Skip to document
Welcome to StudocuSign in to access the best study resources
Guest user
0followers
Upload
HomeMy LibraryAsk AI
  • You don't have any recent items yet.
My Library
  • You don't have any modules yet.
  • You don't have any books yet.
  • You don't have any Studylists yet.

Introduction to Biomedical science

Practice questions to test your knowledge
Module

introduction to biomedical sciences

10 Documents
Students shared 10 documents in this course
Academic year: 2016/2017
Listed bookMolecular Biology of the Cell
Uploaded by:
Anonymous Student
This document has been uploaded by a student, just like you, who decided to remain anonymous.
University of Sunderland

Comments

Please sign in or register to post comments.

Students also viewed

Related documents

Preview text

Biomedical science notes Lecture one 1 What can be used to mostly infer primary structure The DNA sequence 2 What are the two ways of predicting the secondary structure of a protein Can be determined from the primary structure de novo or by alignment with other proteins of known structures using a website database 3 helices are formed by hydrogen bonding within the polypeptide chain, known as intra-chain hydrogen bonding, T or F T 4 What can be said about the direction of hydrogen bonds in ? helices They are vertical hydrogen bonds 5 What is the major disadvantage of X-ray crystallography Extremely expensive (£200,000 in the lab, >£300m for professional synchrotron sources) 6 What is meant when referring to ? helices as heptad structures 7 amino acids for every two turns of the helix 7 The more ordered and symmetrical the protein specimen is that is used in cryo-EM, the easier the averaging process, T or F T 8 Describe the structure of a ? sheet Beta strands are connected laterally by backbone hydrogen bonds 9 What is the main function of circular dichroism Used to induce secondary structure in proteins 10 In what plane do the hydrogen bonds between ? sheet polypeptide chains occur Horizontal hydrogen bonds 11 Which amino acid residues form hydrogen bonds with water molecules and are exposed on the outside of the proteins Hydrophilic polar side chains 12 Which types of amino acids residues are found in the middle of the ? strands/sheets and give examples Aromatic residues such as tyrosine, phenylalanine, tryptophan, valine and isoleucine 13 How can CD be used to infer the stability of a protein upon heating Less stable proteins will lose its characteristic CD spectrum upon heating 14 Describe the structure of a triple-coiled-coil protein Another stable structure formed by ? helices. This is where 3 amphipathic helices twist around a central axis with the hydrophobic side chains of all three exposed in the centre of the structure. This creates a stable hydrophobic core 15 23 What are the different domains of the src-tyrosine kinase Large kinase domain, small kinase domain, SH2 and SH3 24 What is the main advantage of NMR The process is very dynamic and can be used to determine protein structure in solution 25 How can CD be used to look at changes in protein structure CD can be used to investigate the effects on protein structure due to changes in pH and temperature. For example, increasing pH increases helix formation whilst decreasing ? sheet formation. In addition, it can be used to visualise protein unfolding due to increasing temperatures Two which terminus of the ? sheet do the arrows seen in ribbon diagrams point to Study These Flashcards Carboxyl (C) – terminus 27 Describe how Edman degradation can be used to obtain the primary protein structure Study These Flashcards Using phenyl isothiocyanate (PCT) to bind to and break away the terminal amino acid in a step by step process you can determine the unique sequence by high performance liquid chromatography (HPLC). This is done based on the molecular weight of each residue 28 Define the tertiary structure of a protein Study These Flashcards The way in which individual secondary structural elements pack together within a protein and between sub-domains of proteins 29 What is the name of the enzyme responsible for catalysing the conversion of sugar(s) into ethanol and carbon dioxide often used in wine making Study These Flashcards Zymase 30 Describe an ? helical structure Study These Flashcards Spiral conformation in which every backbone amino group donates a hydrogen bond to the backbone carboxyl group of the amino acid located 3-4 residues earlier in the protein sequence 31 Explain how NMR can be used to determine protein structure Study These Flashcards Specific isotopes of carbon and nitrogen (13C and 15N) are introduced into the protein of interest by growing bacteria in a medium containing nutrients with these specific isotopes only. The subatomic particles of these isotopes possess a quantum-mechanical spin. These spin vectors are aligned with a large magnetic field in a number of configurations determined by energy state. Radiowaves are then used to resonate with the natural frequency of these particles spins and cause a transition in spin vector orientation to a high energy conformation. The NMR machine then records the different frequencies required for resonance to occur. This attribute, known as chemical shift, is dependent on the local environment and can be used to determine protein structure. 