Download Biology 2

Biology 101
2 – 25 – 99
1st lecture for test two/Thursday
DNA Structure and Replication
We have 23 paternal chromosomes and 23 maternal chromosomes from dad and mom.
The chromosomes are chosen randomly on the chromatin chain by enzymes. Reason
why we are unique. We have 3 billion nucleotides in DNA.
The 5 Carbon sugar structure is part of the double helix structure. Know how to label
all 5 sides and their base is made out of. C1 is the nitrogenous base, A, C, T, G or U on
RNA. C2 is the sugar minus the oxygen atom. C3 is -OH and C4 is a phosphate.
A connects to T; C connects to G
The DNA nucleotide has three main groups, a nitrogenous base, a sugar, and a
phosphate group. The nucleotides are joined by covalent bonds between the sugar of
one nucleotide and the phosphate of the next. This results in a sugar – phosphate
backbone. DNA ligases ties the single DNA strand into one covalently bonded strip
during replication.
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DNA polymerases/Replication
DNA replication begins at specific sites on the double helix, called origins of
replication. Then replication proceeds in both directions, creating replicating bubbles.
The parental DNA strands open up as the daughter strands elongate on both sides of
each bubble. Thousands of bubbles can be present at once. Eventually, all the bubbles
merge, yielding two completed daughter DNA molecules.
The DNA structure is universal; the sequence is unique to everyone else, except for
twins. All have the same diameter of 2 nanometers.
Each strand has a 31 (three-prime) end and a 51 end. The prime numbers refer to the
carbon atoms of the nucleotide sugars. At one end of each DNA strand, the sugar’s 3
prime carbon is attached to an –OH group. At the other end, the sugar’s 5 prime carbon
has a phosphate group. The opposite orientation of the strands is important in DNA
replication. The enzymes that link DNA nucleotides to a growing daughter strand,
called DNA Polymerases, add nucleotides only to the 3 prime end, never to the 5 prime
end. So 3 to 5, then the daughter strand can only grow in the 5 to 3 direction. 30
enzymes do this break up. She wants us to know two, DNA polymerases and DNA
ligases.
As one strand goes up the other goes down, in between are the DNA nucleotides
connected by weak Hydrogen bonds. The strong covalent bonds are the backbone of the
double helix (sugar covalently bonded to a phosphate, sugar – phosphate – sugar –
phosphate). This mirror image of the strands is called ANTI – PARALELLISM. Then the
two strands coil into the famous double helix.
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Each strand is made up of an old and new strand called the “Semi – Constructive
Model”. There are minor and major grooves on the DNA ladder. The major grooves are
fatter than the minor ones.
Replication
We’re going to open up the DNA strand in the middle. During replication an enzyme
arbitrarily chooses a sight on the strand the DNA opens up in the middle because of the
weak H bonds. If the backbone were to break, some of the DNA would get lost. When
we’re finished we’ll have two sets of chromosomes.
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Biology 101
3 – 2 – 99
nd
2 lecture for test two/Tuesday
Meiosis – cell division in gametes, where the number of chromosomes is reduced by ½.
Mitosis is for growth and repair, as in skin cells. It results in two daughter cells. It starts
with one cell and gets two cells that are identical. Complete set is Meiosis involves only
the sperm and eggs, the gametes and results in 4 cells. Each with 46 chromosomes (2n).
• n= 23 Haploid number
• 2n = complete chromosomes for humans.
MITOSIS
Chromosomes duplicate and then split in two as a cell divides.
Before a eukaryotic cell begins to divide, it duplicates all of its chromosomes. The DNA
molecule of each chromosome is copied. The result is that each chromosome now
consists of two copies called Sister Chromatids. They are joined together at a
specialized region called the centromere. The fuzzy appearance of the chromosome
comes from the twists and folds of its chromatin fibers.
