Protein Synthesis and Bacterial Transfer of DNA

Question 1

Gene

Answer 1

segment (sequence) of DNA that is transcribed into an mRNA that may or may not be translated into a polypeptide
(Genes are recipes for proteins)

(a sequence of DNA that codes for a protein)

Question 2

Where does transcription take place?

Answer 2

inside the nucleus for eukaryotic cells
in the cytoplasm for prokaryotic cells

Question 3

what is the central dogma

Answer 3

the concept that cells are governed by a cellular chain of command:
DNA –> RNA –> protein

Question 4

Why is there only 20 amino acids when it seems like there would be 64 based on the amount of codons?

Answer 4

Its a redundant code:
different codons can code for the same amino acid

Question 5

What codon means start?

Answer 5

AUG

Question 6

Gene expression

Answer 6

the process by which DNA directs protein synthesis,
includes two stages: transcription and translation

Question 7

What is transcription

Answer 7

the synthesis of messenger RNA (mRNA) from a segment (template strand) of DNA

Question 8

What is translation

Answer 8

the synthesis of a polypeptide, using information in the mRNA

Question 9

Template strand

Answer 9

On of the two DNA strands in transcription,
provides a template for ordering the sequence of complementary nucleotides in an RNA transcript

always the same strand for a given gene

Question 10

codons

Answer 10

mRNA base triplets that are read in the 5’ to 3’ direction during translation

Question 11

RNA polymerase

Answer 11

The enzyme that catalyzes RNA synthesis:

pull the DNA strands apart (breaking hydrogen bonds) and joins together the RNA nucleotides

Question 12

Does RNA polymerase need a primer?

Answer 12

no

Question 13

Where does RNA polymerase bind?

Answer 13

an area on the DNA called the promoter

Question 14

Promoter

Answer 14

Sequence of DNA upstream of the transcription unit (part that will ultimately get translated into a string of amino acids)

Question 15

What are the steps of transcription (what does RNA polymerase do)?

Answer 15

1. binds to promoter
2. pulls apart the two different strands of DNA
3. Reads DNA from 3’ to 5’ direction, builds RNA in 5’ to 3’ direction
4. enzyme pops off at area called terminator leaving piece of RNA (pre-mRNA since still has to be processed)

Question 16

What happens in RNA processing

Answer 16

The 5’ end receives a modified guanine nucleotide 5’ cap

the 3’ end gets a poly-A tail (extra adenine nucleotides added to the 3’ end)

Question 17

What are the functions of the modifications that occur in RNA processing?

Answer 17

they help mRNA get out of the nucleus and into the cytoplasm

They protect mRNA from hydrolytic enzymes (enzymes that destroy mRNA)

They help ribosomes attach to the 5’ end

(both the 5’ tail and poly-A tail help with all 3 of these things)

Question 18

Once the mRNA gets into the cytoplasm where it will be transferred into the protein, why would you want to destroy that mRNA (hydrolytic enzymes)?

Answer 18

Just because the cell wants to make a protein right now, doesn’t mean it wants to make it forever

hydrolytic enzymes help minimize this

Question 19

introns

Answer 19

long noncoding stretches of nucleotides that lie between coding regions

(they are in the way, so you cut them out and throw them away, and then splice back together the exons)

Question 20

exons

Answer 20

all regions that aren’t introns

Question 21

Spliceosomes

Answer 21

consist of a variety of proteins and several small snRNPs that recognize the splice sites

Question 22

What are snRNPs made up of

Answer 22

proteins and a special kind of RNA called snRNA

Question 23

What is the role of the snRNP?

Answer 23

decide what is the intron, cut it out, and splice back together the exons

Question 24

Three properties of RNA that enable it to function as an enzyme

Answer 24

1. it can form a three-dimensional structure because of its ability to base-pair with itself
2. some bases. in RNA contain function groups that may participate in catalysis
3. RNA may hydrogen-bond with other nucleic acid molecules

Question 25

tRNA and what it does

Answer 25

a type of RNA that functions as an interpreter in translation Each tRNA molecule has a specific anticodon, picks up a specific amino acid, and conveys the amino acid to the appropriate codon on mRNA

Question 26

how do tRNAs figure out what their appropriate amino acid is?

Answer 26

they look at their Anticodon and figure out based on what the nitrogenous bases would bond to E.G in picture it would be UUC (amino acid Phe) because A(U)A(U)G(C)

Question 27

Name 3 ways in which bacteria can perform horizontal gene transfer

Answer 27

1. transformation 2. transduction 3. conjugation

Question 28

Transformation (1 way that genes can move from one bacterial cell to another)

Answer 28

the incorporation of foreign DNA from the surrounding environment (in the form of a fragment from another bacterial cell)

Question 29

Transduction (1 way that genes can move from one bacterial cell to another)

Answer 29

The transfer of bacterial genes by a phage: when new viruses are being assembled in an infected bacterial cell, a fragment of DNA belonging to the host cell may be mistakenly packaged within the phage’s coat along with the phage’s own DNA. When the phage infects a new bacterial cell, the DNA stowaway from the former host cell is injected into the new host.

