Lecture 1: Biomolecules Flashcards
1
Q
What are the 4 major classes of chemicals in biochemistry
A
- Lipids (smallest), Carbs, Proteins, Nucleic acids (biggest)
- All are polymers (Except lipids: oligosaccharides because too small)
- All are macromolecules (except lipids: they are smaller than 5000Da)
- All are hydrolyzable
2
Q
Water as a solvent
A
- Water is a good solvent as it is small, abundant, and sticky (polar)
- As a solvent, it allows solvation (hydration) reactions to occur which causes a solvation (hydration) shell
3
Q
Hydrolysis vs dehydration
A
- Hydrolysis: exergonic (energy released)
- Dehydration: endergonic (energy put in)
4
Q
Lipid structure & function
A
- Structure: Any biological molecule with low solubility (doesn’t dissolve in water) because they have a large portion of hydrocarbons (high diversity: only need to have hydrocarbon)
- Function:
- Membrane structure: Major components of cell wall: phospholipids, glycolipids, cholesterol
- Energy storage: due to them being anahydrous (have no water) we can store them without them being too heavy
- Hormone signalling: ex: steroids, prostaglandins
5
Q
The two types of lipid derivatives are:
A
- Fatty acid derivatives: carboxylic acid+ long hydrocarbon chain
- terpene derivatives: 2 5C isoprenes together
6
Q
Fatty acids
A
- Unbranched, hydrocarbon chain ending in carboxylic acid
- Chains vary in length (most are 12-24 even number C)
2a. Short (<5C): infinitely soluble in water
2b. Medium (6-12)
2c. Long (14-20):
2d. Very long (22, 24): very very low solubility - Fatty acids are synthesized via 2C acetyl CoA
7
Q
Fatty acid saturation
A
- Saturated: only single carbon-carbon bonds (ex: palmitic acid (16:0))/not flexible
- Unsaturated: has double bonds
2a. Nomenclature: triangle^(double bond position)
2b. Synthesis of double bonds beyond carbon 9 isn’t possible in humans (get those from diet)
2c. Cis double bonds create a kink=increases fluidity=lowers melting point of double bond
2d. Types: Monounsaturated (only 1 double bond) & Polyunsaturated: more than 1 double bond
8
Q
Fatty acid transport in blood
A
- Most common way of transport: fatty acid derivatives in lipoproteins
- Albumin: binds noncovalently to up to 7 fatty acids
- Free fatty acids: very few
9
Q
Fatty acid derivatives: eicosanoids
A
- DAG/phospholipids->archinodic acid->eicosanoids (20C): ex->prostaglandin
- prostaglandins (20C):
2a. Prostaglandins structure: polyunsaturated fatty acid derivatives that have a cyclopentane ring
2b. Prostaglandins function: do vasodilation (lowers blood pressure), increase pain/inflammation, controls smooth muscle contraction (peristalsis), induces labour
2c. Prostaglandins are blocked by aspirin
10
Q
Fatty acid derivatives: Saponifiable lipids
A
- Soponification: ester (RCOOR) + water = fatty acid (RCOOH) + alcohol (HOR)
1a. In lab: Soponification occurs in basic conditions…overall exergonic (protonation step at end)
1b. In cell: Soponification occurs in neutral conditions so it needs a catalyst (lipase) - Fatty acid derivatives (soponifiable lipids): fatty acids are attached to a glycerol (3OH+FA), sphingosine(attaches at amine+FA) and alcohols (OH+FA=wax)
11
Q
Fatty acid derivatives: Waxes structure & definition
A
- Long chain fatty acids esterified to a long chain alcohol: very low solubility (many hydrocarbons)
- Waxes are structural lipids that are hydrophobic (water resistant) and malleable at room temp
- Function: used on outside of organism for cleaning and lubrication
12
Q
Fatty acid derivatives: Glycerolipids
A
- Structure: fatty acids forming ester linkages with 3C glycerol (carb+3OH) backbone
- Types: triacylglycerol (glycerol+3FA), Glycero-phospholipids, glyceroglycolipids
13
Q
Fatty acid derivatives: Glycerolipids: TAG & DAG
A
- TAG: 3FA+ glycerol (3C+3OH): dehydration reaction that forms 3 acyl (-COR: alcohol) groups that attach to glycerol (triacylglycerol/TAG)
