Term
| how many codons are there? |
|
Definition
|
|
Term
| how many codons code for AA? |
|
Definition
|
|
Term
| what are the stop codons? |
|
Definition
|
|
Term
| What is the initiation codon? |
|
Definition
|
|
Term
| What are the 4 characteristics of genetic code? |
|
Definition
| Specificity, universality, redundancy, non-overlapping and commaless |
|
|
Term
| What is genetic code specificity? |
|
Definition
| Specific codon always codes for the same AA |
|
|
Term
| What is genetic code universality? |
|
Definition
| code is evolutionarily conserved |
|
|
Term
| What is genetic code redundancy? |
|
Definition
| AA may have more than one codon coding for it |
|
|
Term
| What is genetic code non-overlapping or commaless? |
|
Definition
| Read as a continuous sequence of bases |
|
|
Term
| What are the three types of point mutation? |
|
Definition
| silent, missense, nonsense |
|
|
Term
| What is a silent mutation? |
|
Definition
| changed base but still codes for same AA |
|
|
Term
| What is a missense mutation? |
|
Definition
|
|
Term
| What is a nonsense mutation? |
|
Definition
|
|
Term
| What is a frameshift mutation? |
|
Definition
| One of two (not three) bases have been deleted or added - affects all sequences downstream |
|
|
Term
|
Definition
| Codon is repeated multiple times. extra copies of AA in protein |
|
|
Term
| What are three examples of tandem repeats? |
|
Definition
Huntington - CAG repeats coding glutamine
Fragile X - CGG repeats
Myotonic Dystrophy - CTG repeats |
|
|
Term
| What does it mean if a tRNA is charged? |
|
Definition
| it has an AA on its 3' end |
|
|
Term
| mRNA is read in what direction? |
|
Definition
|
|
Term
| tRNA pairs with mRNA how? |
|
Definition
| 3' to 5' (antiparallel and complimentary) |
|
|
Term
| What is aminoacyl-tRNA Synthetase? |
|
Definition
| covalently attaches a AA to its corresponding tRNA. Specific for tRNA and AA. Requires ATP/GTP. only one per AA |
|
|
Term
| For a prokaryotic ribosome, how many (S) is the completed ribosome? |
|
Definition
|
|
Term
| For a prokaryotic ribosome, how many (S) is the small subunit and what is it made of? |
|
Definition
|
|
Term
| For a prokaryotic ribosome, how many (S) is the large subunit and what is it made of? |
|
Definition
| 50S = 5S + 23S + 32 proteins |
|
|
Term
| For a eukaryotic ribosome, how many (S) is the completed ribosome? |
|
Definition
|
|
Term
| For a eukaryotic ribosome, how many (S) is the small subunit and what is it made of? |
|
Definition
|
|
Term
| For a eukaryotic ribosome, how many (S) is the large subunit and what is it made of? |
|
Definition
| 60S = 5S + 5.8S + 23S + 50 proteins |
|
|
Term
| What are the three components for translation? |
|
Definition
| Ribosome, protein factors, energy |
|
|
Term
| Which nucleotide base in the anticodon of a tRNA wobbles? |
|
Definition
| first nucleotide base (5' end) |
|
|
Term
| What is the purpose of a wobbling base? |
|
Definition
| allows for nontraditional pairing (tRNA can recognize more than one codon for a specific AA) |
|
|
Term
| the origin of replication |
|
Definition
| At rich, recognized by initiator proteins, only one in bacteria - 10k in human. Replication is bidirectional - 2 replication forks |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Binds to ssDNA exposed from unzipping and stabilizes it |
|
|
Term
|
Definition
| makes short RNA primers that prime DNA polymerase |
|
|
Term
|
Definition
| Keeps DNA polymerase on template (trails DNA polymerase) |
|
|
Term
|
Definition
| seals nicks from the okazaki fragments |
|
|
Term
| DNA polymerase energy source? |
|
Definition
| powered via energy from triphosphate bond of added nucleotide |
|
|
Term
| How does DNA polymerase grow DNA? |
|
Definition
|
|
Term
| What is an okazaki fragment? |
|
Definition
| its the completed DNA from the lagging strands |
|
|
Term
| Does the leading or lagging strand use DNA primase? |
|
Definition
|
|
Term
| How does DNA polymerase proofread? |
|
Definition
| It has an exonuclease that can 3' to 5' cleave nucleotides from the new DNA if there is an error. |
|
|
Term
| how many nucleotides per error does 5' to 3' polymerization in DNA synthesis happen? |
