Cellular level of organization II, Molecular biology of cels
bounded by double membrane,contains the materials needed to control all part of cell
Stores genetic material (DNA)
Makes: DNA and 3 types of RNA
packed form of DNA
DNA plus histone proteins
Comes in two forms: euchromatin or heterochromatin
unspooled, open, ready chromatin
clustered, clumped up form of DNA packaging
Think of it being "hetero"... so it's not loose, it's straight (ok, clustered straight)
a single, continuous DNA strand w an unbroken backbone of deoxyribose-phosphate
two linked in the middle (by centromere) make up the chromosome
so, one chromatid makes one part of the "x" of a chromosome
consist of two identical chromatids
only visible during mitosis; packaging of DNA and histones into X-shaped structures
joins two chromatids to make chromosome
Where mitotic spindle attaches in cell division, tears 2 chromatids apart
special proteins which carry a lot of positive charge... double helix wraps around these proteins
*Recall DNA is acid and carries multiple negative charges
Therefore, histones screen off the negative energy DNA gives off to enable DNA backbones to sit close for cell division and storage (where normally they would repel each other)
"ribosome factory", where ribosomes are made
Rough endoplasmic reticulum, involved in synthesis of proteins
the complex of ribosomes plus membranes
continuous w golgi complex
together, the ribosomes, RER and Golgi make system designed to make proteins for export, to be embedded in cell membrane, or to be recycled if malformed
Proteins in need of some special sort of processing, such as additional sugars, etc... go through Golgi complex
*most abundant in RER is rRNA
taking heterochromatin and pack as tightly as possible
*Only time DNA is visible through light microscope, when packaged into chromosomes during cell division
Genetics: the central dogma...
"DNA makes RNA makes protein"
Defines relationship between these three parts
DNA is made into RNA by transcriptionRNA is made into protein by translation
the process by which DNA makes RNA
copying from one form to another in the same language
Ex: your friend wants to borrow class notes. You say "all i have is a recording, you'll have to transcribe them."
Same language, different format
"DNA writes RNA a prescription"
Language sequence" A,C,G,T
the conversion of an RNA code to protein
"converting one 'language' to another.... Translating
Ex: a brazilian friend want to borrow notes. You say "Mas eles esteja em... blah blah" (their in english, not portugese, you will have to translate them)
Different language: sequence of A,C,G,U converted to amino acids
Steps of the Central Dogma (supporting structures)
1. Transcription - inside nucleus
2. Translation - occurs outside the nucleus, in cytoplasm. Responsibility lays with ribosome.
*In order for RNA to accomplish the function of making protein, needs to be taken out of the nucleus where it's made, through nuclear pore, out into cytoplasm to it can be translated by the ribosome
Can the central Dogma system ever be ran backwards? Can protein ever make RNA, RNA ever make DNA?
Yes, there are exceptions to central dogma
Some viruses use RNA as their genetic material
Some viruses carry this enzyme in their genetic material, converts RNA to DNA
The DNA is then inserted into host cell
Destructive process for host cell; damage to host cell DNA is common and results in diseases such as cancer
is an enzyme (ends in "-ase")
reverse transcriptase= reverses
viruses which are capable of reverse transcriptase
tend to cause human cancers
AIDS, HIV, cervical cancer, HPV
DNA vs. RNA structure
DNA: a double helix; two strands are antiparallel
RNA: Consists of only one strand
(referring to DNA) means that one strand (of the double helix) goes up, the other goes down
*we define up and down by the numbering of carbons on the sugar part of the backbone
What method is DNA & RNA always made and always read?
