Question | Answer |
Purines? | adenine / guanine |
Pyrimidines? | cytosine / thymine |
Repetitive sequence DNA | noncoding DNA |
Old strand has more ____ groups than new strand | methyl |
semi-conservative replication | heavy --> intermediate --> intermediate and light |
replisome | -protein that governs DNA replication |
Site of transcription, DNA replication, translation, recombination for prokaryotes? | Protplasm |
Site of transcription, DNA replication, recombination for eukaryotes? Translation? | -Nucleus
-cytoplasm |
DNA gyrase / topoisomerase | relieves overwound DNA with negative supercils |
RNA Primase | Creates RNA primer for DNA polymerase |
How does DNA polymerase read DNA and make DNA? | Reads 3'-->5' and synthesizes 5' --> 3' |
What energy drives DNA replication? | hydrolysis of phosphodiester link to free pyrophosphate |
DNA ligase | fills in gaps of okazaki fragments with nucleotides and sugar phosphate backbone |
DNA polymerase proofreading activity is also known as? | 3' - 5' exonuclease activity |
WHich strand is more subject to errors? | lagging strand |
Replication-origin of replication and chromosome: prok vs. euk | -prok-circular / one origin
-euk - multiple origins |
Telomerase | -enzyme that elongates telomeres by adding nucleotides (5'-->3')
-reverse transcriptase activity to elongate 5'--> 3' strand |
What type of cells are telomerase found in? | cells with high growth potential
-early embryonic cell, germ, stem, cancer cells |
Location of DNA and RNA? | -nucleus and mito matrix
-nucleus and cytoplasm |
Where does transcription take place? Translation? | -nucleus
-cytoplasm |
Monocistronic - what is it and where is it found? | -eukaryotes - each mRNA translates to only one product |
polycistronic - what is it and where is it found? | -prokaryotes - each mRNA leads to multiple products |
What is antisense strand? | template strand with sequence complementary to RNA produced |
RNA produced is same as ______ | sense strand (coding strand)
-protects against degradation |
How do polymerases act for DNA and RNA | Move in 3'-->5' direction but build new strand in 5'-->3'direction |
How do the types of RNA polymerases compare between prok and euk? | Prok - one polymerase
Euk-3 polmerases |
What is newly formed RNA called? | hnRNA |
How does transcription know where to start / end ? | promoters (consensus sequence) and termination sequence
-variation from consensus seq causes RNA poly to bind less tightly |
Difference between promoter and primer. | Promoter - tells RNA poly where to start transcription
Primer - short piece of RNA that starts replication |
What are differences between transcription and replication in terms of speed and proofreading? | -transcription is slower and doesn't proofread |
How is transcription regulated? | activators / inhibitors bind to DNA close to promoter to activate / repress RNA poly |
Exons / introns are cut out? How to remove? | -Introns --> only exons code
-snRNPs form spliceosome |
T / F: Post-transcriptional processing occurs in both euk and prok? | TRUE |
Does the 5'cap and poly A tail added before or after mRNA is completely transcribed? | before |
What is function of 5'cap? | attachment site for px synthesis and protects against exonucleases |
Where are introns / exons found? | -introns stay in nucleus
-exons exit nucleus |
Start Codon / stop codons? | -start: AUG
-stop: UAA, UGA, UAG |
How to create sticky ends? | use restriction enzymes to cut at palindromic sequences |
What does lacZ enable? | enable to digest x-gal sugar |
PCR steps | -95 degrees: denature DNA
-60 degrees: cool to anneal primers
-72 degrees: activate heat-resistant polymerase |
Restriction fragment length polymorphisms | DNA of different individuals have different restriction sites and varying distances between restriction sites |
Besides cytoplasm, where else can translation occur? What locations on ribosomes? | -mito matrix
-free floating ribosome or ribosome attached to rough ER |
How to make a ribosome? | combine rRNA with protein |
____ end of codon lines up with _______ end of anticodon | 5' and 3' |
tRNA synthetase | enzyme that helps bind a.a. to tRNA (use GTP) |
Prok vs. Euk ribosomes subunits | Prok: 30 + 50 = 70
Euk: 40+ 60 = 80 |
Initiator tRNA activates translation at which site? | P-Site --> once filled A-site can now be filled |
Steps for initiating translation. | 1.) 5'end attaches to small ribosome
2.) start tRNA settles in P-site
3. Signals for large subunit to join |
How to create a peptide bond and what enzyme used? | -C-terminal attaches to N-terminal through dehydration reaction
-peptidyl transferase (ribosome) |
How to terminate translation? | Release factor binds to termination codon so water can be added to stop |
In what direction does ribosomal assembly move? | 5' --> 3' |
What does ribosome bind to initiate translation in prokaryotes? Eukaryotes? | -Shine Delgarno and AUG
-5'cap and AUG |
nonsense mutations | change codon to a stop codon for early termination |
missense mutation and at what position does it occur ? | -one a.a. is substituted for another to produce different a.a.