When the cell divides, the sister chromatids of a duplicated chromosome separate
from each other, Once separated from its sister, each chromatid is now called a
chromosome and is identical to the chromosome we started with.
In our own body, millions of cells must divide every second to maintain the total
number of 60 trillion cells. Specialized cells such as nerve and muscle do not regenerate
themselves. Eukaryotic cells undergo a CELL CYCLE, an orderly sequence that extends
from the time a cell divides to form two daughter cells to the time those daughter cells
divide again.
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Most of the time, the cell cycle is spent in INTERPHASE. The cell’s metabolic rate is
very high – chromosomes replicate during this time and serves as the basis for dividing
interphase into three subphases, G1, S, G2 and M
G1 is the period before DNA synthesis begins. G stands for gap. S is when DNA
Synthesis occurs. At the end of this phase, the chromosomes are double each other.
Each consisting of two sister chromatids.
In a process called Mitosis, the nucleus and its contents, including the duplicated
chromosomes, divide and are evenly distributed into two daughter nuclei. In a second
process called cytokinesis, the cytoplasm divides in two. Together, these two cycles are
called the mitotic phase, M of the cell cycle.
MITOSIS: The Five Stages of Division
1. Interphase – it is a period of growth when the cell synthesizes new molecules and
organelles. The cell contains two microtubule – organizing centers (MTOC’s), which
are clouds of cytoplasmic material that contain centrioles.
2. Prophase – Within the nucleus, the chromatin fibers become more tightly coiled and
folded, forming discreet chromosomes that can be seen easily. Each duplicated
chromosome appears as 2 identical sister chromatids joined at the centromere. The
mitotic spindle begins to form as microtubules grow out from the MTOC’s which move
to the poles.
Then the nuclear envelope starts to disappear so the microtubles from both ends can
reach into the chromosomes, now highly condensed. At the centromere region, each
sister chromatid has a protein structure called the kinetochore. The spindle fibers attach
on to this kinetochore. However some do not grab on. These are called the polar
microtubules (PMTS).
3. Metaphase – The mitotic spindle is fully formed, with its poles at opposite ends of the
cell. The chromosomes convene on the metaphase plate, right in the center of the cell.
The KMT attached to a particular chromatid all come from one pole of the spindle. And
those attached to its sister chromatid come from the opposite pole.
4. Anaphase – Begins when the two centomeres of each chromosome come apart,
separating the sister chromatids. Once separated, each sister chromatid is now a fullfledged daughter chromosome. Anaphase is over when the equivalent and complete
collections of chromosomes have reached the poles of the cell.
5. Telophase & Cytokinesis – The end of cell division. Roughly the reverse of prophase.
The nuclear envelope starts to reappear and the chromatin fiber of each chromosome
uncoils itself. The mitotic spindle also disappears. Cytokinesis, the division of the
cytoplasm, occurs along with telophase, with 2 daughter cells completely separating at
the end of mitosis.
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Review:
On test two, this will be matching. Identify G1, working and growth. It stands for gap. S
is DNA synthesis. DNA replication takes place before cell division. G2 is when the cell
prepares to divide. It spans the time from completion of DNA synthesis to the onset of
cell division. G2 is also a time of metabolic activity.
Know these points.
• The plasma nuclear membrane disappears in late prophase.
• The centromere will be the region where the kinetochore lies. The kinetochore is the
“handle” the MT will grab a hold on to. The kinetochore reinforces the DNA.
• There are two kinds of microtubules. The kinetochore microtubules which attach to
the centromere and the polar microtubules are the ones that don’t grab on to them.
• The polar MT makes the membrane become more oval because they are getting
longer.
• Going into prophase, when the nuclear membrane is gone, the MT attaches on to the
kinetochore.
The chromosomes are going to wind up into little balls. We are shortening and
condensing the DNA. This is why we can see the X structure so clearly.
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Continue review:
• In metaphase, a short phase, some of the MT grab onto the kinetochore. Those that
don’t, the polar MT, will go to the poles and overlap each other. All the DYADS are
lined up in the middle.
