Download UBC BIOL 200 Midterm: Cell Structure & Function Guide and more Exams Molecular biology in PDF only on Docsity!
BIOL 200 UBC Midterm Questions And Answers With
Latest Set
What bonds form in a primary protein structure? ANS covalent bonds between the backbone, peptide bonds What bonds form in a secondary protein structure? ANS non covalent bonds between backbone What bonds form in a tertiary protein structure? ANS covalent bonds between R groups (i.e. disulfide), non-covalent bonds between backbone, R groups What bonds form in a quaternary protein structure? ANS - covalent bonds between R groups (i.e. disulfide), non-covalent bonds between backbone, R groups
- between 2+ polypeptides How is a peptide bond formed? ANS condensation reaction between alpha amino group of one amino acid and carboxyl group of another Why are some folding patterns not obtainable by primary structures? ANS resonance between C- O and C-N constrains flexibility, no free rotation around C-N axis What bonds stabilize primary structures? ANS peptide bonds What bonds stabilize secondary structures? ANS H-bonds between N-H, C=O groups What types of structures result from secondary protein folding? ANS alpha helix, beta sheet Describe the bonds of an alpha helix. ANS carbonyl forms H-bond with H from N-H of a residue, 4 residues further on sequence (in same chain), side chains point outward
Describe the bonds of a beta sheet. ANS polypeptide folds back on itself, H-bonds form between N-H and C=O on neighbouring polypeptide strands, side chains project upwards & downwards What factors determine which structure forms in secondary folding? ANS interactions between side chains of amino acid residues in polypeptide such as: steric hinderance, charge repulsion, proline presence, presence of other chem groups What bonds stabilize tertiary structures? ANS ionic bonds between side chains, H-bonds, LDF (weaker so need more to stabilize), covalent disulfide bond between cysteine How does hydrophobic interactions take part in tertiary formation? ANS most stable when hydrophobic residues face inwards, surrounded by other parts of the protein What bonds stabilize quaternary structures? ANS ionic bonds between side chains, H-bonds, LDF, disulfide bonds Describe the structure of quaternary folding. ANS multiple polypeptide chains, ea. a subunit, form a dimer, tetramer, etc., can be all same polypeptide or different Why are disulfide bonds not found in the cytosol? ANS not an oxidizing environment like lumen of ER What amino acids are acidic? ANS aspartic acid (Asp), glutamic acid (Glu) What amino acids are basic? ANS arginine (Arg), lysine (Lys), histidine (His) Do acidic amino acids lose or gain protons? Where? ANS lose protons from COOH Do basic amino acids lose or gain protons? Where? ANS gain protons on NH What are the functions of membranes? ANS - transport of molecules, cell products
Are unsaturated or saturated fatty acids more useful in maintaining fluidity in a bilayer in subzero temps? ANS unsaturated fatty acids compress in low temps, creating kinks in the tails which creates spaces, less LDFs, therefore increasing fluidity Where does glycosylation occur? What does it do? ANS Golgi, adds carbs to lipids and proteins Where are phospholipids made? ANS cytoplasmic face of the ER Where are carbs made in the cell? ANS non-cytosolic side What enzyme helps establish the lipid bilayer asymmetrically? ANS flippases What molecules can pass freely through the bilayer? ANS gases, small uncharged and hydrophobic molecules How are peripheral proteins attached to the membrane? ANS non covalent bonds Which protein structure has repetitive bonds between atoms in the peptide backbone? ANS secondary Which protein structures can be altered when a protein is reversibly denatured? ANS secondary, tertiary, quaternary How does FRAP work? ANS bleach fluorescently labelled membrane proteins with a laser beam, observe unbleached fluorescently labelled proteins migrate into the bleached area until it is recovered What is FRAP? ANS allows tracking of fluorescently labelled lipids or proteins Is the permeability greater or less in a phospholipid bilayer compared to a biological membrane? ANS less than because biological membranes have pores and channels to allow more movement through
What are hydropathy plots used for? How? ANS to predict alpha helix transmembrane domains
- based on properties of primary sequence and how it interacts with water What techniques can be used to study membrane proteins? ANS SDS-PAGE, hydropathy plots, fluorescent staining, carb staining for glycoproteins (PAS) What type of amino acid side chains will be found in the inner core of a barrel pore? ANS hydrophilic, polar What type of amino acid side chains will be found on the outside of the barrel? ANS hydrophobic, non polar What type of amino acid side chains will be found at the top & bottom of the barrel? ANS hydrophilic, polar What kinds of molecules need to get into the nucleus? ANS nucleotides, ATP, transcription factors, water, ribosomal proteins, nucleases, histones What molecules need to exit the nucleus? ANS mRNA, tRNA, ribosomal subunits What does the nuclear pore use to differentiate between molecules leaving and coming in? ANS NLS on proteins directs them into the nucleus What is the sequence for the NLS? ANS KKKRK What constitutes transmembrane domains? ANS alpha helices or beta barrels What determines how a protein folds? ANS chemical properties of each amino acid