-first or second position in codon |
silent mutation | no detectable change |
transposons | DNA segments can excise themselves and reinsert at another location |
forward mutation | change organism from original state (wild type) |
backward mutation | revert organism back to wild type |
Where do px made by free-floating ribosome in cytosol function? | cytosol |
Where do px made from rough ER become? | injected into ER lumen and become mem-bound px of ER, golgi, plasma mem, etc. |
Signal peptide | direct ribo to attach to ER or stay on free-floating ribosome |
translocation | DNA segment inserts into another chromo |
nucleosome | eight histones wrapped in DNA |
4 stags of cell cycle? | G1 (pre-synthetic)
S (or Go) (synthesis)
G2 (post-synthetic)
M (mitosis) |
What is restriction point not met? What type of cells are in here? | -enter Go phase
-liver cells, mature nx, muscle cells |
What does G1 phase do? | create organelles and double in size |
What does S phase do? | -duplicate DNA to create 2 identical sister chromatids
-centrioles also duplicated |
How many chromosomes and chromatids at S-stage? | 46 chromo and 92 chromatids |
When is tubulin px for microtubules made during interphase? | G2 stage |
During interphase, is DNA condensed or loose? | loose --> transcribe |
What is chromatin? | DNA wrapped around histone proteins to allow DNA to fit into cell |
Why is condensed DNA important for cell division? | don't lose any gnetic material |
4 stages of mitosis? | Prophase, Metaphase, Anaphase, Telophase |
What happens during prophase? | -chromatin condenses and centrioles move to opp. ends of cells to form spindle apparatus
-nuclear mem breaks down |
Aster / centrioles / kinetochore / centromere | Aster rays project from centrioles and attach to kinetochore on centromere to pull them apart |
How does spindle apparatus attach to centromere? | Spindle microtubules attach to kinetochore microtubules |
Do chromosomes uncoil before cytokinesis? | yes! |
When does nuclear membrane disappear / reform? | prophase / telophase |
What is sister chromatid? | identical copies of chromosome |
What are homologous chromosomes? | -have same genes in different allelic forms
-2 pairs of sister chromatids form a tetrad |
When does synapsis occur? | Prophase |
Binary fission produces | equal replication with 2 idential daughter cells |
budding produces | equal replication (same DNA as parent) with unequal cytokinesis |
How to accomplish regeneration? | mitosis |
Number of chromosomes will be diploid for parthenogenic animal? | FALSE - parthenogenesis means adult organism develops from unfertilized egg (haploid) |
How many cells does mitosis / meiosis create? | 2 and 4 |
Can synapsis occur btwn sister chromatids? | NO --> only homologous chromo |
Meiosis I produces? | 2 haploid daughter cells |
What does spermatocyte form at end of meiosis? | 4 sperm cells |
What does oocyte form at end of meiosis? | single ovum and 3 polar bodies |
The law of_____ ( segregation or independent assortment) is dependent on the separation of members of homologous pairs. | segregation |
the law of _______( segregation or independent assortment) is dependent on the random arrangement of homologous chromosomes at the metaphase plate. | assortment |
When does nondisjunction occur for Down's syndrome? | meiosis 2 |
Alleles | alternative copies of same gene |
When do alleles segregate? | meiosis |
Meiosis I is _____ division | reductional |
What are linked genes in terms of segregation? | cannot segregate independently |
What does it mean when 2 genes are 25 map units apart? | 25% of total gametes between 2 genes recombine |
What creates codominance? | multiple coding alleles for a gene |
penetrance vs. expressivity | -penetrance: people who straight up express phenotype
-expressitivity: varying expression of phenotype |
Most recessive diseases are _____ acting while dominant diseases are _____ acting. | early / late |
Who determines the sex of a child? | father |
Most sex-linked traits are on __ chromosome and recessive / dominant? | X and recessive |
Can fathers ever be carriers for sex-linked traits? | NO |
What are viruses made of? | px coat (capsid) and either DNA or RNA (never both!) |
where does virus get lipid-rich envelope? | borrowed from hose mem or made in host cyto (envelope has virus-specific px)
-virus buds off host |
Do viruses have ribosomes or proteins? | NO and yes (enzymes like integrase and reverse transcriptase) |
DNA/RNA + capsid = ? and does it have to kill host cell? | nucleocapsid (naked virus) and yes |
nucleocapsid + lipid mem. with glyco px = ? and does it have to kill host cell? | enveloped virus and NO |
