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BIOL225 > Topic 2 Biomolecules > Flashcards

Topic 2 Biomolecules Flashcards

1
Q

Covalent Bonds

A

-strongest bond, sharted e- pairs

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2
Q

Van Der Waal’s Interactions

A
  • lots of low energy interactions
  • interactions between molecules with temporary charges
  • peaks at van der waals contact distance
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3
Q

Hydrogen Bonding in Water

A
  • can form max 4 bonds (ice) but avg. 3.4 bonds with other water molecules; these constantly changing bonds are called flickering clusters (high entropy)
  • high specific heat, requires high input to raise temperature
  • high heat of vapourization
  • water will form highly ordered cages around hydrophobic alkyl chains
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4
Q

residues

A

monomers of a polymer
- ie. amino acids in protiens

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5
Q

native conformation

A

lowest energy state (lowest gibbs free energy) of a protien

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6
Q

amino acid

A
  • properties determined by R group
    -NH3(+)C(alpha)HCOO(-)R
  • alpha carbon is potential stereocentre
    -l-isomer (NH3 is on left) is the only form found in protiens produced by ribosomes
    -
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7
Q

Nonpolar amino acids (hydrophobic)

A

glycine gly g
alanine ala a
valine val v
leucine leu l
isoleucine ile i
methioine met m
phenylaine phe f
tryptophan trp w
proline pro p

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8
Q

Polar, uncharged amino acid (hydrophilic)

A

serine ser s
threonine thr t
cysteine cys c
asparagine asp n
glutamine gln q
tyrosine tyr y

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9
Q

polar, charged amino acids (hydrophilic)

A

aspartate asp d
glutamate glu e
lysine lys k
arginine arg r
histidine his h

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10
Q

peptide bond

A

c(-)-n(+) bond joined covalently in dehydration rxn (carboxyl and amine group react, water is released)
- linear, unbranched chain (polar)
- very stable (half life about 7 years)
- n terminus is amine (+ charge) and c-terminous is carboxyl group (- charged)

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11
Q

Primary Structure

A

includes all covalent bonds; defined by amino acid sequence (linear, unbranched)
- has a distinct amino (n) terminus and carboxyl (c) terminus

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12
Q

Secondary Structure

A

regular, repeating structure adopted by single polypeptide due to hydrogen bonds
- alpha helix: carbonyl oxygen bonds to an amino terminus hydrogen four monomers away
OR
- beta-pleated sheet: requires at least 2 beta-strands (antiparallel or parallel) with interactions between NH and CO groups in adjacent polypeptide regions

  • bonds involved: hydrogen, between N and C terminuses in the backbone
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13
Q

Tertiary Structure

A

Three-dimensional folding of a single polypeptide chain;
- bonds involved (nearly all) : disuphide bonds, hydrogen bonds, ionic bonds, van der waals interactions, hydrophobic interactions
-ie. tobacco mosaic virus coat protien (mostly a); hexokinase (a and b); immunoglobin (mostly b)

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14
Q

Quaternary Structure

A

Association of multiple polypeptides to form a multimeric protein;
- bonds involved (nearly all) : disuphide bonds, hydrogen bonds, ionic bonds, van der waals interactions, hydrophobic interactions

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15
Q

van der waals contact distance

A

the distance between atoms at which the force becomes repulsive rather than attractive as the atoms approach one another
- potential energy of system at this point is lowest, so molecules are at their most stable

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16
Q

protien functions

A

• catalytic rxns of enzymes
• motility / movement
• transport of substances
• receptors / cell signalling
• storage of amino acids
• structural support
• regulatory proteins
• hormonal (metabolic ctrl)
• defense (antibodies)

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17
Q

Denaturation/Renaturation Expiriment (Anfinsen)

A
  • all that is needed to determine the 3-dimensional structure of a ribonuclease polypeptide was the primary structure
  1. Denaturing:
    - folded polypeptide exposed to denaturing conditions (heating), disrupting noncovalent interactions between amino acid r-groups causing it to have no fixed shape or enzymatic activity
  2. Renaturing:
    - renaturing conditions (cooling) allowed renewed interactions between amino acid r-groups; polypeptide returned spontaneously to its native conformation and enzymatic activity
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18
Q

Afinsen’s Dogma

A

All the information needed to determine the 3-dimensional structure of the protein was in the primary structure!

