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Molecular Biology

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Joel Hutson

on 26 October 2016

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Transcript of Molecular Biology



Main Point#1:

Be able to explain
why a universal (i.e.,
all known life uses it)
genetic code provides
overwhelming supportive
evidence for evolution.
by Joel David Hutson
BIO 110
Elgin Community College

Chapter 10 Learning Objectives:
Explain how the structure of DNA facilitates its replication.
Be able to describe the process of transcription,
i.e., how DNA is copied into RNA.
Diagram the process of translation;
that is, how the "language" of DNA
& RNA is translated into the "language"
of proteins.
Chapter 10 Learning Main Points:
The evidence that all life uses the same
genetic "language" of DNA & RNA is one
of the most powerful pieces of supporting
evidence that all known life is descended
(i.e., evolved) from one common ancestor.
Mutations (the ultimate starting point for evolution),
are misspelling in the words (genes) of DNA.
DNA is the molecule that carries all of the inherited information in cells.
Your cells “read” DNA and it tells them what to do in several ways
An everyday analogy:
CDs &
A cell's enzymes
can "read" the bumps
& grooves
in unzipped DNA
Each of the 4
"letters" of DNA
has a different shape
Detectors "read"
the bumps &
grooves burned
into discs too
DeoxyriboNucleic Acid = DNA

DNA was described as “nucleic acid”—an acidic material in the nucleus in the late 1800’s.
Its importance wasn’t discovered until later. For a long time, DNA was considered too simple to carry genetic information in the hunt to find the hereditary
material of life.
Experimental tests using bacteria and bacteriophages (viruses that attack bacteria) showed that DNA is the hereditary material in living organisms

E.g., Hershey and Chase’s experiments
A Bacteriophage
(eater of bacteria) virus
Is protein the
hereditary material?
Is DNA the
hereditary material?
Later work corroborated (backed up, verified) that the hereditary material of life is DNA.
The Race was then on to
describe the structure of DNA
A DNA molecule consists of two
strands of nucleotides, coiled into
a double helix (like a right-handed
spiral staircase)
Each nucleotide has:
A five-carbon sugar
A phosphate
A nitrogen-containing base (adenine, thymine, guanine, or cytosine)
The 4 Bases of DNA
Base Pairing:

Bases of two DNA strands pair in only one way,
a complementary (one fits the other) way.

Adenine pairs with thymine (A-T)
Guanine pairs with cytosine (G-C)
You could visualize complementary
base pairing as a lock and key model
The DNA sequence (order of bases) varies among species and individuals, but NOT this complementary base pairing!
However, complementary bases
also act like magnets.
Hydrogen bonds are very common in organic molcules

(+) Hydrogens are attracted
to exposed (-) Oxygen or Nitrogen electrons
These bonds & their
associated electrons
& atoms also provide
the bumps & grooves
that enzymes "read" on
unzipped DNA molecules

Likewise, complementary base pairing immediately suggests how DNA must copy itself when cells reproduce

A cell must replicate (copy) its DNA
before dividing during mitosis or meiosis.

A cell must also continously repair
mutations in its DNA throughout its life.

How is this accomplished?
Enzymes (ATP-powered protein machines) unwind & unzip the double helix
Double Helix
- DNA polymerases assemble complementary DNA strands on templates from free nucleotides
- DNA ligase seals gaps in new DNA strands

Two double-stranded DNA molecules result
One strand of each is new
The energy for DNA replication comes from the nucleotide precursors. They all have 3 phosphates on them, like ATP, and 2 of the phosphates are removed to make the DNA.
A simple view of
DNA replication
New DNA is assembled
continuously on only one
of the two parent template
strands. It is assembled on
the other parent template
strand in short fragments.
DNA ligase seals the gaps
between the fragments.
Why discontinuous assembly?
DNA synthesis occurs only in the 5’ to 3’
direction. Prime symbols (') stand for the
carbons on a base ring.

