chp.13 bacterial genome replication and expression

Question 1

Explain the central dogma of molecular biology

Answer 1

DNA is the template for its own replication – known as DNA replication, RNA (mRNA, tRNA, rRNA) known as transcription, mRNA is the template for proteins known as translation

Question 2

DNA replication is done by DNA polymerase

Answer 2

Transcription is done by RNA polymerase

Question 3

What is the “transformation test”? Who was it conducted by?

Answer 3

the change of nonvirulent organisms into virulent ones via “transformation”
1944- griffith

Question 4

What did the Hershey-Chase experiment find?

Answer 4

1952- used bacteriophage T2 infection as model, DNA was labeled with 32P, the protein coat was labeled with 35S•only the labeled DNA entered the bacterial cell, labeled protein remained outside of the cell

Question 5

Mention similarities and differences between DNA and RNA:

Answer 5

1.The nitrogenous bases they contain  RNA: adenine, guanine, cytosine, and uracil DNA: adenine, guanine, cytosine, and thymine 2.The sugars they contain RNA: ribose DNA: deoxyribose 3.Whether they are single or double stranded  RNA: single stranded DNA: double stranded

Question 6

What are the three components of nucleotides?

Answer 6

carbon sugar, nitrogen base (purine or pyrimidine), phosphate

Question 7

Beginning of the nucleic acid strand is known as the 5’ end and the end is known as the 3’ end

Answer 7

There are 2 hydrogen bonds between A and T and 3 hydrogen bonds between G and C

Question 8

How does a nucleoside differ?

Answer 8

Nitrogen base – pentose sugar

Question 9

Proteins are polymers known as polypeptides made up of monomers of amino acids

Answer 9

Contain covalent peptide bonds

Question 10

Structure of primary proteins:

Answer 10

peptide bonds only

Question 11

Structure of secondary proteins

Answer 11

alpha helices and beta sheets by hydrogen bonds

Question 12

Structure of tertiary proteins:

Answer 12

give the structure and function, noncovalent bonds + disulfide

Question 13

Structure of quaternary proteins:

Answer 13

not all proteins have it, can have same type of bonds as tertiary

Question 14

Explain the process of DNA replication. Consider key players involved in the process, and unique characteristics.

Answer 14

DNA is its own template for replication, Mediated by DNA polymerase, DNA replication is semi-conservative, Replicates the whole genome, process is dependent on a lot of different proteins, It only happens once during cell replication

Question 15

Complementary DNA/ sense strand

Answer 15

have the same nucleotide sequence as mRNA

Question 16

Promoter

Answer 16

is located at the start of the gene, responsible for the recognition/binding site for RNA polymerase

Question 17

Leader sequence

Answer 17

transcribed into mRNA but is not translated into amino acids, contain the Shine-Dalgarno sequence important for initiation of translation

Question 18

Stop codon:

Answer 18

coding region ends with a stop codon followed by a terminator sequence used to stop transcription

Question 19

DNA sequence that codes for tRNA and rRNA

Answer 19

Genes coding for tRNA may code for more than a single tRNA molecule or type of tRNA

Question 20

What are ribozymes?

Answer 20

Spacers between the coding regions of both are removed after transcription, some by the use of special ribonucleases

Question 21

Explain the process of transcription. Also mention the difference between polycistronic and monocystronic mRNA

Answer 21

RNA synthesis under the direction of DNA, RNA produced has complementary sequence to the template DNA, Three types of RNA are produced: a)mRNA carries the message for protein synthesis b)tRNA carries amino acids during protein synthesis c)rRNA molecules are components of ribosomes

Question 22

What are the 3 rules of the genetic code?

Answer 22

Rule 1: codons are read 5’ to 3’, Rule 2: codons are non-overlapping, message has no gap, Rule 3: message is translated in a fixed reading frame

Question 23

What is a codon?

Answer 23

A codon is part of the genetic code “word”, 3 base pairs long, specifies an amino acid

Question 24

What is an anticodon?

Answer 24

on tRNA is complementary

Question 25

What is a sense codon?

Answer 25

61 codons that specify the 20 amino acids

Question 26

What is a start codon?

Answer 26

start site for translation, always AUG, encodes for methionine

Question 27

What is a stop codon (nonsense codon)?

Answer 27

three codons used as translation termination signals: UGA, UAG, and UAA, do not encode for an amino acid

Question 28

What are codon exceptions?

Answer 28

Some protists use a single stop codon; the other two code for amino acids instead, Some microbes incorporate two rare amino acids into polypeptides, selenocysteine (Sec, U), pyrrolysine (Pyl, O)

Question 29

What is code degeneracy?

What causes it?

Answer 29

Since there are more codons (61) than amino acids (20), multiple codons can specify the same amino acid
Wobble position

Question 30

Explain the process of translation.

Answer 30

Synthesis of polypeptide is directed by the sequence of nucleotides in the mRNA, direction of synthesis: N to C-terminal, The ribosome is the site of translation, coupled transcription/translation in Bacteria/Archaea, polyribosome is a complex of mRNA with several ribosome

Question 31

What is non-coding RNA?

Answer 31

a functional RNA molecule that is transcribed from DNA but not translated into proteins.

Question 32

Explain the process of protein maturation

Answer 32

Splicing is the removal of a part (or parts) of a polypeptide before folding, inteinsare the removed portion, exteinsare the portions that remain in protein, Protein function depends on the 3D shape, shape occurs as post translational event, requires folding, association with other proteins (chaperones), delivered to proper subcellular or extracellular

Question 33

What are molecular chaperones?

What are its functions?

Answer 33

Molecular chaperones are proteins that help other proteins fold, Including: trigger factor, DnaK, DnaJ, GroEL and GroES

protects the cell from thermal damage (heat-shock proteins (HSPs)), aid in transport of proteins across membranes (SecA)

Question 34

What is protein translocation? Secretion?

Answer 34

Translocation is the movement of proteins from the cytoplasm to plasma membrane or periplasmic space by enzymes known as translocases, Sec system is a general secretion pathway, Tat system secretes only folded proteins, Secretion is the movement of proteins from the cytoplasm to external environment

Question 35

Explain the process of protein secretion in gram negative bacteria:

Answer 35

Requires crossing two membranes, Some proteins cross in a two-step process: a) translocation to the periplasm by the Sec or Tat system b) secretion across the outer membrane, One-step processes involve structures composed of multiple polypeptides that completely span the periplasm

Question 36

Macromolecule transport moves proteins that

Answer 36

not been folded yet

Question 37

Secretory systems:

Answer 37

both exports and inserts integral proteins into the cell membrane

Question 38

Name the different systems and their specific functions:

Answer 38

SecY, E, G: transmembrane transporter, SecA: recognizes the signal, ATP hydrolyzing enzyme, SecB: prevents folding of the protein, SecD & F: use the proton motive force for translocation

Question 39

Transported proteins are synthesized as pre-secretory proteins called preproteins

Answer 39

They have a signal peptide at the N-terminus which is recognized by SecA

Question 40

What is the Tat system?

Answer 40

Translocate folded proteins with “twin” arginine residues (tat) in their signal sequence, Found in Bacteria and some archaea, both Gram-negative and Gram-positive, Moves folded proteins across the plasma membrane