Why are viruses non-living | -require host-cx machinery to reproduce
-do not metabolize organic nutrients
-no cx wall /mem
-never possess both DNA and RNA
-can be crystallized and still infect |
What do viruses absolutely need on host to infect? | specific glycopx chemical receptor |
How do bacteriophages and euk viruses compare? | -bacteriophages inject nucleic acid through tail after viral enzymes digest hole in cx wall
-euk viruses are engulfed by endocytotic process |
How do lytic vs. lysogenic infections compare? | -lytic-virus takes over host machinery to make new viruses
-lysogenic-viral DNA incorporated into host with reverse transcriptase |
Prions | naked px that can reproduce without DNA or RNA |
Viroids | rings of naked RNA with no capsid that can only infect plants |
Plus strand RNA and example | -virus mRNA is same sense as mRNA so px can be directly translated from RNA
-AIDS |
minus strand RNA and example | -virus RNA is complementary to mRNA and must be copied to plus RNA before being translated
-flu |
What is vaccine? | -injection of non-pathogenic virus with same capsid and envelope that forces immune system to create own antibodies
-OR injection of antibodies |
What are difficulties with viral infections? | -rapidly mutating spike proteins
-more than one animal acts as carrier population |
T/F: Viral genomes are more diverse than euk? | TRUE - can be single or double stranded DNA or RNA |
Can a virus infect cell with no glycoprotein receptors? | NO |
What is it called when viral DNA is incorporated into host DNA during lysogenic cycle? | dormant, latent, provirus |
Do euk. have the enzyme to replicate RNA? What do viruses do? | NO --> viruses bring RNA replicase into cell |
Do retroviruses have proteins? | YES --> bring in reverse transcriptase |
Why don't antibodies always work? | RNA poly doesn't proofread so changes in spike proteins are common
->spike proteins are what antibodies recognize when fighting infection |
What are 2 ways body fights viral infections? | -antibodies
-cytotoxic T-cells |
What are 4 forms of genetic recombo for bacteria? | -binary fission
-conjugation
-transformation
-tranduction |
transformation | bacteria integrates foreign DNA from environment into host genome |
conjugation | -2 cells form cytoplasmic bridge (sex pili) so + --> - genetic material
-one bacterium must have plasmid that codes for sex pilus |
What is best-studied sex factor? | F-factor |
transduction | when bacteriophages infect new bacterium, inject harmless bacterial DNA fragments |
binary fission | 2 DNA polymerases begin at single origin of replication to create 2 DNA-double-stranded circles |
What is the lac operan about? | regulation of genes that control the digest of lactose
-no glucose --> turn on genes
-glucose --> turn off genes |
Constitutive genotype? | always on |
What are operator and promoter part of operon? | -operator: binds repressor px
-promoter: binds RNA poly |
What is the process for fixing NItrogen? | N2 --> ammonia --> nitrate |
What type of genetic material do prok have? | single, circular double strand DNA |
What are the main differences btwn prok. and euk. in terms of cell wall and membrane? | -cell wall with peptidoglycan
-plasma mem. without cholesterol |
What regulate fluidity in membrane? | -hopanoids in prok
-cholesterol in euk |
periplasmic space | space btwn cx wall and plasma membrane with many px |
hydrostatic pressure vs. osmotic pressure | -pressure fluid exerts on wall vs. pressure required to prevent flow of water across semipermeable mem. via osmosis |
peptidoglycan | -disaccharide polymer chain connected by a.a. cross-links |
gram positive bacteria are what and stain what color? | -thick peptidoglycan cell wall and purple |
gram negative bacteria are what and stain what color | -thin peptidoglycan cell wall and pink |
capsule + peptidoglycan cell wall + plasma mem = | gram positive |
capsule + phospholipid bilayer + cell wall + plasma mem = | gram negative |
Differences in flagella between prok and euk? | -prok: made of flagellin
-euk: made of microtubules (9 +2) |
Fungi | eukaryotic multicx. heterotrops made of hyphae that obtain food by absorption than ingestion |
When do fungi perform sexual vs. asexual reproduction? | -bad conditions vs. good conditions |
Does diploid / haploid dominate in fungi? | haploid stage dominates and is growth stage |
Can fungi have diploid stage? | YES - sexual reproduction when 2 hyphae grow towards each other to form zygospore |
What are four main types of connective tissue? | blood, lymph, bone, cartilage |