Free nucleotides can be
added only to the —OH group at
the 3’ end of a growing strand.
Thus, DNA replication proceeds "downhill", from 5'
to 3' carbons.
This is also why DNA replication
may happen at many different sites,
or "bubbles".
DNA repair is very similar to DNA replication:

Newly forming DNA strands are monitored for errors, most of which are corrected
DNA repair mechanisms fix DNA damaged by chemicals (like oxidants, water is an example, or radiation such as sunlight)
Proofreading by DNA polymerases corrects most base-pairing errors

Uncorrected errors are mutations

Any change in the base sequence of a DNA molecule is a mutation. Mutation is a completely random process: any DNA base can be mutated, whether it is in a gene or not.
Basic types:
1. base substitutions: convert one base into another, such as changing an A into a G.
2. Insertions or deletions of large pieces of DNA.
3. Combining parts of 2 different genes together.
Mutations are very common & unavoidable: they are occurring constantly day and night in every one of your trillions of cells; every cell contains multiple mutations, which slowly add up as you age… Also, everyone is genetically different from every other person due to the accumulation of mutations, even identical twins (clones).

Question: If mutations add up as you age, how come
our gametes (eggs & sperm) don't become defunct?
Genetic load: on average, each person has 3 recessive lethal mutations in all cells. We survive because the dominant normal alleles cover up the recessive lethals. Also, most of them are extremely rare and so don’t come from both parents during fertilization.

Inbreeding—mating with close blood relatives—often causes homozygous recessive children because the recessive lethals inherited from the common ancestor become homozygous.
Ellis-van Creveld syndrome is common amongst the Amish.
It involves not only short stature but polydactyly (extra fingers or toes), abnormalities of the nails and teeth, and, in about half of individuals, a hole between the two upper chambers of the heart. The syndrome is common in the Amish because of the "founder effect," which we will discuss later.
Gene Expression:

“Expressed” = making
the protein product
Recall that each gene is a short section
of a chromosome’s DNA that
codes for a polypeptide.
Recall, that polypeptides are linear chains of amino acids, and that proteins are composed of one or more polypeptides, sometimes with additional small molecules attached. The proteins then act as enzymes or structures to do the work of the cell.
All cells have the same genes. What makes one type of cell different from another is which genes are expressed or not expressed in the cell. For example, the genes for hemoglobin are on in red blood cells, but off in muscle and nerve cells.
Genes are expressed by first making an RNA copy of the gene (transcription) and then using the information on the the RNA copy to make a protein (translation).

RNA is a nucleic acid, like DNA, with a few small differences:
i) RNA is single stranded, not double stranded like DNA
ii) RNAs are typically short, not more than 1 gene long, whereas DNAs are very long and contain many genes
iii) RNA uses the sugar ribose (hence RiboNucleic Acid) instead of deoxyribose in DNA. This, among other things, causes RNA to pair up less readily & tightly to itself or other RNAs
iv) RNA uses the base uracil (U) instead of thymine (T) in DNA.
There are 3 types of RNA in the cell that we will be
learning about because they are directly related to
replication, transcription & translation:
1) messenger RNA(mRNA): single-stranded copies of the individual genes
mRNA copy
2) ribosomal RNA (rRNA): part of the ribosome organelle, a big enzyme made up of protein and rRNA that translates mRNA into protein
3) transfer RNA (tRNA), which is an adapter between the mRNA and the protein links (amino acids) it codes for

= copying (not exact replication, but in to RNA).

In genetics, transcription is the process of making an mRNA copy of a single DNA gene.

Question: Do you think it matters which strand of the DNA double helix is copied?
The transcription (copying) is done by an enzyme: RNA polymerase. Recall that in replication, a DNA copy of DNA is made by the enzyme DNA polymerase.
The bases of mRNA pair with the complementary bases of DNA: A with T (or U in RNA), and G with C.
RNA polymerase attaches to a signal at the beginning of the gene, the promoter. Then RNA polymerase moves down the gene, adding new bases to the RNA copy, until it reaches a termination signal at the end of the gene.
More Transcription:
mRNA processing:

Oddly, most genes in eukaryotes are not continuous. They are interrupted by long regions of DNA called “introns”. Introns may provide a means of controlling or modifying gene expression.