32 Which two amino acid residues have low helix forming propensities Study These Flashcards Proline and glycine 33 Give an example of a triple-coiled-coil structured protein and its role in the body Study These Flashcards 39 The hydrogen bonds that form in ? sheets form between polypeptide chain and are referred to as intra-chain hydrogen bonds, T or F Study These Flashcards F – the hydrogen bonds do form between polypeptide chains but are referred to as inter-chain hydrogen bonds 40 What method other than Edman degradation (chemical disruption) can be used to infer primary structure of a protein Study These Flashcards Physical disruption through mass spectrometry 41 Random coils are another secondary structure of proteins and can connect ? sheets together, T or F Study These Flashcards T 42 Coiled-coils are often found in soluble proteins, T or F Study These Flashcards F – they are often found in elongated, fibrous proteins 43 CD spectroscopy measures the differential absorption of linearly polarised light, T or F Study These Flashcards F – measures the differential absorption of circularly polarised light 44 Lecture 1 Qn 18 Determine which representations of ? sheet protein structures the following images correspond to Study These Flashcards Backbone, sticks, space filling, ribbon 45 How often do hydrogen bonds occur in the primary sequence of an ? helix Study These Flashcards Every 3 residues 46 Describe the structure of a coiled-coil Study These Flashcards Two ? helices wrap around eachother to form a stable structure. One side of each helix contains mostly aliphatic amino acids (such as leucine and valine). The other side contains mostly polar residues. The two helices are amphipathic and contain distinct hydrophobic and polar side chains. These two amphipathic helices align with hydrophobic residues packed tightly in the centre of the structure and polar hydrophilic faces exposed to the solvent. 47 How can CD be used to determine protein refolding capabilities Study These Flashcards Cooling the protein down can be used to determine the ability of the protein to refold by seeing if it can regain its characteristic CD spectrum 48 What is the difference in the structures of the two kinase domains of src-tyrosine kinase Study These Flashcards The large kinase domain is mostly ? helical in structure whereas the smaller kinase domain is mostly a ? sheet 49 How does cyro-electron microscopy enable the derivation of average protein shape Study These Flashcards Vitreous ice is used to preserve/freeze the protein specimen. Electrons are then shone onto the frozen specimen and the average shape of the protein is determined. 50 56 Which amino acid residues have high helix forming propensities Study These Flashcards Methionine, alanine, leucine, lysine and glutamate 57 What is meant by the term secondary protein structure Study These Flashcards Local folding of the primary amino acid sequence into three different types of structures; ? helices, ? sheets and random coils 58 What does the prediction of the secondary structure rely on in order to achieve desired structures Study These Flashcards The tendency of particular amino acids to form particular structures 59 Explain how CD works Study These Flashcards CD spectroscopy uses far-UV radiation (190-250nm) to reveal the secondary structures of proteins. Each type of secondary structure has a unique and characteristic CD spectrum. ? helices have two-peak spectrums at 208 and 225nm whereas, ? sheets give a single peak between 216-218nm. Random coils also have a unique CD profile 60 What are the regulatory domains of src-tyrosine kinase and to what do they bind to Study These Flashcards SH2 binds to phosphorylated tyrosine residues and SH3 binds to other proteins involved in regulation Lecture 2 1 Explain how zinc finger domains interact with DNA Zinc fingers consist of an ? helix and a ? sheet region linked together. The ? helical region rests in the major groove of the DNA with amino acid side chains that interact directly with DNA bases via hydrogen bonds. The identity of these interacting side chain amino acids in the helical region of the domain determines which bases it interacts with. 2 Give some examples of aromatic amino acids Tyrosine, proline 3 Which metal ions bind to their binding domain and have a structural role, give some examples of protein that contain these domains Zn2+ ions bind to zinc domains. Examples of proteins with these domains include botulinum toxin, zinc fingers and DNA binding proteins 4 Give