|
Definition
|
|
Term
| How many nucleotides per error occur from 3' to 5' exonucleolytic proofreading in DNA synthesis? |
|
Definition
|
|
Term
| how many nucleotide per error occur from strand directed mismatch repair in DNA synthesis? |
|
Definition
|
|
Term
| What is the total number of nucleotides per error in DNA synthesis? |
|
Definition
|
|
Term
| How does DNA deal with the problem of primase not being able to lay down the final RNA primer for the final Okazaki fragment? |
|
Definition
| Telomerase adds repetitive DNA to chromosome ends |
|
|
Term
| What are all of the examples of how DNA can be damaged? |
|
Definition
| oxidative cleavage, hydrolytic attack, methylation, depurination, deamination, thymine dimerization |
|
|
Term
| What is depurination of DNA? |
|
Definition
| purine base (guanine) removed from deoxyribose sugar via hydrolysis of glycosidic linkage. The base is replaces with hydroxyl group |
|
|
Term
| What is deamination of DNA? |
|
Definition
| hydrolysis of cytosine's amino group converting cytosine to uracil |
|
|
Term
| What is thymine dimerization of DNA? |
|
Definition
| it results from UV damage. It is the bonding of adjacent (usually thymine) residues |
|
|
Term
| What are the general results of DNA damage? |
|
Definition
Most common = base substitution
all others = deletion |
|
|
Term
| What are the general repair mechanisms for DNA? |
|
Definition
| excision, resynthesis, and ligation |
|
|
Term
| What things are involved in DNA damage repair? |
|
Definition
| AP endonuclease and phosphodiesterase, DNA helicase, DNA polymerase, DNA ligase |
|
|
Term
| What is base excision repair in DNA? |
|
Definition
AP endonuclease and phosphodiesterase cut DNA backbone containing damaged or missing BP.
DNA polymerase fills the gap
and DNA ligase seals the nick |
|
|
Term
| What is nucleotide excision repair in DNA? |
|
Definition
1. DNA nuclease cuts DNA backbone containing damaged or missing DNA
2. DNA helicase unwinds DNa to allow DNA pol access
3. DNA pol fills gap
4. DNA ligase seals nick |
|
|
Term
| What is nonhomologous end joining in DNA? |
|
Definition
| it fixes broken DNA but is not effective for coding DNA (because what is inserted is non-specific) |
|
|
Term
| What is homologous end joining in DNA? |
|
Definition
uses second chromosome to restore the broken or missing DNA chromosome.
This is essential for coding DNA |
|
|
Term
| What are the two types of DNA recombination? |
|
Definition
| general (homologous) and site-specific |
|
|
Term
| What is general or homologous DNA recombination? |
|
Definition
| it occurs between DNA with SIMILAR sequences |
|
|
Term
| What is site-specific DNA recombination |
|
Definition
Occurs between DNA with DISSIMILAR sequences.
seen with mobile genetic elements: transposons in bacteria and viruses for eukaryotes |
|
|
Term
| What are the steps in homologous recombination? |
|
Definition
1. double strand is broken. (2 of the 4 strands - *2 chromosomes are exchanging DNA*)
2. uneven single strand 3's
3. Pairing with homologous chromosome
4. joint molecule is between two chromosomes
5. nicks are sealed producing the cross-over |
|
|
Term
| What is the intermediate in homologous recombination? |
|
Definition
| cross-strand exchange or holiday junction |
|
|
Term
| What is a holiday junction? |
|
Definition
AKA cross-strand exchange.
Branch migration occurs here |
|
|
Term
| What are the outcomes of a holiday junction? |
|
Definition
no rotation, cut, reseal= NO exchange
rotation, cut, reseal=minimal exchange
rotation, branch migration=major exchange |
|
|
Term
| What are the three types of mobile genetic elements that complete site specific recombination? |
|
Definition
DNA only transposons
retroviral-like retrotransposons
nonretroviral retrotransposons |
|
|
Term
| what is the deal with DNA only transposons? |
|
Definition
They are in bacterial genomes
They encode transposase which forms the active transposase complex and transfers the transposon from the donor to the target chromosome
they have short terminal inverted repeats (IRs)
Excision or replicative pathway
Examples: Tn3, P elements, Tam3 |
|
|
Term
