1.
- THE
IDEA OF A PROTEIN STORED IN DNA
- Where the idea lives: genes on chromosomes
- Chromosomes
- prokaryotes,
chloroplasts and mitochondria, and some viruses in
- are found in cells of
- prokaryotes in
- eukaryotes in
- have a structure
including a:
- circular form made from
- double stranded DNA
- single stranded DNA
- linear form made from
- double stranded DNA
- along
with histone proteins which are used to supercoil the DNA into
chromosomes
- single stranded DNA
(viruses)
- single stranded RNA
(viruses)
- double stranded RNA
(viruses)
- vary in number between
species
- such as 23 chromosomes in
duplicate in humans, and 24 chromosomes in duplicate in chimpanzees, (REF)
- and
are named by length of metaphase chromosome shown in a karyotype (See
Figures at the right.)
- stay constant in number
between normal members of the same species.
- An online karyotyping
exercise is available
- More details about banding patterns in chromosomes: CLASSIFICATION, KARYOTYPING, BANDING, and IDIOGRAMS.
- Where the idea for a protein lives: Genes are
sections of chains of nucleotides called nucleic acids.
- Nucleic acids are found
in nature as
- ribonucleic acids (RNA)
or
- deoxyribonucleic acid
(DNA)
- Nucleic acids are found
in nature as polymers of
monophosphate nucleotides
held together between 5' carbons on one nucleotide and the 3' carbon of
the adjacent nucleotide via a bond known as a phosphodiester bond.
- Nucleotides are
- three-component molecules
made of
- a) one sugar, either
- b) one nitrogenous base,
either
- purines
- adenine, or
- guanine
- or...
- pyrimidines
- cytosine, or
- thymine, or
- uracil
- c)
one or more phosphates,
- OR...
- two-component molecules made of
- a) one nucleoside,
- which is one sugar bonded
to one nitrogenous base,
- such as with ribose called:
- adenosine (with base
adenine)
- guanosine (with base
guanine)
- cytidine (with base
cytosine)
- uridine (with base
uracil)
- such as with deoxyribose called:
- deoxyadenosine (with
base adenine)
- deoxyguanosine (with base
guanine)
- deoxycytidine (with base
cytosine)
- deoxythymidine (with base
thymine)
- b) one or more phosphates
- Nucleotide examples are
- ribose based and found in RNA
- adenosine monophosphate
(AMP)
- guanosine monophosphate (GMP)
- cytosine monophosphate (CMP)
- uridine monophosphate (UMP)
- deoxyribose based and found in
DNA
- deoxyadenosine
monophosphate (dAMP)
- deoxyguanosine
monophosphate (dGMP)
- deoxycytosine
monophosphate (dCMP)
- thymidine monophosphate (dTMP)
- A 3-page Summary of Nucleotides is available: Nucleotides
- Nucleotides are also used
as single molecules
- single (ribose based):
- ATP
- ADP
- AMP
- GTP
- GDP
- GMP
- UTP
- UDP
- UMP
- ITP (using base inosine)
- IDP
- IMP
- cyclicAMP (cAMP)
- cyclicGMP (cGMP)
- coenzymeA
- or in modified double
nucleotides such as:
- double
(ribose based)
- NAD+
- NADH
- NADP+
- NADPH
- FAD
- FADH2
- There are two types of
nucleic acids known as
- deoxyribonucleic
acid (DNA),
- which
is a polymer of monophosphate deoxyribonucleotides (MDNs) such as:
- dAMP (abbrev: A)
- dGMP (abbrev: G)
- dTMP (abbrev: T)
- dCMP (abbrev: C)
- and
is found in eukaryotic nuclei with a double-stranded structure,
with each strand arranged so that the structure of double stranded DNA
is "anti-parallel" where
- the
"parallel" aspect comes from the fact that opposite DNA strands are
equidistant all along the molecule.
- This
occurs because opposite strand bases are arranged with one purine
(single ring) with a pyrimidine (double ring) so that opposite strands
are approximately 3 base rings appart all along the DNA molecule.
- the
"anti" aspect comes from the fact that opposite strands run in
opposite directions 3'-5' and 5'-3'
- and the double stranded
DNA is twisted into a helix which gives DNA its "double helix" name
- and one DNA molecule is
found in each chromosome.
- ribonucleic acid (RNA) ,
- which
is a polymer of monophosphate ribonucleotides (MRNs) such as:
- AMP (abbrev: A)
- GMP (abbrev: G)
- UMP (abbrev: U)
- CMP (abbrev: C)
- and examples are;
- hnRNA,
- mRNA,
- tRNA,
- rRNA,
- snRNA
- which are found as
single or double stranded molecules or single stranded molecules folded
back into loops in molecules such as
- The locations where
- DNA
is found in cells are:
- the nucleus
- mitochondrial matrix (REF)
- chloroplast stroma
- RNA
is found in cells are:
- the nucleus
- hnRNA
- mRNA
- rRNA
- snRNA
- tRNA
- the cytoplasm
- mitochondrial matrix
- chloroplast stroma
- ribosomes
- The synthesis of
nucleic acids such as:
- DNA is called DNA
Synthesis or Duplication or Replication and occurs wherever the
original DNA resided with the help of
- the enzyme DNA
polymerase
- and building blocks
triphosphate deoxyribonucleotides (TdRNs):
- dATP--> dAMP + PP
- dGTP--> dGMP + PP
- dTTP--> dTMP + PP
- dCTP--> dCMP + PP
- which are used to make
polymers of monophosphate deoxyribonucleotides (MdRNs) using:
- dAMP
(abbrev: A)
- dGMP
(abbrev: G)
- dTMP
(abbrev: U)
- dCMP
(abbrev: C)
- and several protein helper molecules
- Animation Overview for DNA duplication
- RNA is called RNA
Synthesis or Transcription and occurs wherever the DNA which
contains the gene being transcribed resided.
