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
Chain form
Ring form
Aldose
CH2OH
Aldose (glucose) ketose (fructose)
H
H C O
H C OH
H
C
OH
HO
C
H
H
C
H
H
O
HO
C
H
OH
H
C
OH
C
OH
H
C
OH
C
H
OH
H
C
H
OH
O
H
OH
OH
OH
(α-D-glucose)
CH2OH
OH
(α-D-fructose)
CH2OH
H+
O
C
O
O OH
－
H
C O
OH
C
OH
H
OH
OH
OH
OH
－
OH
OH
OH
O
C
OH
HO2HC
O
OH
CH2OH
H
CH2OH
O
C
CH2OH
ketose
H+
OH
OH
OH
OH
α-glucose
OH
β-glucose
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)
CH2OH
O
OH
O－H
HO
OH
OH
CH2OH
O
O
OH
OH
OH
Condensation
Hydrolysis
HO2HC
(cellobioses make up cellulose)
2. Polysaccharides
CH2OH
O
C４
OH
Lactose (milk sugar);β-galactose ＋β-glucose (β-1,4-glycosidic linkage) OH
Cellobiose; β-glucose ＋β-glucose (β-1,4-glycosidic linkage)
C1
O
OH
OH
OH
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
OH
3. Lipids
・Hydrophobic organic compunds
・Energy storage
・Component of cellular membrane, bile, hormone
6 main groups
①Neutral fats
Fatty acids
Glycerol
O
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
2H
C
O
C
O
H
C
O
C
O
2H
C
O
C
ester bond
Fatty acids
Glycerol
1 glycerol ＋ 2 fatty acids ＋ 1 phosphate group
Amphipathic
O
2H
C
O
C
O
H
C
O
C
C
H2
Main component of cell membrane
③Carotenoids
P
Isoprene
hydrophobic
hydrophilic
β－carotene
Pigments (yellow, orange)
Consist of isoprene units.
Ex. vitamin A (retinal), β-carotene
OH
O
CH2
④Steroids
CH
Steran frame
Vitamin A
Retinal
Synthesized from isoprene units
Ex. Cholesterol (component of cell membrane), sex hormones, bile, cortisol
CH3
⑤Sphingolipids
(CH2)12
Sphingomyelins; sphingosine ＋ phosphate ＋ lecithin
Cerebrosides; sphingosine ＋ hexose
CH
HC
CH-OH O
CH-NH-C-R
→membrane or myelin sheath in nerve tissue
CH2-O-
- P ＋ lecithin
or
- glucose
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 protein joined by peptide bond.
H
20 common amino acids
H2N
Polar － asparagine(Asn), glutamine(Gln), etc.
Acidic － aspartic acid(Asp), glutamic acid(Glu)
Contain surfer － cysteine(Cys), methionine(Met)
COOH
R
Non-polar － alanine(Ala), valine(Val), etc.
Basic － arginine(Arg), lysine(Lys), histidine(His)
C
O
H2N
C
C
O
N
C
COOH
H
peptide bond
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
purine
pyrimidine
N
N
N
adenine
guanine
N
O P O
N
O
CH2
N
tymine
cytosine
A base and a pentose together called nucleoside
5’
→ nucleotide = nucleoside ＋ monophosphate.
Nucleotides are joined by phosphodiester bonds.
Complimentary base pairing
A = T (2 hydrogen bonds), G ≡ C (3 hydrogen bonds)
N
N
N
O
N
nucleoside
O
nucleotide
Phosphodiester
bond
O P O
O
N
CH2 O
N
3’
O
7. RNA
A family of single stranded polynucleotide that function mainly in protein synthesize.
Structure; similar to the DNA
Differences
・ribose (instead of deoxyribose in DNA)
・Uracil (instead of Tymine in DNA)
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
adenine
NH2
N
N
N
ribose
O
N
Structure
adenosine
H2C O P O
O
O
O
O
P O
P O
O
O
Adenosine (adenine ＋ ribose) ＋ triphosphate
ATP is synthesized through the cell respiration.