The other parts of the gene, the parts that code for proteins, are called “exons”. Some genes are more than 99% introns, with only 1% of the gene coding for exons.
The entire gene, introns and exons, is transcribed into an mRNA copy, but the introns need to be removed before it can be converted to protein.
After transcription, another type of RNA helps remove (excise) the exons from the introns, leaving only the protein coding portion of the gene in the mRNA.
Also, the cell adds a protective cap to one end, and a tail of A’s to the other end. These both function to protect the mRNA from enzymes that would degrade it starting on an end and moving inward
Thus, an initial mRNA copy of a gene is converted into a final mRNA by doing 2 things:
1. cut out the introns.
2. add protective bases to the ends.
Transcription & mRNA processing occur in the nucleus. After this, the mRNA moves to the cytoplasm for translation
DNA Replication and Repair:
The Genetic "Code"

How does the language of DNA
& RNA get translated into the
language of proteins?
The Problem:
There are only 4 bases in DNA and RNA, but there are usually only 20 different amino acids that go into proteins in most known species of life. How can DNA code for the amino acid sequence of a protein?

Through experimentation, researchers realized that
bases form words of three bases each to code for
one amino acid.
Each amino acid is coded for by a group of 3 bases, a codon. 3 bases of DNA or RNA = 1 codon.
Since there are 4 bases and 3 positions in each codon, there are 4 x 4 x 4 = 64 possible codons.
This is far more than is necessary, so most amino acids use more than 1 codon.
3 of the 64 codons are used as STOP signals; they are found at the end of every gene and mark the end of the protein.
One codon is used as a START signal: it is at the start of every protein.
What does the actual translating?

Useful mnemonic: the (t) in transfer RNA (tRNA)
can also be remembered as standing for
tRNA molecules act as adapters between the codons on mRNA and the amino acids. tRNAs are the physical manifestation of the genetic code.
Each tRNA molecule is twisted into a knot that has 2 ends
At one end is the “anticodon”, 3 RNA bases that matches the 3 bases of the codon. This is the end that attaches to mRNA
At the other end is an attachment site for the proper amino acid
A special group of enzymes (which we won't be learning) pairs up the proper tRNA molecules with their corresponding amino acids
tRNAs bring the amino acids to the ribosomes, which are rRNA/protein hybrids that move along the mRNA, translating the codons into the amino acid sequence of the polypeptide (protein chain)

Three main players here: mRNA, the ribosome, and the tRNAs with attached amino acids
First step: Initiation.

Ribosomes are composed of 2 subunits (large and small), which come together when the mRNA attaches during the initiation process
Step 2 is Elongation:

the ribosome moves down the mRNA, adding new amino acids to the growing polypeptide chain
The mRNA binds to a ribosome, and the tRNA corresponding to the START codon binds to this complex.
The ribosome has 2 sites for binding tRNA. The first tRNA with its attached amino acid binds to the first site, and then the tRNA corresponding to the second codon bind to the second site
The ribosome then removes the amino acid from the first tRNA and attaches it to the second amino acid
At this point, the first tRNA is empty: no attached amino acid, and the second tRNA has a chain of 2 amino acids attached to it
The ribosome then slides down the mRNA 1 codon (3 bases)

The first tRNA is pushed off, and the second tRNA, with 2 attached amino acids, moves to the first position on the ribosome
The elongation cycle repeats as the ribosome moves down the mRNA, translating it one codon and one amino acid at a time
Repeat until a STOP codon is reached
The final step in translation is termination. When the ribosome reaches a STOP codon, there is no corresponding tRNA
Main Point#2:

Mutations, or mispellings
in the 4 DNA bases,
provide the material for
natural selection to work
Helicase = unwinds the helix first
Full transcript