ALWAYS 5′-prime to 3′-prime direction, both by humans and by enzymes (only way the enzymes work... )
*in organic chemistry, when there are carbon containing compounds in ring structure, carbons are numbered
Carbons on bases are numbered 1,2,3,4... etc
Carbons on sugar are numbered 1′, 2′, 3′, 4′, etc
5′ carbon ~ 3′ carbon
pronounced "5-prime" ~ "3-prime"
Referring to DNA, 5′ where we start reading, and where the enzymes that work on DNA start their work
referring to "reading" DNA, 3′-prime where the reading stops
4 bases involved with DNA
Adenine, Cytosine, Guanine, Thymine (DNA only)
Reading order: A,G,C,T (5′ to 3′) ~ where A -T only bind to each other, and G - C only bing to each other.
Think of Dana Thelander (for DNA)
4 bases involved w RNA
Adenine, Cytosine, Guanine, uracil (RNA only)
For reading order: A, G, C, U (5′ to 3′) ~ where A-U only bind together, and G - C only bind togetherThink of "R U Dana Thelander?" (RNA)
*Recall... when you see four lines (in a chemical structure) coming together, not labeled ON ORGANIC MOLECULE
it's assumed there is a Carbon there
region of DNA that codes for a protein
messenger RNA ~ the final edited version
carries the code for a primary sequence of amino acids in protein
responsible for being copied and carrying that information out of the nucleus, into the cytoplasm, where the ribosomes can act on it.
Leaves nucleus through nuclear pores
How is mRNA made?
In the DNA sequence of the gene, it has both exon and intron sections.
We take several of these exon regions and, through RNA processing (editing), cut them out and splice them together to form the final mRNA which is translated into a polypeptide or protein
After which, the mRNA can pass through the nuclear membrane into the cytoplasm and be translated.
**Note that although introns were transcribed, they will not be translated.
Exon vs. Intron sections of DNA
Exon it the portion of DNA that is expressed, or made into protein
introns is the portion of DNA that is not made into protein & must be edited out
Recall the RNA transcribed from DNA has regions that are not used to code for protein synthesis (introns)
Therefore, "editing" must take place (where the exons are "snipped" from the introns and spliced together)
an ordered sequence of amino acids when they are strung together in to a polypeptide
When a gene is very busy, what happens to transcription?
It's being transcribed at multiple sites
"first draft" of RNA is
a direct copy of DNA
from here, it is edited down to final version
The enzyme which makes RNA from DNA template; makes an RNA polymer (taking DNA monomers and stringing them together into RNA polymers)
Specialized sites on DNA promote RNA polymerase binding & release
*NOTICE "-ase" ending --> meaning it's an enzyme
site where RNA synthesis is started
so, this is the start of a segment of DNA that will eventually code for a protein
*process begins as the DNA double helix is opened up. only one DNA strand is read
site where RNA synthesis is stopped
As RNA polymerase travels along DNA, the RNA strand gets longer. Therefore:
The longer RNA strands are, the "older" they are
*Recall that only one strand of DNA is read at a time.
therefore, the strand being read is the "coding strand", since it carries the "genetic code"
Starting at promoter region, new RNA strand is built, in 5′-to-3′ direction, ending at the terminator
the RNA which will be used to make a protein
expressed region of DNA, which is made into a protein
Like example which editing a video, this is the part that we see
introns which have been removed from the first version of RNA during the editing stage
they are recycled by the cell
the portion of the DNA that is not made into protein and must be edited out
Like editing a movie, the part of the video that gets taken out and we never see
When they are removed (becomeing excised introns)the cell recycles them.
In order to create mRNA from hnRNA...
the introns must be sliced out and the exons stitched together.