| whats the deal with retroviral-like retrotransposons? |
|
Definition
EUKARYOTE TYPE THAT ARE NOT TRANSPOSONS BUT TRANSPOSABLE SEQUENCE
they encode reverse transcriptase and resemble retrovirus
have Long Terminal Repeats (LTRs)
Moves with RNA intermediate
HAVE NO PROTEIN COAT
Example: Ty1 of yeast |
|
|
Term
| Whats the deal with nonretroviral retrotransposons? |
|
Definition
EUKARYOTE TYPE THAT ARE NOT TRANSPOSONS BUT TRANSPOSABLE SEQUENCE
HAVE NO PROTEIN COAT
Poly A tail at 3' end
Truncated 5' end
Encodes reverse transcriptase - RNA is made and attached to RT and then inserted into DNA
Moves with RNA intermediate
Ex: L1 element (15% human genome), Alu element (11% human genome) |
|
|
Term
| How does reverse transcriptase work? |
|
Definition
1. Make DNA/RNA
2. Make DNA/DNA helix |
|
|
Term
| What does the positioning of transposable elements in humans and mice suggest? |
|
Definition
| They are a recent evolutionary acquisition |
|
|
Term
| What are the two major events in the cell cycle? |
|
Definition
|
|
Term
| What is the main idea behind interphase? |
|
Definition
| It increases the cell size and content and replicates genetic material (karyokinesis) |
|
|
Term
| What is the main idea behind mitosis? |
|
Definition
Cell division of nucleus and cytoplasm (cytokinesis)
Short part of a cell's life here |
|
|
Term
| What are the three phases of interphase? |
|
Definition
Gap 1 phase, Synthetic phase, Gap 2 phase
G1, S, G2 |
|
|
Term
| What is the G1 phase of interphase? |
|
Definition
synthesis of components for DNA replication
synthesize RNA, regulatory proteins, and enzymes for replication
Cell volume increases
Nucleoli reestablished
Centrioles duplicate
OCCURS DIRECTLY AFTER MITOSIS |
|
|
Term
| What is the Synthetic phase of interphase? |
|
Definition
DNA is replicated and synthesized
Necessary material (histones, nucleoproteins) are imported into nucleus
Chromatin formed |
|
|
Term
| What is the Gap 2 phase of interphase? |
|
Definition
Preparation for mitosis
cell division molecules (RNA, proteins) are made
energy is stored
tubulin is made for microtubules
check for and repair DNA replication errors |
|
|
Term
| What is the resting phase (G0) of interphase? |
|
Definition
| highly differentiated cells that may temporarily or cease to undergo mitosis |
|
|
Term
|
Definition
Ligands bind to cell surface receptors activating signal transduction paths
Cascade of protein kinases activate nuclear transcription factors
proto-oncogenes which regulate cell division become expressed |
|
|
Term
| What is the cyclin and cyclin-dependent kinases (CDKs) activity in the G1 to S phase? |
|
Definition
Cyclin D - binds to CDK4 and CDK6 during early G1
Cyclin E - Binds CDK2 during late G1
These complexes permit S phase entry |
|
|
Term
| What is the cyclin and cyclin-dependent kinases (CDKs) activity in the S to G2 phase? |
|
Definition
Cyclin A - binds CDK2 and CDK1
Cyclin B - formed |
|
|
Term
| What is the cyclin and cyclin-dependent kinases (CDKs) activity in the G2 to M phase? |
|
Definition
Cyclin B - Binds CDK 1
Complex permits mitosis to begin |
|
|
Term
| What do the quality control mechanisms regulate during mitosis? |
|
Definition
| Adequate cell growth, correct DNA synthesis, and proper chromosome segregation |
|
|
Term
| What are the phases of mitosis? |
|
Definition
| PPMAT; Prophase, prometaphase, metaphase, anaphase, and telophase |
|
|
Term
| What happens during prophase of mitosis? |
|
Definition
1. chromosomes condense and become visible
2. nucleus dissapears
3. centrosome divides into the two poles
4. astral rays and spindle fibers develop
5. kinetochore forms at each centromere
6. spindle fibers bind to kinetochore to cause karyokinesis |
|
|
Term
| During prophase, two identical chromatids are joined by what? |
|
Definition
| centromere. a kinetochore forms here in prophase |
|
|
Term
| when centrosomes divide during prophase, what goes to each pole? |
|
Definition
| two centrioles and one microtubule-organizing center (MTOC) |
|
|
Term
| Where do astral rays and spindle fibers develop from? |
|
Definition
| mitotic spindle apparatus |
|
|
Term
|
Definition
microtubules that radiate from the pole of the spindle.