- The
focus of this course is the events associated with gene
transcription into tRNAs, rRNAs, and mRNAs and the subsequent
translation of mRNAs into polypeptides and proteins, AND their
functions.
- The following section
is a review of genes and transcription.
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Human
Chromosomes 1-22, X & Y (*1)
The human karyotype of the 22
chromosomes (1-22) found in duplicate in every diploid cell plus
either two X chromosomes or one X and one Y chromosome. The only
exceptions are gametes (sperm and ova) that contain only one set of
chromosomes 1-22 plus either an X or a Y chromosome. In addition,
because human red blood cells (RBCs) do not contain any organelles
including nuclei, they do not contain any DNA at all.
Human and chimp karyotypes show that
chromosome 2 appears to have broken into two chromosomes in
chimpanzees. Humans and chimps have about the same number of
genes.
(Click on the graphic above to learn more.)
Do
you know what these letters represent?
A nucleic acid (DNA or RNA) is a polymer of
monophosphate deoxyribonucleotides held together between 5' carbons on
one
nucleotide and the 3' carbon of the adjacent nucleotide via a bond
known as a phosphodiester bond. When the identity of the
nucleotides in a nucleic acid is determined, it is known as a sequence,
and it is simplified to show only the identities of the bases attached
to each sugar of each nucleotide.
For instance AAGGAC really stands for
AMP-AMP-GMP-GMP-AMP-CMP in RNA and dAMP-dAMP-dGMP-dGMP-dAMP-dCMP in DNA
Are the letters in the figure above, part
of a DNA or RNA strand?
A DNA sequence is shown above in the box because it
includes
T which represents dTMP which is found only in DNA. It is
possible for a sequence of DNA, if short enough, to not show any Ts, so
you should also look to see if any Us exist. If a U is shown,
then
you will know that the sequence is RNA because RNA contains UMP, and no
TMP.
It is possible that a short sequence of nucleic acid would have neither
T or U, and therefore, you would not be able to decide if the sequence
was DNA or RNA. You would need to determine which sugar was used
to make the nucleotides.
If you see a sequence showing BOTH
T and U, then the sequence is not a naturally occuring DNA or RNA.
A sequence is often shown in groups of
10 bases. For instance, the sequence below is the first 30 nucleotides
in a human double
stranded mitochondrial DNA.
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1 GATCACAGGT CTATCACCCT ATTAACCACT
2 CTAGTGTCCA
GATAGTGGGA TAATTGGTGA
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Note
that below strand 1, strand 2 has a different base. The
relationship
between bases is that whenever there is a purine (A or G) the opposite
base is a pyrimidine (C or T). This is known as Chargaff's Rule
and
the relationship between A and T and G and C is called complementary
base pairing. The binding of two complementary bases to form a ladder
rung is called a base pair. The binding occurs via hydrogen
bonding which is shown in the figure below.
What is a genome?
The Human Genome Project, or any other Genome Project
is an attempt to
determine the base sequence of each strand of DNA within each
chromosome in one cell of a species. Note that each chromosome contains
only one DNA molecule.
On
June26, 2000, the
Human Genome Project reached
an historical
point. To check on its progress, visit
the NCBI Human
Genome
Sequencing
website.
Within
a species, individual differences are due to different base
sequences in certain genes. Many other genes may be identical
because, for instance, everyone needs the same gene for the enzyme
hexokinase which is the enzyme that first processes glucose in the
glycolytic pathway.
What does DNA look like?
DNA
CHEMISTRY
In DNA, the left strand runs so that the 5' end is at the top and 3'
end is at the bottom. The right strand is upside down so its 3'
end is at the top and the 5' end is at the bottom. 5' and 3'
refer to the carbons in the sugar, Carbon 1' is the location
where the bases attach. Carbons 3' is the bottom left carbon on
each deoxyribose sugar (on the left stand of DNA) . Carbon 5' is
the carbon shown as a CH2 connected to the left carbon (4')
in the sugar. Therefore you can see that the backbone of each DNA
strand is an alternating deoxyribose sugar- phosophate chain. So
each sugar is connected to the next sugar via a phosphate. The
connection is called a phosphodiester bond.
Note also that the bases are connected in a way that a double ring base
(a purine base such as adenine and guanine) is connected via dotted
hydrogen bonds to a single ring base (a pyrimidine such as thymine or
cytosine).
To learn more about nucleotides, nucleosides and nucleic acid
chemistry, please visit my website: Nucleotides
The twisted ladder idea for DNA structure.
DNA synthesis occurs when a triphosphate deoxyribonucleotide arrives
near the DNA polymerase enzyme (not shown). [Green and Yellow
bases: are pyrmidines, and Pink and Blue bases are purines.] The triphosphate deoxyribonucleotide releases energy and two
phosphates, and the remaining monophosphate deoxyribonucleotide becomes the next building block
in the nucleic acid chain.
DID
YOU NOTICE...
that the third attempted nucleotide addition did not work
because a pyrimidine was unable to be matched to another pyrmidine on
the right side?
How do you know this is DNA synthesis and not RNA synthesis?
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