This is accomplished by the spliceosome
hnRNA = heterogeneous RNA
made upof several small nuclear ribonucleoprotein particles, or snRNP's ("SNURPS")
slices out the introns and stitches in the exons in order to create mRNA from hnRNA
structure (a "loop" in hnRNA) that is formed to cut out the intron, and stitch the ends of the exon together
formed by snRNP (snurps)
the first draft version made of RNA (from copying DNA)
called heterogeneous nuclear RNA or pre-mRNA
long transcripts formed in the nucleus which will be processed to mRNA molecules by splicing.*SO THE UNEDITED CUT OF RNA
pronounced "snurp", a small nuclear ribonucleoprotein (it's small, in the nucleus)MAKES UP SPLICEOSOME!!!
a special type of RNA combined w a protein
participates in the editing process that cuts and splices pre-mRNA into mRNA
"the scissors and paste" responsible for building mRNA
it removes the introns by forming lariats
blood disorder in which the blood is unable to carry normal amounts of oxygen (symptom of anemia)
results from the abnormal transcription and/or translation of α- and β-globin genes
When the 2 types of globin proteins are formed, if one is a mutation, then they can't fit together right to form the hemoglobin molecule.
If the mutation is with the α-globin, then it's called alpha-thalassemia
If the mutation is w the beta-globin, then it's called β-thalassemia
Beta-globin: a protein that makes up half of hemoglobin (the oxygen carrying protein of red-blood cells)
Alpha-globin: the protein which makes up the other half of hemoglobin
Abnormal splicing of β-Globin gene produces...
an abnormally short globin mRNA
this lead to an abnormally short β-globin protein that cannot bind O2 properly
a condition when the blood is unable to carry normal amounts of oxygen
iron containing, oxygen containing group w/in hemoglobin
Hemoglobin molecule w/o the hemo group
2 forms: α & β
the segment of DNA before the translated part (remember, we always move 5′ to 3′)
Ahead of the first exon, here the promoter is found
At front end of the gene
(3′ UTR) ~ the segment of DNA after the gene contains signal for the termination of transcription
probably contributes to stability of RNA
is after terminator
at the back end of the gene
Some mRNAs need to hang around for a long time & get translated over & over, others disappear after they're used once
What does translation of mRNA do?
changes the A,C,G,U language (the nucleic acid "language") to the amino acid language.
4 bases are translated into 20 amino acids
occurs through the action of a ribosome
translation process which changes the nucleic acid "language" to amino acid language
Letters in RNA: A,C,G,U
Protein polymer is output: 20 different types of amino acids strung together in a specific order make up protein's primary structure
3 types of RNA that are players in protein synthesis
mRNA ~ messenger RNA
rRNA ~ ribosomal RNA
tRNA ~ transfer RNA
messenger RNA ~ carries coded message from nucleus to ribosome
very unstable, allows for transcriptional control of protein production
made by RNA polymerase II
ribosomal RNA ~ w proteins, forms ribosomes (protein factories); small and large subunits
more stable than mRNA, (mostly) made by RNA polymerase I
transfer RNA ~ "trucks" to bring amino acids to the growing protein strand
supplies ribosomes w correct amino acid
each has a unique anticodon
RNA folded up into a cloverleaf-shaped: one loop of RNA forming a "leaf" (anticodon) matches the mRNA message (codon)
The acceptor arm "stem" carries an amino acid
shape held together by hydrogen bonds
Notice each tRNA has a particular pairing of anticodon and amino acid
more stable, made by RNA polymerase III
one of the loops of the "clover leaf" shape of the tRNA
has a set of three ribonucleotides, which will bind to the mRNA (by it's codon)
pared w a specific amino acid which binds to an acceptor arm
Process of ribosome assembly on RNA
*recall ribosomes r made up of RNA and protein, have two parts, large and small.
When these come together on either side of the mRNA, protein syntheses (translation) occurs
when they detach, translation stops
large subunit of the ribosome
has two special sites, termed "P" and "A"
P site is where the growing polypeptide chain is made
A site is where the new
amino acids are added
A site of large subunit of ribosome
where single tRNAs carrying their amino acid cargo are docked
"TRUCK PARKING SPACES"
P site of large subunit of RNA
where the tRNA carrying the growing polypeptide chain is located
"TRUCK PARKING SPACES"
steps of ribosome attachment to mRNA
1. Ribosome finds start, assembles
2. Ribosome reads along mRNA and decodes mRNA to make polypeptide (immature protein)
3. Ribosome finds "stop"
4. Ribosome disassembles and translation stops
three base pairs on mRNA, coding for an amino acid, matches up with tRNA (at anticodon)
the sequence in mRNA which codes for a protein
on one end of the transfer RNA's, lines up w the mRNA codon
the complementary sequence (for the codon) found on tRNA
codon and anticodon held together by...