They orient the MTOC at the pole of the cell |
|
|
Term
| What happens during prometaphase? |
|
Definition
1. nuclear envelope disappears
2. mitotic spindle microtubules attached at the kinetochores assist in proper chromosome orientation
3. Polar microtubules (not part of the mitotic spindle apparatus) maintain space between poles during mitosis |
|
|
Term
| What happens during metaphase? |
|
Definition
1.Chromosomes condense and line up at the metaphase plate
2. spindle microtubules still attached to kinetochore |
|
|
Term
| what happens during anaphase? |
|
Definition
1. sister chromatids pulled apart and begin migration to opposite poles
2. microtubules shorten (depolymerization) causing migration of chromatids
3. Late in this stage, cleavage furrow forms at cell membrane (plasmalemma) |
|
|
Term
| What happens during telophase? |
|
Definition
1. chromosomes uncoil and organize into heterochromatin and euchromatin
2. Nucleolus-organizing regions (NORs) on 5 human chromosomes develops the nucleolus
3. Cytokinesis happens |
|
|
Term
| What happens during cytokinesis? |
|
Definition
1. cleavage furrow deepend and only midbody and polar microtubules attach daughter cells
2. actin and myosin filaments compose contractile ring just inside plasmalemma
3. Each daughter call contains a diploid (2n) number of chromosomes and are identical |
|
|
Term
| How does the nuclear envelope disappear? |
|
Definition
| The nuclear lamins phosphorylated |
|
|
Term
| how much DNA and chromosomes are in a cell at the beginning of meiosis? |
|
Definition
| 4n DNA and 4n chromosomes |
|
|
Term
| How much DNA and chromosomes are in a cell at the end of meiosis? |
|
Definition
| haploid (n) for both DNA and chromosomes |
|
|
Term
| Why does recombination occur during meiosis? |
|
Definition
| for gene variability and gene pool diversity |
|
|
Term
| What are the stages of meiosis? |
|
Definition
Meiosis 1: PMAT 1
Meiosis 2; PMAT 2 |
|
|
Term
| When does meiosis 1 begin? |
|
Definition
| at the conclusion of interphase |
|
|
Term
| What happens during meiosis 1 in general? |
|
Definition
There is a reductional division: HOMOLOGOUS pairs of chromosomes separated going from 2n to 1n.
The DNA content goes from 4n to 2n |
|
|
Term
| What are the five phases of Prophase 1 in meiosis? |
|
Definition
Leptopene, zygotene, pachytene, diplotene, and diakinesis
(lesbian zebras push donkey dildos) |
|
|
Term
| What phase of prophase I is where crossing over occurs? |
|
Definition
|
|
Term
| What happens in Leptopene? |
|
Definition
| Individual chromosomes composed of two chromatids joined at centromere condense and form long strands |
|
|
Term
| What happens during Zygotene? |
|
Definition
| Homologous pairs of chromosomes line up gene locus to gene locus and form SYNAPSES via the synaptical complex to form TETRADS |
|
|
Term
| What happens during Pachytene? |
|
Definition
| Chromosomes condense further and form cross over sites called chiasmata for exchange of genetic material between homologous chromosomes |
|
|
Term
| What happens during Diplotene? |
|
Definition
| Chromosomescondense further and begin to separate revealing the chiasmata |
|
|
Term
| What happens during Diakinesis? |
|
Definition
| Chromosomes condense and nucleus and nucleolus disappear |
|
|
Term
| What happens during Metaphase 1? |
|
Definition
Homologous pairs of chromosomes line up at metaphase plate
spindle fibers attach to kinetochores |
|
|
Term
| What happens during anaphase 1? |
|
Definition
homologous chromosomes migrate to opposite poles
(keep in mind that each chromosome still consists of two chromatids (but nor sister because of genetic exchange) |
|
|
Term
| What happens during telophase 1? |
|
Definition
cytokinesis occurs resulting in two daughter cells
cell posses haploid number of chromosomes but each chromosome has two chromatids sooo... still diploid amount of DNA |
|
|
Term
| What happens during meiosis II? |
|
Definition
occurs without DNA synthesis
Rapid progression through phases forming 4 daughter cells with haploid (n) chromosome number and haploid (n) DNA material |
|
|
Term
| How many strands does RNA typically have? |
|
Definition
|
|
Term
| What does the sugar part of RNA look like? |
|
Definition
| composed of ribose with -OH group at 2' carbon |
|
|
Term
| What does uracil replace? |
|
Definition
|
|
Term
| What structures can RNA have? |
|
Definition
harpin by base pairing with same RNA
Double helix by pairing with DNA, RNA, or the same RNA
Can also form tertiary structures |
|
|
Term
|
Definition
| 32 or more (48 in humans) |
|
|
Term
| tRNA can come from up to how many genes? |
|
Definition
|
|
Term
| How many nucleotides are there per tRNA? |
|
Definition
