Section 1 Flashcards
1
Q
What type of polymers are DNA, RNA and proteins?
A
informational biopolymers
2
Q
What is a informational Polymer?
A
Polymers: Covalent bond-linked chain of monomers
Informational: more than 1 kind of monomers, order of them IS the information
All monomers have common element (forms the backbone by covalent bonding of common element) + characteristic element
3
Q
How many joining sites are needed for different polymers?
A
The joining sites on the common elements react together and bond
1 joining site = max 2 monomers in polymers
2 joining sites = linear polymers
3 joining sites = branched polymers (complex carbs)
*Informational polymers are LINEAR
4
Q
Why are informational polymers always linear?
A
It is more efficient for handling and packaging (DNA has a huge length so need efficient use of space)
Most cases, have 2 ends but can be circular (but still unbranched) ex: genomic DNA of some bacteria and some virus such as E.coli
5
Q
How does the joining sites configuration affect the growth?
A
Assymetry of the monomers → assymetry of the polymer
(2 different joining sites)
growth occurs only at one end/ unidirectional (right end by convention)
6
Q
What are the 2 major information biopolymer monomer units?
A
nucleotides (nucleic acids, DNA, RNA) and amino acids (proteins)
DNA = longest chains, then RNA, then proteins
7
Q
What is the structure of nucleotides?
A
Characteristic element: heterocyclic base (A, C, G, T) attached to the 1’ Carbon of the ring
Common element: pentose sugar phosphate
for DNA → Deoxyribose
for RNA → Ribose
8
Q
What are the joining sites nucleotides?
A
5’ phosphate (ACID in “nucleic acid”, doubly Negatively charged on 2 O)
3’ OH (hydroxyl)
*We talk of 5’ end and 3’ end
Addition of monomers ALWAYS to the 3’ end.
9
Q
What is the difference between DNA and RNA nucleotides?
A
The pentose sugar differs at C 2’
Ribose: OH attach to 2’ (RNA)
2-Deoxyribose: only H attached to 2’ (DNA)
*Absence of 2’-OH makes DNA much more resistant to chain cleavage by hydrolysis (more stable)
10
Q
Which are the heterocyclic bases of nucleotides?
A
PURINES (A, G) = double cyclic rings (9C)
PYRIMIDINES (U (in RNA), T (in DNA), C) = Single ring (6C)
11
Q
What is the difference between U and T?
A
There is a methyl on 5’ C in T, and not in U
*T in DNA instead of U makes chemical damage easier to repair
12
Q
How do we call the bond between the heterocyclic base and the common element?
A
N-glycosidic bond (bonded to a sugar on the 1’C)
13
Q
What is the name of the bonds between nucleotides?
A
Phosphodiester bond
Because phosphate is joined in an ester to the 5’OH and to the 3’OH
14
Q
What are the monomers of proteins?
What are their structure?
A
Amino acids (Only L stereomers, not D)
Common element: H2N - CH - COOH
Joining sites: H2N (amino group/n-terminus) and COOH (carboxyl group)
Always adds onto Carboxyl group
Characteristic element: R side chain
15
Q
Which are the different classes of amino acid side chains? (How many of each?)
A
20 different side chains total
- Hydrophobes (8)
- Hydrophilic (acidic and basic, 9)
- Special (3)
16
Q
How do we call the link between adjacent amino acids?
A
peptide bond
O=C (plus rest of chains) - NH
COOH end is chained to just C=O when in chain
17
Q
What are Nucleotide monomers named in the form of high-energy?
A
nucleoside triphosphate (NTPs) = chain of 3 phophates - pentose - base
The outer phosphates are kicked-out when NTP is incorporated in the chain (energizing group is on the 5’ end)
*Revoir ATP, CTP, GTP, UTP
18
Q
What are amino acid monomers in the form of high-energy? (needed to incorporate the chain)
A
amino acyl-tRNA esters
high energy ester bond on the C-terminus!
tRNA bonded to the single bonded O of the COOH group
tRNA molecule is kicked-out when the next amino acid is incorporated at the end of a growing protein chain (they add to the c-terminus)
19
Q
Can energized monomers join a growing chain by themselves?
