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119 Cards in this Set
- Front
- Back
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An A-B toxin ___________________. |
is a two component toxin |
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The site of ricin’s action in rRNA inhibits ___________________ A) the binding of release factors to the ribosome B) the binding of initiation factors to the ribosome C) the binding of codons to the ribosome D) the binding of elongation factors to the ribosome |
D |
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What is the function of the sec61 complex? |
involved in moving ricin into cytosol because the proteins are unable to fold correctly in the ER. Once in cytosol they are degraded by proteasomes. |
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Lectin |
sugar-binding protein |
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One of the potential uses of ricin is as an immunotoxin. What might be the utility of such a compound? |
used as an anti-cancer agent |
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A glycosidase is an enzyme that breaks a bond between a sugar and another molecular group. The A-chain of ricin has glycosidase activity targeted for ________________ A) The deoxyribose sugar found in DNA B) The ribose sugar found in adenine of mRNA C) The ribose sugar found in adenine of rRNA D) the deoxyribose sugar found in adenine of rRNA |
C |
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Which of the following is an important component of ricin’s mode of action? A) It involves retrograde transport through the endomembrane system. B) It binds to to tRNAs C) It involves anterograde transport through the endomembrane system. |
A |
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A ricin molecule with a mutated B-chain that interfered with lectin activity _________. A) would be able to enter a cell at a high efficiency B) would fail to bind rRNA C) would be more toxic D) would be less toxic |
D. Because both chains need to be mutated in order to fail in binding. |
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"RIP".. A) is a lipid-binding protein B) can describe ricin C) More than one answer is correct D) means “ribosomal inactivating protein" |
C |
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What is the field of epigenetics study and how is it different compared to “genetic” studies? |
Epigenetics- study of cellular and normal trait variations that are due to environmental factors Genetic studies- look at changes in function or regulation of molecules due to the altering primary sequences. |
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Gene VS Allele |
Gene- piece of DNA that codes for a RNA or protein product and determines a certain trait. Allele- an alternate form of the same gene due to a mutation in gene sequence |
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What is the "code" for the genetic code? |
The nucleotide sequence of a gene’s DNA which specifies the amino acid sequence for a protein. Nucleotides are in sets of three, called codons, and each set corresponds to one out of the twenty amino acids. |
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In addition to protein-coding DNA, what other regulatory sequences may be present in a gene (please be specific)? |
UTRs |
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What two types of molecules typically bind to promoter regions to facilitate transcription? |
transcription factors and RNA polymerase. |
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TRUE OR FALSE. Enhancers are always located close to the start of the gene. |
False |
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What type of macromolecule are transcription factors? What do transcription factors bind to and why? |
proteins bind to DNA to initiate or repress transcription |
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_______________ proteins bind to enhancers to increase the initiation rate of transcription, while ____________ proteins bind to silencers to decrease the initiation rate of transcription. |
Activator Repressor |
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What genetic components are seen in mature mRNA? |
UTRs and exons |
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Define operon. What group of organisms has operons? |
An operon is piece of DNA that contains a collection of genes that are under control of one promoter. Found in prokaryotes, rare in eukaryotes |
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Process of Gene Expression |
1. Transcription 2. Translation |
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What are possible products of gene expression? |
RNA or protein |
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3 co(post)-transcriptional modifications that occur to mRNA and what is their main result? |
1. 5’capping- adds guanine in place of free phosphaet to the 5' end. The cap shields the 5’ end of the primary RNA transcript from the attacks of ribonucleases. 2. 3'polyadenylation- involves cleavage of the 3’ end and then adding around hundreds adenine residues to create a poly(A) tail.This protects the 3’ end from what is called ribonuclease digestion. 3.RNA splicing- pieces of RNA that do not code for protein, known as introns, are eliminated from the pre-mRNA and the remaining exons re-arrange and link to form a single molecule. |
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What shape does prokaryote chromosomes have? Do they have single-stranded or double-stranded DNA? |
Circular chromosomes and have double-stranded DNA |
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What are eukaryote chromosomes called? What shape does eukaryote chromosomes have? Do they have single-stranded or double-stranded DNA? |