Question 30

Conjugation (1 way that genes can move from one bacterial cell to another)

Answer 30

when two bacterial cells "mate" and transfer DNA: there is a gene called an F factor, and if a bacterial cell has this gene, it enables it to grow a conjugation tube that connects to another cell, and allows some of the original DNA to go through and into the other cell

Question 31

ribosomes

Answer 31

a cell structure consisting of RNA and protein organized into two subunits and functioning as the site of protein synthesis in the cytoplasm

Question 32

Plasmid

Answer 32

a small circular DNA molecule separate from the bacterial chromosome

Question 33

F Factor

Answer 33

A piece of DNA that can exist as a bacterial plasmid

Question 34

What are the steps of translation in order?

Answer 34

1. The small ribosomal subunit binds to the mRNA in a region that encompasses the start codon 2. The first tRNA with the complementary anticodon (UAC), which is already carrying a methionine (met amino acid), will come in and hydrogen bond with the codon 3. The large ribosomal subunit comes in with 3 sites: A site, P site, E site builds amino acid chain (reads 5’ to 3’) anticodon builds 3’ to 5’

Question 35

How does the amino acid chain get built (during translation)?

Answer 35

There is already a tRNA with the anticodon UAC hydrogen bonded to the start codon (AUG) at the P site. The next 3 nucleotides after AUG are the next codon. A tRNA with the appropriate anticodon will come and hydrogen with that next codon at the A site. The amino acid on the first tRNA will pop off and connect to the amino acid on the new tRNA at the A site (forming chain). The whole mRNA shifts (including the tRNAs). The tRNA that no longer has an amino acid will then be in the E site (Exit site), and it will pop off and leave. The tRNA with the growing chain of amino acids will now be in the P site, and the A site will be empty waiting for a tRNA with the appropriate anticodon for the NEXT codon. The process repeats (GTP powers this)

Question 36

When does the process of building the amino acid chain stop? what happens when it stops?

Answer 36

It stops when it reaches a stop codon release factor comes in (not a tRNA) and goes into the A site and breaks whole thing apart leaves free polypeptide which can then fold and become a protein

Question 37

What proteins have to be made in the Rough ER?

Answer 37

proteins that have to be packaged into a vesicle

Question 38

How are proteins made in the rough ER?

Answer 38

first several amino acids in the chain will be called signal peptides signal peptide is recognized by a protein called SRP (signal recognition particle), grab onto the signal peptide and drag it to the rough ER (will bring to one of the pores in the membrane of the rough ER) the ribosome will be making the polypeptide chain but feeding it into the lumen of the rough ER when the whole thing breaks apart (reaches stop codon), the polypeptide will end up inside the rough ER (in the lumen)

Question 39

Mutations

Answer 39

changes in the genetic material of a cell or virus

Question 40

Point mutations/base pair mutations

Answer 40

the wrong nitrogenous base is put in: change in just one base pair of a gene can be good, bad, or indifferent indifferent - SILENT MUTATION if the code is redundant (if you change one letter it might end up coding for the exact same amino acid) Good - change amino acid so that the protein is slightly different and better than it used to be (at whatever it's job is) Bad - change amino acid and make protein slightly different but worse than what it used to be at its job

Question 41

Silent mutation (type of point mutation)

Answer 41

when a mutation is indifferent: the change of the codon (or the base of the codon) codes for the same amino acid (redundant code)

Question 42

Frame-shift mutation

Answer 42

removing or inserting a base (or any amount that isn't 3) a whole: changes whole reading frame and screws up everything after the removed base (changes all the amino acids)

Question 43

Which would matter more: a mutation during DNA replication or a mutation during protein synthesis (transcripiton)? why?

Answer 43

the one during DNA replication would be much worse. If it happens during the making of mRNA (protein synthesis), its not really a big deal because that one protein will be bad, but when you try to make protein again, the original recipe (the DNA) is fine, and you could copy it correctly the next time if it happens during DNA replication then the mutation is in the recipe, meaning every time you try and make protein using that DNA it will make the wrong recipe

Question 44

Missense mutation (type of point mutation)

Answer 44

The mutation still codes for an amino acid, but not the correct one

Question 45

Nonsense mutation (type of point miutation)

Answer 45

the mutation changes the amino acid codon to a stop codon, nearly always leading to a nonfunctional protein

Question 46

Advantage of horizontal gene transfer

Answer 46

genetic diversity

Question 47

When do mutations occur?

Answer 47

it occurs during transcription but could also occur during DNA replication

Question 48

What mutations are most impactful?

Answer 48

one that happens during S phase of DNA replication before meiosis or very early on in embryonic development when the first cell will start dividing (before mitosis during S phase)

Question 49

when are mutations least impactful?

Answer 49

when they effect the 99% of DNA that doesn't code for anything when the mutation doesn't affect the amino acid sequence of the protein (redundant code)