A
No, reaction needs to be canalized by specific enzymes
20
Q
Which biopolymer is associated with which template and enzyme?
A
B: DNA, T: DNA, E: DNA polymerase
B: RNA, T: DNA, E: RNA polymerase
B: protein, T: mRNA, E: ribosome
21
Q
How are the 2 antiparallel DNA strands held together?
A
By Watson-Crick base pairs
2H bonds between A&T
3H bonds betwen C&G
*Bases are stacked on the inside
22
Q
How are base-pairs «read» in interior of DNA?
A
By DNA-binding protein binding to major or minor grooves and identify specific sequence without separating the strands
Groove = space between curls of the backbone?
23
Q
How is strand separation called? What is used for?
A
It is called melting or denaturation
Done by breaking individually weak H-bonds
When they re-associate = renaturation
Important for replication and transcription
24
Q
What is Tm? How does the composition of DNA affects it?
A
Temperature at which 1/2 of DNA is melted
Depends on composition
Higher G-C proportion = higher Tm bc more H-bonds, so more energy needed to separe the strands
25
Why is it important that DNA can bend?
Important in DNA-protein interaction and in folding DNA into compact structures
Can bend easily bc no H-bonds alond the backbone
26
Which protein is responsible for bending DNA?
TATA box-binding protein
27
By what chain of structure do gene develop to generate organisms?
DNA —> RNA —> protein (def of Physiology)
28
What is the definition of replication?
Making a perfect copy of DNA
DNA —> DNA
28
What is transcription?
Rewriting in a different nucleotide font (deoxyribose = DNA font, ribose = RNA font)
DNA —> RNA
29
What is translation?
rewriting in a different language (nucleotide —> amino acid)
for protein synthesis (mRNA —> Protein)
30
What type of molecule are RNA polymerase and DNA polymerase?
What is the composition of ribosomes?
RNA pol and DNA pol: proteins
ribosomes: protein + RNA
31
How does the process of Transcription work?
Direct interaction of template with rNTP (nucleoside triphosphate)
Base waits for perfect Watson-Crick base pair nucleotide to attach to the specific base by H-bond
When right Watson-Crick base pair attached by H-bond, Polymerization happens
Polymerization: 3’-OH attacks alpha phosphate, beta and gamma diphosphate are dropped from rNTP
32
What is the transcription bubble? How the Transcription work?
RNA polymerase causes helicase (local unwinding of duplex DNA) —> exposes template DNA strand
Transcription bubble is the local unwond part of DNA
Unwoumded strand = template strand
Transcription bubble moves UNIDIRECTIONALLY along DNA with RNA polymerase
After transcription, re-forming of the duplex behind polymerase, « kicks out » the newly-synthesized RNA strands
33
How do the starting site and stop site of RNA polymerase work?
Sites are on the template strand
Starting: promotors (specific DNA sequences facilitate the intial binding of RNA polymerase to DNA
Stopping: Certain DNA sequences destabilize the attachement of RNA polymerase to the DNA so it falls off and releases RNA chain
34
What is helicase?
Helicase is the process of unwinding DNA duplex locally to expose template
35
What direction is the new strand synthesized? (on template and growing chain)
Addition to the 3’-end of the growing chain
Template read from 3’ to 5’ bc anti-parallel
**By direct interaction (Watson-Crick base pairing)**
36
What are the differences between DNA transcription anfd DNA replication?
Tr monomers = rNTP, Rep monomers = dNTP (ribose and deoxyribose)
Transcription: Start and stop sites on template
Replication: Start sites (origins), but no stop sites
Transcription: new strand (RNA) separates from template
Replication: new strand (DNA) never separates from template
Transcription: Only 1 strand is a template
Replication: 2 strands independently serve as templates
37
How is called protein synthesis?
Translation
1 language (nucleotides) to another (amino acids)
38
How are amino acids read?
3-character sequences of nucleotides : codons
20 different amino acids so same amino acids for multiple combinations of nucleotides
39
What are the punctuation codons?
Stop codons: UAA, UAG, UGA
Start codons: Methyionine (AUG) (can also be present within the protein chain)
Does protein synthesis require direct or undirect interaction between template and incoming monomer?
tRNA acts as an adaptor between template and growing chain
40
What is the role of Aminoacyl tRNAs in protein synthesis?