|
|
Term
| What structure does tRNA have? |
|
Definition
3D=L shape
3 unpaired loop regions
paired regions form double helix |
|
|
Term
| What are psuedouracil and dihyrouracil? |
|
Definition
| unusual bases produced via chemical modification after tRNA synthesis |
|
|
Term
| what is aminoacyl tRNA synthetase? |
|
Definition
|
|
Term
| Where does aminoacyl tRNA synthetase bind on tRNA? |
|
Definition
| 5-CCA-3 at 3' end (short arm) |
|
|
Term
| how specific is aminoacyl tRNA synthetase? |
|
Definition
| one aminoacyl tRNA synthetase catalyses reaction between one specific AA and all tRNAs that code for that AA |
|
|
Term
| What are the rRNA in eukaryotes? |
|
Definition
|
|
Term
| What are the rRNA in prokaryotes? |
|
Definition
|
|
Term
| how many copies of rRNA are synthesized in each cell generation? |
|
Definition
|
|
Term
| how many copies of rRNA are in the human genome? |
|
Definition
| 200 gene copies on 5 chromosomes |
|
|
Term
| Describe Eukaryotic rRNA ribosomal subunits |
|
Definition
18 S + 30 proteins = small ribosomal subunit (40 s)
28 S, 5.8 S, 5.0 S, and 45 proteins = large subunit (50 S) |
|
|
Term
| Describe Prokaryotic rRNA ribosomal subunits |
|
Definition
16 S + 21 proteins = small ribosome subunit (30 S)
32 S, 5 S + 35 proteins = Large subunit (50 S) |
|
|
Term
|
Definition
only RNA that codes protein
Poly A Tail = long Adenine tail at 3' in EUKARYOTES |
|
|
Term
|
Definition
|
|
Term
| What direction is RNA synthesized? |
|
Definition
|
|
Term
| What is a start RNA polymerase signal? |
|
Definition
|
|
Term
| What determines which DNA strand is template in RNA synthesis? |
|
Definition
| The orientation of the promoter |
|
|
Term
| When attaching a ribonucleotide in RNA synthesis, what happens? |
|
Definition
| pyrophosphate is cleaved from the triphosphate ribonucleoside forming a phosphodiester bond between the 3'-OH and the ribose phosphate on C5 |
|
|
Term
| where is a promoter located? |
|
Definition
| actually in DNA upstream of a gene |
|
|
Term
| What is made of the four subunits; 2 alpha, beta, and beta'? |
|
Definition
| the core enzyme of prokaryotic RNA polymerase |
|
|
Term
| What is prokaryotic RNA polymerase able to do? |
|
Definition
| contains necessary enzymes for RNA synthesis but NOT DNA PROMOTER BINDING! needs a sigma factor for that... |
|
|
Term
|
Definition
| The 5th subunit of the prokaryotic RNA polymerase. Binds promoters and facilitates initiation |
|
|
Term
|
Definition
| prokaryotic RNA polymerase + sigma factor |
|
|
Term
| Are there different sigma factors? |
|
Definition
| Yes and they recognize different DNA promoters. |
|
|
Term
| What do bacterial promoters look like? |
|
Definition
| hexameric sequence 10 base pairs and 35 base pairs (-10, -35) upstream of first nucleotide to be transcribed (+1) |
|
|
Term
| What are some common bacterial promoters? |
|
Definition
(sigma)70=most common
(sigma)F aka (sigma)28
(sigma)H aka (sigma)32
(sigma)N aka (sigma)54 |
|
|
Term
| What are the prokaryotic RNA polymerase steps in transcription? |
|
Definition
1. (sigma) factor binds to RNA polymerase
2. Haloenzyme binds promoter forming the closed complex
3. unwinding of DNA from -10 to 0 forming the open complex
4. rNTP pairs with +1 base on DNA template folowed by base addition to 3' end of growing chain |
|
|
Term
| How is prokaryotic transcription terminated? |
|
Definition
| factor (rho) independent or dependent |
|
|
Term
| What is Rho independent termination? |
|
Definition
stem loop hairpin followed by U repeat residues in growing RNA chain
RNA polymerase pauses at hairpin and U-A basepairing at active site is interrupted |
|
|
Term
| What is rho dependent prokaryotic termination of transcription? |
|
Definition
rho protein stops transcription upon certain sequence recognition
Does not need hairpin structures or U repeats |
|
|
Term
| What are the different types of eukaryotic RNA polymerase and what to they transcribe? |
|
Definition
1. RNA polymerase I - transcribes genes for rRNAs (5.8 S, 18 S, 28 S)
2. RNA Polymerase II - Transcribes protein-coding genes mRNAs and some snRNAs
3. RNA Polymerase III - Transcribes tRNAs, 5 S, rRNA and some snRNAs |
|
|
Term
| What is a general transcription factor? (TF) |
|
Definition
| in eukaryotes. they are protein factors that help position RNA polymerase at the promoter gene |
|
|
Term
| What do promoters look like in eukaryotes? |
|
Definition
TATA boxes. Alternating repeat of Ts and As. 25 bases upstream of TSS (transcription start site)
-There are other promoters that are GC rich |
|
|
Term
| How is eukaryotic RNA polymerase transcription initiated? |
|
Definition
TATA binding proteins (TBPs) bind TATA box to initiate transcription.