What is most common extracx matrix structural protein? | collagen |
most proteins used by mito are from? | nuclear DNA |
What are desmosomes? | join 2 cells at a point but do not create watertight seal |
What are microtubules used for? | mitotic spindle, flagella, cilia |
Where are cilia found? | fallopian tubues and respiratory tract |
What are microfilaments used for? | muscle, phagocytosis, cytokinesis |
In muscle, smooth ER is known as ____ and controls? | sarcoplasmic reticulum and controls calcium |
What do secretory vesicles do? | supply cx membrane with integral px and lipids |
What is the ER contiguous with? | cell membrane and nuclear membrane |
What is an axoneme? | major part of cilia / flagella with 9+2 arrangement connected by dynein |
What end does DNA polymerase add to in growing strand? | 3'-OH end |
nucleoside vs. nucleotide | -base + sugar
-base + sugar + phosphate |
What gives DNA its acidity? | phosphate group |
What unwinds DNA and relaxes supercoils ahead of replication fork? | DNA gyrase (class II topoisomerase) |
What unwinds DNA at replication fork? | helicase |
Replication occurs _____ every cell generation during ___ phase. | -once
-S phase |
DNA polymerase III can add new deoxyribonucleotides only to a free ____ | 3' OH end |
Which DNA polymerase adds new deoxyribonucleotides and which removes the RNA primer? | -DNA poly 3
-DNA poly 1 |
If DNA replication were completely conservative, what would be seen? | Only heavy and light DNA |
If DNA replication were dispersive, what would be seen? | everything intermediate weight |
If DNA replication is semi-conservative what would be seen? | intermediate weight after first round, intermediate and light weight after second round |
DNA polymerase has what kind of proofreading activity? | 3' - 5' exonuclease
-scans and backs up to fix mistake |
The DNA polymerase that replaces the RNA primer has what kind of activity? | 5'- 3' activity |
What leads to DNA damage? | -attack by water, chemical damage, radiation damage |
Mismatch repair | enzymes cut out stretch of DNA with mismatch
-polymerase adds correct nucleotides |
How does enzyme know which strand of DNA to cut during mismatch repair? | methylation |
Base-excision repair | -damaged base gets cut out and replaced |
Nucleotide excision repair | -similar to mismatch repair
-used for damages like thymine dimers |
nick translation | -5'--3' exonuclease activity coupled to polymerase activity
-polymerase chews off bad nucleotides and replaces with new nucleotides |
SOS response in E.Coli | -so much DNA damage that instead of correcting DNA damages during replication, polymerase replicates over damaged DNA as if it were normal |
What is benefit / disadvantage of SOS response? | -better than not replicating at all but high error rates |
restriction enzymes / endonucleases | - cut double stranded DNA at palindrome sequences |
Can sticky / blunt ends hybridize? | sticky ends only |
What does the plasmid need to have for gene cloning? | -restriction site to insert gene
-origin of replication to clone gene
-antibiotic resistant gene to kill competing, useless bacteria
-replicate independently of genomic DNA of bacteria |
Steps for PCR | -denature - heat to 90C to separate DNA
-anneal - cool so primers can anneal to ss DNA
-elongation - use heat stable polymerase to extend primers |
Why don't the separated strands reanneal in PCR? | excess amount of primers used |
What is the amplification of DNA after "n" cycles? | 2^n |
Where is mRNA made? Where does translation occur? | nucleus / cyto |
What are characteristics of codons? | continuous, non-overlapping, and degenerate |
Where is start codon AUG located? | downstream of Shine Dalgarno sequence in prokaryotes
-Kozak sequence for eukaryotes |
Is there a tRNA codon complementary to stop codon? | NO |
Where does wobble exist? | on anticodon on 5' position --> creates degeneracy |
Does prok mRNA have 5' cap or polyA tail? | NO |
What does 5'cap and 3'poly A tail for? | protects against exonuclease degradation |
What is structure of tRNA | -anticodon at the tip
-amino acid at 3' tail |
How is amino acid attached to 3'OH end of tRNA? | ester linkage |
What are mRNA, tRNA, rRNA made of? | nucleotides |
What catalyzes peptide bond formation in translation? | rRNA of large ribosomal subunit |
How does transcription initiate? | RNA poly binds to promoter (TATA box) of ds DNA and dsDNA opens up |
What are 2 ways that transcription can terminate? | 1. intrinsic termination
2. rho dependent termination |
intrinsic termination | termination sequences create stem-loop structure on RNA that causes to slip off template |