Eukaryote chromosomes are call nuclear chromosomes. They have linear chromosomes and have double-stranded DNA |
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Prokaryote plasmids are what shape and are they single-stranded or double-stranded DNA? |
circular & double-stranded DNA |
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Prokaryotes have _______ non-coding DNA while Eukaryotes have _________ non-coding DNA |
limited large amount |
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Are nuclear chromosomes the only kind of DNA in Eukaryotes? |
No |
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Viruses have what shape chromosome and and have _________non-coding DNA. Do viruses have single-stranded DNA or double-stranded DNA? |
linear limited can be single-stranded or double-stranded |
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What is in a prokaryotic gene? |
promoters/operators terminators UTRS some archae have introns protein coding sequence |
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Prokaryotes tend to organize genes in functional units called ________ |
operons |
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Operon |
many genes under control of a single promoter and operator |
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Genes are common to a metabolic function and only are turned on when needed |
blank |
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What is in a eukaryotic gene? |
enhancers/repressors promoters terminators introns UTRs exons (coding region) |
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Genome |
complete genetic material of an organism |
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Genome size tends to ________ with multi cellularity |
increase |
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As genome size increase there is a ________________ in non-coding DNA related to regulation of gene expression |
increase |
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Somatic cells (i.e., non-gameticcells ex. eye) all have the same DNA content in their cells. |
True |
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Cells of a multicellular organismwill express all the genes present in their nuclei? |
False. Genes are only turned on (expressed) when needed |
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Even though all cells have the same DNA, not all cells express the same genes |
blank |
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Gene Expression |
the process of synthesizing a protein from a gene |
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What must occur to allow for the initiation of transcription? |
DNA-histone interactions must loosen (euchromatin) |
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Process of transcription |
uses RNA polymerase enzyme -DNA provides information -RNA polymerase adds nucleotides to 3' end of mRNA |
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Transcription |
process of making RNA from DNA template |
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When considering the process oftranscription, the newly synthesized mRNA will have the same sequence (with theexception of U’s for T’s) as the _____________ strand. |
sense (coding strand/DNA strand) |
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To initiate the process oftranscription, which enzyme is required to allow RNA polymerase access to thesingle-stranded template strand? |
helicase (help unpackage an organisms genes) |
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Can transcription faction be expressed? |
Yes based on the environment, development timing, or communication from other cells |
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Name the transcription factors |
basal transcription factors, activators, repressor, and co-activators |
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TATA Box |
DNA sequence about 25 bps upstream of gene start |
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Co-Activators (In transcription pre-initiation complex) |
bridges the signals between the activators andthe basal transcription factors |
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Activators (In pre-initiation complex) |
bind at enchancers and increase rate of transcription |
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Repressors |
bind to silencers and decrease the rate of transcription |
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Basal transcription factors |
help position RNA polymerase at the start of transcription and initiate the transcription process |
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Transcription rate is determined by what? |
by number of times mRNA synthesis occurs. If activators or repressors are present it will alter transcription rate |
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In a tissue, a repressor protein normally binds to a silencer to regulate transcription. If the repressor became mutated so it did not bind to the upstream sequence, ___________. |
transcription would speed up |
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If all components of the transcription initiation complex are present in a cell and the DNA is in a heterochromatin state, will transcription occur? |
No must be in euchromatin state for transcription to occur |
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Transcription termination in eukaryotes is related to the polyadenylationsignal |
•PolyA-signal and PolyA-sitehelp position proteins involved in adding the Poly A tail. •RNA polymerase will dissociate from theDNA template after these sequences are transcribed |
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Major Role of Splicesome |