OH OH
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.
triphosphate
9. Comparison of prokaryotic cell and eukaryotic cell
Prokaryotes
Eukaryotes
YES
endomembrnane system
NO
(nuclear envelope, ER, golgi, lysosome,
chloroplast, mitcondria)
chromatin with proteins
DNA structure
circular
mitotic spindle
NO
YES
ribosome units
70S (30S ＋ 50S)
80S (40S ＋ 60S)
(histone, scafolding protein)
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
medial cysteinae
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.
cis-face
trans-face
→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)
①
Signal sequence
Golgi-apparatus
lumen
Cis-face
②
RER
SRP
(Signal recognition particle)
Translocon
(channel protein)
Receptor
for SRP
phosphorylation
Ribosome
core
③
ｍ-ＲＮＡ
polypeptide
polypeptide
polysaccaride
vesicle
RER → Golgi－apparatus
Polypeptide with polysaccaride is packaged into vesicle.
Vesicle fuses with cis-face of Gorgi-apparatus.
Lysosome
３
４
Signalize (phosphorilation, pruning, addition of sugars).
２
１
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.)
５
Lysosomal enzymes are synthesized in 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 apparatus where they receive a mannose-6-phosphate tag
(phosphorilation of mannose) that targets them for the lysosome.
16. Mitochondria
Mitochondria are the membrane-enclosed organelle, found in most eukaryotic cells.
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, which the major functions include oxidation of pyruvate and fatty acids, and the
citric acid cycle, ribosomes, tRNA, and several copies of the mitochondrial DNA genome.
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 (α and β-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 secretary vesicles 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
High
concentration
Ｎａ＋
Low
concentration
glucose
outside
inside
High
concentration
High
concentration
Ｎａ＋
Ca2+
Ｎａ＋
Ca2+
outside
Ｎａ＋
Low
concentration
inside
glucose
High
concentration
Low
concentration
Low
concentration
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.
②
Ligand
(LDL particle)
Clathrin recycled
①
③
LDL
receptor
Clathrin
④ ⑤
Endosome
Lysosome
Free
cholesterol
⑦
⑥
※receptor recycled
23. Endergonic and exergonic reactions
Exergonic reactions (spontaneous; energy releasing)
An exergonic reaction releases energy.
Free energy
reactants
energy
The total free energy in its final state is less than the
products
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.
Free energy
energy
products
The free energy of the products greater than the free energy
of the reactant.
Ex) anabolisum
[⊿G is positive]
reactants
24. Enzymes (structure, role)
Biological catalysts
active site
Increase the speed of the chemical reaction
substrate
apoenzyme
without being consumed by the reaction.
Decrease the activation energy.
consist of only protein. Ex. pepsin
have two component; apoenzyme + cofactor
cofactor
allosteric site
Neither the apoenzyme nor cofactor alone has catalytic activity.
※Cofactor; additional chemical component
inorganic; metals. Ex.magnesium ion, calcium ion, iron, copper, zinc
organic
coenzyme. Ex. NADPH, NADH, FADH2 ATP
prosthetic group. Ex. heme
※Coenzyme: An organic, nonploypeptide compound that binds to the apoenzyme and serves as a cofactor
25. Regulation of enzymatic activity
Activation of proenzyme. Ex. pepsinogen → pepsin
Allosteric modulation. Ex. cAMP dependent protein kinase (cAMP removes allosteric inhibitor)
feed back inhibition
Phosphorylation
Genetic control
induction
repression
Inhibition of enzyme
Reversible inhibition
competitive inhibition
noncompetitive inhibition
→(some feature in common with allosteric inhibition)
Irreversible inhibition
Feedback inhibition
1 Reversible inhibition (competitive, noncompetitive inhibition)
●competitive inhibition
In competitive inhibition, the inhibitor competes with the normal substrate for binding to the active site
of the enzyme
●noncompetitive inhibition
In noncompetitive inhibition, the inhibitor binds with the enzyme at site other than active site and
noncompetitive inhibition has some feature in common with allosteric inhibition
2 Irreversible inhibition
In
irreversible
inhibition,
an
inhibitor
permanently
inactivates
or
destroys
an
enzyme.
