Download Biotechnology Unit 3: DNA to Proteins Essential Cell Biology

Biotechnology Unit 3: DNA to Proteins
From DNA to RNA
I.
After the discovery of the structure of DNA, the major question remaining was how does the
__________________ stored in the 4 letter code of DNA direct the __________________ and
__________________ of an entire organism
II. The central dogma of molecular biology
a. There are 2 general steps to the production of a
__________________ from a __________________
i. Genes code for __________________
(__________________)
ii. RNA codes for the __________________
(__________________)
b. So, the flow of genetic information is from
__________________  __________________ 
__________________
i. This is known as the __________________ of
molecular biology
c. Together, transcription and translation are the means by
which cells __________________ their genetic information
i. This is known as gene __________________
III.
__________________ of DNA into RNA
a. RNA is an __________________ produced from DNA in the process of protein
__________________
i. RNA can have many forms and an incredibly wide range of __________________ within
the cell
b. Like DNA, RNA is a linear __________________ made up of four different
__________________ linked together by phosphodiester bonds
i. There are two major __________________ differences between DNA and RNA
1. The nucleotides in RNA are __________________ instead of
deoxyribonucleotides
a. They contain the 5-carbon sugar __________________ instead of
deoxyribose
2. The bases involved in the ribonucleotides are A, C, G, and ____
(__________________)
a. Uracil replaces __________________ and complimentarily binds with
__________________ with 2 hydrogen bonds just like thymine
ii. There is also a fairly major __________________ difference between DNA and RNA
1. RNA is __________________ stranded instead of being a double helix like DNA
a. This allows RNA to __________________ into many different shapes to
accomplish many different __________________
c. All RNA in a cell is made by __________________
i. There are several similarities between transcription and DNA __________________
1. A small portion of the DNA double helix is opened up and __________________
to expose the bases of the DNA
2. One of the two strands acts as a __________________ and ribonucleotides are
added using __________________ base-pairing
3. The new RNA molecule (called a __________________) grows one nucleotide at
a time
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
a. The enzyme responsible for reading the template and building the new
RNA molecule is called __________________ and it reads from
__________________ and builds from 5’ to 3’ like DNA polymerase
i. RNA polymerase uses energy from ribonucleoside
__________________ for energy just like DNA polymerase
ii. Transcription does differ from DNA replication in some __________________ ways
1. The RNA transcript that is formed does not stay __________________ bonded to
the template strand like DNA does
a. The RNA ends up being __________________ stranded
b. Just behind the region where nucleotides are being added, the RNA
transcript is __________________ and the DNA double helix
__________________
2. Only one side of the DNA molecule acts a __________________ during
transcription
a. Both sides can be templates for different genes at different
__________________ on the chromosome however
b. The __________________ or __________________ strand is the strand
that is __________________ by the RNA polymerase
c. The other strand is called the __________________ or
__________________ strand and is the __________________ for the
RNA molecule
3. RNA molecules are only transcribed from __________________ regions of DNA
a. This means that transcription only produces a __________________
segment of not more than a few __________________ base-pairs and not
an entire DNA molecule
4. Transcription of the same gene can occur __________________ by several
different RNA polymerases
a. Because the transcripts are released almost __________________,
transcription can start over shortly after the RNA polymerase has moved
on from the starting point
b. It takes approximately __________________ to transcribe a molecule of
RNA from a __________________ sized gene of 1500 nucleotide pairs
i. As many as 15 RNA polymerases can __________________ be
transcribing this gene at any one give time
ii. This means over __________________ can be synthesized in a
hour
5. RNA polymerase is very similar in its action as DNA polymerase but there are a
couple key __________________
a. RNA polymerase polymerizes __________________ instead of
deoxyribonucleotides
b. RNA polymerase does not require RNA __________________
i. Because RNA does not __________________ store genetic
information, the necessity of __________________ in
transcription is lower than in DNA
1. RNA polymerases make approximately 1 mistake in every
__________________ compared to the rate of one mistake
in 107 nucleotides by DNA polymerase
iii. Several types of RNA are __________________ in cells
1. The vast majority of genes in a cell’s DNA code for the amino acid sequence of
__________________
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
a. The RNA molecules that are copied from these genes are called
__________________ RNA (__________________)
i. In __________________, each mRNA carries information from
just one gene, coding for just one protein