conduct splicing, a process of removing introns from transcribed pre-mRNA. |
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Two Major Molecules in Splicesome |
protein complexes & snRNAs |
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snRNA vs snRNP. How are they related? |
snRNA-small RNA molecules found in the splicing speckles and Cajal bodies of the nucleus of eukaryotic cells. snRNP- small nuclear ribonucleic proteins-complexes of RNA-protein that join with other protein&unmodified pre-mRNA to create a spliceosome. Related because snRNA creates snRNP |
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In terms of post-transcriptional processing, what's the importance of nucleotides GU and AG within an intron? |
Splicosomes distinguish the sequences at the 5’ of the splice site because introns always begin with GU nucleotide sequence and end with AG (3’ end splice site) nucleotide sequence. |
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One end of a tRNA contains __________ while the other contains_______________________ |
anticodon the amino acid that corresponds to the anti codon seq. |
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What is the function of aminoacyl-tRNA synthetase? |
functions to attach the proper amino acid on its corresponding tRNA |
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4 Major Stages of Translation |
initiation- ribosome binds to mRNA elongation- messaged translated into polypeptide chain translocation termination- ribosome dissociates, polypeptide released |
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The first codon on virtually all mRNAs is _____________ |
the start codon (AUG) |
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TRUE OR FALSE Ribosomes present in the RER are stable and associate with the RER over a long period of time. |
False associate for short periods |
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What types of molecules make up the “translocon”? |
complex of proteins |
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Two Major Functions of Translocon |
transport ribosome to ER Second function: ask LA? |
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What interactions contribute to the overall shape (folding)of a protein? What is folding sensitive to? |
hydrogen bonding, ionic interactions, hydrophobic packing, and Van der Waals forces Folding sensitive to ionic interactions, PH, heat |
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What makes up the primary structure of a protein? What bonds contribute to this structure? |
consists of a sequence of amino acids in the polypeptide chain. Covalent bonds like peptide bonds contribute to this structure |
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What are the two main types of secondary structure? What bonds contribute to this structure? |
Alpha helix and beta sheets are two main types of 2nd structure. Hydrogen bonds in this structure |
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What forces are involved with formation of protein tertiary structure? |
hydrogen bonds, ionicinteractions, disulfide bonds and/or hydrophobic/hydrophilicinteractions |
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What is quaternary structure of a protein? |
multi-subunit protein made of many polypeptide chains This uses disulfide bonds as well as the same non-covalentinteractions used in the tertiary structure |
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Protein Structural Domain. Define it. Why are they important? |
folds independently of the rest of the protein change and is independently stable Are important because they are needed in avariety of proteins as they aid in the biological function of their protein |
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Synonymous Mutation |
the mutated codon has the same meaning as the original codon and therefore does not change the amino acid. |
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Ifall components of the transcription initiation complex are present in a celland the DNA is in a heterochromatin state, will transcription occur? |
No. Things needed for transcriptioncannot physically get in if it is in heterochromatin state |
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Where do the steps of pre-mRNAprocessing occur? |
nucleus *Processing occursin the nucleus, andthe functional mRNA produced is transported to the cytoplasm |
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What type of lipid would have the highest fluidity? |
unsaturated (short C chain length), short (mult. double bonds) |
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What does 3' Polyadenylation aid in? |
aids in nuclear export, stability, translation |
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hnRNP |
ribonucleic proteins that help prevent the mRNA fromassociating with itself or other mRNAs |
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What is splicing dependent on? |
RNA & snRNP snRNPs bind to intron on conserved sequences (RNA) interactions between RNA and snRNPs cause intron to bend Requires ATP Bending facilitates splicing |
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What do snRNPs contain? |
RNA and protein
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What would you predict would happen if a conserved region at the 5’ splice site of an intron was mutated? A.The intron would be excised B. The intron may not be excised |
B |
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How is an intron removed? (shape) |
as a lariet, NOT LOOP |
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There is a conservation of introns suggesting introns play a role in gene regulation |
blank |
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Pre-mRNA (3) vs mRNA (4) |
