Biology oral exam 2006-07 semifainal
1. Mono－and disaccharides
Monosaccharides which typically contain from three to seven carbon atoms are the sugars than cannot be
degraded by hydrolysis to simpler sugar.
Classify
Triose (3 carbons) →glyceraldehyde (C3H6O3; constituent of neutral fat, intermediate of glycolysis)
Pentose(5 carbons) →ribose (C5H10O5; constituent of RNA), deoxyribose (C5H10O4; constituent of DNA)
Hexose (6 carbons)→glucose and galactose (C6H12O6; they are epimers), fructose(C6H12O6)
Aldose; C1=aldehyde →glucose, galactose
Ketose; C2=ketone →fructose, dihydroxyacetone
Structure
A disaccharide contains 2 monosaccharides joined by glycosidic linkage.
Maltose (molt sugar);α-glucose ＋α-glucose (α-1,4-glycosidic linkage)
Sucrose (table sugar);α-glucose ＋β-fructose (α-1,2-glycosidic linkage)
Lactose (milk sugar);β-galactose ＋β-glucose (β-1,4-glycosidic linkage)
Cellobiose; β-glucose ＋β-glucose (β-1,4-glycosidic linkage)
(cellobioses make up cellulose)
2. Polysaccharides
Polysaccharides are the polymer of monosaccharides.
Starch →stored energy in plants
Amylose: contain onlyα-1,4-glycosidic linkage
Amylopectin: containα-1,4-glycosidic linkage and α-1,6-glycosidic linkage (branched)
Glycogen→stored energy in animals
More branched than starch
Cellulose→cell wall of plants
Modified saccharides:Galactosamines, N-acetyl glucosamines(chitin), Glycoproteins, Glycolipids
3. Lipids
・Hydrophobic organic compunds
・Energy storage
・Component of cellular membrane, bile, hormone
6 main groups
①Neutral fats
Usually triacylglycerol (triglyceride)
1 glycerol ＋ fatty acids (usually three)
Joined by ester bonds
2 types of fatty acids
・Saturated fatty acids; no double bonds
・Unsaturated fatty acids; contain one or more double bonds
②Phospholipids
1 glycerol ＋ 2 fatty acids ＋ 1 phosphate group
Amphipathic
Main component of cell membrane
③Carotenoids
Pigments (yellow, orange)
Consist of isoprene units.
Ex. vitamin A (retinal), β-carotene
④Steroids
Synthesized from isoprene units
Ex. Cholesterol (component of cell membrane), sex hormones, bile, cortisol
⑤Sphingolipids
Sphingomyelins; sphingosine ＋ phosphate ＋lecithin
Cerebrosides; sphingosine ＋ hexose
→membrane or myelin sheath in nerve tissue
⑥Prostaglandins
Unsaturated fatty acid ＋ cyclopentane
4. Amino acids
Organic compounds containing amino group and carboxyl group on the same carbon atom.
Make up peptides or proteinjoined by peptide bond.
20 common amino acids
Polar － asparagine(Asn), glutamine(Gln), etc.
Non-polar － alanine(Ala), valine(Val), etc.
Acidic － aspartic acid(Asp), glutamic acid(Glu)
Basic － arginine(Arg), lysine(Lys), histidine(His)
Contain surfer－ cysteine(Cys), methionine(Met)
10 essential amino acids (adult; 9, child; 10)
バス雨降り一色
バ(Val; valine)･ス(Thr; threonine)･ア(Arg; arginine→child only)･メ(Met; methionine)･フ(Phe; phenyl alanine)･
リ(Lys; lysine)･ヒ(His; histidine)･ト(Trp; tryptophan)･イ(Ile; isoleucine)･ロ(Leu; leucine)
5. Proteins
Basically polymer of amino acids (polypeptide) making up globular or fiber proteins.
4 levels of structure
①Primary
Sequence of amino acids joined by peptide bond.
②Secondary
Regular (repeating) structure
Hydrogen bond between amino acids
α－helix; elastic
β－pleated sheet; flexible but not elastic
triple helix; collagens
③Tertiary
3-D structure of the whole polypeptide
The bonds stabilizing tertiary structure of protein are;
Ionic bond
Disulfide bond (－S－S－)
Hydrogen bond
Van der Waals force
④Quaternary
More than 2 polypeptide chains (subunits).
Simple protein; composed of only amino acids
Complex protein; not only amino acids. →prosthetic group other organic compounds(saccharides, lipids)
Metal
Domain →the parts responsible for function.
Primary structure determines 2, 3, 4 structures helped by chaperons (heat shock protein).