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19
Q

Chaperone System

A

a group of proteins that have functional similarity and assist in protein folding
- very tightly folded, will not unfold under heat-shock conditions; system upregulates chaperone production when experiences increased heat
- energy-dependant

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20
Q

Ubiquitin

A

small protein chain containing 76 amino acids
- “ubiquitous” among organisms
- can form chains (form an isopeptide bond with itself)

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21
Q

Ubiquitination

A

A form of post-translational modification in which the ubiquitin-protein is attached to a substrate protein.
Three-step/enzyme process:
ubiquitin-activating enzyme (E1): ubiquitin is activated by attatching to E1 via ATP
ubiquitin-conjugating enzyme (E2): ubq. is transferred to E2
ubiquitin-protein ligase (E3): E2 ubq. is linked via E3 to a lysine residue in a target protien; E2 and E3 detatch. additional ubq. molecules are added, forming small chains
The chains then serve as target signals to be recognized by protien-degredating/amino-acid liberating proteasomes

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22
Q

Vitamins and Minerals

A

enzyme co-factors; cannot produce all required, so must recieve them through diet and microbes
- some enzymes will also require metals to function

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23
Q

Vitamin K

A

carboxyglutamate localizes factors to the wound via interactions with calcium
- warfarin (rat poison) and dicoumarol (blood thinner) inhibit this, decreasing clotting

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24
Q

Mg2+

A

Required for DNA and RNA.