(General TFs, TFIIA, TFIIB, TFIIE, TFIIH, and RNA polymerase meet at promoter forming the basal transcription complex) |
|
|
Term
| What is the basal transcription complex? |
|
Definition
| General TFs, TFIIA, TFIIB, TFIIE, TFIIH, and RNA polymerase meet at promoter forming the basal transcription complex |
|
|
Term
| After initiation, how is RNA polymerase transcription completed in eukaryotes? |
|
Definition
1. A short sequence is made initially
2. RNA polymerase conformation change to "elongation mode"
3. Activators and enhancers interact with RNA polymerase to increase the rate of synthesis
4. modifying proteins help uncoil DNA chromatin |
|
|
Term
| How does RNA polymerase in eukaryotes have a conformation change to elongation mode and what is the result? |
|
Definition
-RNA polymerase tail is phosphorylated at C-terminal domain (CTD) via TFIIH
-results in tighter interaction with DNA
-General TFs release and elongation factors (EFs) bind |
|
|
Term
| What are the three types of RNA post-transcriptional processing? |
|
Definition
| mRNA Capping, RNA splicing, and polyadenylation |
|
|
Term
| In what cells does RNA post-transcriptional processing occur? |
|
Definition
|
|
Term
|
Definition
| modification of the 5' end of mRNA with methylguanine nucleotide |
|
|
Term
| What enzymes are involved in mRNA capping? |
|
Definition
| phosphatase, guanyl transferase, and methyl transferase |
|
|
Term
| What is the process of mRNA capping? |
|
Definition
1. 25 nucleotides added
2. 1 phosphate cleaved from 5' end
3. Guanyl transferase adds GMP in a reverse linkage (5' to 5') which is atypical
4. Methyl transferase adds methyl to guanosine |
|
|
Term
|
Definition
On a basic level, just removes introns and leaves exons from pre-mRNA.
-provides another mechanism for the regulation of gene expression in a eukaryotic organism |
|
|
Term
|
Definition
| primary RNA transcript containing both introns and exons |
|
|
Term
|
Definition
|
|
Term
| What does a spliceosome look like? |
|
Definition
| 5 snRNAs are involved in formation (U1, U2, U4, U5, U6) |
|
|
Term
| What is a small ribonucleoprotein (snRNP)? |
|
Definition
| each snRNA + protein subunit |
|
|
Term
| How is the splice site determined by specific sequences in pre-mRNA? |
|
Definition
| 5' splice site, 3' splice site, and the branch point |
|
|
Term
| How is the splicing reaction catalyzed? |
|
Definition
it is catalyzed by RNA not proteins
-two transesterfication reactions occur
1. joins 5' end of cut intron to branch point
2. joins 3'-OH of exon to 5' of next exon
-The intron is removed as a lariat (loop) |
|
|
Term
|
Definition
| A loop of intron RNA (5' end bonded to branch point) that is removed during splicing |
|
|
Term
| What is the splicing process? |
|
Definition
1. Binding of point binding proteins (BBPs) to pre-mRNA
2. snRNAs are recruited and the spliseosome forms and splices |
|
|
Term
| What is alternate splicing? |
|
Definition
| Inconsistent splicing of introns during RNA splicing this increases the number of potential gene products that can be expressed from a single gene |
|
|
Term
|
Definition
| Yes. during crossing over. |
|
|
Term
| What is one way for a single gene to express multiple proteins? |
|
Definition
| RNA splicing (in particular alternate splicing) |
|
|
Term
|
Definition
| When a Poly A Tail is added to a piece of RNA after it has been synthesized |
|
|
Term
| How long can a Poly A Tail be? |
|
Definition
| as many as 200 Base A repeats |
|
|
Term
| How does polyadenylation occur? |
|
Definition
Poly A polymerase adds nucleotides using ATP for energy.
-CstF and CPSF bind 3' end of RNA as it leaves RNA pol II
-Poly A binding proteins bind RNA as tail is added (these determine length of Poly A tail |
|
|
Term
| What proteins are involved in polyadenylation? |
|
Definition
| Poly A polymerase, Cleavage stimulatio factor (CstF), cleavage and polyadenylation specific factor (CPSF), and binding proteins |
|
|
Term
| Where do the CstF and CPSF come from? |
|
Definition
| They are part of basal transcription complex at tail of RNA Polymerase II |
|
|
Term
| What does the initiation codon code for? |
|
Definition
|
|
Term
| What does polycistronic mean? |
|
Definition
it means that mRNA has several coding regions.
-only in Prokaryotes
-each coding region has its own initiation codon and makes separate polypeptide |
|
|
Term
| What are the steps in protein synthesis? |
|
Definition
| initiation, elongation, termination |
|
|
Term
| What is the process of initiation in protein synthesis? |
|
Definition
1. IFs aid in formation of 30S initiation complex
2. GTP is cleaves and IFs leave upon binding of 50S to 30S (forming 70S)
3. EFs direct tRNA binding to A site |
|
|
Term
| What is the shine-delgarno sequence? |
|
Definition
Type of ribosomal binding sire (RBS) used for recognition and attachment of mRNA to the 16S rRNA of the ribosome.