Ex. sickle－cell anemia
glutamic acid (ionic)→(change to)→valine (hydrophobic)→less soluble in water→hemoglobin crystallized
External factors result in changes
Denaturation (irreversible coagulation); heat, heavy metals, strong acid
Reversible coagulation; light metals, weak acid
6. DNA
Antiparallel, double stranded (double helix) polynucleotide (hetero polymer).
Contains genetic information coded in specific sequence of bases.
Structure;
Each nucleotide composed of 1 base, 1 sugar (pentose), 1 phosphate
・base purine; A, G
pyrimidine; T, C
・pentose; deoxyribose
・phosphate
A base and a pentose together called nucleoside
→nucleotide = nucleoside ＋ monophosphate.
Nucleotides are joined by phosphodiester bonds.
Complimentary base pairing
A = T (2 hydrogen bonds), G ≡C (3 hydrogen bonds)
7. RNA
A family of single stranded polynucleotide that function mainly in protein synthesize.
Structure; similar to the DNA
Differences
3 types of RNA
①m－RNA (messenger RNA); transcribe genetic information from DNA
②t－RNA (transfer RNA); bring amino acids to the ribosome. Have anticodon.
③r－RNA(ribosomal RNA);component of ribosome which catalyze the transformation of amino acids(ribozyme)
8. ATP and coenzymes
(1)ATP
Energy source of an organism.
Contains chemical energy between phosphate; macroenergic bond
Structure
Adenosine (adenine ＋ ribose) ＋ triphosphate
ATP is synthesized through the cell respiration.
ATP releases energy as exergonic reaction. ATP →ADP ＋ Pi ＋ Energy
This energy is used in endergonic reactions.
(2)Coenzyme
The organic, detachable cofactors which attach to the allosteric site of apoenzymes.
Regulate the activity of enzymes. Ex. NAD＋, FAD, Coenzyme A →see also 24.
9. Comparison of prokaryotic cell and eukaryotic cell
Prokaryotes / Eukaryotesendomembrnane system / NO / YES
(nuclear envelope, ER, golgi, lysosome, chloroplast, mitcondria)
DNA structure / circular / chromatin with proteins
(histone, scafolding protein)
mitotic spindle / NO / YES
ribosome units / 70S (30S ＋ 50S) / 80S (40S ＋ 60S)
10. The cell nucleus
Control center of the cell
Prokaryotes; no envelope, floating in cytosol.
Eukaryotes;
Nuclear envelope (double membrane)
Lamina fibrosa (one of intermediate filament) attaching inner envelope stabilizes the structure.
Pores; responsible for selective transport of materials (RNA, protein, etc.)
Outer envelope is connected to the ER
Nucleolus
Chromatin structure (DNA＋protein) euchromatin (not visible)
Hetelochromatin (visible)
Nucleoplasm
11. Rough endoplasmic reticulum
An organelle participating in endomembrane system.
Its cytosolic surface looks like rough because many ribosomes attach to the RER.
Responsible for modification of polypeptides.
→N－glycosilation (adding saccharides to the nitrogen of side chain of certain amino acids, mostly asparagine)
Polypeptide (synthesized by ribosomes using the information of m-RNA) with SRP (signal recognition particle) at its head is injected to the lumen (inner space of RER).
→see also 14.
12. Smooth endoplasmic reticulum
An organelle participating in endomembrane system.
Its surface looks like smooth because ribosomes do not attach.
Responsible for lipids synthesis phospholipids
fatty acids
steroids
detoxification
→large amount in liver cells.
13. The Golgi complex
An organelle participating in endomembrane system.
Responsible for transport of polypeptides;
・vesicles with glycosilated polypeptide from RER fuse with
cis－face of golgi.
・modified polypeptides in golgi go to their termination through
trans－face of golgi.
→see also 14.
14. Protein traffic with in the cell
Cytosol → RER (rough endoplasmic reticulum)
①Proteins (polypeptides) are produced by ribosome using the information of RNA in cytosol.
②SRP (signal recognition particle) binds to the signal sequence of 5’ end of polypeptide.
③SRP binds to the receptor on RER.
④Polypeptide is injected into lumen of RER through translocon (channel protein).
⑤Signal sequence is removed by enzyme (signal peptidase)
⑥Modification of protein. (N-glycosilation, pruning (removal of some sugars), addition of other sugars)
RER →Golgi－apparatus
Polypeptide with polysaccaride is packaged into vesicle.
Vesicle fuses with cis-face of Gorgi-apparatus.
Signalize (phosphorilation, pruning, addition of sugars).
1.default (no-signal addition) →cell membrane
2.M-6-P (Mannose-6-Phosohate) →lysosome
3.special signals →RER (back to the RER)
4.special signals →stay in Gorgi
5.special signals →outside the cell (export protein)
Signalized protein reaches their terminal.
15. The lysosomes
Lysosomes are organelles that contain digestive enzymes (acid hydrolases).