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25
Nucleic Acids as Carriers of Chemical Energy (function)
- ATP: a nucleotide trisphosphate; hydrolysis of the phosphoanhydride bonds in ATP is a universal mechanism for releasing the energy required by many catalyzed reactions - CoA: common carrier of 2-carbon groups - NADH & NADPH: common electron carriers
26
Nucleic Acids as Modes of Informational Storage and Retrieval (functions)
The linear sequence of nucleotides in polynucleotides dictates the primary structure of proteins, performs many roles in its own expression, & also encodes many nonprotien products. -central dogma of biology
27
Nucleotide Compostion
Nucleotides: nucleic acid molecules - nitrogenous base - pentose (5C sugar) - 1+ phosphate groups (PO4-2) - nucleosides are NOT nucleic acids (lack an acidic phosphate group)
28
Proteosome
a protein complex in cells containing proteases; it breaks down proteins that have been tagged by ubiquitin.
29
5" position
addition of a phosphate group on C5 of the pentose (counting clockwise from top oxygen)
30
Polynucleotides
made up of nucleotides covalently linked by phosphodiester bonds (5' to 3' carbons of ribose) - single (ss) (ie. ssDNA or ssRNA) or double (ds) stranded (ie. dsDNA or dsRNA)
31
Nucleotide Sugars
purines
32
purines
adenine (A) guanine (G)
33
pyrimidines
thymine (T) uracil (U) - T has methane group, U has H - cytosine (C)
34
Chargaff's Rules
A=T G=C
35
Stacking Interactions
Bases (or base pairs) are planar, and these planes stack at contact distance (about 3.4 Angstrom), excluding water and maximizing Van der Waals interactions.
36
minor/major groove
areas where the nitrogenous bases in DNA are exposed
37
A/B/Z DNA
B: standard dna shape A: major and minor grooves roughly same size, molecule looks thicker Z: major and minor grooves roughly same size, molecule looks skinnier
38
downstream (DNA)
5' to 3', direction of transcription
39
DNA Transcription Regulation
- activators (bind to sequence of DNA called promoter) and inhibitors (protiens) determine where rna polymerase begins and ends transcribing
40
Exogenous Addition of GFP
GFP is inserted into a reporter gene on the end of a gene of interest, not affecting the protien production output of the gene onto which it is attatched but being produced in equal quantites - usually extrachromosomal
41
Monosaccharides
- major cell nutrients - carbon skeletons can be used as raw material for building other organic molecules - classified by two features: 1. number c atoms, 2. chemical nature of carbonyl group (ie. aldoses are aldehydes, ketoses are ketone)
42
Classifications of monosaccharides based on their total number carbons:
3: trioses 4: tetroses 5: pentoses 6: hexoses 7: heptoses 8: octoses
43
alpha vs. beta glucose
alpha: OH below glu beta: OH above
44
Anomeric Carbon
The carbon atom bonded to two oxygens in the ring-form of the sugar; carbonyl carbon (C1 on aldose C2 on ketose) in the open-chain form of the sugar (fisher projection); alpha: OH below beta: OH above -if there is an OH on an anomeric carbon, the ring can open, and is called a reducing sugar
45
Stereoisomers
same chemical formula, different structure - enantiomers: nonsuperimposable mirror images - diastereomers: not mirror images
46
Epimers
differ in configuration at one of several chiral carbons
47
Diasteroisomers
stereoisomers that are not mirror images - epimers: differ at one of the several chiral carbons - anomers: differ at a new chiral carbon atom formed on ring closure (ie. alpha or beta glucose)
48
Disaccharides
Sucrose: glucose + fructose Lactose: galactose + glucose Maltose: 2 glucose linked via α-1→4 glycosidic bond. Isomatose: 2 glucose linked via α-1→6 glycosidic bond Cellobiose: 2 glucose (Hs on consecutive glucoses in the glycosydic linkage are alpha/beta, rather than beta/beta as with maltose)
49
Oligosaccharides
several monosaccharides covalently linked - cell surface receptors: often found linked to noncytoplasmic side of protiens (forming glycoprotiens) and lipids (forming glycolipids) - important in molecular recognition
50
Starch
storage polysaccharide - principle storage polysacc. of plants - digested by amylases - a mixture of very long helical glucose polymers - 2 forms: amylose and amylopectin
51
Amylopectin
branched-chain polymer of D-glucose subunits with an occasional α-1→6 bond causing branching
52
Amylose
straight-chain polymer of D-glucose α-1→4 subunits - form of starch
53
Glycogen
principle storage polysaccharide of animals similar to amylopectin, but α-1→6 branch points are more frequent
54
Cellulose