ii. In __________________, several adjacent genes are often
transcribed together into a single mRNA which carries the
information for several different proteins
2. In other genes, the final product of the gene is the __________________ itself
a. These nonmessenger RNAs can serve a __________________,
__________________, and __________________ components of cells
and they are important to the translation of proteins and the regulation of
gene expression
b. __________________ RNA (__________________) forms the central
core of the ribosomes where mRNA is translated into proteins
c. __________________ RNA (__________________) for the adaptors that
hold the amino acids in place on the ribosome so they can be incorporated
into the protein
d. __________________ (__________________) serve as regulators of
eukaryotic gene expression
d. __________________ in DNA tell RNA polymerase where to start and finish
i. Because of the fact that not all of the DNA of an organism __________________ for
proteins and because not all of the genes are __________________ in all cells, there has
to be a __________________ to tell RNA polymerase where to begin transcription
ii. The beginning of a gene must be __________________ in order for transcription to begin
iii. This process is different in __________________ and __________________
1. In procaryotes, when RNA polymerase collides with a DNA molecule it attaches
itself very __________________ and moves along the DNA until it finds a
specific region called a __________________
a. At the promoter, the RNA polymerase binds __________________ and
opens up the double helix in front of itself
i. Promoter regions are __________________ which prevents
transcription from occurring in any direction other than 5’ to 3’
b. The RNA polymerase then moves along the DNA double helix reading the
__________________ strand and producing the __________________
RNA transcript until it reaches another specific region called the
__________________ or stop site
i. At the terminator site, the RNA polymerase __________________
from the DNA double helix
c. The procaryotic RNA polymerase has a special subunit called a
__________________ that helps to identify the promoter region
i. Once the promoter is identified, the sigma factor
__________________ itself from the RNA polymerase until
transcription is __________________ and the polymerase has
disengaged
2. In eucaryotes, the process is much more __________________
a. Unlike procaryotes, eucaryotes have __________________ different RNA
polymerases
i. RNA polymerase I and RNA polymerase III are responsible for
transcribing __________________, __________________, and
__________________
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
ii. RNA polymerase II is responsible for transcribing
__________________
b. Another difference from procaryotes is that eukaryotic RNA polymerase
doesn’t have a sigma factor and therefor is dependent upon a large group
of accessory proteins called transcription __________________ which
assemble at the __________________ before transcription can occur
i. A group of __________________ __________________
__________________ assemble at a short section of DNA located
25 base-pairs upstream of the gene
1. This region is usually rich in A and T nucleotides and is
called the __________________
ii. Once the RNA polymerase II is bound to the transcription factor
complex, it is __________________ by adding a phosphate to its
tail and that allows it to break away from the transcription factors
and begin transcription
1. The transcription factors then release and are available to
__________________ at another promoter region
c. The __________________ of eukaryotic chromosomes also affects
transcription because the individual genes are spread out considerably
more than they are in procaryotes
i. This allows for almost unlimited combinations of
__________________ sequences for individual genes
d. Finally, the __________________ of the eukaryotic chromosomes adds a
level of complexity to transcription
e. __________________ of transcripts
i. In prokaryotes, the DNA is already in the __________________ and exposed to
ribosomes
1. __________________ can attach to the 5’ end of the transcript and begin the
process of protein synthesis while transcription is still going
ii. In eucaryotes, the DNA is __________________ inside the nucleus and is not exposed to
the ribosomes until it leaves
1. Eucaryotic transcripts go through several steps of RNA __________________
before they can leave the nucleus
a. These steps take place while transcription is occurring because the
enzymes are attached to the __________________ of the RNA
polymerase
b. RNA __________________ involves adding methylated
__________________ to the 5’ end of the transcript
c. __________________ involves cutting a small portion off of the 3’ end of
the transcript and then adds a few hundred __________________ creating
a poly-A tail
d. Both RNA capping and polyadenylation are thought to add
__________________ and to help with the __________________ of the
mRNA out of the nucleus
2. Most eukaryotic genes are __________________ with noncoding regions that
need to be __________________ from the transcript before translation can occur
a. The noncoding regions are called __________________ and the coding
regions are called __________________
i. The introns are usually much __________________ than the exons
Essential Cell Biology Chapter 7
IV.