an example of protein that contains EF-hand domains and describes its role Calmodulin kinase – requires Ca2+ binding for its structure and regulation. Calmodulin is formed of a single polypeptide chain and SH3 domains bind to proline-rich motifs (poly-proline regions) and acts as an adaptor domain to link proteins together 10 Which metal ion(s) bind to catalytic metal ion domains Fe2+ or Cu2+ 11 Describe the role of zinc finger domains Zinc finger domains are found in the most frequency classes of transcription factors and are DNA binding domains that recognise 3base pairs of double-stranded DNA 12 Phosphatases and kinases used PH domains and have a direct role in lipid signalling, T or F F – kinases and phospholipases contain PH domains involved in lipid signalling 13 What does SH3 stand for Src homology 3 domain 14 Describe the basic structure of an EF-Hand domain Consists of two ? helices linked by a short loop region of around 12 amino acids that bind to Ca2+ 15 What are EF Hand domains Ca2+ binding domains that have a regulatory or structural function 16 What do SH2 domains bind to Phosphorylated tyrosine residues 17 EF-Hand motifs bind cations via 5 oxygen containing amino acid side chains, T or F Study These Flashcards T 18 What do SH3 domains bind to Study These Flashcards Proline-rich motifs 19 What do PH domains bind to Study These Flashcards Phosphoinositide lipids 20 What does SH2 stand for Study These Flashcards Src homology 2 domain 25 What is the significance of tandem zinc finger repeats usually found in proteins Study These Flashcards Tandem zinc finger repeat domains occur as part of larger DNA binding regions. Proteins with more zinc fingers can recognise longer sequences 26 How do aromatic amino acids interact with water Study These Flashcards They don’t, aromatic amino acids are hydrophobic 27 What is meant by the minimum consensus sequence for SH3 Study These Flashcards The smallest region which SH3 will bind to. This is the P-x-x-P motif consisting of a 4 residue sequence with first and last residues being prolines 28 To which domain does Zn2+ bind in a structural mode Study These Flashcards Zinc finger domains 29 Different sizes and valencies of metal ions are liganded by different numbers of amino acids and have different structural requisites, T or F Study These Flashcards T 30 SH3 recognises proline-rich motifs, how does aromatic stacking account for the interdigitating of tyrosine residues with the target poly-proline domains Study These Flashcards Aromatic stacking is the process by which the tyrosines contained within the SH3 domain interdigitate with proline residues within the binding proteins target domain. This is caused by an interaction between the aromatic side chains of tyrosine and proline residues with hydrogen atoms attached to the adjacent aromatic ring. This interaction is a dipole-dipole interaction due to the ?- aromatic rings and the ?+ hydrogen atoms. The aromatic residues (tyrosine) of the SH3 domain are positioned so that they can stack with aromatic (proline) residues contained in the proline-rich motifs 31 As well as being involved in linking signalling components, what other role does SH3 have Study These Flashcards Also as a structural role in maintaining multiprotein complexes 32 Recall how Zn2+ ions interact with zinc finger domains Study These Flashcards LECTURE 3 1 What post-translational modification targets proteins for transport to the nucleus of the cell SUMOylation 2 What does SDS-PAGE stand for Sodium Diethyl Sulphate Poly-Acrylamide Gel Electrophoresis 3 The poly-acrylamide gel has a sieving effect and protein migration through the gel in the presence of SDS is proportional to molecular mass, T or F T 4 Which two amino acids can be phosphorylated Serine and threonine 5 Describe how 2D gel electrophoresis can be used to separate proteins

Was this document helpful?

Introduction to Biomedical science

Module: introduction to biomedical sciences

10 Documents
Students shared 10 documents in this course

University: Sheffield Hallam University

Was this document helpful?
Biomedical science notes
Lecture one
1
What can be used to mostly infer primary structure
The DNA sequence
2
What are the two ways of predicting the secondary structure of a protein
Can be determined from the primary structure de novo or by alignment with other
proteins of known structures using a website database
3
helices are formed by hydrogen bonding within the polypeptide chain, known as
intra-chain hydrogen bonding, T or F
T
4
What can be said about the direction of hydrogen bonds in ? helices
They are vertical hydrogen bonds
5
What is the major disadvantage of X-ray crystallography
Extremely expensive (£200,000 in the lab, >£300m for professional synchrotron
sources)
6
What is meant when referring to ? helices as heptad structures
7 amino acids for every two turns of the helix
7

Students also viewed

Related documents