Bio 315- Exam 1
What is a codon and how many codon possibilities are there?
1 codon= combination of 3 nucleotides= 1 reading frame
Name the 4 steps of translation
1. New tRNA lands in A site of ribosome. tRNA in P site has growing polypeptide chain 2. Ribosome catalyzes peptide bond formation between amino acid in A site and amino acid in P site. 3. Large ribosomal subunit shifts right three nucleotides 4. Small ribosomal subunit shifts right three nucleotides. tRNA with polypeptide chain is now in P site. Uncharged tRNA is ejected from ribosome
The covalent modification of a protein, such as phosphorylation, ubiquitylation and acetylation, may affect its location A. True B. False
A
The gene encoding DNA polymerase can be inactivated by a mutation in a cell. The cell attempts to replicate its DNA. What will likely happen in the absence of DNA polymerase? A. No replication can take place at all. RNA primers will be laid down at the origin of replication B. The lagging DNA strand will consist of newly synthesized fragments with both DNA & RNA
A
What are the three main domains of the living world?
Bacteria, archaea & eukaryotes
Explain the origin of mitochondria & chloroplasts
Bacterium absorbed- this is why they are double membraned
Evolutionary distance between species is reflected in the sequence & organization of DNA but functionally important sequences are conserved, why is this?
Because they do not react well to a sequence change, a change disrupts the function of the transcribed proteins/RNAs -> cell dies
Describe the consequences that would arise if a eukaryotic chromosome lacked one or both telomeres A. The rate of DNA replication would severely limit the rate of cell division B. Many mutations occur during DNA replication C. The chromosome ends would gradually shrink. Eventually, essential genes would be lost, leading to cell death D. Newly replicated chromosomes could not be partitioned accurately between 2 daughter cells
C
The alpha helix & beta sheet are found in many different proteins because they are formed by A. Noncovalent interactions between aa side chains & the polypeptide backbone B. Ionic structures between charged aa side chains C. Hydrogen bonding between atoms of the polypeptide backbone D. Hydrophobic interactions between the many non polar aa's
C
What is the function of DNA polymerase?
Catalyze the addition of new nucleotides to growing strand -Energy for bond from P-P cleavage -Repair (allosteric) -Creates phosphodiester bond between 3' -OH of new strand and 5' phosphate of incoming nucleotide -Synthesis in 5'-> 3' direction
Name four structures in plant cells that are NOT in animal cells
Chlorophyll, plasmodesmata, cell wall & vesicle
How does a transcription regulator control transcription from a distance and how can a single regulator affect several genes?
DNA wraps around so transcription regulator is at transcription site Regulator binds to mediator which is bound to RNA pol II Mediator translates signals to RNA pol II for how to proceed with transcription A final transcription activator protein can work for different genes Activation of transcription for various genes via a common signal
What are some common types of DNA damage and the steps of a DNA repair mechanism?
Depurination: loss of purine bases Deamination: loss of amino (NH2), leads to A-T pairing Thymine dimers: 2 adjacent T's, cross linked, stalls replication Repair: excision (nuclease), resynthesize (repair DNA polymerase), ligation
What is differentiation?
Differentiation = specialization The process by which a cell becomes specialized to perform a specific function. Cells function is determined by gene regulation
What is a horizontal gene transfer? How can antibiotic resistance be transferred in this pathway?
Donor Bacteria use sex pilus to attach to another bacterial cell -> draws recipient cell closer Transcription and translation of antibiotic resistance occurs in recipient bacteria
Describe characteristics of DNA?
Double helix, 4 types of bases (H-bonded), nucleotide structure, backbone made of alternating sugar & phosphate groups (covalently bonded w/ phosphodiester bond)
What type of microscopy would you use to view fine structures?
Electron microscopy
What is the biggest class of proteins?
Enzymes
What is a consequence of exon shuffling?
Exons from one gene move to another (recombination) Short repeated homologous sequence on either side of exon (in introns) facilitate movement 1 exon = 1 domain Add new domain to a gene
What are different components of the replication machine?
Helicase: unzips dsDNA ssDNA-binding proteins: binds exposed single strand, prevents repairing & keeps elongation Sliding clamp: keeps DNA polymerase attached to template Clamp loader: hydrolysis ATP each time clamp locks - leading strand= one time - lagging strand= every time new Okazaki fragment is started Topoisomerase: relieves torsional stress
Why are mitochondria folded?
Increase surface area
How does DNA polymerase synthesize the lagging strand compared to the leading strand?