(Ex)inhibitor …heavy metals (Hg, Pb )
3 Feedback inhibition
A type of enzyme regulation in which the accumulation of the product of a reaction inhibits an earlier
reaction in the sequence also known as product inhibition.
26. Steps of aerobic respiration
The chemical reaction of the aerobic respiration of glucose are grouped into four stage that are Glycolysis,
Formation of acetyl CoA, Citric acid cycle and Electron transport chain. In eukaryotes, the first stage take place
in the cytosol and the rest stages take place inside mitochondria.
During aerobic respiration, nutrients are catabolized to carbon dioxide and water.
①Glycolysis
Series of reaction in which glucose is degraded to pyruvate.
(net profit of 2ATP;hydrogen atoms are transferred to carries; can proceed anaerobically )
②Formation of acetyl CoA
Pyruvate is degraded and combined with coenzyme A to form acetyl CoA
(hydrogen atoms are transferred to carries; CO2 released)
③Citric acid cycle
Series of reactions in which the acetyl portion of acetyl CoA is degraded to CO2
(hydrogen atoms are transferred to carries; ATP is synthesized)
④Electron transport chain
Chain of several electron transport molecules; electron are passed along chain; released energy is used to
form proton gradient; ATP synthesized as proton diffuse down gradient; oxygen is final electron acceptor.
glucose
2ATP
④Electron transport chain
G-3-P ×2
①Glycolysis
4ATP
2NAD+
2NADH+H+
H+ ＋
pyruvate ×2
cytosol
1
O ＋ e2 2
H2O
mitochondria
②Formation of acetyl CoA
ADP ＋ Pi
2CO2
2coA
2NAD+
ATP
2NADH+H+
acetyl－coA ×2
citrate
(C6)
oxaloacetate
(C4)
×２
③Citric acid cycle
2ATP
6NADH+H+
2FADH2
27. Glycolysis
Glycolysis is the first stage of respiration, literally splitting sugar.
In glycolysis, glucose is converted to two molecules of pyruvate in the cytosol and there is a net yield of 2 ATP
and 2 NADH molecules
Glycolysis is divided into two major phases, the energy investment phase and the energy capture phase.
Glycolysis
C6H12O6 + 2 NAD++ 2ADP → 2C3H4O3 + 2NADH + 2 ATP
Glucose
pyruvate
(1)The energy investment phase (＝endergonic reaction )
①In two separate phosphorylation reaction, a phosphate group is transferred from ATP to the sugar.
→substrate-level phoshorylation; ATP formed when a phosphate group is transferred to ADP from
phosphorylated intermediate.
[glucose → fulctose-1,6-bisphosphate]
2 ATP are used
②The fulctose-1,6-bisphosphate is converted to 2 glyceraldehyde phosphate(G3P)
(2)The energy capture phase (exergonic reaction)
G3P is converted to pyruvate.
4 ATP and 2 NADH + H+ are produced.
NADH + H+ produced in glycolysis is used in electron transport chain.
Cells in the heart, the liver, the kidney
Electrons stored in NADH + H+ are transported through malate－asparatate shuttle.
→ 3 ATP are synthesized from 1 NADH + H+
Cells in others
Electrons stored in NADH + H+ are transported through glycerophosphate shuttle.
→ 2 ATP are synthesized from 1 NADH + H+
28. Citric acid cycle
Citric acid cycle is series of chemical reaction in aerobic respiration.
In citric acid cycle, acetyl coenzyme A is completely degraded to carbon dioxide and water (NADH, FADH2) with
the release of metabolic energy that is used to produce ATP.
To summarize, citric acid cycle yields 4CO2, 6 NADH, 2 FADH2 and 2 ATP per glucose molecule.