3-nucleotide anticodon sequence complementary to the codon
tRNA with matching anti-codon has amino acid attached to it
Amino acid reacts with protein chain (n-terminus attacks C on the c-terminus)
Indirect contact between amino acid chains (reacts in the big subunit) and mRNA template (in small subunit)
Reads from 5’ to 3’
41
What is the effect of a single base deletion?
Because the reading frame is 3 bases at the time, changes all the amino acid sequence (tout décalé)
42
What are basic biological roles of DNA, RNA and proteins?
DNA and RNA: synthesis of specific proteins
proteins: to carry out the physical and chemical functions of cells
43
What is the size range of proteins?
smallest = 40 amino acids
average = 300-400 amino acids
largest known = 30 000 amino acids (muscle protein Titin)
44
What is the primary structure of a protein?
The specific sequence of amino acids
This sequence will determine how it folds into a definite 3D strcture
This 3D overall shape determines its function
45
Explain the Hydrophobic effect
Water molecules surrounding hydrophobic molecules arrange in a cage-like very ordered manner
If every molecule is separated, more water molecules are ordered so lower entropy, nature wants higher entropy so molecules aggregate to have a bigger cage around all (need less molecules so more of them free) = Hydrophobic aggregation
46
What is the Oil drop model?
Seen because cytoplasm is fundamentally an aqueous solution (water)
It is the fact that proteins fold in order to have hydrophobic amino acids on the inside so that water is in contact with the hydrophilic molecules on the outside
Specific protein structure is based on general oil drop model
47
What determines the secondary and tertiary structure of a protein?
And Quaternary?
Specific, local, structural interactions which determine path of the peptide "backbone"/ overall shape
Secondary = local folding + H-bonding
Tertiary = overall conformation of a single polypeptide
Quaternary = interaction between polypeptides to form bigger proteins
48
What are different functions a protein can have?
- Structural
- Movement (cause mvt of other particles)
- Molecular transformation (catalysts)
- Transport
- Signaling
49
Which level of structure are alpha helix and beta sheets part of?
secondary structure
50
What is a domain in a polypeptide?
*Tertiary Structure*
The domain is a region of the protein that is held together by interactions between the SIDE CHAINS
It can stay together independently of the interactions in the rest of the molecule
51
What is a homodimer?
2 of the same polypeptide which amino acids sticking out the backbone interact to hold them together
*Quaternary Structure*
Can have homotrimer or heterodimer
52
DNA part of the protein does DNA determine?
Only the amino acid sequence which determines the 3D structure, which determines the function
53
Explain the process by which an amino acid intergrates a polypeptide chain.
1. O- on the C-terminus of the chain reacts with H+ on the NH3+ (n-terminus) of the amino acid to create a peptide bond by dehydration (H2O is produced)
Peptide bond between C-N (both connected to their respective alpha carbons (each amino acid has an alpha carbon)
3D Structure very important: Carbonyl Oxygen (C=O) and Amino Hydrogen (NH) ar sticking out opposit directions in same plan, perpendicular to R sticking out on the other plan alternating up, down
When attached to the chain, tRNA + anticodon that was attached to the O- leaves the ribosome
54
What does the secondary structure of a protein refer to ?
Local conformation of the peptide chain backbone
2 major peptide chain BACKBONE conformations: (together = 60% of length of average polypeptide)
*Based on H-bonding* between Carbonyl Oxygen and Amino Hydrogen
- alpha-helix
- beta-sheet
Secondary structure = local, most polypeptides have multiple
54
What is the alpha helix structure?
Helix backbone structure where amino acid n, H-bonds with amino acid n+4 by tilted verical bond
Can't bend it, because would have to break the H-bonds
Periodicity of 3.6 residues/turn (bc tilted axis of H-bond)
Surface properties = dependant on side chains sticking out = propensity of a-helix to form and interactions with other parts of the protein/stability
55
What is the beta-sheet structure?
H-bonds between Carbonyl Oxygen and Amino Nitrogen link 2 adjacent beta-strands, R chains stick out above and below sheet (determining interactions and stability)
Strands can parallel or antiparallel forming different popypeptides)
*Like multiple stripes of paper beside each other on a table
56
What is the tertiary structure of a polypeptide?