• In anaphase, the chromosomes come apart, separating the sister chromatids. The
PMT get longer and longer and the KMT will get shorter and shorter as the pull the
chromosomes to the poles.
• In telophase, the chromosomes unwind and the nuclear membrane reforms. The
microtubules will fall into their tubulin form.
• In cytokinesis, ACTIN separates the cell into two.
On test 2, explain the importance of 46 DYADS in metaphase in mitosis. It’s so we
have the correct 46 chromosomes in each cell.
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Biology 101
3 – 4 – 99
rd
3 lecture for test two/Thursday
MEIOSIS
Meiosis is the reproduction of gametes, sperm and ova. The result is four haploid cells
with 23 chromosomes each. An egg and sperm have 23 chromosomes each, so a zygote
will have 46 chromosomes.
Cells whose nuclei contain 2 homologous sets of chromosomes are diploid cells, and the
total number of chromosomes is called the diploid number (2n). In humans the diploid
number is 46.
Under a microscope, we can see our chromosomes match up as 23 pairs. They are
similar in length, centromere position and staining pattern. Metaphase chromosomes can
be matched up and called homologous chromosomes. They are called homologous
because they both carry GENES controlling the same inherited characteristics.
The locus is a particular point for both chromosomes that have this gene for a trait.
For example, eye color. We inherit one chromosome of each homologous pair from our
mother and the other chromosome of the pair from our father.
Our 23 pairs of homologous chromosomes are of two general types. 22 pairs consist
of autosomes, found in both males and females. The other pair of chromosomes are the
GAMETES, the sex cells. XX – female. XY – male. Each gamete has a single set of
chromosomes, 22 autosomes plus a single sex chromosome, either X or Y. A cell with a
single set is called a haploid cell, n=23.
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During sex, a haploid sperm cell fuse with a haploid egg cell of the mother during
fertilization. Results in a zygote, with a diploid number of 46. Mitotic cell division
ensures that all somatic cells of the body receive copies of all the zygote’s 46
chromosomes.
Having haploid gametes keeps the chromosome number from doubling in each
succeeding generation. 46, 92, 184…
… We don’t have a human with 184 chromosomes.
Haploid gametes are produced by a special sort of cell division called meiosis, which
occurs only in reproductive organs. The cells divide into four cells either in the female
ovaries or in the male’s testes.
So, whereas mitosis produces daughter cells with the same numbers of chromosomes as
the parent cell, meiosis reduces the chromosome number by half. In meiosis, a cell
undergoes 2 consecutive divisions, called meiosis I and meiosis II. Four daughter cells
result from these divisions.
MEIOSIS I
• Interphase I – chromosomes duplicate here. At the end of interphase, each
chromosome consists of 2 genetically identical sister chromatids.
• Prophase I – most complex. Accounts for 90% of meiosis. In a process called
SYNAPSIS, homologous chromosomes (each composed of two sister chromatids)
pair up. They form a structure called a TETRAD. Each TETRAD has four
chromatids. During synapses, chromatids of homologous chromosomes exchange
segments, in a process called CROSSING OVER. VARIABILITY #I takes place here.
• Then the MTOC’s (microtubule – organizing centers) move away from each other
and a spindle starts to form between them. The nuclear envelope disappears and the
chromosomes tetrads, captured by spindle microtubules, are moved toward the center
of the cell.
The random alignment of maternal or paternal DYADS is called INDEPENDENT
ASSORTMENT. This is to ensure everyone is different. A TETRAD IS TWO DYADS.
• Metaphase I – The random attachment to the kinetochore results in the randomness
of variability. Each chromosome is condensed and thick, with its sister chromatids
attached at their centromeres by spindle microtubules. VARARIABLITY #2 takes
place here.