Citric acid cycle
Acetyl CoA + 6 H2O → 4 CO2 + 6 NADH + 2 FADH2 + 2 ATP
electron transport chain
NADH+H+
acetyl－coA C2
citrate
C6
C4
isocitrate
oxaloacetate
FADH2
C4
NADH+H+
C6
C4 malate
C4 fumarate
succinate
8 H2O
ADP
ATP
GTP
GDP
α-ketoglutarate C5
succinyl-coA
C4
NADH+H+
29. The electron transport chain
The series of redox reactions which hydrogens or their electrons are passed along from one electron acceptor to
another, finally electrons are accepted by oxygen and form water.
During these reactions, protons are transported actively from matrix to inter membrane space, causing a
concentration gradient of H+.
H+ Concentration gradient causes energy for ATP synthesis by passing through the enzyme complex.
(ATP synthase)
NADH + H+ donates its electrons to the complexⅠ → 3 ATP are produced from 1 NADH + H+
FADH2
donates its electrons to the complexⅡ → 2 ATP are produced from 1 FADH2
H+
H+
H+ intermembrane space
H+ H+ H+ H+ H+
H+
complexⅠ
CoＱ
NAD+
H+
Ⅲ
Ⅳ
H+
2H+
complexⅡ
H+
NADH+H+
FADH2
FAD
matrix
H+ H+
H+
1
O
2 2
H+
H+
H+
inner
membrane
H2O
ATP synthase
H+
ADP + Pi
ATP
30. Fermentation
An anaerobic process for producing ATP
Final electron acceptor is organic compound, not oxygen.
①Lactate fermentation; microbes, human(muscle cells, red blood cells)
glucose
cytosol
2ATP
G-3-P ×2
4ATP
2NADH+H+
2NAD+
2NAD+
pyruvate ×2
lactate ×2
Lactates are formed from pyruvates in order to oxidize NADH + H+ to NAD+, and NAD+ are recycled.
②Alcohol fermentation; microbes(bacteria, fungi)
glucose
cytosol
2ATP
G-3-P ×2
4ATP
2NAD+
2NADH+H+
2NAD+
ethanol ×2
pyruvate ×2
CO2
Ethanols are formed from pyruvate in order to oxidize NADH + H+ to NAD+, and NAD+ are recycled.
31. The catabolic pathways of proteins and fats in the cell
Protein consist of amino acid and that are metabolized by reaction in which the amino group (-NH2) is first
removed, a process called deamination.
Therefore amino acid divided into amino group and carbon chain.
The amino group is converted to urea and excreted, but the carbon chain is used as a reactant in one of step of
aerobic respiration such as Glycolysis, Acetyl CoA and Citric acid cycle.
Ex) The catabolic pathway of proteins
Carbon chain
Step of aerobic respiration
Glycolysis
alanine
⇒
glutamate
⇒
Citric acid cycle
aspartate
⇒
Citric acid cycle
leucine
⇒
acetyl CoA
Fat which consists of Glycerol and fatty acid are also used fuel.
Phosphate is add to Glycerol, converting it to G3P (glyceraldhyde-3-phosphate) or another compound that
enters glycolysis.
Fatty acids are oxidized and split enzymatically into two-carbon acetyl groups that are bond to coenzyme A.
This process which occurs in the mitochondrial matrix is called β-oxidation.
32. Comparison of anabolic and catabolic reactions in the cell
Metabolism
Anabolism; simple → complex (endergonic)
Primary; inorganic → organic (photosynthesis; plants only)
Secondary; organic → organic (glucose → starch, glycogen; plants, animal, fungi)
Catabolism; complex → simple (exergonic)
Cellular respiration
33. The cell cycle
The cell cycle is the period from the beginning of one division to the beginning of the next.
Interphase(G1 phase → S phase → G2 phase) → M phase
①G1 phase (first gap phase)
The cell is carrying out its normal function.