1a. Functions of TAG: Store energy (oxidation of fatty acid releases large energy) and provide thermal insulation - Diacylglycerol (DAG): only 2 acyl groups attach to 2 C’s from the glycerol (one of the C’s in the glycerol remains empty)
14
Q
Ester linkage
A
- A bond between oxygen and carbon dioxide
- -oate
15
Q
Fatty acid derivatives: Glycerolipids: Glycerophospholipids
A
- Phosphatidic acid (no head group): Has a phosphate attached to the third carbon of a glycerol backbone of a diacylglycerol (2 acyl groups)
- Glycerophospholipids (have a head group attached to the phosphate):
2a. choline: positive (named phosphatidylcholine): amine+2methyls->Most abundant phospholipid
2b. ethanolamine: positive (named phosphatidylethanolamine): amine
2c. serine (named phosphatidylserine)
2d. inositol (OH on hexane ring; phosphatidylinositol): intracellular signalling
16
Q
Fatty acid derivatives: Glycerolipids: Glycero-glycolipids
A
- Carb (water and carbon) is attached directly to the third carbon of a diacylglycerol
- NOT found in humans
17
Q
Fatty acid derivatives: Sphingolipids
A
- Lipids with sphingosine backbone (18C; Has amine (NH2) on carbon 2 and a trans double bond between C4-5)
- Every sphingolipid is derived from a ceramide (sphingosine+ fatty acid attached to amine)
18
Q
Fatty acid derivatives: Sphingolipids: sphingo-phospholipid
A
- Sphingosine backbone of a ceramide + first C is attached to a phosphate and the phosphate is attached to a head group
- Only sphingophospholipid in humans is sphingomyelin with a choline backbone (ethanol+quaternary amine (+))
19
Q
Fatty acid derivatives: Sphingolipids: sphingo-glycolipids
A
- When first carbon on sphingosine backbone of a ceramide is attached to a head group (carbohydrate)
- All glycolipids without a phosphate group, important in Brain/neural tissue
- Types:
3a. Cerebrosides (simple carbohydrate): one carbohydrate
3b. Globosides (simple carbohydrate): more than one carbohydrate
3c. Gangliosides (charged on headgroup(+)): more than one carbohydrate + sialic acid
20
Q
Terpene derivatives
A
- Terpene: polymers of isoprene (horse shape if cis) that are nonsaponifiable
1a. Terpenes formula is (C5H8)n where n=2+ - Terpene ->cholesterol (a steroid) -> sterols (vitamins A, D, E, K, B-carotene, Qionone/coenzyme Q, squalene, bile acids)
2a. Cholesterol: 4 rings where 3 are 6C and 1 is 5C: head group=alcohol: 6+2 carbon tail: methyl in 2 groves
2b. Cholesterol ester (wax/saponifiable/less soluble): fatty acid attaches to head group alcohol on cholesterol - Steroids: their skeleton is the 3 6C and 1 5C rings we see in cholesterol
21
Q
Terpene derivatives: cholesterol
A
- Cholesterol is a terpene derivative with 6 isoprene units
- Function:
2a. maintains stability of cellular membranes: decreases fluidity at high temperatures and increases it at low temperatures
2b. Precursor to steroid hormones: testosterone and estrogen
22
Q
Membrane (structural) lipids
A
- Structural lipids include Phospholipids (80%), glycolipids (5%) and cholesterol (15%), waxes
- These lipids are Amphipathic molecules: polar at one end and nonpolar at others:
2a. Form micelles: By being amphiphatic, they aggregate in water where their polar heads go towards the solution and non polar tails are away=forms spherical Micelle spontaneously
2b. Liposomes: vesicle surrounded by aqueous solution: surrounded by 2 layers of phospholipids (phospholipid bilayer) - Structural lipids combine to form the fluid mosaic model:
3a. Electrostatic forces (van der Waals) and ionic forces hold heads together
3b. Hydrophobic effect holds both leaflets together to form the lipid bilayer
23
Q
Lipoproteins
A
- Big micelles that are Water soluble lipid transporters that are made in liver and intestines
1a. Monolayer composed of phosphatidylcholine, sphingomyelin, cholesterol and apolipoproteins
1b. Core is filled with TAGs and cholesterol esters - Types
2a. Chylomicrons (least dense/largest): made in smooth ER of enterocytes…deliver TAG to adipose, muscle tissue and liver
2b. VLDL: made in liver and transport endogenous lipids and cholesterol from liver to tissues (as they lose TAGs they become IDL (VLDL remnants) which are taken up by liver and metabolized to LDL)
