Biotechnology Unit 3: DNA to Proteins
Structure of DNA
I. __________________
a. Nucleic acids are macromolecules used for __________________ and __________________ of
genetic information
b. Nucleic acids are composed of monomers called __________________
i. Nucleotides are composed of __________________ components
1. A __________________ carbon sugar molecule
a. __________________
b. __________________
2. __________________ group
3. __________________ base
a. Double ring __________________
i. __________________ (A)
ii. __________________ (G)
b. Single ring __________________
i. __________________ (T)
ii. __________________ (C)
c. __________________ __________________ (DNA)
i. Primary function is __________________ of genetic material
ii. Forms a helical structure called a __________________
iii. Contains the sugar __________________ and bases __________________
iv. __________________ stranded molecule with bases facing __________________ from a
phosphate backbone
1. The backbone consists of alternating __________________ and
__________________ molecules attached __________________
2. The __________________ ends are called the 3’ and 5’ ends and sequences of
bases are always written from 5’ to 3’
3. Relative positions on a DNA strand are referred to as being either
__________________ (closer to the 5’ end) or __________________ (closer to
the 3’ end)
v. Bases are connected on the __________________ of the helix by __________________
bonds
1. __________________ always pair with __________________ to maintain a
constant helix diameter
a. __________________ (C) always pairs with __________________ (G)
b. __________________ (A) always pairs with __________________ (T)
2. This pairing is called __________________ base pairing and means that the two
strands of DNA are always complimentary
3. High __________________ and __________________ extremes can cause
__________________ of DNA by breaking the hydrogen bonds
vi. DNA molecules are also __________________ because the two strands are
__________________
1. One strand runs __________________ and the other is __________________
vii. Only __________________ of human DNA is made up of protein coding regions called
__________________
1. The rest is composed of __________________, short __________________
sequences, tRNA and rRNA coding sequences, and __________________ and
__________________ sequences
Essential Cell Biology Chapter 5
Biotechnology Unit 3: DNA to Proteins
Structure of Eucaryotic Chromosomes
I. Incredibly __________________ amounts of DNA are needed to __________________ the information
needed to make an organism
a. A human cell has approximately __________________ of DNA and the nucleus is only
__________________ in diameter
b. This is similar to folding __________________ of fine thread into a tennis ball
II. In __________________ cells, DNA molecules are packaged into structures called
__________________
a. __________________ carry their genes on a single “chromosome” that is __________________
in shape
i. This is not the same as a eukaryotic chromosome because it is __________________
very differently
b. Eucaryotes carry their DNA on long __________________ threads of DNA that are
__________________ and __________________ into a compact structure by proteins
i. The DNA and protein complex is called __________________
ii. The DNA in the chromosome is densely packed to save __________________ but it is
also __________________ for all of its functions
c. Human have __________________ chromosomes (22 autosomal and 2 sex)
i. With the exception of __________________ and __________________ cells, each
human cell, has 2 copies of each chromosome
1. One from the __________________ and one from the __________________
2. These maternal and paternal pairs are called __________________ chromosomes
(or __________________)
3. The sex chromosomes in males (X and Y) are the only __________________
human chromosomes
ii. Each chromosome is numbered (1-22) and is different in size and can be
__________________ using a variety of techniques so they can be __________________
Essential Cell Biology Chapter 5
Biotechnology Unit 3: DNA to Proteins
1. A display of all 46 human chromosomes in a human cell is known as a
__________________ and can be used to look for chromosomal abnormalities
III. The most important function of chromosomes is to carry __________________
a. A gene is a section of DNA that carries the __________________ for a protein or a group of
proteins
i. Some genes carry information for the production of special types of
__________________ with diverse functions
b. The __________________ of an organism is the total collection of its genetic material
i. In general, the __________________ of the genome and the complexity of the organism
are related
1. Simple bacteria have around __________________ genes packed into relatively
small molecules of DNA
2. Humans have between __________________ genes with huge amounts of DNA
that is not used for coding proteins
a. The function of this “__________________” is not yet well understood
but each year we learn more about its role
3. This is not always true, however
a. Some plants have __________________ more genes than humans and
some amoebas have __________________ as many genes!
ii. There is no correlation between number of __________________, number of
__________________, and total __________________ size
IV. Chromosomes exist in different __________________ throughout the life of a cell
a. Chromosomes become more or less densely __________________ depending on what they are
doing
i. During the phase of cell division where the chromosomes are replicating
(__________________), the chromosomes are more __________________ packed
ii. During the stage where the chromosomes for the two __________________ cells are
being pulled apart, they are more __________________ packed
V. Chromosome __________________
a. __________________ are the major group of proteins used in chromosome structure
i. The mass of the __________________ in a chromosome is roughly the same as the mass
of __________________
ii. The histone and DNA complex (along with other proteins) is called
__________________
b. The first level of chromatin packing is called the __________________
i. The DNA strand wraps around histone based structures called nucleosome
__________________ particles
1. Commonly called “__________________ on a __________________”
ii. The __________________ charge on the DNA backbone is attracted to the
__________________ charge of the nucleosome core particle
iii. Individual nucleosome core particles are linked together by chains of DNA of varying
length called __________________
c. Linker histones then connect nucleosome core particles together to form an even more densely
packed structure called a __________________
d. The 30 nm-fibers are folded into a series of __________________ to further condense the
structure
i. The __________________ for this is not fully understood
e. There is one more level of folding that is also not yet __________________
Essential Cell Biology Chapter 5
Biotechnology Unit 3: DNA to Proteins
DNA Replication
I.
