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65 Cards in this Set

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Gene
series of DNA nucleotides that generally codes for the production of a single polypeptide or mRNA, rRNA (in ribosomes) or tRNA

-Eukaryotes have more than one copy of some genes

-prokaryotes have only one copy of each gene
Eukaryotic genes being actively transcribed
-associated with euchromatic regions of DNA
Eukaryotic genes not being actively transcribed
-associated with tightly packed regions of DNA called heterochromatin (repetitive sequence DNA)
Genome
-entire DNA sequence of an organism
Central Dogma of gene expression
DNA is transcribed to RNA (nucleus or mitochondrial matrix only)
-RNA translated to amino acids forming protein (ribosome)
DNA
-composed of Adenine guanine (purines) cytosine and thymine (pyrimidines) nitrogenous bases,
-double helix held together by phosodiester bonds between nucleoutides and hydrogen bonds (base pairing) across two strands of nucleotides strands
-one less hydroxy group than RNA

-5' -> 3' directionality
-two strands lie antiparralel to each other
DNA Replication
-semiconservative: contains one strand from original DNA and one newly synthesized strand
-two replisomes proceed in opposite directions on chromosomes creating a bidirection process containing a leading and lagging strand
-RNA polymerase builds primer
-DNA polymerase assembles leading (new strand) and lagging strands
-primers removed
-okazaki fragments are joined by DNA ligase
-process called semidiscontinuous because one strand is formed and the other fragmented
-fast and accurate
Enzymes in DNA replication
-DNA helicase unwinds double helix
-DNA polymerase builds new DNA strand, can only add nucleotides to an existing strand and needs Primase an RNA polymerase to create an RNA primer to get started
-DNA ligase moves along lagging strand and ties okazaki framgents together
DNA polymerase
-adds deoxynucleotides to the RNA primer and moves along DNA strand reading them from 3-5 and creating the complimentary 5-3.
Telomeres
-repeated six nucleotide units that protect chromosomes from eroding after numerous replications
DNA vs. RNA
Characteristic of DNA vs. Characteristic of RNA

made from deoxyribose vs. made from ribose

double stranded vs. single stranded

Thymine vs. Uracil

produced by replication vs. transcription

only in nucleus and mitochondrial matrix vs. also in cytosol

one type of DNA vs. 3 types of RNA

use primer during replication in nucleus vs. use promotor during translation in ribosome
RNA
-one more hydroxyl group than DNA
-RNA not confined to nucleus
-3 forms: mRNA, rRNA, tRNA
-uracil instead of thymine (common cause of mutation in DNA)
mRNA
delivers DNA code from amino acids to the cytosol where proteins are manufactured
rRNA
ribosomal RNA
-combines with proteins to form ribosomes that direct synthesis of proteins
-synthesized in nucleolus
tRNA
transfer RNA
-collects amino acids in cytosol and transfers them to ribosomes for incorporation into a protein
Transcription
-process by which RNA is manufactured from DNA template
-in eukaryotes, DNA cant leave nucleus or mitochondrial matrix which limits transcription to these places

-requires promoter (instead of primer for DNA replication) to tell RNA where to begin transcription.
-after binding to promoter RNA polymeraze unzips DNA and elongation begins
-end of transcription is called termination and separates RNA polymerase frmo DNA

-transcription is what decides whether genes are activated or deactived via activators and repressors (regulated by cAMP) and bind to dna to close the promoter and activate or repress RNA polymerase activity

-amount of given type of protein or gene expression is related to how much mRNA is transcribed. mRNA has short hlaf life in cytosol and many proteins can be transcribed from single mRNA
Elongation
-occurs in transcription when RNA polymerase transcribes only one strand of the DNA nucleotide sequence into a complementary RNA nucleotide sequence (only one strand called template or antisense strand is transcribed of the double stranded DNA, the other called the sense strand or coding strand)
-reads 3-5 just like DNA polymerase during DNA replication to make a 5-3 copy
Gene regulation in prokaryotes
-prokaryotic mRNA typically include several genes in one transcription while eukaryotic mRNA include one gene.
-operon (prokaryotic gene regulation)
genetic unit usually sequence of DNA consisting of operator promoter and genes that contribute to single prokaryotic mRNA

-example is lac operon:
low glucose -> high cAMP ->activates CAP -> binds to CAP site, promoter activated

operator-> binding site for lac repressor -> inactivated by presence of lactose

lactose can induce transcription for lac operon only when glucose is not present
Post transcriptional processing
prokaryotes- rRNA and tRNA undergo post transcrip. processing while mRNA directly translated to protein while all eukaryotic RNA undergo post transcript. processing.