They digest excess or worn out organelles, food particles, and engulfed viruses or bacteria.
Lysosomes can fuse with vacuoles and dispense their enzymes into the vacuole, digesting its contents.
(Primary lysosome + endosome →socendary lysosome)
The interior of the lysosomes (pH 4.8) is more acidic than the cytosol (pH 7).
(The constant pH of 4.8 is maintained by proton pumps and Cl- ion channels.)
Lysosomal enzymes are synthesizedin the rough endoplasmic reticulum(RER) and modified by N-glycosilation.
(adding sugars to the Nitrogen of R-chain of certain amino acids (Asparagine))
→Transported and processed through the Golgi apparatuswhere they receive a mannose-6-phosphate tag
(phosphorilation of mannose) that targets them for the lysosome.
16. Mitochondria
Mitochondriaarethe membrane-enclosed organelle, found in most eukaryoticcells.
Structure
A mitochondrion contains inner and outer membranes.
The inner mitochondrial membrane contains proteins with four types of functions;
1. Those that carry out the oxidation reactions of the respiratory chain.
2. ATP synthase, which makes ATP in the matrix.
3. Specific transport proteins that regulate the passage of metabolites into and out of the matrix.
4. Protein import machinery.
The inner mitochondrial membrane is compartmentalized into numerous cristae, which expand the surface
area of the inner mitochondrial membrane, enhancing its ability to generate ATP.
The matrix is the space enclosed by the inner membrane.The matrix contains a highly concentrated mixture
of hundreds of enzymes, whichthe major functions include oxidation of pyruvate and fatty acids, and the
citric acid cycle, ribosomes, tRNA, and several copies of the mitochondrial DNAgenome.
Functions
・Production of ATP (convert organic materials into cellular energy in the form of ATP)
This is done by oxidizing the major products of glycolysis: pyruvate and NADH that are produced in the
cytosol. This process of cellular respiration, also known as aerobic respiration.
・Apoptosis－programmed cell death
・Heme synthesis ・Steroid synthesis
17. Cytoskeleton
Cytoskeleton is a dense network of protein fibers, gives cells mechanical strength, shape, and their ability to move. Also function in cell division and in the transport of materials with in the cell.
Cytoskeleton is dynamic internal framework made of 3 types of protein filaments; microtubules,
microfilaments, and intermediate filaments. Both microtubules and microfilaments are formed from beadlike, globular protein subunits, which can be rapidly assembled and disassembled. Intermediate filaments are made from fibrous protein subunits and are more stable than the others.
(1) Microtubules
Hollow cylindrical fibers consisting of tubulin protein subunits (αandβ-tubulin), major components of the
cytoskeleton and found in mitotic spindles, cilia, flagella, centrioles, and basal bodies.
MAPs (microtubule associated proteins)
Structural proteins helps regulate microtubule assembly and cross-link microtubules to other cytoskeletal
polymers.
Motor proteins, kinesin and dynein, produce movement by using ATP.
(2) Microfilament
Thin fibers consisting of actin protein subunits, are important in cell movement.
They are found in muscle cells associated with another protein, myosin.
In cytokinesis, they produce cleavage furrow to separate into two daughter cells.
(3) Intermediate filament
They are intermediate in size between microtubules and microfilaments.
They strengthen the cytoskeleton and stabilize cell shape, examples are lamina fibrosa inside the nuclear
envelope, neuron filaments in axons of neuron cells, and keratin in hairs, nails, and skin.
18. Centrosome
In animal cells, centrosome is the main part of MTOCs (microtubule-organizing centers), the region of the cell
from which microtubules are anchored and possibly assembled.
It contains 2 centrioles which are oriented at right angles to each other.
(each centriole has a 9×3 structure consisting of 9 sets of three attached microtubules arranged to form a hollow cylinder)
During the cell division, centrosomes move to the poles of the cell and make up the mitotic spindle.
19. The cell membrane
The cell membrane is composed of phospholipid bilayer, cholesterols, proteins, and carbohydrates.
①Phospholipids (lipids in which 2 fatty acids and a phosphorous- containing group are attached to glycerol)
They associate as bilayers in water because they are roughly cylindrical amphipathic molecules
(The hydrophobic fatty acid chains associate with each other and are not exposed to water.
The hydrophilic phospholipid heads are in contact with water.)
The ordered arrangement of phospholipid molecules makes the cell membrane a liquid crystal.
(The hydrocarbon chains are in constant motion, allowing each molecule to move laterally on the same side of
the bilayer.)
Various transport and secretaryvesicles form from phospholipid bilayers and also merge with membranes of
the ER and Gorgi complex, facilitating the transfer of materials from one compartment to another.
Phospholipid bilayer presents a barrier to most polar molecules because the interior of it is hydrophobic.