Lagging: short "backstitching" steps, much slower, pieces joined continuously Nuclease, repair polymerase, ligase
What is fluorescence in situation hybridization used for?
Locate genes on isolated chromosomes
Where would a transcription regulator bind to DNA?
Major groove
How does gene duplication result from homologous recombination?
Misalignment leads to unequal crossing over
During which stage of the cell cycle is DNA the most condensed? Why?
Mitosis, needs to seperate
What are point mutations & what effect can they have?
Mutation in a single nucleotide Can be beneficial or detrimental Usually neutral Can be regulatory
What mechanisms produce genetic changes that have evolutionary effects?
Mutations within a gene Mutation within the regulatory DNA of a gene Gene duplication Exon shuffling Transposition Horizontal gene transfer
What is an Operon? Do eukaryotes have operons?
Operon: cluster of genes within on mRNA (several proteins transcribed & translated at a time), eukaryotes do not have operons but bacteria do
What is the name of the bond between aa's? How is it formed?
Peptide bonds form from condensation reaction
What is the function of eukaryotic transcription factors?
Position polymerase, pull apart double helix, launch poly, activators (TBP, TFIIH)
What are the 3 ways the cell ensures gene regulation is passed to daughter cells?
Positive feedback loops Heterochromatin DNA methylation
What are the four levels of protein organization?
Primary: aa sequence Secondary: local folds (a helix & b sheets) Tertiary: long-range interactions (loops & folds) Quaternary: subunit of 1+ polypeptide chain
What is the main difference between prokaryotes and eukaryotes?
Prokaryotes: no organelles, DNA not organized in nucleus, single celled, two domains: bacteria and archaea Eukaryotes: distinct organelles, double membrane-bound nucleus, both single and multicellular organisms
Which of the nucleotides are purines and which are pyrimidines?
Purines: Adenine, Guanine Pyrimidines: Cytosine, Uracil, Thymine
What are some differences between DNA polymerase & RNA polymerase
RNA pol: makes more errors, uses ribose-bound bases DNA pol: uses deoxyribose, short section
What is the function of the spliceosome?
RNA processing, snRNAs + snRNPs
What is the function of repressor and activator proteins?
Regulate amount of transcription Repressors: inhibit transcription by blocking RNA pol binding site Activators: promote transcription by helping RNA pol bind better to DNA
Where do replication, transcription and translation take place in eukaryotes?
Rep & transcription take place in nucleus Translation takes place in cytosol
What are 3 distinct sequences required on chromosomes for replication?
Replication origin (multiple), centromere (1) and telomere (2)
Name differences between replication and transcription
Replication: full DNA copied Transcription: DNA helix reforms after, RNA is a much shorter product
What is a ribosome and what is a proteasome?
Ribosome: E,P,A binding sites, does translation Proteasome: degrade proteins
What determines how a protein folds?
The low energy, bonds
Comparing the eukaryotic transcription with the bacterial transcription, which statement is NOT true? A. Bacterial cells contain a single RNA polymerase whereas eukaryotic cells have 3 B. Bacterial RNA polymerase can not initiate transcription without the help of many general transcription factors C. In eukaryotic cells, gene regulatory proteins can influence transcription initiation thousands of nucleotides away from the promoter whereas bacterial regulatory sequences are very close to the promoter D. Eukaryotic transcription is affected by chromatic structure and nucleosomes whereas bacterial transcription is not
B
Noncovalent bonds are too weak to influence the 3D structure of macromolecules, such as the protein complex A. True B. False
B
The difference between multicellular organisms are largely explained by the different kinds of genes carried on their chromosomes A. True B. False
B
The most reliable feature distinguishing a eukaryotic cell from prokaryotic cell is the: A. Presence of plasma membrane B. Presence of a nucleus C. Eukaryotic cells larger size D. Presence of DNA
B
The replication fork is asymmetrical because it contains two DNA polymerase molecules that are structurally distinct A. True B. False
B
Which of the following is NOT part of the Cell Theory? A. All organisms are made up of one or more cells B. Genes dictate cell structure & function C. The cell is the structural unit of life D. Cells can only arise by division from pre-existing cell
B
Which of the following statements is NOT true about his tones? A. They are rich in positively charged aa's B. There is a great deal of diversity in histones from various eukaryotes C. They form dimers through "handshake" interactions D. The modification of histone tails, such as methylation, acetylation, phosphorylation, or the removal of these functional groups, is important for the regulation of chromatin structure and gene expression
B
What can we use to study protein-protein interactions? To see where proteins bind to DNA?