-mRNA and 16S form complimentary BPs
-Located on the mRNA upstream of the start codon |
|
|
Term
| What is an initiation factor? |
|
Definition
-They are the proteins used during initiation of protein synthesis.
-They aid in formation of 30S initiation complex (small ribosomal subunit) |
|
|
Term
| What are the prokaryotic initiation factors (IFs)? |
|
Definition
|
|
Term
| What are the eukaryotic initiation factors (IFs)? |
|
Definition
|
|
Term
| What is the first AA in protein synthesis and how are eukaryotic and prokaryotic start AAs different? |
|
Definition
Methionine.
-prokaryotes have formulated methionine (fMET) which ensures N to C elongation. Formylated by transformylase (N^10 formyl tetrahydrofolate is the carbon donor)
-euks have regular met |
|
|
Term
| What are the antibiotic actions at initiation of protein synthesis? |
|
Definition
Streptomycin - binds 30S and distorts structure
Tetracyclines - small ribosomal subunits blocking tRNA from mRNA-ribosome complex |
|
|
Term
| Elongation adds AAs to which side of the amino acid? |
|
Definition
| The carboxyl end (not the N end) |
|
|
Term
| ribosomes read mRNA from which direction? |
|
Definition
|
|
Term
| What facilitates the delivery of aminoacyl-tRNA (charged) to the ribosome? |
|
Definition
Elongation factors (EF-Tu and EF-Ts)
-requires GTP |
|
|
Term
|
Definition
moves ribosome 3 nucs on mRNA
-requires GTP |
|
|
Term
| Uncharged tRNA is released from what site on the ribosome? |
|
Definition
|
|
Term
| How are the sites arranged on the RNA? |
|
Definition
| E-P-A (A being where the charged tRNA attaches, P is where the peptidyl-tRNA attaches, and E is where the uncharged tRNA is attached) |
|
|
Term
| What antibiotic action is possible during elongation? |
|
Definition
-puromycin - resembles aminoacyl-tRNA and causes inhibition of elongation via incorporation in peptide chain (prok and euk)
-Chloramphenicol - inhibits peptidyltransferase (prok)
-clindamycin/erythromycin - irreversibly bind 50S inhibiting translocation
-diphtheria toxin - inactivates euk eEF-2 preventing translocation |
|
|
Term
| Which elongation antibiotics only affect prokaryotic organisms? |
|
Definition
| chloramphenicol, clindamycin, and erythromycin |
|
|
Term
| Which elongation antibiotics only affect eukaryotic organisms? |
|
Definition
|
|
Term
| Which elongation antibiotic affects both euks and proks? |
|
Definition
|
|
Term
| When does termination occur during protein synthesis? |
|
Definition
| When the termination sequence enters A site |
|
|
Term
| What are the steps in protein synthesis termination in prokaryotes? |
|
Definition
1. the termination codon is recognized by RF (RF 1,2 helped by RF-3)
2. mRNA is released
3. ribosome dissociated (70S dissociates into 30S and 50S) |
|
|
Term
|
Definition
| release factor. facilitates termination of protein synthesis |
|
|
Term
| What are the types of postranslational modification after protein synthesis? |
|
Definition
| trimming and covalent alterations |
|
|
Term
| what is protein trimming and why does it occur? |
|
Definition
| -some proteins are synthesized as inactive. they become active upon endoprotease cleavage (trimming) in ER, Golgi, Vesicle, Post-secretion |
|
|
Term
|
Definition
Inactive precursor of secreted enzyme. Needs to be trimmed in order to be active.
Example: trypsinogen--> trypsin |
|
|
Term
| What are examples of covalent alterations in proteins after protein synthesis? |
|
Definition
| phosphorylation, glycosylation, and hydroxylation |
|
|
Term
|
Definition
phosphate group added to AA
-Common in tyrosine and serine |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Proline, lysine in collagen formation |
|
|
Term
|
Definition
|
|
Term
|
Definition
one or more cistrons that are co-transcribed into single mRNA.