2c. LDL: have apoB100 to deliver cholesterol to tissues
2d. HDLs (most dense/smallest): made in peripheral tissues and they transport excess cholesterol to liver (act as negative feedback signal to reduce cholesterol synthesis)
24
Q
Apolipoprotein function
A
- Structure: bind lipids together, stabilize lipoproteins
- Communication: interacting with lipoprotein receptors on cell surfaces, initiating uptake and clearance of lipoproteins
- Metabolism: serve as cofactors for enzymes that metabolize lipoproteins
25
Q
Amino acids
A
- Amino acids/residues are linked by peptide bonds (N-C) to form a polypeptide=long polypeptide is called a protein
- 20 alpha amino acids with carboxyl group (2), amino group (9), hydroxyl group and R group (all chiral except glycine)
2a. Polar: STCNQ
2b. Nonpolar: LIMP VAG
2c. Charged: DEKRH
2d. Aromatic: WYF
26
Q
Relative configuration: D or L
A
- D or L: all 19 common amino acids are L amino acids (since glycine isn’t chiral, it doesn’t have a configuration)
1a. Levorotatory (-): plane of polarized light rotates counterclockwise and dextrorotatory (+): plane polarized light rotates clockwise - Steps:
2a. Number all carbons: carbonyl carbon should be lowest number possible
2b. If carbonyl carbon is on bottom, rotate structure 180 degrees so its at top (or at end just change lettering: D->L or L->D)
2c. Find chiral carbons: look at one with highest numbering
2d. If OH is on Right of chiral carbon=D…if OH is on left of chiral carbon=L
27
Q
Isoelectric point (PI)
A
- Amino acids are amphoteric (can donate acid or base) and amphiprotic
- Have specific pKa for each regions: amino (+)=9, carboxylic acid (-)=2
2a. PH>Pka: deprotonated
2b. PH<PkA: protonated - Isoelectric point (PI) is the pH where 100% of an amino acid are zwitterions (net charge=0): vertical in titration
3a. PI=(pKa1+pKa2)/2
3b. When PI=Ph: equivalence point on titration curve
28
Q
Primary structure of protons
A
- The number/sequence of its amino acid residues: disulphide bonds covalently connect residues
- Native conformation of a protein is determined by its amino acid sequence
2a. Proteins can vary making them polymorphic but even they have crucial/conserved regions called consensus sequence (most common amino acid sequence)
29
Q
Secondary structure of proteins
A
- Backbone: Refers to identifiable, localized spatial arrangements of atoms of the backbone
- Amino acids are connected by a peptide bond (N-C): trans configuration exists 99.6% of the time except when in proline
- Types: held via H bonding
3a. Alpha helix: right handed spiral with negative c term and positive N term for a dipole: held together by hydrogen bonds
3b. Beta pleated sheets: parallel and antiparallel (2 hydrogen bonds/amino acids)
3c. Beta turns: on outside of protein so polar/charged residues common (proline and glycine common here)
30
Q
Tertiary structure of proteins
A
- 3d shape of a protein: native conformation if a protein
- Forces that contribute to tertiary structure:
2a. hydrophobic effect: most important for structure formation/folding, water allows R groups to turn inward to protein and pack tightly
2b. van der Waals: hold core together)
2c. hydrogen bonds/ion pairing (salt bridge: increases entropy of the solvation layer
2d. disulfide bonds: covalent so strongest bond; formed via oxidation reaction between cysteines in ER
31
Q
Quaternary structure of proteins
A
- 2+ polypeptide chains that associate to form one protein
32
Q
Denaturation
A
- Denaturation is when a protein loses its 2, 3, or 4 structure due to heat, salt or pH
1a. Urea: H bonds
1b. Salt/pH change: ion pairing
1c. Mercaptoethanol: disulfide bonds
1d. Organic solvents: hydrophobic forces
1e. Heat: all forces
33
Q
Classification of proteins
A
- Globular (corpuscular): soluble in water, function as enzymes, hormones, membrane pumps/channels, membrane receptors, inter/intracellular transport/storage, osmotic regulators, immune response etc.