Two-hybrid system, DNA foot printing
What does it mean to use the Sanger method to sequence DNA?
Using dideoxy method that terminates at ddNTP
What are the levels of control of gene expression from DNA->RNA->Protein?
When and how often transcribed How RNA is spliced or processed Selection for export from nucleus Selective degradation of mRNAs Selection for which mRNAs are translated at the ribosome Regulating protein degradation Selectively activating or inactivating protein after produced
What is heterochromatin?
densely packed, unacetylated chromatin that is inactive, can silence genes permanently
What's the difference between a gDNA library & cDNA library?
gDNA: all DNA, cDNA: only genes expressed as RNA
What are the products of transcription and translation?
mRNA & proteins
Name a method used to study gene expression
mRNA microarray, RNA seq. reporter genes
Nucleus acid hybridization is used to isolate or identify specific DNA fragment by base-pairing between complementary DNA or RNA probes and the DNA of interest A. True B. False
A
Small non-protein coding RNAs, such as miRNAs can regulate expression of protein-coding genes by controlling mRNA stability and translation A. True B. False
A
What 3 things take place as part of RNA processing?
5' capping (methylated guanine) Splicing Polyadenylation
Each eukaryotic chromosome must contain the following DNA sequence elements: multiple origins or replication, two telomeres and one centromere A. True B. False
A
For each statement below, which one is false? A. All highly conserved stretches of DNA in the genome are transcribed into RNA B. To find functionally important regions of the genome, it is more useful to compare species whose last common ancestor lived 100 million years ago rather than 5 million years ago C. Most mutations & genome alterations have neutral consequences D. Proteins required for growth, metabolism and cell division are more highly conserved than those involved in development and in response to the environment
A
From the list below, select the one cellular structure or compartment that is not found in animal cells: A. Plasmodesmata B. Golgi apparatus C. Endoplasmic Reticulum D. Plasma membrane
A
It is possible for a codon region of a gene to be present in a genomic library prepared from a particular tissue, but not to be represented in a cDNA library prepared from the same tissue A. True B. False
A
The sugar-phosphate backbone of the DNA double helix contains many negative charges, and is hydrophilic A. True B. False
A
When a mutation arises, it can have 3 possible consequences: A. Beneficial to the individual, B. Selectively neutral, or C. Detrimental. The spread of a mutation in subsequent generations will, of course, depend on its consequences to individuals that inherit it. Order the 3 possibilities above from that which is most likely to spread & become over-represented in subsequent generations to that which is most likely to become under-represented or disappear from the population. A. A,C,B B. A,B,C C. B,C,A D. C,B,A
A
How does DNA replication begin and how does the cell identify replication origins?
At replication origins-> opening of double helix to expose unpaired bases for replication-> recruitment of initiator proteins Bacteria have 1 replication origin, humans have 10,000
Name different levels of protein regulation
Amount of protein in the cell, condition of sub cellular compartments, altering the shape Methods: feedback inhibition, allosterism, negative/positive regulation
What is epigenetic inheritance & why is it important?
Accumulation of regulators that determine fate and function are passed on to daughter cells This ensures that a cell produces a cell with the correct function
How do we know that all globin proteins come from a common ancestral gene?
All have very close amino acid sequence
Which of the model organisms we've discussed would you use to study flower development? Vertebrate development?
Arabidopsis & zebrafish
How does the cell prepare chromatin for transcription?
Chromatin remodeling complexes (decondense chromatin) Histone covalent modifying enzymes Histone acetylases (HAT) - activate
What allows DNA to condense and re-condense?
Chromatin-remodeling complex for decondensing and covalent modifications on histone tails
What is chromatin? What makes up a chromosome?
Chromatin= DNA + nucleosomes wrapped around Chromosomes include fully packaged proteins
What does allosterism refer to?
Conformational change in active/binding site due to binding of a compound on NOT the active binding site
What does it mean to charge a tRNA?
Covalently linking an amino acid to the 3' end of the tRNA. This is done by amino acid specific aminoacyl tRNA synthetase
What is the function of a chromosome telomere in the presence of telomerase?
Signals true end and not break
What is the difference between Southern, Northern & Western blots?
Southern: DNA fragments, Western: protein, Northern: RNA
Compare Transmission Electron Microscopy & Scanning Electron Microscopy
TEM: Electrons going through specimen; need very thin specimen SEM: Looking at surface detail; electrons aimed back and forth across specimen