Are histones negative or positive proteins? ANS mostly positive so that they can bind to the negative backbone of DNA What is heterochromatin? Euchromatin? ANS heterochromatin-highly condensed form of interphase chromatin euchromatin-exists in an extended state How do histone tail modifications play a part in chromatin structure? ANS they attract certain non-histone proteins What are some examples of reversible chemical modifications of histones? ANS acetylation, phosphorylation, methylation What is the purpose of the 5' cap? ANS stabilizes the transcript, helps bind mRNA to export protein, attracts ribosome What is the purpose of the poly-A tail? ANS stabilization, helps indicate when the ribosome should leave What does it mean to have a double membrane? ANS surrounded by 2 lipid bilayers Is the nucleolus a membrane bound organelle? ANS no What is the purpose of the nuclear lamina? ANS maintains the nuclear structure (i.e. if the envelope is degraded, the nucleus will remain intact), gene expression, DNA replication, transcription Describe the process of a protein entering the nucleus. ANS - NLS of a protein binds to the NIR
- complex binds to fibril on annular ring
- fibril guides the protein into nucleus via a GTP-driven reaction
- ranGTP binds to NTR, releasing cargo
- ranGTP-NTR complex returns to cytosol through pore Where is the NLS found in a protein? ANS primary sequence How are the terms 'necessary' and 'sufficient' related? ANS Things that are sufficient are also necessary, but things that are necessary aren't always sufficient What does a gain-of-function experiment tell you? ANS If the component added is sufficient What does a loss-of-function experiment tell you? ANS If the component removed is necessary What histones make up the octamer that forms a nucleosome? ANS 2 copies of H2A,H2B,H3,H Where would you find the amino acids of a histone to reside? ANS on the surface of the histone What is the difference between the 10nm fiber and the 30nm fiber? ANS the 30nm fiber has the H1 histone attached How is the histone octamer formed? ANS primarily b/c of hydrophobic interactions between tertiary structures of the 8 polypeptides Where on the chromosome is heterochromatin likely found? ANS near centromeres and telomeres Which direction is DNA read? synthesized? ANS read 3' to 5' and synthesized 5' to 3' Which direction is mRNA read? ANS 5' to 3'
- U1 snRNP binds to 5' splice site, U2 binds to branch
- U4,5,6 come and bind to intron
- 5' splice site is cut and curls to bind to A in branch site
- U1,U4 leave and 3' site is cut, exons connected
- U5,U6,U2 dissociate and lariat is degraded How does alternative splicing occur? ANS - controlled by proteins that activate, repress, silence or enhance splicing by binding on mRNA
- secondary structures of pre-mRNA can mask or bring together certain acceptor/donor sites Does a tRNA molecule recognize only one mRNA codon sequence? ANS no there are multiple codon sequences for one amino acid Where does assembly of rRNA and proteins occur? ANS nucleolus Describe how rRNA is processed. ANS 45S transcript split into 18S (used in small ribosomal subunit), 5.8S, 28S (used in large subunit w/additional 5S) Describe what can be seen with each of the 4 types of microscopy. ANS Brightfield- cell/nucleus level, resolution 0.2um Fluorescence- tagging SEM- 3D images, dead sample, no moisture, high vacuum, stained surface w/heavy metal, resolution ~0.2nm TEM- 2D images, grainy, organelles, dead specimen How does indirect immunofluorescence work? ANS - uses 2 antibodies: primary AB, secondary AB has a fluorophore attached
- multiple secondary AB bind to the primary AB, therefore amplified signal
- primary AB can't be from same species b/c of cross reactivity
What are the advatages of GFP? ANS heritable, small, visible in live tissues, non-invasive What membranes specialize in ATP? Why? ANS Mitochondria for oxidative phosphorylation, chloroplasts for photosynthesis How do organelles move along filaments in the cell? ANS residual energy from ATP hydrolysis What is the function of protein translocators? ANS move proteins from cytosol to mitochondria, ER and chloroplasts How are chromatin fibers made more accessible to proteins? ANS histone tail modifications affect stability of the fiber (not nucleosome) and recruit proteins to decondense/condense When does RNA splicing occur? ANS after 5' capping, but before polyadenylation, as transcription continues What happens to mRNA after transcription? ANS mRNA translated many times, eventually degraded into nucleotides Describe the regulatory sequences. ANS - promoter attracts RNA pol.
- activators bind to enhancers, aid in assembly of GTFs and RNA Pol at promoter
- repressors decrease transcription by blocking mediator
- histone acetylases alter chromatin structure to make DNA accessible What is combinatorial control? ANS when complexes of proteins work together to determine gene expression How do you isolate a protein in a sample? ANS solubility properties (differs between peripheral and integral proteins)
