How cells work

Question 1

What’s the central dogma of how cells work?

Answer 1

Replication, Transcription, Translation

Question 2

Give a brief description of the central dogma on how cells function

Answer 2

Information is stored on the DNA molecule. That information can be replicated directly to form a second identical molecule. Segments of the DNA molecule can be transcribed to yield RNAs.Using a variety of RNA’s, this information is translated into proteins. The proteins then perform a structural or enzymatic role, mediating almost all the metabolic functions in the cell. Some of the proteins interact with DNA to control which genes are transcribed

Question 3

What are nucleotides?

Answer 3

genetic information is stored on DNA strands in the chromosomes as sequences of nucleotides

Question 4

What are the different letters of nucleotides?

Answer 4

A - adenine
T - thymine
G - guanine
C - cytosine

Question 5

Which letter nucleotides H bond together?

Answer 5

A and T
G and C

Question 6

How many nucleotides make up a codon (word)?

Answer 6

3 letter nucleotides.
Therefore there are 64 words possible

Question 7

What do codons put together in a sequence create?

Answer 7

Genes (sentences)

Question 8

What does each step of information and transfer require?

Answer 8

Macromolecular template

This is how genetic-level language is preserved and expressed

Question 9

Describe the process of DNA replication

Answer 9

Replication normally begins at a predetermined site, the origin of replication.
Initiator proteins bind to DNA at the origin of replication, break hydrogen bonds, in the local region of the origin and force the two DNA strands apart.
The two strands form a Y- shaped structure called a replication fork.
This separation of the strands is facilitated by the enzyme DNA gyrase and other unwinding enzymes.

Question 10

What are the needed ‘ingredients’ for DNA replication?

Answer 10

Enzyme DNA polymerase is responsible for covalently linking the nucleotides E.coli has (Pol I, II, III)
RNA polymerase makes RNA primer
Pol III mediates addition of nucleotides to an RNA primer
Pol I hydrolyzes an RNA primer and duplicates single stranded DNA regions
The enzymatic reaction requires energy. The activated monomers are the nucleotide triphosphates. The formation of the 5’-3’ phosphodiester bond to link a nucleotide with the growing DNA molecule results in the release of a pyrophosphate which provides the energy for such a biosynthetic reaction. The resulting nucleoside monophosphates are the constituent monomers of the DNA molecule.
To initiate nucleotide synthesis an RNA primer is required which is made by the enzyme RNA polymerase.
Once a short RNA strand is made, DNA is synthesized using DNA polymerase (Pol III). Next, the RNA piece is degraded by (Pol I) and DNA is synthesized in its place

Question 11

Figure showing DNA replication and a bit more info

Answer 11

In part A of figure - Newly polymerized DNA strands (wavy lines) are synthesized in the 5’ to 3’ direction using the preexisting DNA strands (solid lines) as template. The process creates two replication forks which travel in opposite directions until they meet on the opposite side of the circular chromosome
In part b, more detail of the replicating forks which shows the process by which short lengths of DNA are synthesized and eventually joined to produce a continuous new strand of DNA. Four short segments are illustrated at various stages. In (1), primer RNA (thickened area) is being synthesized by an RNA polymerase Successively in (2) DNA is being polymerized to it by DNA polymerase III (PollII).In (3) a preceding RNA primer is being hydrolyzed, while DNA is being polymerized in its place by DNA polymerase I (PolI).Finally, the completed short segment of DNA (4) is joined to the continuous strand (5) using another enzyme DNA ligase

Question 12

Diagram of DNA replication happening

Answer 12

Question 13

What are the activated monomers in DNA replication?

Answer 13

The activated monomers are the nucleotide triphosphates. The formation of the 5’-3’phosphodiester bond to link a nucleotide with the growing DNA molecule results in the release of a pyrophosphate, which provides the energy for the biosynthetic reaction.The resulting nucleoside monophosphates are the constituent monomers of the DNA molecule.

Question 14

Draw a diagram for the DNA elongation reaction

Answer 14

Question 15

What is the core principle of DNA transcription?

Answer 15

How this genetic information that’s been replicated can be transferred

Question 16

What are the 3 products of transcription?

Answer 16

Messenger RNA, m-RNA - the encoding of a chemical “blueprint” for a protein product.mRNA is transcribed from a DNA template.

Transfer RNA, t-RNA – recognizes three-letter codes and provides the corresponding amino acid

Ribosomal RNA, r-RNA – is the central part of the ribosome equipment for producing proteins.

Question 17

What enzyme mediates RNA synthesis from DNA?

Answer 17

RNA polymerase

Question 18

What is RNA polymerase’s 2 major subcomponents?

Answer 18

• Core enzyme: contains the catalytic site.
• Sigma factor: a protein which is essential for locating the appropriate beginning for the message.

The two parts together are called the holoenzyme

Question 19

What direction does the RNA polymerase read?