- Fibrous (fibrillation)/structural: made from long polymers, maintain/add strength to cellular/matrix structures, insoluble in water
34
Q
Carbohydrates
A
- Sugars or saccharides Cx(H20)x: carbon + water (so polar and water soluble)
- Nomenclature:
2a. Anomeric carbon: (ring) attached to 2 oxygens or (linear) carbon double bonded to oxygen…this carbon has lowest numbering possible
2b. D vs L: (ring) if C6 above=D, below =L or (linear) if OH is on right of biggest number chiral carbon (D) if on left (L)
2c. Alpha vs beta: (ring) alpha is opposite of C6 and beta is same side as C6
35
Q
Monosaccharides
A
- Glucose: 6C, OH down
- Galactose: 6C, OH up
- Fructose: 5C
36
Q
Disaccharides
A
- When monosaccharides form glycosidic bonds: Can be alpha (OH down) or beta (OH up) linkages (different anomers)
- Types
2a. Sucrose: glucose + fructose (a 1, 4)
2b. Lactose: galactose + glucose (b 1,4)
2c. Maltose: glucose + glucose (a 1,4)
37
Q
Glycogen
A
- Glycogen: branched glucose polymer found in muscle and liver cells
1a. Better energy storage than fat because its short term efficient, energy readily available because it produces ATP faster through glycolysis, can provide energy without oxygen
1b. HOWEVER, fat is better for long term energy storage because its anhydrous so its lighter - Forms a1,4 and a1,6 bonds
38
Q
Plant polysaccharides
A
- Starch: stores energy
1a. Has alpha linkages and comes in 2 forms: amylopectin (branched link glycogen: a 1, 4 linkages and a 1, 6 linkages) and amylose (not branched so only a 1, 4 linkages) - Cellulose: builds cell wall
2a. Not branched so b 1, 4 linkages: since beta animals can’t digest cellulose
39
Q
Nucleotides
A
- Building blocks of nucleic acids (DNA and RNA) and play a role as energy carriers and cell signaling
- Nucleotide Structure: 5C sugar called ribose, nitrogenous base and 1, 2, or 3 phosphate groups (nucleosides don’t have phosphate group)
2a. Phosphate groups are linked together by phosphodiester bonds (these bonds can be hydrolyzed in exergonic reactions)
2b. Nitrogenous base: organic base with nitrogen and there are 2 types->pyramidines (Single ring-cytosine, thymine, uracil) and purines (double ringed-adenine and guanine)
40
Q
DNA vs RNA
A
- RNA has hydroxy group at 2’ C
- RNA is always single stranded in human
- RNA uses uracil not thymine
- RNA may leave nucleus but DNA doesn’t
- RNA is transcribed from DNA template; DNA is replicated from DNA template
41
Q
DNA structure
A
- Primary: sequence of nucleotides
1a. Each nucleotide is bound to the next via a phosphodiester bond between the 5C and 3C carbons which creates 5’->3’ directionality: results in sugar phosphate backbone - Secondary: any recognizable structure achieved by a string of nucleotides (1 double helix=1 chromosome)
- Tertiary: folding patterns of large chromosomes
42
Q
Watson crick model of DNA
A
- 2 strands lie antiparallel which forms dsDNA: sequence is written 5’->3’
- 2 strands are held together by hydrogen bonds between purines and pyramidines
2a. Base pairing: Adenine makes 2H bonds with thymine, guanine makes 3H bonds with cytosine (higher melting temperature) - Complementary strands (when bases match up) curl into double helix with polar phosphate sugar backbone towards aqueous solution
43
Q
DNA tertiary structure
A
- Chromosome: single molecule of DNA in a double helix and it is bound to proteins and small amounts of RNA (DNA-protein-RNA material: chromatin)
- Chromatin
2a. Heterochromatin: tightly condensed, not transcribed … 2 types of heterochromatin->faculative (can become euchromatin) and constitutive (remains condensed always: centromere and telomeres)
2b. Euchromatin: relaxed state, transcribed - Histones: protein in chromatin that has many positive amino acids (arginine, lysine) which attracts negative phosphates on DNA backbone which causes helix to wrap tight around histones
3a. Histones group together in octamers called nucleosome
44
Q
CDNA cloning process:
A
- Uses DNA polymerase, DNA ligase and reverse transcriptase