principal structural component of plant cell walls - linear unbranched polymer of glucose - not helical - broken down by cellulase - β-1→4
55
Chitin
principal structural component of invertebrate exoskeletons (also: cell walls of fungi, some algae) - homopolymer of GlcNAc (linked via β-1→4 bonds)
56
Bonds and Interactions Involved in Protein Folding and Stability
The initial folding and subsequent stability of a polypeptide depends on (a) covalent disulfide bonds (ie. S-S between 2 cystiene residues) as well as on several kinds of noncovalent bonds and interactions, including (b) hydrogen bonds, (ie. C-terminus to OH) (c) ionic bonds, (ie. N-terminus to C-terminus) (d) van der Waals interactions, and hydrophobic interactions (ie. methyl R groups)
57
Disulfide Bonds
- forms between the sulfur atoms of two cysteine amino acid residues under oxidizing conditions - become covalently linked (strongly stable) following an oxidation reaction that removes the two hydrogen atoms from the sulfhydryl groups of the two cysteines, forming a disulfide bond
58
Ionic Bonds/ Electrostatic Interactions (Protien Structure)
Polypeptide folding is dictated in part by attractive interactions between +/- charged R-groups and repulsive interactions between +/+ or -/- groups - strength of interactions allows them to exert attractive force over greater distance and less rigidly defined angles than other non covalent or covalent bonds - denaturation in high or low pH occurs due to loss of ionic bonds
59
Denaturation in high or low pH occurs due to:
loss of ionic bonds
60
Hydrophobic Interactions (protien structure)
Tendency of hydrophobic molecules or parts of molecules to be excluded from interactions with water. - amino acids with hydrophillic R groups tend to be located near the surface of a folded polypeptide, where they can maximally interact with water, whereas those with hydrophoblic R groups are usually on the inside of the polypeptide - if most amino acids in a polypeptide are hydrophobic, it would be found in a nonpolar environment (ie. membrane protiens) - if most are hydrophillic, it will likely be loosely folded and in an aqueous environment
61
Ball-and-Stick Model
- s backbone carbon and nitrogen atoms plus the carbonyl oxygen: gray - hydrogen bonds between CO and NH groups: dotted lines - R-groups important for catalytic activity: purple - disulfide bonds for tertiary structure: gold
62
Richardson Diagram/ Spiral-and-Ribbon Model
- a-helical regions: blue spirals or cones - b-sheets: purple ribbons with arrows pointing to c-terminus - amino r-groups and disulfide bonds: omitted for clarity
63
Protein Domains
- 50 to 350 amino acids in length - discrete, conformationally stable, locally folded unit of tertiary structure that usually has a specific function - modular - proteins with similar functions usually have common domains containing sequences of identical or very similar residues
64
Fibrous Protiens
Long strands; reptitive with limited range of R-groups - help maintain cell shape - (generally) insoluable
65
Globular Protiens
Roughly circular, irregular and wide range of r-groups - carry out specific biological function - (generally) soluable
66
Mechanisms for Gain of Protien Domains
1. gene fusion 2. exon extension 3. exon recombination 4. intron recombination 5. retroposition
67
In Vivo
in the cell
68
Molecular Chaperones
Protiens that facilitate the correct folding and assembly of protiens and protien structures which are not themselves components of assembled structures. - bind to specific regions that are exposed only in the early stages of assembly, thereby inhibiting unproductive assembly pathways that would lead to incorrect structures.
69
Tobacco Mosaic Virus (TMV)
- when disassembled, reforms spontaneously, showing that complex biological structures can reassemble without external information - many disks made of coat protiens (17 per layer) each associate with a 102 nucleotide sequence of viral, single stranded RNA
70
Ubiquitination Susceptability
- certain N-terminus amino acids cause rapid ubiquitination/degredation due to E3 recognition - presence of degrons (internal amino acid sequences) - defective newly synthesized protiens (up to 30%)
71
Central Dogma of Biology
A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein. 1. DNA Replication 2. DNA Transcription 3. RNA Translation
72
Nucleic Acids as Cell Signallers (functions)
cAMP & cGMP are common cytosolic "second messengers" in signal transduction cascades
73
Structure of ATP
- triphosphate (held together by phosphoanhydride bonds) - ribose (held to phosphates by phosphoester bond) - adenine
74
DNA vs. RNA Composition