What are different possible representations of the tertiary structure of a polypeptide?
Spaical organization of the multiple secondary structures --> Structure driving interactions between Amino Acid side chains
Representations:
- Ca backbone trace (not showing the side chains)
- Ball and Stick model
- Ribbon diagram (Shows only backbone structure)
- Water-accessible surface (amino Acids chains filles in distribution of +/- charges)
- Hybrid model
*AA side-chains mediate interactions between different parts of the protein and between the protein and its ligand
57
What are possible Structure-driving interactions among amino acids in a potein?
**Most of the are non-covalent bond**
Non-convalent:
- H-bond among peptide backbone (a-helix, b-sheet)
- H-bond between R with polar side chains
- Ionic bonds between basic (+) and acidic (-) side chains
- Van des Waals interactions between hydrophobic R
58
What is an important covalent bond driving-structure side-chain interaction ?
covalent S-S (disulfide) within the chain or with other side chains
SH + SH → S-S + H2
Intrachain: Tertiary structure
Interchain: Quaternary Structure
Ex: in humain insulin
59
What are Motifs?
Combination of secondary structures forming distinct local 3D structures
Examples:
- Coiled-coil motif (2 proteins with same pattern of hydrophobic Rs come together to protect), hydrophobic R follow a pattern 1 and 4 out of 7, others are hydrophilic (Heptad repeat)
Looks like double stranded helix (3.5 average R between each hydrophobic which is on the inside, similar to 3.6 of a-helix)
- EFhand/helix-loop-helix motif: a-helix + loop around a Ca2+bc the specific amino acids of the chain interact with it and the a-helix continues 90˚ from where it started
- Zinc-finger motif: Common in transcription factors, binds to DNA/RNA
a-helix Histamines and Cys from the loop of a b-sheet interact with Zn2+ (U shape manner)
60
What is a supramolecular complex?
Multiple proteins associating for one specific purpose.
They each have a function of their own and at specific times, associate for a more complex task and dissociate afterwards
As opposed to Quaternary structure that will not dissociate
Ex: transcription initiation complex = RNA polymerase + multiple General transcription factores + Mediator complex
60
What is the difference between the Motifs and a Domains of a protein structure?
Motifs = NOT structurally independent entities (don't stay in shape if cut away from rest of protein, to small and unsufficient strong bonds, rest of protein contributes to stability of local motif)
Domains are strcturally independent entities, but still convalently bonded to the rest of the protein (rest of protein also helps its stability, just not essential)
61
What are 4 major classes of proteins?
1. Fibrous proteins
2. Globular proteins
3. Intergral membrane proteins
4. Intrinsically disordered proteins
62
What is the structural definition of a domain?
- More than 40 aa-long region
- Compactly folded
- can be made of various motifs
ex: Globular domain, fibrous domain, etc.
Can be found in diverse protein that may or may not be a source of that particular domain (can also have multiple of the same domain in 1 protein)
ex: EGF precursor = chain of EGF that can be cut from the protein and used in other proteins
EGF = epidermal growth factor
Used in Neu oncogene protein and TPA (tissue plasminogen activator)
63
What is the most common sign of misfolding?
hydrophobic patches at the surface of protein (in contact with water)
makes the protein insoluble in cytoplasm
Causes aggregation of misfolded proteins to protect the hydrophobic zones
*Urea can cause misfolding*
64
What is the timing of folding vs synthesis of proteins during initial formation?
Folding starts as soon as the new peptide is out of the ribosome, don't wait for all of the protein to be synthesized, secondary structure starts as soon as it can
Folds following the "folding pathway"
64
By which process can a native protein become misfolded?
Denaturation (Urea) followed by renaturation (wrong conformation)
Can go both ways and reform a misfolded protein
65
What are chaperones?
Chaperons roles:
- fold new proteins
- refold misfolded
- unfold proteins to return on proper folding pathway before they are destroyed
- disassemble toxic protein aggregates
Without them, all slightly misfolded proteins would be destroyed (ex: they recognize exposed hydrophobic patches)
Chaperones upragulated in conditions that favour misfolding of proteins (ex: heat-shock)
Work through ATP-dependent cycles of binding to and release from misfolded proteins by blocking the exposed hydrophobic patches (protects from aggregation until properly folded)
66
What are the 2 major classes of chaperones?