Pre-mRNA 5' & 3' UTR Introns Exons mRNA 5' & 3' UTR Exons 5' guanine cap 3' poly-A tial |
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Codon |
sequence of 3 nucleotides that code for an amino acid
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4 nucelotides. How many different codons can they produce? |
64 |
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Are there more codons than amino acids? |
Yes |
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How are all 61 codons used withonly 45 tRNAs? |
anti-codon can recognize more than one codon due to "wobble" |
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Where are tRNAs located? |
with an amino acid |
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What strand does translation occur on? |
mRNA |
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tRNA contains.. |
anti-coding region amino acid binding region has a super secondary structure |
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"charged" tRNA |
has an amino acid bound completed by aminocyl tRNA synthetase |
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What is a ribosome composed of? What is a ribosome considered as? What does the large subunit bind to? What does the small subunit bind to? |
RNA and protein subunits Considered as an enzyme Large subunit binds to tRNA Small subunit binds to mRNA |
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Where does the small ribosomal subunit bind to on the mRNA? What does initiation of translation require? |
It binds to 5' guanine cap Requires initiation factors and tRNA-Methionine |
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What happens in the initiation of translation? What energy is required for the initiation stage of translation? |
The small ribosomal subunit associated with the 5' cap of mRNA Initiation factors and tRNA-Methonine are there too Initiation factors create GTP to form ribosome Once formed initiation factors leave and large ribosomal subunit binds GTP-GDP |
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Translation starts in what part of the cell? Where does it end? If a signal peptide binds to the subunit where will translation end? |
Translation starts in cytoplasm and ends in cytoplasm or ER Rough ER lumen |
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Is there a tRNA for a stop codon? |
No. For termination, a release factor binds to codon in the A site.Triggers hydrolysis of GTP and ribosome complex dissociates. |
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Super Secondary Structures |
Multiple(2-4) secondary structures forming regular patterns |
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How many protein domains can an organism have? |
one many or no domains |
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Structural Motif |
functional part of protein that is defined by a super secondary structure CANNOT function without the rest of the protein |
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What kind of transport is used after translation? a. Reterograde b. Anterograde |
Anterograde transport ER, golgi, vesicle, plasma membrane |
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Transition Temperature |
the temperature at which a membrane changes from a gel to a liquid |
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In which direction is template strand read? |
3' to 5' |
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In which direction is mRNA synthesized |
5' to 3' |
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Fatty acid chains are ____________ hydrophobic or hydrophillic? |
Hydrophobic |
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What role to membrane sterols play? Where are they located? |
alter fluidity of membrane plasma membrane |
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A normal cell membrane is ________ Fluid Gel Crystal |
fluid. |
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What types of proteins do membranes contain? |
integral proteins- permanent peripheral proteins- temporary |
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Movement of phospholipids within the bilayer causes.. What types of movement can they do? |
it to be fluid it to be temperature sensitive essential for membrane function rotational *common lateral diffusion *common transverse diffusion *rare |
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Why is membrane fluidity important? |
important for cell division, cell signaling, motility, protein function |
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Peripheral membranes can associate with the membrane in several ways. Name four ways. |
1. Alpha-helix domain
2. Hydrophobic loop domain 3. Lipidation 4. Electrostatic interaction via calcium ions |
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What enzyme can release lipidated proteins from membrane? |
Lipases |
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Largest receptor protein family in Eukaryotes? |
GCPRs they are integral proteins |
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TRUE OR FALSE Invertebrates have more GPCR’s thanvertebrates |
False |
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At whichcodon position would you expect to see a synonymous substitution? |
3 because it doesn't matter what codon that is anyway |
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TRUE OR FALSE G-protein signaling evolved after theevolutionary split of plants, fungi and animals |
FALSE |
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Ka/Ks What does each stand for? 1 < (Ka/Ks) means...? 1 > (Ka/Ks) means...? |
Ka- non-synonymous Ks- synonymous Changing Conserved |
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Are Ka mutations noticeable? Are Ks mutations noticeable? |
Ka- YES Ks- NO |