Biotechnology Unit 3: DNA to Proteins
b. The __________________ length of a gene is transcribed including both
introns and exons
c. The introns need to be removed by RNA __________________
i. There are sequences within the introns that __________________
them as the regions that need to be cut out
ii. The splicing of mRNA is done by other RNA molecules called
small nuclear RNAs (__________________) that combine with
proteins to form small nuclear ribonucleoprotein particles
(__________________) (pronounced “snurps”)
iii. The cutting follows what is known as a __________________ cut
3. __________________ splicing provides the ability for one mRNA to be used to
produce several different __________________
a. Splicing the RNA __________________ (keeping different exons)
provides many different functional mRNA molecules
b. It is estimated that ________ of human genes undergo alternative splicing
iii. Once RNA processing and splicing is complete, the mRNA must __________________
the nucleus to join with ribosomes to be translated into proteins
__________________ is the process of converting the RNA sequence into a __________________
a. Translation involves a much more __________________ change than transcription
i. The “__________________” used to carry the code in DNA and RNA is based on 5 (but
only 4 at a time) __________________
ii. The “__________________” used to build proteins is composed of 20
__________________
1. There cannot be a one to one relationship between RNA and proteins so we need
what is referred to as the __________________ __________________ that is
identical in nearly all life forms
a. The mRNA sequence is read in consecutive groups of 3 nucleotides called
__________________
i. There are 4x4x4 = __________________ for codon combinations
ii. Because there are only 20 amino acids, there is a built in
__________________ meaning come amino acids are coded for by
more than one codon
b. This allows for three unique __________________ __________________
depending on where the reading begins
i. There is a __________________ start codon that identifies the
proper reading frame for each protein
b. The rapid __________________ of mRNA into a protein requires a molecular
__________________ that moves along the RNA, captures and holds tRNA molecules, and
__________________ links the incoming amino acids
i. __________________ RNA (tRNAs) molecules match amino acids to the proper mRNA
codons
1. tRNAs are molecules roughly 80 nucleotides long that act as
__________________ to bring in the correct amino acid that is coded for by each
codon
a. Each tRNA contains a region known as the __________________ which
is complimentary to the codon on the mRNA
b. The 3’ end of the tRNA holds a specific __________________ molecule
c. tRNA molecules are said to be __________________ when the amino
acid is attached
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
i. This is done by enzymes called aminoacyl-tRNA
__________________
ii. Each amino acid has a __________________ synthetase that is
responsible for connecting that amino acid to the tRNA molecules
with the proper anticodons
ii. __________________ are the protein manufacturing machine
1. They are made of over 50 different __________________ and several
__________________ RNA (rRNA) molecules
2. Typical cells have __________________ of individual ribosomes
a. Both eucaryotic and procaryotic ribosomes are similar and are made up of
a __________________ subunit and a __________________ subunit
i. The small subunit pairs the __________________ to the mRNA
codons
ii. The large subunit links the __________________ into the
polypeptide chain
b. The ribosome attaches near the __________________ of the mRNA and
then pulls the mRNA through while it __________________ the
appropriate amino acids
i. Eucaryotic ribosomes can add about __________________ per
second
ii. Procaryotic ribosomes can combine up to __________________
per second
3. Along with the binding site for the mRNA, the ribosome has
__________________ sites for tRNAs
a. The __________________ is where the new tRNA comes in and binds to
the anticodon and brings in the new amino acid
b. The __________________ is where the previous tRNA is held until the
new amino acid can be linked onto the chain
c. The __________________ holds the tRNA until it is ejected
d. The mRNA moves through these sites __________________ until the
polypeptide chain is complete
4. Codons in mRNA signal where to __________ and _________ protein synthesis
a. Translation always begins with the codon __________________
i. The __________________ tRNA carries the amino acid
methionine and attaches to the AUG codon
ii. This initiator tRNA is different from the normal
__________________ carrying tRNA
iii. The __________________ ribosomal subunit attaches to the 5’end
of them RNA (signaled by the 5’ cap) and then
__________________ along until it finds an AUG
b. It then reads along adding all the necessary amino acids until it reaches a
__________________ codon
i. __________, __________, and __________ are the stop codons
ii. Stop codons do not correspond to a tRNA and instead signal the
ribosome to stop __________________
iii. __________________ factors (proteins) bind to the stop codon in
the A-site and cause the __________________ and the
__________________ to be released from the mRNA
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
Essential Cell Biology Chapter 7
Biotechnology Unit 3: DNA to Proteins
Overview of Gene Expression
I.
Every cell in an organism has a complete set of the __________________ for that organism but not all
of the __________________ are needed within the cell
a. Different cell types produce different sets of __________________
b. The __________________ of each protein that the cell needs is different at different times
c. The control of gene __________________ is how the cell deals with these issues
i. Cells can change the expression of genes in response to __________________ signals
II.