When cells __________________, they must accurately reproduce the __________________
material so both cells contain __________________ DNA copies
II. The replication of DNA requires __________________
a. This energy is created by converting the incoming deoxynucleoside __________________
into deoxynucleoside __________________
III. Replication is __________________
a. This means the two strands __________________ and each becomes a
__________________ for a new strand
b. This results in two __________________ molecules, each with one __________________
strand and one __________________ strand
IV. Replication begins at a specific site called an __________________ of __________________
a. The DNA strands are separated into two _________________ ___________________
b. __________________ DNA (in eukaryotes) has __________________ origins of replication
and is replicated __________________
i. This creates small fragments called __________________
ii. Replicons are __________________ when they meet
c. __________________ DNA (in prokaryotes and in mitochondria) has one origin of
replication and is also replicated __________________
i. This is called __________________ replication because it looks like the Greek letter

V. The replication process is __________________ by __________________
a. __________________ and DNA __________________ (__________________) unzip and
unwind the DNA
i. __________________ binding proteins bind to the DNA to prevent it from
__________________
ii. This produces two replication __________________ moving in
__________________ directions
b. __________________ are attached to the template strand to allow the binding of the new
nucleotides
i. An enzyme called __________________ synthesizes small fragments of RNA
(usually 10 bp or less) that are __________________ to the 3’ end of the DNA
c. DNA __________________ is a large enzyme that allows the production of the
__________________ strand of DNA during replication
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
i. DNA polymerase can only attach to a __________________ region of DNA
1. This is why the RNA __________________ are important
ii. Alone, DNA polymerase will usually fall off a DNA molecule after making only a
short string of nucleotides
1. Another replication protein called a __________________ surrounds the
DNA and hold on to the DNA polymerase
iii. DNA polymerase only works in __________________ direction
1. Therefore, DNA polymerase moves __________________ the replication fork
on one strand (__________________ strand) and __________________ from
the replication fork on the other strand (__________________ strand)
2. Replication on the lagging strand can only occur in short fragments called
__________________ fragments
a. Each Okazaki fragment requires an __________________ to begin is
replication
b. The RNA primers have a high rate of mistakes and cannot be left in
the finished DNA
c. A __________________ breaks up the primers after the Okazaki
fragment is complete and then a __________________ polymerase
replaces the RNA nucleotides with DNA nucleotides and then finally,
the fragments are connected together by DNA __________________
iv. New nucleotides are added to the daughter strand on the __________________
1. This means replication occurs from __________________
v. DNA polymerase is incredibly __________________, it makes only one error in
every 107 nucleotide pairs
1. This rate is lower than the __________________ of complimentary pairing
a. A-T and C-G are the most __________________ pairs, but other can,
and do, occur
2. DNA polymerase is capable of __________________ by double checking the
previous pair before forming the next
d. __________________ replicates the ends of eukaryotic chromosomes
i. The end of the __________________ strand is a problem for normal replication
because there is nowhere to place the RNA __________________
ii. Because prokaryotes have __________________ DNA molecules, this is not a
problem for them
iii. The ends of eukaryotic chromosomes has special structures called
__________________
1. Telomerase is an enzyme that adds a chain of __________________
nucleotides to the template strand of the DNA so that DNA polymerase can
then __________________ the replication
2. These repeated regions of DNA allow the cell to __________________ the
true end of the chromosome
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
DNA Repair
I.