• Anaphase I – the chromosomes are then moved toward opposite ends of the cell. In
contrast to mitosis, the sister chromatids making up each doubled chromosome
remain attached at their centromeres. The dyads are still held together at their
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kinetochore. Only the TETRADS, pairs of homologous chromosomes split up. Thus,
you still see the 2 doubled chromosomes, the haploid #, moving toward each spindle
pole.
• Telophase & cytokinesis – In telophase I, the chromosomes arrive at the poles of the
cell. When the chromosomes finish their journey, each pole of the cell has a haploid
chromosome set. Usually cytokinesis occurs along with telophase I and the two
haploid daughter cells are formed. No chromosomes duplication ocurrs between
telophase I and the onset of meiosis II.
MEIOSIS II
After a pause in meiosis I, the chromosomes condense again and the nuclear
envelope breaks down during prophase II. In any case, meiosis II is essentially the same
as mitosis. Meiosis II separates the sister chromatids of the haploid number of
chromosomes in the two starting cells, resulting in 4 daughter cells that have the haploid
number of single daughter chromosomes. The important difference is that meiosis II
starts with 2 haploid cells (23 chromosomes in each) that divide and produce 4 daughter
cells with 23 chromosomes each.
Lecture:
• We have tetrads in meisosis and dyads in mitosis
• They’ll be a short answer question on meiosis on test 2
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3 – 9 – 99 /4th lecture for test two/Tuesday
DNA
Transcription in the nucleus and Translation in the ribosomes.
Transcription produces genetic messages in the form of RNA.
Transcription, the transfer of genetic information from DNA to RNA, occurs in the
cell nucleus. As with replication the two DNA strands unwind but only one-strand
serves as a template for the newly forming RNA strand.
The RNA nucleotides are linked by the transcription enzyme RNA Polymerase. The
“start transcribing” signal is a nucleotide sequence called a promoter, which is located
in the DNA. The first phase of transcription, called initiation, occurs when RNA
polymerase attaches to the promoter DNA. – INTIATION.
During the 2nd phase of transcription, the RNA elongates. Then in the 3rd phase,
termination, the RNA polymerase reaches a special sequence of bases in the DNA
template called a terminator. This sequence signals the end of the gene on the DNA! So
the RNA strand detaches from the gene AND the RNA polymerase to go outside the
nucleus into the cytoplasm. ELONGATION AND TERMINATION AND THE
COMPLETED RNA STRAND.
There are 3 types of RNA
• Messenger RNA – the ticker tape message that goes to the ribosome to be translated
• Transfer RNA – the interpreter of the MRNA message that puts down the correct
bases on the constructing protein strand.
• Ribosome RNA – the stuff that RNA is made out of.
RIBOSOMES build polypeptides
A ribosome consists of 2 subunits, each made up of proteins and rRna. Its large subunit
has binding site for tRNA and the small subunit binds for mRNA. On the large subunit
are the P and A sites. The P site is where holds the tRNA carrying the growing
polypeptide chain, while the A site holds the tRNA carrying the next amino acid to be
added to the chain. The A guy hands over the bases, (AUG etc.) over to the P site who
actually puts the chain together by the tRNA.
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An initiation codon marks the start of an mRNA message.
Translation can be divided into the same three phases as transcription: initiation,
elongation and termination. An mRNA molecule binds to a small ribosomal subunit. A
special initiator tRNA locates and binds to the specific codon, called the start codon,
where translation is to begin on the mRNA molecule.
A special sequence of nucleotides on a gene are not part of the message but helps the
mRNA bind to a ribosome. The role of the initiation process is to determine exactly
where translation will begin, so that codons on the mRNA are translated into the correct
sequence of amino acids.
ELONGATION ADDS AMINO ACIDS TO THE POLYPEPTIDE CHAIN
Until a stop codon terminates translation.
Once initiation is complete, amino acids are added one by one to the initial amino acid.
Each addition occurs in a 3-step elongation process.