the "stem" part of the "clover-leaf" shape of tRNA
carries the amino acid
5′-AUG-3′ is always the start codon for mRNA translation
matches up to anticodon (5′-CAU-3′) on tRNA
UAA, UAG OR UGA means STOP
an amino acid carried by a tRNA
always the first amino acid in any growing polypeptide
Steps in Translation
1. Ribosome attaches to mRNA
2. AUG start codon matches up to tRNA- which is carrying methionine (in parking spot P, parking spot A is empty)
3. Next tRNA-amino acid arrives (pulls into parking spot A)
4. Peptide bond forms (the two amino-acids in the parking spots decide they should bond. synthesis begins)
5. Ribosome shifts three mRNA bases (met-tRNA is released to bonded amino-acid, leaves parking spot P so other tRNA in parking spot A can now park in P, and empty parking A can be occupied by new amino acid - tRNA
6. Process continues, polypeptide is growing
7. stop codon is reached, polypeptide is released
closer look at Step 4 in Translation
The amino acids who find themselves snuggled together in the parking spots P & A decide to bond, thus synthesis of protein begins.
The tRNA holding the methionine lets go of the methionine (since the "meth" is now bonded) and leaves to go get another amino acid.
This leaves the P parking site open; The tRNA from parking spot A slips over into parking spot P... and thus the cycle continues
self-assembly of the ribosome
triggered by the binding of met-tRNA
large (60S) ribosomal subunit always assembles so the Met-tRNA is enveloped in the P site
what something is like when it is born
closer look at Step 7 in translation
the stop codon is reached, the polypeptide is released.
This polypeptide is the "primary sequence" of the amino acids that have formed the "nascent" polypeptide
polypeptide will be altered, or edited, later
having more information than we need
referring to genetic coding, and the ability to code for 64 amino acids when we only have 20
the three-base sequence representing each amino acid
*4 bases taken 3 at a time can code for 64 amino acids, which is more than enough to code for 20 amino acids, which is why the genetic code is called degenerate ~ meaning we have more info than we need (we have 64 different ways of representing Amino acids, but we only need 20)
lets us use multiple combos to code for same amino acid
That's why codons have 3 bases in them
Like a "french to english" dictionary, or vise versa
the code used to convert mRNA message to amino acid sequence
Ex: AUG means "start"; UAA, UAG, UGA means "stop"
GGG means glycine
a change in the sequence of DNA, which changes the mRNA made from the coding strand
most are silent, that is, they do not change the primary protein sequence
some cause noticeable changes in the organism, called mutations
when gene polymorphism causes noticeable changes, a defect or disease
Two types: point mutation and frameshift mutation
3 bases are read at a time, so "frame"
Ex: CAT CAT CAT CAT
do not change reading frame; only change a single base
Ex: CAA CAT CAT CAT
Sometimes they do not change protein sequence (silent mutations)
Sometimes they do change protein sequence (missense and nonsense mutations)
A point mutation (which only changes a single base) that doesn't change the protein sequence
A point mutation (which only changes a single base) that changes the protein sequence
*change one amino acid to another*one of these mutations which results in the disease of sickle cell anemia
A point mutation which changes the protein sequence
changes codon that codes for an amino acid to stop codon, resulting in abnormally short protein
changes reading frame
Two types: deletion or insertion
If we introduce a mutation after the start codon, that either adds or subtracts a base, the entire frame is shifted so that all amino acids downstream from the mutation are wrong
type of frameshift mutation in which one base is removed
Ex: CAT C⌈TC ATC ATC
type of frameshift mutation where one base is added
Ex: CAT CCA TCA TCA
a point mutation, missense
only one codon is altered, completely changing the structure of hemoglobin (forms rod-like structures instead of spheres)