Answer 19

reads from 3’ to 5’ direction so it reads in opposing direction on complementary strands

Question 20

Give the 3 stages of the transcription process

Answer 20

Initiation, elongation and termination

Question 21

Describe the process of transciption

Answer 21

The RNA polymerase moves down the DNA chain causing a temporary opening of the double helix and transcription of one of the DNA strands.
The sigma factor recognizes a specific sequence of nucleotides on a DNA strand called the promoter region. A strong promoter is one with a high affinity for the holoenzyme. The rate of transcription initiation is directly linked to promoter strength.
After the initiation is recognized, elongation of the transcript begins. Once elongation is established, the sigma factor is released so that it can be reused. Energy for the growth of the RNA molecule is provided by activated triphosphate monomers.
The transcript is made until the RNA polymerase encounters a stop signal (the transcript or terminator). At this point, the RNA polymerase disassociates from the DNA template and the RNA transcript is released. In some cases, an additional protein called the rho protein is required for termination.
Terminator sequences can also be strong or weak and these also need to be considered in the design of recombinant systems.
The transcripts formed are m-RNA, t-RNA or r-RNA.

Question 22

Diagram for messenger RNA synthesis

Answer 22

Question 23

What’s an example of the difference of transcription in eukaryotes and prokaryotes?

Answer 23

in procaryotes, related proteins are often encoded in a row without interspacing terminators

Question 24

What is the result of proteins encoded in a row without interspacing terminators

Answer 24

Thus, transcription from a single promoter may result in a polygenic message (each gene encoding a different message). Furthermore, in procaryotes there is no physical separation of the chromosome from the cytoplasm and ribosomes. Often an m-RNA will bind to a ribosome and begin translation immediately, even while part of it is being transcribed.

However in eukaryotes a nuclear membrane separates the chromosomes and ribosomes, and the m-RNA is subject to processing before translation. Furthermore, the DNA can encode for a transcript with an intervening sequence (an intron) in the middle of the transcript. This intron is cut out and the remains are spliced together (m-RNA splicing)

Question 25

Diagram of eukaryotic cells and RNA synthesis

Answer 25

Question 26

Diagram of overview of information transfer from DNA to proteins

Answer 26

Question 27

What codon does all protein synthesis begin with?

Answer 27

AUG (or CUG) codon on the m-RNA

Question 28

What does the initiation of polymerization in procaryotes require?

Answer 28

An initiation complex composed of a 30S ribosomal unit and 50S ribosomal unit, three proteins called initiation factors (IF1, IF2, IF3), and the phosphate bond energy from GTP.

Question 29

What does elongation of amino acids use as decoders?

Answer 29

t-RNAs. One end of the t-RNA contains the anticodon, which is complementary to the codon on the m-RNA. The other end of the t-RNA binds a specific amino acid. The t-RNA is called charged when it is carrying an amino acid. The binding of an amino acid to the t-RNA molecule requires the energy from two phosphate bonds and enzymes known as aminoacyl-t-RNA.

Question 30

Give further info on how proteins are made

Answer 30

The actual formation of the peptide bond between the two amino acids occurs on adjacent sites on the ribosome: the P or peptidyl site and the A or aminoacyl site.

The growing protein occupies the A site. As the peptide bond is formed, the t-RNA associated with the P site is released, and a rachet mechanism moves the m-RNA down one codon so as to cause the t-RNA that was in the A site to be in the P site.

Then a charged t-RNA with the correct anticodon can be recognized and inserted into the A site. The whole process is then repeated. The cell expends a total of four phosphate bonds to add one amino acid to each growing polypeptide (two to charge the t-RNA and two in the process of elongation).(This accounts for most of the cellular energy expenditure in bacteria. When a stop codon is reached, the protein is released from the ribosome with the aid of a protein release factor (RF). The 70S ribosome then dissociates into 30S and 50S subunits. An m-RNA typically is being read by many (e.g. 10-20) ribosomes at once; as soon as one ribosome has moved sufficiently far along the message that the ribosome binding site is not physically blocked, another ribosome can bind and initiate synthesis of a new polypeptidechain.

Question 31

Diagram of translation relating to protein synthesis

Answer 31

Question 32

Diagram of translation relating to protein synthesis. part 2

Answer 32

Question 33

What is Post-Translational Processing?

Answer 33

• Essential for protein functionality
• Occurs after protein synthesis
• Includes protein folding and modifications
• Ensures proper protein conformation and activity
• Involves signal sequences for protein targeting
• Signal sequences guide proteins to correct cellular locations
• Pre-form proteins transition to mature, active forms
• Modifications include glycosylation, lipid addition, and phosphorylation
• Glycosylation adds sugar molecules to proteins
• Crucial for protein structure and function
• Considerations for protein production in biotechnology
• Host organisms affect post-translational modifications