• Step one – Codon recognition. The anticodon of an incoming tRNA molecule,
carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome.
The A site has the amino acids that are the opposite of the mRNA chain. So if the
mRNA has AUG then the anticodon translation will be UAC respectively.
• Step two – Then comes the PEPTIDE BOND formation. The polypeptide separates
from the tRNA to which it was bound, the one in the P site, and attaches by a peptide
bond to the amino acid carried by the tRNA in the A site. A first then P.
• Translocation – the P site now leaves the ribosome and the A site tRNA, carrying the
growing polypeptide, is translocated to the P site. A moves to P.
Elongation continues until a stop codon reaches the ribosomes A site. Stop codons,
UAA, UAG, UGA and ACT do not code for amino acids but instead signal translation
to stop. The completed polypeptide is freed from the last tRNA and from the ribosome,
which splits into its subunits. During and after translation, the polypeptide coils and
folds into a tertiary and then later forming a quaternary structure.
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MUTATION
A change in the DNA sequence that affects the structure of the proteins.
Almost all the nonsense amino acids, 70%, will be miscoded and usually new stops
result in the codon.
In cystic fibrosis, the condition can be traced back through the difference in a protein
to one tiny change in a gene. In the hemoglobin molecule, the sickle cell child has a
single different amino acid, a Val, instead of a Glu. This difference is caused by the
change of a single nucleotide in the coding strand of DNA.
We now know that the alternative alleles of many genes result from changes in single
base pairs in DNA. Any change in the nucleotide sequence of DNA is called a mutation.
It can involve large regions of a chromosome or just a single nucleotide.
Mutations within a gene can be divided into two general categories: Base
Substitutions and Base Deletions. A base substitution is the replacement of one
nucleotide with another. If an mRNA codon is GUA, instead of GAA, then CAT,
mutant hemoglobin, results instead of CTT, normal hemoglobin. It may result in no
change at all or an insignificant amount or life threatening.
Mutations involving the insertion or deletion of one or more nucleotides in a gene
often have disastrous effects. Because mRNA is read as a series of nucleotide triplets
during translation, adding or subtracting nucleotides may alter the reading frame (triplet
grouping) of the genetic message. All the nucleotides that are “downstream” of the
insertion or deletion will be regrouped into different codons. The result will most likely
be a no0nfunctional polypeptide.
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3 – 11 – 99 /5th lecture for test two/Thursday
INHERITANCE
Genetics – What you see expressed. The genes that are used by the organism. In
contrast to the Genotype – All the genes of any organism that are passed down through
offspring. Gregor Mendel discovered the fundamental principles of genetics breeding
garden peas. The paternal parents are called the P Generation, and their HYBRID
offspring are the F1 generation. Then when the F1 offspring mate, they produce the F2
generation.
A monohybrid cross has one trait, while a dihybrid cross has 2 traits.
Mendel’s Hypothesis
• There are alternative forms of genes, the units that determine heritable traits. Ex. The
gene for flower color exits in one form for purple and another for white. We now call
alternative forms of genes ALLELES.
• For each inherited characteristic, an organism has two genes, one from each parent.
These genes may both be the same allele or they may be different alleles.
• A sperm or egg carries only one allele for each inherited trait, because allele pairs
separate from each other during the production of gametes. When they unite, each
contributes its allele, thus restoring the paired condition in the offspring.
• When the two genes of a pair are different alleles, one is fully expressed and the
other has no noticeable effect on the organism'’ appearance. These are called the
DOMINANT ALLELE and the RECESSIVE ALLELE respectively.
A true breeding organism, which has a pair of identical alleles for a characteristic, is
said to be homozygous for that characteristic. Ex. AA or aa. While an organism with 2
different alleles for a characteristic, such as a pea plant with alleles P and p, is said to be
heterozygous for that characteristic. There is a 3:1 ratio in the F2 generation, the Punnet
Square shows the 4 possible combinations. The Punnet Square indicates the proportions
of F2 plants predicted by Mendel’s hypotheses.