Gene expression can be __________________ at many different levels or step within the
__________________ from DNA to RNA to protein
a. __________________ control
i. Transcription is controlled by __________________ binding to __________________
DNA sequences
1. Remember that in order for transcription to begin, RNA __________________
must attach and __________________ itself at the promoter region of the gene
2. The simplest regulatory sequences are only __________________ long
a. These are most common in __________________
3. In eucaryotes, the regulatory sequences can be up to __________________
nucleotide pairs and can interact with a wide variety of signals
4. Transcription __________________ are proteins that bind to specific regulatory
DNA sequences to act as a __________________ for the control of transcription
a. Different proteins recognize different __________________ based on the
shape of the protein
ii. In procaryotes, __________________ control the expression of groups of genes
1. There is a region at the start of the operon called the __________________ which
is where transcription of the entire group of genes will begin
2. Operators are controlled by __________________ and __________________
a. A repressor is a __________________ that when bound to the operator
does not allow transcription to begin by blocking the
__________________ of RNA polymerase
b. An activator is a protein that allows transcription to occur by allowing for
__________________ attachment of the DNA polymerase
c. Some operons use __________________ repressors and activators
3. Operon __________________
a. __________________ operon
i. This operon uses a __________________ and it controls a group
of five genes that are necessary for the production of the amino
acid tryptophan
ii. When tryptophan is in __________________ in the cell, it can
bind to the repressor protein which will then bind to the operon and
__________________ transcription
iii. When tryptophan is in low concentration, it cannot bind to the
repressor protein and the repressor protein then cannot bind to the
operator and transcription will occur __________________ for the
production of tryptophan
Essential Cell Biology Chapter 8
Biotechnology Unit 3: DNA to Proteins
b. Lac operon
i. This operon uses both a __________________ and an
__________________ to control the transcription of several genes
used to break down __________________ which is a food source
for bacteria
ii. __________________ is the bacterial cells first choice for food so
when glucose is presence the Lac operon is switched off because it
is lacking a necessary __________________ protein that is only
available when glucose is absent
iii. The operon is also switched off by a repressor protein that can only
be removed when __________________ is present
iv. The only time the Lac operon is active, is when both the activator
is bound (__________________ not present) and the repressor is
not bound (__________________ is present)
Essential Cell Biology Chapter 8
Biotechnology Unit 3: DNA to Proteins
iii. __________________ also use transcription regulators (both repressors and activators)
but they do not use __________________ to control groups of genes
1. These sites are called __________________
2. Eucaryotic transcription regulators can work from a __________________
a. The binding of activators or repressors in eucaryotes does not need to be
__________________ to the gene of interest or even be
__________________ from it
b. In many instances the transcription regulators are long distances away but
there is a __________________ that occurs to allow for the initiation of
transcription
b. __________________ -transcriptional control
i. These are controls that occur __________________ the RNA polymerase has already
started synthesizing the mRNA
ii. Some mRNA molecules contain __________________, short RNA segments that can
change their conformation when certain chemicals are present and therefore can control
their own expression
1. There are no __________________ involved in this type of regulation
iii. Controlling __________________
1. Repressor proteins can bind onto the __________________ in eucaryotic mRNA
and regulate when the ribosomes can attach to carry out translation
2. RNA __________________ (RNAi) is one way organisms can control translation
a. Many __________________ have double stranded RNA (dsRNA)
i. completely or just parts
ii. As a defense against these viruses, cells have the ability to
__________________ dsRNA and trigger the RNAi response
b. A nuclease named “__________________” recognizes and cuts dsRNA
into small pieces called __________________ RNAs (siRNA) that are
usually around 20 base pairs long
i. This is a highly conserved nuclease found in
__________________ organisms
1. It probably evolved __________________ to the
divergence of plants, animals, and fungi
2. Recently, a similar enzyme has been found in
__________________
ii. siRNAs from dicer combine with a group of proteins to form a
complex known as __________________ (RNA-induced silencing
complex)
1. The siRNA is __________________ into a single strand
a. In some systems there is __________________
selection of strands but in most both an and are used
2. One of the key proteins is a protein called
“__________________”
iii. The RISC complex then uses the single stranded siRNA to bind to
the __________________ mRNA
iv. Slicer then __________________ the mRNA and the cell
__________________ the sliced transcripts
c. Another type of double stranded RNA exists that is found naturally in
many cells called __________________ (miRNA)
i. These are expressed from __________________ regions of the
genome and make natural double stranded RNA
Essential Cell Biology Chapter 8
ii.
iii.
iv.
v.
vi.
Biotechnology Unit 3: DNA to Proteins
miRNAs are also recognized by dicer and target other genes as a
__________________ form of controlling gene expression without
cleavage
miRNAs do not induce cleavage of the mRNA because they are
not __________________ complimentary
1. Instead they are involved in translational
__________________
2. Specific type of miRNA called a small temporal RNA
(stRNA)
Dicer interacts with the stRNA or other mRNA and then they enter
the RISC complex and bind to mRNA but __________________
translation instead of cutting
There is __________________ recognition so slicing does not
occur
This allows for the same miRNA to target several different
__________________ or __________________ of genes
Essential Cell Biology Chapter 8