same phosphate (PO4-2) deoxyribose in DNA (H on C2), D-ribose in RNA (OH on C2) purines: adenine (A), guanine (G) pyrimidines: cytosine (C), thymine (T) (in DNA) and uracil (U) in RNA
75
Adenine Nucleoside/Nucleotide Nomenclature Example
RNA: (nucleoside) adenosine or (nucleotide) adenosine monophosphate DNA: (deoxynucleoside) deoxyadenosine or (deosynucleotide) deoxyadenosine monophosphate
76
Structure of DNA
- Nobel Prize (Physiology or Medicine) awarded to Francis Crick, James Watson and Maurice Wilkins in 1962 for postulating the anti-parallel double-stranded helical structure for DNA - rosalind franklin did x-ray crystallography image (photo 51)
77
Bonds in DNA
- phosphodiester (between pentose 5C and 3C and phosphate in backbone) - hydogen bonding between base pairs
78
Carb Functions
- energy storage (storage polysacchrides) - fuel storage (monosaccharides) - structural support (storage polysacchrides) - molecular recognition (ie. parts of receptors for extracellular signalling molecules)
79
Fisher Projection vs. Haworth Projection
Fisher: provides clear view of stereochemistry at each carbon in the open-chain form of the sugar Haworth: allows visualization of closed-chain form of the sugar
80
Haworth Projection
at top of vertical stick: above plane of carbon ring at bottom of vertical stick: below plane of carbon ring allows visualization of closed-chain form of the sugar
81
Reducing Sugar
A sugar that can open or close from its closed-chain ring form; anomeric carbon has an OH group (aldose or ketose) attatched which can reduce other compounds. - all monosacchrides except sucrose
82
Most of the sugars in nature are in which conformation?
D
83
Isomers
Same molecular formula but different arrangement of atoms and thus different physical / chem properties. - "structural isomers" - possible isomers = 2^n n= number chiral carbon atoms
84
Chiral Carbon Centers
- an asymmetric carbon (4 different groups attatched to it) - possible isomers = 2^n n= number chiral carbon atoms
85
Glycoprotiens
N (ie. asparagine) or O (ie. serine) linked to amino acid - can be found in noncytoplasmic side of membrane protiens
86
Lipid Functions
- energy storage - fuel - membrane formation - communication (cell signaling) - protection of organs - thermal insulation
87
Lipids as Energy Stores (functions)
- very compact fuel reserve - per gm, fats have 2x as much energy as polysaccharides
88
Lipids as Fuel Molecules (functions)
- fatty acids (released from fats) are oxidized in the mitochondria to form acetyl-CoA for the Krebs cycle (aerobic respiration)
89
Lipids as Membranes (functions)
-phospholipids & glycolipids spontaneously self-seal into bilayers in aqueous solutions
90
Lipids for Communication (functions)
- steroid hormones - some second messengers
91
Lipids as Organ Protection (functions)
- adipose tissue cushions many organs
92
Lipids as Thermal Insulation (functions)
-adipose tissue decreases thermal conductivity of body coverings
93
Triglycerol Synthesis
1 glycerol + 3 fatty acid chains (2 saturated, one unsaturated) with an ester linkage
94
Fatty Acids
- compounds with a hydropilic carboxyl group and unbranched, hydrophobic hydrocarbon group - amphipathic (amphiphilic): possess both polar (hydrophilic, carboxyl) and nonpolar (hydrophobic, hydrocarbon) domains
95
Generalized Formula for Saturated Fatty Acid
CH3(CH2)nCOOH, no double bonds/ branching on hydrocarbon
96
Structural Variation in Fatty Acids
– length (# carbon atoms) – saturated, monounsaturated, or polyunsaturated – if unsaturated, location(s) of C-C double bond(s) – if unsaturated, cis- vs. trans- – presence of other groups... rings, -OH groups, -CH3 groups (branches)
97
Phosphoglyceride
phosphatidic acid (2 fatty acid chains with a glycerol attatched to a ch2 - phosphate) with a head/r group attatched - most common r/head groups are serine, ethanolamine, choline, and inositol
98
Phospholipids
Include phosphoglycerides (glycerol group below phosphate and r, bonded to fatty acid via ester linkage, e.g. phosphatidylcholine) & phosphosphingolipids (sphingosine group instead of glycerol, bonded to fatty acid via amide bond, e.g. sphingomyelin- only one fatty acid); - amphipathic ( hydrophobic fatty acids, hydrophillic glycerol, phosphate, and r group)
99
Glycolipids !
sphingolipids; head group + sphingosine + fatty acid (linked via amide bond) - glycosphingolipids, cerebrosides, gangliosides
100
Sterols
- serve as fluidity buffer - cholesterol, phytosterols, ergosterols, hopanoids
101
Steroid Hormones Derived From Cholesterol
102
Ester Linkage (lipids)
- formed between the oxygen molecules of glycerol and the hydroxyl molecules of fatty acids

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