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