this, in turn, causes overall structure of red blood cell to change from biconcave disk to a ragged, sickle shape which is susceptible to damage as it passes through narrow capillaries
happens in TROPICAL areas
relationship btwn malaria and sickle-cell anemia, argument over natural selection
sickling protects red blood cells against malaria parasite
There is a good distribution in the population btwn where there is malaria and where there is sickle-cell anemia
Area's where malaria isn't a threat to the population, the people w sickle cell did eventually get eliminated from the population
Thus, where there is more malaria, there is more sickle cell
Stability btwn DNA and RNA
DNA is very stable, lasts millions of years
RNA is unstable, lasts long enuf to make protein, then destroyed
relates to fact mRNA is very unstable
most messages are destroyed immediately after use, allows cell to change it's protein composition dynamically by changing how much message is made
Cell division after birth:
some continue to divide: skin, bone marrow, intestinal lining
Others cannot divide after birth: muscle, heart muscle, brain
Mitosis and interphase
takes approx. 24hr to complete
part of cell cycle, DNA is in euchromatin form
Consists of 3 stage when cell is not actively dividing
-G1 (also called "growth-1" or "gap-1")
-S (replication of DNA)
-G2 (growth-2 or "gap-2")
happens after mitosis, first growth (or gap) phase; called "Gee-one"
takes 8 - 10 hours to complete
Cell duplicates organelles and cytoplasmic components
In order to enter S phase, cell must pass "checkpoint"
"checkpoint" in interphase
btwn G1 and S, also btwn S and G2
Similar to going through customs at airport... hitting many checkpoints
a resting state, cell is incapable of cell division, parked in cell cycle called G0
If cell cannot pass the G1/S checkpoint, or is quiescent (not actively dividing) remains in G0
where cell exits cell cycle, gets "off merry-go-round"
*G0 Lock happens when a cell never comes out, or never divides again. Like neurons spend lifetime here
Other cells (like liver, kidney) may wait here for up to several years but can prepare for division if needed
phase in interphase, stands for "synthesis" (for DNA)
replication of DNA so it can divide equally btwn daughter cells (went from 46 to 92 chromatids)
takes 8 hours
last part of interphase, finalizes it's preparations for mitosis
Cell now carries double amount of normal DNA
Duplication of centromeres, now has 92 DNA molecules
Second checkpoint must be crossed
takes 4 - 6 hours
Each daughter cell must have appropriate amount of DNA: two copies of each gene, called a diploid # (2n)
Cells which have only one copy of each chromosome are called haploid (sperm n egg)
process by which DNA molecules increase to 92
these 92 molecules are packed into 46 chromosomes and when chromatids are ripped apart at anaphase, each daughter cell gets 46 DNA molecules.
*since dna is only synthesized in one direction (5′ to 3′), this creates problem since strands are antiparall.
Specific base pairing rule w DNA replication
and vice versa: T-A, G-C
*REMEMBER: A always binds to the base that is different btwn RNA and DNA. Therefore, it will always bind w either a T or U. G and C stay together.
Mitosis vs. Cytokinesis
Mitosis: process of nuclear division. Genetic material must be parcelled equally btwn cells, chromosomes form, get pull apart, dissolve
Cytokinesis: process of cell division (happens at end of mitosis, in cytoplasm & organelles). plasma membrane of cells tightens like rubber band and pinches off two cells. Separates genetic material cytoplasm and organelles into two equal daughter cells.
how daughter cells move apart.
the process in S phase when DNA is replicated
Each DNA strand is used as template to make new strand of DNA, so amount of DNA is doubled.
# of DNA molecules increases to 92 (so when cell goes through mitosis, and rips apart, each daughter cell w have 46 DNA molecules)
M phase ~ the actually, active process of cell division