Molecular chaperones: operate as single molecules
Chaperonins: form multisubunnit "refolding" chamber
67
How the Hsp70 work? What type of molecule is it?
It is a molecular chaperone part of the Heat Shock Proteins (upregulated in high temperatures), Has a Substrate-binding subunit, a Nucleotide-binding domain and a unamed part (1 single polypeptide chain with 3 parts)
*Can be used for misfolded or nascent proteins directly out of the ribosome
HSP70 cycle:
1. ATP bound to it, substrate-binding site is open and empty
2. protein binds to it at needed site
3. releases 1 phosphate (now ADP) and substrate-binding site closes
4. ADP released, ATP replaces it, unfolded protein is released
68
What are Hsp60's?
They are another word for Chaperonins: enclosed chamber formed of inward facing protein-binding subunits (ATP based) → isolated environment ideal for proper folding
GroES (2 caps) + GroEL (2 independent folding chambers)
Each = 7 protein chain/cycle (quaternary structures)
1. misfolded protein comes into the upper chamber (open lid)
2. ATP hydrolysis closes the cap
3. Folding within the Heterocyclic-octomeric folding chambers
69
What are the 2 groups of chaperonins
Group I chaperonins = bacteria, mitochondria
Group II chaperonins = eukaryotic cytoplasm
70
What is Ubiquitin?
What stands for E1, E2 and E3 in Ubiquitin system for protein degradation?
Ubiquitin = 76-residue protein, can be convalently linked to lysine residues on target proteins
E1 = Ubiquitin-activating enzyme
E2 = Ubiquitin-conjugating enzyme
E3 = Ubiquitin ligase
71
What Steps are involved in Ubiquitination? (Which leads to degredation of proteins by protease)
Step 1:
Poly-ubiquitin "tags" damaged/misfolded proteins for degradation (binding to the lysine residues on it)
- E1 (Ub-activating enzyme) + ATP bind to the C-terminus of Ub protein
- E1 passes Ub protein to E2 (Ub-conjugating enzyme)
- E2 and E3 catalyse the bonding of Ub to the target protein (Isopeptide bond bc between Ub and side chain, not a backbone)
- Repeat n times until sufficient amount of Ub tp be recognized by chamber
Step 2:
Ubiquitin-tagged proteins fed into a multisubunit chamber, in which subunits form inward-facing proteases
72
What is the role of E3 Ubiquitin ligase?
Recognizes misfolded or damaged proteins, by recognizing exposed hydrophobic patches (other E3 might recognize oxidized amino acids)
Approx. 600 gene encoding different E3 to recognize different forms of aberrant protein structures
When some of these gene are mutated, can cause diseases. ex: Parkinson's disease = mutation E3 Ub ligase parkin
Some E3 Ub ligases recognize and target for degredation of "normal" protein that cell needs to degrade for regulation.
73
What is Proteasome and its structure?
What is its role
Protein complex which has proteases (chamber)
2x 19S caps + 20S core
Proteins in cap:
- recognize + bind polyubiquitin
- Remove targeting Ub by hydrolysis
- Unfold target proteins (ATP based)
- Pass them onto the central chamber of the 20S core.
20S core subunits form inward-facing proteases that degrade proteins → amino acids or short oligopeptides
*Chamber provides isolated environment (safer)
74
What happens to protein that cannot be properly refolded with chaperone assistance?
Ideally degraded by multiubiquitination/proteasome mechanism
But imperfect system, so sometimes get aggregates of insoluble proteins (slower bc chaperones)
75
What are amyloid?
An accumulation of misfolded proteins that aggregate in a specific formation → Formation of Amyloid protofilament → aggregate to form Amyloid fbrils which are resistance to proteolysis (very bad)
Amyloid protofilament looks like a double helix of beta-sheets
*Important aspect of several neurodegenrative diseases (Alzheimer, Parkinson, mad cow, etc.)
76
How are Amyloid deposits visible in brain tissue?
- Plaques
- Tangles
77
What are the 2 principle quaternary structures that respond to protein misfolding?
