synthesized by the enzyme

Question 50

define leading and lagging strand

Answer 50

The polymerases make this strand in short lengths that are synthesized in the direction opposite to that of DNA unwinding (see Figure 11.14). The short lengths produced by this discontinuous replication are then covalently linked into a single continuous polynucleotide chain. The short lengths are called Okazaki fragments, after Reiji Okazaki, the scientist who first detected them. The new DNA strand synthesized in the direc-tion of DNA unwinding is called the leading strand on; the template for that strand is the leading strand template. The strand synthesized discontinuously in the opposite direction is called the lagging strand; the template strand for that strand is the lagging strand template.

Question 51

how many replication origins do bacteria chromosomes have? eukaryotic?

Answer 51

Bacterial Chromosomes Have a Single Replication Origin; Eukaryotic Chromosomes Have Multiple Replication Origins

Question 52

transcription vs DNA replication

Answer 52

he machinery is used for making an RNA transcript of a gene to be used in gene expression, not for cell division as in DNA replication;
● start codon. By
analogy, if you read the message SADMOMHASMOPCUT-OFFBOYTOT three letters at a time, starting with the first let-ter of the first “codon,” you would find that a mother reluctantly had her small child’s hair cut. However, if you start incorrectly at the second letter of the first codon, you read the gibberish message ADM OMH ASM OPC UTO FFB OYT OT.
STUDY BREAK QUESTIONS 1. On the basis of their work with auxotrophic mutants of the fungus Neurospora crassa, Beadle and Tatum proposed the one gene–one enzyme hypothesis. Why was this hypothesis updated subsequently to the one gene–one polypeptide hypothesis?
2. Why is the sequence of bases in the mRNA different from that in the DNA of a given gene?
●
for a given gene, only one of the two DNA nucleotide strands acts as a template for synthesis of a complementary copy, instead of both, as in replication;
only a relatively small part of a DNA molecule—the sequence encoding a single gene—serves as a template, rather than all of both strands, as in DNA replication;
●
RNA polymerases catalyze the assembly of nucleotides into an RNA strand, rather than the DNA polymerases that cata-lyze replication;
●
the RNA molecules resulting from transcription are single polynucleotide chains, not double ones, as in DNA replication;
●
wherever adenine appears in the DNA template chain, a uracil is matched to it in the RNA transcript instead of thy-mine, as in DNA replication.
Although the mechanism of transcription is similar in
prokaryotic cells and eukaryotes, watch for the important dif-ferences pointed out in this section

Question 53

3 steps of transcription

Answer 53

Transcription takes place in three steps: (1) initiation, in
which the molecular machinery that carries out transcription assembles at the promoter and begins synthesizing an RNA copy of the gene; (2) elongation, in which the RNA polymerase moves along the gene extending the RNA chain; and (3) termi-nation, in which transcription ends and the RNA molecule—the transcript—and the RNA polymerase are released from the DNA template

Question 54

transcription in eukaryotes vs bacteria

Answer 54

In eukaryotes, RNA polymerase II, the enzyme that tran-scribes protein-coding genes, cannot bind directly to DNA; it is recruited to the promoter after proteins called transcription factors have bound. In bacteria, RNA polymerase binds directly to DNA; it is directed to the promoter by a protein factor that is then released once transcription begins. Binding to a promoter region automatically orients the RNA polymerase in the proper direction on the DNA. When the region unwinds, the polymerase reads whichever strand is running 3ʹ to 5ʹ. This is the template strand.
●
Elongation is essentially identical in the two types of organisms.