-5' cap and poly A tail at 3' end.
-primary transcript cleaved into introns and exons - introns are taken out and do not code for proteins
-occurs in nucleus
nucleic acid hybridization/restriction enzymes
-when strands of DNA are separated they will automatically start base pairing because they prefer to be double stranded
-this allows for nuclear acid hybridization which enables scientists to identify nucleotide sequences by binding a known sequence with an unknown sequence

-restriction enzymes cut at a restriction state on an enzyme and will be a palindromic sequence 4-6 nucleotides long
recombinant DNA
-two DNA fragments cleaved by the same endonucleus can be joined together regardless of origin of DNA
-artifically recombined
-recombinant DNA can be made long enough for bacteria to replicate and then placed within the bacteria using a vector, typically a plasmid or an infective virus and bacteria can form clone of cells containing vector and recombinant DNA and create a clone library

-not all clones take up vector and not all vectors take up DNA..need to be screened with X gal
-clones with active lacZ gene turn blue in presence of X-gal clones with cleaved form of gene do not turn blue including DNA fragment clones.
complementary DNA or cDNA
-bacteria cant remove introns and eukaryotic DNA has introns
what to do?
-mRNA produced by the DNA is reversed transcribed using reverse transcriptase and adding DNA polymerase to create cDNA which is a double strand of the desired DNA without introns
PCR or polyermase chain reaction
fast way to clone DNA
Southern blot vs. Northern blot
-identifies specific sequences of DNA by nucleic acid hybridization while Norther blot uses the same techniques to identify specific sequences of RNA

1. chop up DNA
2. use electric field to separate pieces by size
3. blot it onto a membrane
4. Add a radioactive probe made from DNA or RNA
5. visualize with radiographic film

-uses an electrolytic cell where negative DNA moves to postive anode (opposite charge of anode in galvanic cell)
Western Blot
detects a protein in a mixture of proteins with antibodies
Restriction fragment length polymorphisms (RFLP) "riflips"
-identifies individuals as opposed to specific genes because DNA of individual possess different restriction sites and varying distances between restriction sites
-used in criminal court cases
Genetic Code
the stringing together of mRNA nucleotides which translates the DNA nucleotide sequence copied into an amino acid sequence and then into protein

-4X4X4 for each amino acid so 64 possibilities but there are only 20 amino acids.. some combinations of nucleotides form the same amino acid!=degenerative
-code is universal
stop (termination codons) and start codons
codon: three consecutive nucleotides on a strand of mRNA
-all are amino acids except 3 combinations which are stop codons : UAA UAG UGA
-signal an end to protein synthesis

-start codons
AUG (also codon for methionine)
Translation
-process of protein synthesis directed by mRNA
-mRNA carries genetic code from nucleus to cytosol in form of codons
-tRNA contains a set of nucleotides complementary to codon called anticodon
-tRNA finds amino acid corresponding to its anticodon
-rRNA manufactured in nucleolus in eukaryotes but prokaryotes do not have nucleolus
-tRNA with 5-CAU-3 anticodon will look for AUG strand (because it will pair 3-5) and settles at the P site to form initiation complex.

tRNA with corresponding amino acid attaches to A site where dehydration reaction occurs
Elongation occurs where during translocation the ribosome shifts 3 nucleotides along the mRNA toward the 3' end and tRNA moves to E site
where it exits ribosome
-translocation is repeated until stop codon reaches P site and translation is terminated.

-rRNA makes up ribosome which provides site for translation
Post translational modifications
-proteins began folding even as the polypeptide is translated and is assisted by chaperones