②Cholesterol
Cholesterols play a role as a fluidity buffer.
At low temperature, they act as “spacers”between the hydrocarbon chains, restricting van der Waals
interaction that would promote solidifying.
At high temperature, they connect hydrophilic parts and stabilize membrane.
③Proteins
The 2 major classes of membrane proteins are Integral proteins and Peripheral proteins.
(1)Integral proteins
They are firmly bound to the membrane.
They are amphipathic. (their hydrophilic regions extend out of the cell or into the cytoplasm, while their
hydrophobic regions interact with the fatty acid tails of the membrane phospholipids (α-helix).
Transmembrane proteins; extend completely through the membrane.
Non-transmembrane proteins; do not extend all the way through the membrane.
(2)Peripheral proteins
They are located on the inner or outer surface of the membrane, usually bound to exposed regions of integral
proteins by noncovalent interactions.
Functions of membrane proteins are;
Anchoring (integrin), transport (channel protein, carrier protein), enzymatic activity (membrane-bound enzyme), signal transduction (receptor), cell recognition (antigen), intercellular junction.
④Hydrocarbons
They are exposed on the extracellular surface, and play roles in cell recognition and adhesion as glycolipids (carbonhydrates attached to lipids) or gycoproteins (carbonhydrates attached to proteins).
20. Membrane transport
(1)Passive transport; does not require energy
①Diffusion (or simple diffusion)
The net movement of particles (atoms, molecules, or ions) down its concentration gradient from a region of
greater concentration to one of lower concentration.
(gases (O2, CO2, N2), small polar molecules (H2O, glycerol), larger nonpolar substances (hydrocarbons)
Slightly larger polar molecules (glucose) and charged ions of any size are also pass through but slowly.)
②Facilitated diffusion
The passive transport of ions or molecules by a transport protein in membrane (channel protein, carrier
protein)
As in simple diffusion, net transport is down a concentration gradient, and no additional energy has to be
supplied.(ions, amino acids, sugars, water-soluble molecules)
(2)Active transport; require energy
①Primary active transport (carrier mediated active transport)
The transport of ions or molecules across a membrane against a concentration gradient or electrical gradient.
It requires both a transport protein with binding site for the specific substance and energy directly supplied by ATP.
(Na+－K+ pump, H+ pump (lysosome))
②Secondary active transport (cotransport)
The active transport of one substance against a concentration gradient by coupling its transport to the transport of another down its concentration gradient.
It requires energy but not from ATP directly.
(symport; Na+and glucose in the intestine
antiport; Na+and Ca2+)
21. Types of endocytosis
Endocytosis is the active transport of large substances into the cell by the formation of cytoplasmic vesicles or vacuoles enclosing the material, and then the material is released inside the cell.
There are 3 types of endocytosis; phagocytosis, pinocytosis, and receptor－mediated endocytosis.
①Phagocytosis (literally cell eating)
The plasma membrane encloses a large solid particles, such as a bacterium or food, forms a vacuoles around it, and moves it into the cell. The vacuoles then fuses with lysosomes, and ingested material is degraded.
②Pinocytosis (literally cell drinking)
The cell takes in dissolved materials.
Tiny droplets of fluid are trapped by folds in the plasma membrane, which pinch off into the cytosol as tiny vesicles.
The liquid contents of these vesicles are then slowly transferred into the cytosol.
③Receptor－mediated endocytosis
→see 22
22. Receptor－mediated endocytosis
A type of endocytosis in which extracellular molecules become bound to specific receptors on the cell surface, and then enter the cytoplasm enclosed in vesicles.
①Ligand (a molecule that binds specifically to a receptor) binds to receptors in coated pits of membrane.
②Coated vesicle forms by endocytosis.
③Coating detaches from vesicle.
④Contents are transferred to endosome.
⑤Ligand separates from its receptors.
⑥Endosome fuses with lysosome.
⑦Contents are digested and released into cytosol.
※Receptors are transported to membrane and recycled
Cells take up cholesterols from the blood by this process.
23. Endergonic and exergonic reactions
Exergonic reactions (spontaneous; energy releasing)
An exergonic reaction releases energy.
The total free energy in its final state is less than the
total free energy in its initial state. [⊿G is negative]
Ex) catabolisum
Endergonic reaction (not spontaneous; energy requiring)
An endergonic reaction is a reaction in which there is gain
of the free energy.
The free energy of the products greater than the free energy
of the reactant. [⊿G is positive]
Ex) anabolisum
24. Enzymes (structure, role)
Biological catalysts
Increase the speed of the chemical reaction
without being consumed by the reaction.
Decreasethe activation energy.
consist of only protein. Ex. pepsin
have two component; apoenzyme + cofactor
Neither the apoenzyme nor cofactor alone has catalytic activity.
※Cofactor; additional chemical component