rho-dependent termination | -rho factor travels along synthesized RNA and bumps off polymerase |
Prok: transcription factors bind to ______ and ________ to affect transcription. | enhancers / silencers (DNA) |
Where are enhancers and silencers located in prok. transcription? | close to core promoter |
operon | cluster of genes under control of single regulatory signal or promoter |
transcription attenuation | -Trp operon
-needed - made, not needed - not made |
alpha factors | -how phages control transcription in bacterial host
-by making different alpha factors at different times, phage controls correct sequence of early, middle, and late genes |
What does small subunit of ribo do? | -recognize mRNA and bind to Shine-Dalgarno / Kozak sequence |
What is initiation complex for translation? | mRNA, start tRNA (fmet), ribosome, initiation factors, and GTP |
In what direction is protein made? | N terminus --> C-terminus |
In what direction is mRNA codons read to make proteins? | 5' --> 3' |
HOw to attach a.a. to tRNA? What is required? | -enzymes called aminoacyl-tRNA synthetases attach correct a.a. to tRNA
-ATP |
For tRNA with a.a. to enter A site, what is required? | GTP and elongation factor |
Peptidyl transfer occurs in which site? | A site |
Translocation from P site to E site requires? | GTP --> basically, any mvmt requires GTP |
Translation termination requires what? | water, release factors, and GTP |
histones | responsible for compact packing and winding of DNA
-DNA winds itself around histone octamers |
centromere | links sister chromatids |
What is difference between chromatin and chromosome? | -chromatin is "stuff" chromosomes are made of |
What is difference between euk transcription factors and prok transcription factors? | -euk's can be far away, upstream, or downstream from promoter
-DNA must look back so transcription factor bound to enhancer / silencer can make contact with promoter
-prok's must be at promoter |
angiogenesis | cause new blood vessels to grow to nourish cancer cell |
Proto-oncogen --> oncogene | harmless --> harmful |
Example of oncogene and example of tumor suppressor | -src
-p53 |
mass of hyphae is called | mycelium |
fungi cell wall is made of | chitin |
what are lichens? | fungi + algae |
How do fungi reproduce? | spores or mycelial fragmentation |
What are the types of viral nucleic acid? | DNA or RNA / ss or ds |
Why do certain viruses not have envelope? | cause host cx to burst |
What are 3 structural components to bacteria? | head to store genetic info, sheath to provide way for injection, tail to attach to host |
Viruses are ______ times smaller than bacteria and _______ times smaller than eukaryotic cells | 100 / 1000 |
Does the virus provide anything to replicate? | NO - host provides ribosomes, ATP, nucleotides, and a.a. |
How do new viral particles assemble together? | self-assembly --> no effort required |
What type of nucleic acid do retroviruses have? | ss RNA |
What is process of transduction? | virus infects cx, host DNA fragments packaged by accident, virus progeny infects other cells, fragment enters cells and crosses over |
What type of growth do bacteria exhibit? | exponential and then slows down |
facultative anaerobe | doesn't need oxygen for growth, but grows better with oxygen |
Commensalistic relationship | one benefits while other has no effect |
Plasmids are _______stranded DNA and are _____ essential for growth and reproduction | -double stranded
-not essential |
What does F+ bacteria transfer to F- bacteria? What can it also transfer? | -plasmid with pillus genes
-genomic DNA because F+ plasmid can integrate into chromo |
Where do prok mostly regulate gene expression? | transcription level (i.e. operons) |
Is there any RNA processing in prok? | NO |
When cx if full of TRP, translation occurs fast / slow? When cx is starved of Trp, translation occurs fast / slow? | -fast - causes termination
-slow - causes Trp mRNA to be made to completion |
What causes growth arrest? | -too much genomic mutation / damage causes cx to arrest in M phase
-contact inhibition (too crowded)
-lack of food |
apoptosis | cx death that is clean and healthy
--> activation of caspases that digest cx from within |
How is apoptic cell engulged? | -apoptosed cell releases chemicals that attract macrophages
-gets engulfed |
What causes apoptosis? | -development
-immune response |
What type of bacteria does conjugation occur in? | gram negative |
Virions are obligate____ | parasites |
Are viruses bigger than bacteria? | DEFINITELY NOT |
Viral px are produced by translation of viral or host nucleic acid? | viral nucleic acid |