-if ribosomes attached to the ER, they will inject proteins into ER which is destined for golgi and is to be a membrane protein or protein out of cell
-or protein may just be used in cytosol
-signal peptide may direct ribosome complex to receptor protein on ER
mutations
alteration in the genome
-rare
-in somatic cells not passed to offspring
chromosomal mutation
occurs when structure of a chromosome is changed
mutagen
-physical or chemical substance that increases frequency of mutation above frequency of spontaneous mutations
point mutation
-mutation changes single base pair of nucleotides in DNA
-base pair subsititution mutation is a type of mutation when one base pair is replaced by another
missense mutation
-type of base-pair mutation that occurs in the amino acid coding sequence of the gene
-may or may not alter the amino acid sequence of a protein
-insertion or deletion
-type of point mutation that may result in a frameshift mutation if the insertion or deletion is not a multiple of 3 because genetic code is read in groups of 3 nucleotides
-nonsense mutation
-if base pair substitution or insertion deletion mutation creates a stop codon
-very serious because they prevent translation
chromosomal deletions
-occur when a portion of the chromosome breaks off or when a section of DNA is reversed on the chromosome
translocation and DNA mutations
when segment of DNA from one chromosome is inserted into another chromosome
transposable elements or transposons
-DNA segments that can excise themselves from a chromosome and reinsert themselves at another location
-can contain one or several genes or just a control element
-may copy itself and move
-mechanism by which somatic cell can alter genetic makeup without meiosis
forward mutation or backward mutation
-a second mutation which can further mutate (forward) or mutate to return to original state (backward)
Cancer
-cells that divide indefinetly
-mutagens that cause cancer: carcinogens
histones
-globular proteins are wrapped around by DNA not in use
Nucleosome
Eight histones wrapped in DNA
Chromatin
entire DNA/protein complex
-composed of 1/3 DNA 2/3 protein and small amount of RNA
Chromosomes make up by chromatin
chromosomes have supercoils within them, supercoils have further coiling within supercoils of chromatin, chromatin are made up of histones

-heterochromatin is chromatin condensed as described above
human somatic cell and chromosomes
46 double stranded DNA molecules in nucleus of human somatic cell, chromatin associated with one molecule is called chromosome
-1 chromosome = hundreds or thousands of genes
homologues
-when chromosome has partner that codes for same traits the two such chromosomes are called homologues

diploid= homologues
haploid- cell that does not contain homologues
Cell Life Cycle
G1= growth phase 1
S= synthesis
G2= growth phase 2
M= mitosis or meiosis
C= cytokinesis

G1 + S + G2= interphase
G1
cell just split and begins to grown in size producing organelles and proteins
-rna synthesis and protein synthesis very active

-if conditions are favorable for condition it will enter S, if not it will enter G0
-main triggering factor is cell size based upon ratio of cytoplasm to DNA
G0
-nongrowing state distinct from interphase
S
-cell replicates DNA, organelles and DNA produced more slowly, each chromosome is exactly duplicated
G2
cell prepares to divide, cellular organelles duplicate,
-RNA and protein are actively synthesize
-checkpoint checks for mitosis promoting factor, if high enough mitosis is triggered
mitosis
nucleur division without genetic change
-think PMAT
-Prophase
-Metaphase
-Anaphase
-Telephase
-produces exact copy so diploid cells
Prophase
-condensation of chromatin into chromosomes, centrioles move to opposite ends of the cell
-nucleolus and nucleus dissapear
-spindle apparatus forms consisting of aster or microtubules
Metaphase
chromosomes align along the equator of the cell
Anaphase
-sister chromatids split at their attaching centromeres and move toward opposite ends of cell
-cytokinesis is the actual separation of the cellular cytoplasm due to constriction of microfilaments about the center of the cell
telophase
nuclear membrane reforms by reformation of nucleolus
meiosis
-double nuclear division which produces four haploid cells
-only occur in sex cells or spermatogonium and oogonium, all other cells are somatic cells and undergo mitosis only

-after replication in S phase cell is primary spermocyte or primary oocyte, in female germ cells are arrested at primary oocyte and just before ovulation at puberty it undergoes first meiotic division to become secondary oocyte

-divided into meiosis I and II (two rounds of division
prophase I of meiosis I
-homologous chromosomes line up along each other, crossing over or genetic recombination occurs, exhibit four chromatids and are called tetrads
-genes located close together on a chromosome are more likely to cross over together and are said to be linked
-diploid
metaphase I
-homologues remain attached and move to metaphase plate, instead of single chromosomes lining up like in mitosis, tetrads align in meiosis
anaphase I
separates homologues from partners
-HAPLOID
telophase I
-nuclear membrane may or may not reform and cytokinesis may or may not occur
-in humans cytokinesis occurs and new cells are haploid with 23 replicated chromosomes and are secondary spermocytes or oocytes

-in female 1st oocyte degenerates it is much smaller to conserve cytoplasm
meiosis II
pmat II-
-like normal mitosis
-final products are haploid gametes
-nondisjunction may occur and noe cells will have extra chromatids