-Can be transcribed from more than one promoter |
|
|
Term
| When translating an operon with multiple cistrons, are they all translated in the same proportion? |
|
Definition
| no. they may not be translated at the same level. |
|
|
Term
| Why are not all of the cistrons on an operon translated at the same level? |
|
Definition
repressors and activators could affect the expression of the cistrons. also the shine delgarno site may not be as efficient (may be farther upstream taking more energy for binding)
Also translation may just take longer (some AAs may have only one tRNA, some tRNAs are lower copy number, mRNA may have inhibitory structure) |
|
|
Term
| Can transcription occur at the same time as translation (coupled)? |
|
Definition
In prokaryots - yes - because there is no nuclear membrane
In eukaryotes - no - there is a nuclear membrane |
|
|
Term
| What is translational coupling? |
|
Definition
en example of the cis effect - the ability of a ribosome to translate a gene is dependent on the translation of a gene immediately upstream
Example: If a cistron is not translated it may fold and base pair with RBS of B cistron |
|
|
Term
| how can gene expression be regulated? |
|
Definition
| feedback inhibition and repressors |
|
|
Term
| What is feedback inhibition? |
|
Definition
| the end product of a pathway inhibits 1st enzymatic step of the same pathway |
|
|
Term
| At what level does feedback inhibition take place? |
|
Definition
| at level of protein activity |
|
|
Term
| How is feedback inhibition carried out? |
|
Definition
| allosteric binding of effector molecule - could result in less, more, or different activity |
|
|
Term
| What types of feedback inhibition are there? |
|
Definition
| simple linear and branched |
|
|
Term
| What is simple linear feedback inhibition? |
|
Definition
| one end product affects upstream enzyme |
|
|
Term
| What is branched feedback inhibition? |
|
Definition
| two end products are both needed to inhibit upstream enzyme |
|
|
Term
| What are the types of branched feedback inhibition? |
|
Definition
| cumulative, sequential, and multivalent |
|
|
Term
| What is cumulative branched feedback inhibition? |
|
Definition
| two components partially inhibit an upstream enzyme |
|
|
Term
| What is sequential branched feedback inhibition? |
|
Definition
| two components inhibit their unique branches and then branch point molecule inhibits upstream enzyme |
|
|
Term
| What is multivalent feedback inhibition? |
|
Definition
| two components form complex that then inhibits enzyme |
|
|
Term
| At what level do repressors prevent gene expression? |
|
Definition
| at the transcriptional level |
|
|
Term
|
Definition
| They bind to operator sequences in or near promotors where RNA polymerase binds |
|
|
Term
|
Definition
| It binds repressors including alteration of repressor properties (allostery) |
|
|
Term
|
Definition
| it is the process by which a repressor's properties are altered by an inducer |
|
|
Term
|
Definition
|
|
Term
| What is an example of an inducer? |
|
Definition
|
|
Term
| How does an inducer work? |
|
Definition
| when repressor bound, repressor can not bind to an operator and RNA polymerase can bind to the promoter and transcription can ensue |
|
|
Term
|
Definition
its like an inducer except co-repressors bind to the repressor and ALLOW it to bind to the operator.
This stops transcription. |
|
|
Term
| What is an example of a co-repressor? |
|
Definition
|
|
Term
|
Definition
DNA binding protein that enhances or activates transcription
-They help RNA polymerase begin transcription |
|
|
Term
|
Definition
| They can bind to activators and allow the activator to bind to DNA site and ensue transcription |
|
|
Term
| What is an example of an activator? |
|
Definition
|
|
Term
|
Definition
| operon that encodes enzymes (lacZ, lacY, lacA) needed for breaking down lactose |
|
|
Term
| If there is no lactose, what happens to the lac operon? |
|
Definition
|
|
Term
| If there is lactose around, what happens to the lac operon? |
|
Definition
|
|
Term
| What is the repressor protein for the lac operon? |
|
Definition
|
|
Term
| What is the inducer in the lacZYA example? |
|
Definition
| lactose (actually allolactose) |
|
|
Term
| What is the activator in the lacZYA example? |
|
Definition
|
|
Term
| When is CAP/CRP activated in the lacZYA example? |
|
Definition
| In the presence of glucose, CAP is activated and will bind DNA (upstream of promoter--activating transcription of the lac operon) |
|
|
Term
| In the lacZYA example, how is CAP activated? |
|
Definition
via cAMP (catabolite) which is high during low glucose
high glucose = low cAMP (catabolite)
This is a type of catabolite repression, catabolite referring to cAMP |
|
|
Term
| what is an example of catabolite repression? |
|
Definition
| Glucose and cAMP relationship. the lower the glucose, the higher the cAMP, the higher the glucose, the lower the cAMP. |
|
|
Term
| On what level is the E.Coli trp operon regulated? |
|
Definition
| transcription and translation |
|
|
Term
| what is the feedback mechanism for regulation in the E.Coli trp operon? |
|
Definition
-end product inhibits the very path from which it was created
-end product is a co-represser
-co-repressor inhibits first unique enzyme to the pathway |
|
|
Term
| What are the transcription regulation components of the E.Coli trp operon? |
|
Definition
Repressor-TrpR protein
co-repressor-Tryptophan molecules |
|
|
Term
| How is the trp operon regulated? |
|
Definition
|
|
Term
| What is the point of the E.Coli trp operon? |
|
Definition
| 5 genes encoding 5 enzymes encoded to synthesize AA tryptophan |
|
|