Because an organism’s appearance does not always reveal its genetic composition,
geneticists distinguish between an organism’s expressed traits, PHENOTYPE, and its
genetic make up, GENOTYPE.
One parental trait disappears in the F1 generation of heterozygous, only to reappear in
¼ of the F2 offspring. The mechanism underlying this pattern is stated by Mendel’s
PRINCIPLE OF SEGREGATION – Pairs of genes segregate during gamete formation,
the fusion of gametes at fertilization pairs genes once again.
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MENDEL’S PRINCIPLE OF INDEPENDENT ASSORTMENT
Each characteristic is independently inherited from the parents. The gametes RY and
ry could produce four types of gametes, RY, rY, Ry and ry in equal quantities. The
Punnet Square shows all the possible combinations of alleles that can result in the F2
generation from the union of four kinds of sperm with four kinds of eggs.
The Punnet Square shows that each pair of alleles segregates independently during
gamete formation. This behavior of genes is called Mendel’s Principle of Independent
Assortment.
MANY GENES HAVE MORE THAN 2 ALLELES
Many genes have multiple alleles. Although each individual carries, at most, two
different alleles for a particular gene, in cases of multiple alleles, more than 2 possible
alleles exist. The ABO blood group groups in humans are one example of multiple
alleles. There are four phenotypes for this characteristic: A person’s blood type may be
O, A, B or AB.
O is the universal donor, he produces no sugar. AB can take anybody’s blood but he
can only take AB blood.
A single gene may affect many phenotypic characteristics.
The impact of a single gene on more than one characteristic is called PLEITROPY.
In many cases, one gene influences several characteristics. An example is sickle cell
disease, where a single allele causes numerous health problems because it makes RBC
produce abnormal hemoglobin molecules. These cells are destroyed by the body,
lowering the RBC count causing anemia and general weakening of the body. It kills
100,000 people in the world annually.
A single characteristic may be influenced by many genes
Mendel studied genetic characteristics that could be classified on an either or basis,
such as purple or white flower color in peas. However, many characteristics, such as
human skin color and height, vary in population along a continuum. Many such features
result from polygenic inheritance, the additive effect of two or more genes on a single
phenotypic characteristic. This is the converse of pleitropy.
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3 – 16 – 99 /6th lecture for test two/TUESDAY
HOW ONLY CERTAIN GENES ON DNA ARE EXPRESSED
In both eukaryotes and prokaryotes, cell specialization depends on the selective
expression of genes. The overall process by which genetic information flows from genes
to proteins, from genotype to phenotype is called gene expression.
E. COLI
When we drink milk, we take in lactose. E. coli makes enzymes necessary to absorb
the sugar and use it as an energy source. E. coli can make lactose utilization enzymes
because it has genes that code for these enzymes. E. coli uses three enzymes to take up
and start metabolizing lactose and the genes coding for these enzymes are regulated as a
unit.
Adjacent to the group of lactose enzyme genes are short sections of DNA that help
control them. One stretch of nucleotides is a promoter, a site where the transcription
enzyme, RNA polymerase, attaches and initiates transcription. Between the promoter
and the enzyme genes, a DNA segment called an operator acts as a switch. The operator
determines whether RNA polymerase can attach to the promoter and move along the
genes.
Such a cluster of genes with related functions, along with a promoter and an operator,
is called an operon, operons exist only in prokaryotes.
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3 – 18 – 99 /7th lecture – LAST LECTURE for Test two/Thursday
RECOMBINANT DNA TECHNOLOGY
In the mid-70’s, research on the E. Coli bacteria led to the development of recombinant
DNA technology. This is a set of techniques for combining genes from different sources
– even different species and transferring it into cells. Scientists have already created
genetically engineered bacteria that can mass-produce useful chemicals, including
hormones and certain cancer drugs.
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