On rare occasions, the normal replication and repair processes of the cell __________________ and
changes to DNA called __________________ occur
a. Because each protein depends on its __________________ for its __________________, even a
single base pair change can cause a dramatic effect in an organism
i. Changes in __________________ cells can build up and eventually result in improper
functioning of the cells causing __________________
ii. Changes in the __________________ cells (sperm and egg) will be passed on to all the
cells that are found in the __________________ that develops from that germ cell
b. Even though these mutations can help drive __________________, high __________________
of DNA replication is important to an organism and therefor, cells have sophisticated
mechanisms to __________________ the number of DNA mutations
i. __________________________________ is a mechanism dedicated to finding and fixing
the rare mistakes (1 in 107 nucleotides) of replication that are not caught by DNA
polymerase __________________
1. _____________ of the mistakes missed by proofreading are caught by the DNA
mismatch repair mechanism making the overall mutation rate 1 in 109 nucleotides
2. When a base pair is __________________ during replication, there is a chance of
producing a faulty protein
a. There is also a risk that the DNA
will replicate again and therefore
__________________ the mistake
3. Mismatch repair proteins
__________________ these mismatches
and __________________ a region of the
newly created DNA strand around the
mistake and __________________ it with
the correct sequence
a. It is unclear how the proteins
__________________ which side
is old and which side is new, but it
is thought there are small
__________________ in newly
created DNA that are involved
b. Some types of cancer, including
__________________ cancer, are
the result of mutations in mismatch
repair proteins and therefore
__________________ this repair
ii. Not all DNA damage is the result of mistakes in replication, some damage occurs due to
normal __________________ between molecules
1. Depurination and deamination are common __________________ within DNA
a. __________________ involves the random removal of purines (A and G)
i. This causes __________________ in center of the DNA chain but
does not affect the backbone
b. __________________ involves the removal of an amine group from
__________________ bases and turning them into __________________
2. Some chemical __________________ can also damage DNA
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
3. __________________ from the sun or from synthetic sources can cause mutations
called thymine __________________ where two adjacent thymine molecules are
covalently bonded together
4. Whatever the cause, these changes can have __________________ effects on a
cell if they are not repaired
iii. Although there are a wide variety of specific
__________________ (and
__________________) to repair DNA damage,
there is a basic pathway with three main steps
(step one is the most __________________)
1. __________________ and
__________________ the damaged DNA
a. Usually done by
__________________
2. Fill in the __________________ left by
removing the damage
a. Usually done by
__________________ DNA
polymerases
3. Seal the __________________ in the
DNA strand
a. Usually done by DNA
__________________
II. __________________ strand breaks
a. If both strands of the DNA are broken, there is a great
potential for problems because the
__________________ is broken
i. If left unrepaired, chromosomes would be
__________________ and genes could be
__________________ during cell division
b. __________________ end-joining is the process used to fix double strand breaks
i. Specialized __________________ bring the ends together and they are linked by simple
__________________
ii. This usually results in the loss of some __________________
1. The relatively low percentage of the human genome that codes from proteins
means that simply by __________________, there is a relatively low risk of
losing information from a gene
III.
The high fidelity of DNA replication has led to the fact that most organisms alive today share a
tremendous __________________ of their DNA sequences
a. DNA changes tend to be very __________________ and most changes have no impact on the
organism
i. Those mutations that are __________________ are usually eliminated by natural
selection
ii. Those mutations that have no effect, however, are not acted upon by
__________________
b. Humans and chimpanzees split from a common ancestor about __________________ years ago
and still share 98% of their DNA
Essential Cell Biology Chapter 6
Biotechnology Unit 3: DNA to Proteins
Cutting DNA
I. Many organisms, especially bacteria, are able to __________________ and __________________
foreign DNA
a. There is a special class of __________________ the bacteria use to cut specific sequences of
DNA called restriction __________________ (enzymes)
i. Act like __________________ to cut the sugar-phosphate backbone
ii. Recognize specific __________________ sequences of usually
__________________ pairs
iii. They cut both sides of the DNA by breaking the __________________ bond between
the __________________ of one nucleotide (3’) and the __________________ of
another (5’)
iv. The cutting of the DNA can create either __________________ or
__________________ ends
b. Different species have different restriction endonucleases
i. They are named for the __________________ they come from
What are the products that would result when the following piece of DNA is digested with
EcoRI
AluI
NotI
All three together
5’-AAGAATTGCGGAATTCGAGCTTAAGGGCCGCGCCGAAGCTTTAAA-3’
3’-TTCTTAACGCCTTAAGCTCGAATTCCCGGCGCGGCTTCGAAATTT-5’
Essential Cell Biology Chapter 10a
Biotechnology Unit 3: DNA to Proteins
Separating Restriction Fragments and Visualizing DNA
I. __________________ __________________ is a technique to identify different DNA Fragments
II. When the sequence of the bases is unknown, we must exploit the properties of DNA that we do
know
a. __________________ __________________ of cutting by __________________
__________________
III. Electrophoresis separates fragments based on __________________ and __________________
a. DNA is __________________ __________________ due to phosphates
b. DNA is cut by ____________________________________
c. DNA is placed into small holes called __________________ in an __________________
i. Jello like substance made of interlocking fiber with different sized holes
ii. The size of the holes can be regulated by using different concentrations of agarose
d. An _________________________ is applied to the gel
i. Negative charge by the wells and positive on the other end
ii. This causes the DNA fragments to migrate through the well towards the positive end
iii. Smaller fragments move faster (and therefore farther) than larger fragments because
of the sizes of the holes in the gel
e. DNA can be stained with _______________________________ to show up orange under
UV light or it can be stained to be seen under fluorescent lighting
f. A __________________ is run with the DNA samples to estimate the sizes of the fragments
i. The marker uses a piece of DNA with known fragment lengths from known
sequences and restriction enzymes
Essential Cell Biology Chapter 10a