HTHS Mod 5

• 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

• "DNA makes RNA makes protein"
• Defines relationship between these three parts
• DNA is made into RNA by transcription
• RNA 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

• 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

• 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: 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

• 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

• 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

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)

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 together
• Think of "R U Dana Thelander?"  (RNA)

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

• 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 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

It's being transcribed at multiple sites

• 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

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.

• the introns must be sliced out and the exons stitched together. 
• This is accomplished by the spliceosome
• hnRNA = heterogeneous RNA

• made up of 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

• 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

• just globin. 
• 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

• 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

• 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

• *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

• 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

• where single tRNAs carrying their amino acid cargo are docked
• "TRUCK PARKING SPACES"

• where the tRNA carrying the growing polypeptide chain is located
• "TRUCK PARKING SPACES"

• 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

hydrogen bonds

• 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

• in translation
• UAA, UAG OR UGA  means STOP

• an amino acid carried by a tRNA
• always the first amino acid in any growing polypeptide

• 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

• 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

• 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

• 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

• 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

• 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

• 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"

• 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

• pronounced "Gee-zero"
• 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

• called "n"
• 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.

• A-T 
• C-G
• 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: 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.

• "cell motion"
• 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
• takes about 30 minutes
• 4 stages: prophase,  metaphase, anaphase, telophase
• "please meet aunt teresa"

• referring to the lagging strands of DNA in DNA replication, where it's difficult to follow the 5′to3′ standard
• therefore, little short segments of DNA are made, called Okazaki fragments, are later stitched together to form completed strand

an enzyme which fill in the gaps btwn the Okazaki fragments and stitch the 5′ to 3′ together

In DNA replication, the enzyme which runs in the usual 5′to 3′ direction on the leading strand

• referring to DNA replication
• LEADING STRAND: the strand which is built continuously 5′to3′
• LAGGING STRAND: the strand which uses Okazaki fragments to build short segments which are then stitched together. "lower fork"

enzyme which uncoils the helix of DNA for replication

enzyme which inserts a swivel that keeps the intact double helix from getting supercoiled (knotted) from spinning as replication of DNA proceeds.

• One of 3 enzymes which work to create the lagging strand
• referring to DNA replication

• one of 3 enzymes which work to create the lagging strand
• referring to DNA replication

• one of 3 enzymes which work together to create the lagging strand
• referring to DNA replication

• first phase of mitosis
• DNA is tightly packed into chromosomes
• nuclear envelope breaks down
• mitotic spindle forms

• middle phase of mitosis,
• everything in parent cell lines up in middle
• chromosomes (formed in prophase) move to middle of parent cell and microtubules of mitotic spindle attach to anchors (centromeres) 
• phase used to create karyotype

a picture of chromosomes used in study

down syndrome

• the phase of mitosis where the contents of the two daughter cells move backwards, away from each other
• chromatids are torn apart in two equal pieces

• mitosis is complete ("telo: end")
• cleavage furrow appears, cell split

• sperm and eggs
• carry only one copy of each gene (are haploid)
• Because they bind to form 1, each germ cell needs 1/2 normal amount of DNA (haploid)

• Both are DNA content #'s
• diploid refers to the cells which are somatic, have normal #
• Haploid refers to cells in reproduction, having 1/2 # of normal DNA content. ONLY HAS 1 SEX CHROMOSOME

• Meiosis I (first division)
• *is reduction division (divides DNA content of each daughter cell)
• *Crossing over is an important feature: Non-sister chromatids swap analogous genetic material

• happens in Prophase I
• can be used for gene mapping
• ensures "shuffling" of genetic material, an important benefit of sexual reproduction
• w/o itc some siblings would be identical twins
• Genes which are close together on same chromosome rarely get separated during crossing over
• Genes which are far apart on the same chromosome are more likely to be separated

• Mitosis creates two daughter cells that are identical to the "parent"
• Meiosis halves the DNA content in Meiosis I and then Meiosis II resembles mitosis

• One copy of a gene inherited from the mother, and one copy of a gene inherited from the father.
• each child has 50/50 chance of getting each allele
• *In modern molecular genetics, these are the same as polymorphisms

those where inheriting one copy of the gene, or getting the DNA, which will give you a condition or disease

Only takes one gene to have disease

• those where inheriting one copy of a gene makes you a carrier, 
• inheriting two copies will give you a condition or disease

• used to analyze genetics
• Use capital letter for dominant allele
• Use small letter for recessive allele
• *if disease is dominant, then individuals with AA or Aa will have disease, while those w/ aa will not
• *if disease is recessive, than individuals w AA or Aa will not have disease, but individuals w aa will

• characteristic of lacking skin pigmentation
• an autosomal recessive genetic disease

• means if you inherit one copy of the bad gene, your a little bit sick. 
• If you inherit 2 copies of the bad gene, then your really sick