Proteasome and Chaperonins
78
What is the name of a molecule to which a protein binds and what is the effect of this binding?
What type of particle can it be?
Ligand (can be a macrmolecule, small molecule, ions)
Binding can change confromation of protein (essential for functions of some proteins)
79
What are the 2 properties of ligand-binding?
Specificity: ability of a protein to bind to only 1 PARTICULAR/specific ligand (even if many similar molecules in the environment)
Affinity: tightness/strength of the binding, expressed as dissociation Kd (Stronger interaction = lower dissociation = lower Kd)
80
What is the definition of binding?
Binding is an interaction between COMPLEMENTARY molecular surfaces (side chains)
sum of multiple individually weak (non-covalent) interactions → collectively strong binding → protein binding specificity
ex of weak interactions between the side chains: Ionic bonds (between charged amino acids), Hydrogen bonds, Hydrophobic and van der Waals interaction
81
How can the binding between Antobodies and antigens be qualified?
With high specificity and with high affinity
CDR (complementarity determining region) at ends of the light chains of the antibody involves multiple protein loop
82
What is another name for the ligand of an enzyme?
The substrate of the reaction the enzyme catalyses
83
What is the enzyme active site?
Has 2 part:
Substrate binding site (Complementary to substrate) + Catalytic site
84
What are the definitions of Vmax and Km?
Vmax = maximal rate of catalysis when saturating amount of substrate (depends on amount of E and how fast they can work)
Vmax = turnover number, enzymatic cycle/sec at top speed
Km = substrate concentration supporting rate of 0.5Vmax (measure of affinity of enzyme-substrate)
Doesn't depend on [S]
85
Revenir Slide 8-9 L5
86
WHat can reflect the pH optima for an enzyme?
- Active site acid-base chemistry
- Sensitivity of overall protein conformation ot charge distribution
Ex: trypsin/chymotripsin = acid-base rxn between 2 key active site residues → pH 7 needed, above 9, conformation distrupted because important groups become unprotonated and uncharged
Ex: proteolytic enzyme such as lysosomal hydrolases evolved in more acidic environment (lysosome) so more active in low-pH
87
What are different ways multi-enzymatic reactions can become more efficient?
Slow if reactant has to find 1st enzyme, react, then wait to find 2nd, then react, etc.
Faster:
- Enzymes form quaternary structure so all together
- Enzymes bind to a common "scaffold" protein
- Changing gene structure → Enzyme which where encoded by different genes evolve to be encoded by same → 1 single convalently bounded continuous peptide with multiple domains
87
What is the allosteric effect?
Binding of a ligand on one site → conformational changes → affect binding of another ligand at different site
Conformational switches in regulatory proteins (on and off switches)
ex: Hsp70, when ATP binds → open conformation for misfolded protein to come in, when ADP binds → closed confirmation
88
How does Ca++ binding affect calmodulin?
Calmodulin has 4 EF-hands motifs (Helix-loop-Helix)
When binds to Ca2+ (4 possible sites) → conformational change let target peptide come in the middle → side chains of target peptide are complementary to the side chains of alpha helixes from the EF motifs
*Non-covalent bonding, Allosteric switches*
89
How do G-proteins switch from on → off and inversely?
GTPase bound to GTP = on (more rectangular conformation)
GTPase bound to GDP = off (more rounded confirmation)
GAP = GTPase activating protein helps G-protein to hydrolyse its own GTP → GDP which turn it off
GEF = guanin nucleotide exchange factor
90
Hoe does phosphorylation and dephosphorylation work?
What is their importance?
On-off switch for proteins/cell regulation
Post-translational modification!!
(Change in structure by adding a phosphate group)
Phosphorylation of amino acid side chains = rapidly reversible covalent change in the protein structure
In active state: target protein binds with phosphate group
Protein phosphatase (ephosphorylation) = bring protein to inactive state by changing by reacting with H2O, phosphate bound to the protein becomes an OH
Inactive state: target protein bound to OH
Protein Kinase = use of ATP (→ ADP) to change OH → phosphate (PO4 2-)
91
Which motif is usually found in DNA and RNA binding proteins?
Zinc finger motif
92
Which protein can fold and refold without any help?
Ribonucleases
Others need chaperones and chaperonins