G1
Euchromatin state. (not visible)
S
46 single chromosomes
→ 2n (23 paternal and 23 maternal)
M
G２
46 DNA
②S phase (synthesis phase)
DNA is replicated.
M phase
(Mitosis and cytokinesis)
Still euchromatin state.
46 double chromosomes
→ 2n (23 paternal and 23 maternal)
92 DNA
③G2 phase (second gap phase; shorter than G1 phase)
Enzymes for mitosis are created.
Single chromosomes
G1
S
G２
2n
2n
2n
M
2n
Still euchromatin state.
2n
46 double chromosomes
→ 2n (23 paternal and 23 maternal)
Double chromosomes
92 DNA
④M phase (mitosis phase; contains cytokinesis)
Prophase → metaphase → anaphase → telophase → cytokinesis
→ see 40.
Cells are diploid cells (homologue chromosomes; 2 sets of chromosomes (1 paternal and 1 maternal)) through
the cell cycle.
Cell cycle is controlled by cyclins (regulatory proteins) and cyclin－dependent kinase (protein kinase)
34. DNA synthesis (= replication)
The process by which DNA is duplicated.
Origin of replication
Semiconservative.
⑥DNA polymeraseⅢ
Enzymes needed for replication are;
①topoisomerase → nicks in DNA (relining tension in DNA)
②DNA helicase → unwound DNA strands.
③SSB (single strand binding protein) or helix destabilizes protein
①topoisomerase
→ single strand DNA is fixed by this enzyme
RNA primer
④DNA primase → synthesize short RNA primer
③SSB
⑤DNA polymeraseⅠ
→ gap filling in the places between okazaki fragments.
②DNA helicase
⑥DNA polymeraseⅢ
→ synthesize new DNA strand by adding nucleoside triphosphate
(or nucleotide diphosphate)
(DNA polymeraseⅡ is needed for repairing of DNA)
⑦DNA ligase
→ connect DNA strand and the short section replaced
Direction of replication
by DNA polymeraseⅠ
5’
5’
3’
A
3’
A
T
C
C
A
T
OH
Leading strand
G
G
C
T
A
3’
5’
OH
3’
5’
T
C
G
G
3’
(bidirectional)
5’ 3’
Lagging strand
(Okazaki fragments)
3’
5’
5’
3’
3’ 5’
RNA primer
5’
5’
5’
①RNA primer is made by DNA primase
Direction of replication
②new strands are synthesized by DNA polymeraseⅢ
3’
5’
5’
5’
space of it is replaced by DNA polymeraseⅠ
3’
3’
③RNA primer is degraded,
④strands are combined by DNA ligase
5’
3’
5’
3’
5’
3’
Telomeres; end part of DNA (repeating, non-transcribed sequences)
At each replication, telomeres get a bit shorter.
First primer is not replaced by DNA
DNA
polymeraseⅠ
→ telomeres are used up after a certain number of replications
→ cells die after a limited number of cell divisions
3’
5’
5’
3’
ligase
3’
5’
5’
3’
End of DNA
3’
5’
5’
3’
telomere
3’
5’
5’
3’
35. Transcription in prokaryotes
Transcription is the synthesis of RNA complementary to the template DNA strand.
m-RNA contains information that specifies the amino acid sequences of polypeptide chains.
Transcription in prokaryotes occurs in the cytoplasm alongside translation.
①Initiation
・RNA polymerase (RNAP) recognizes and specifically binds to the
promoter region on DNA. (promoter is not transcribed)
At this stage, the DNA is double-stranded ("closed").
This RNAP/wound-DNA structure is referred to as the closed complex.
・The DNA is unwound and becomes single-stranded ("open") in the
Template strand of DNA
promoter
②Elongation
5’
3’
Translated
region
mRNA
3’
5’
vicinity of the initiation site.
This RNAP/unwound-DNA structure is called the open complex.
mRNA termination
Transcribed sequence
region
leader
sequences
・mRNA is elongated until RNAP recognizes a stop signal termination
trailing
sequences
Start codon Stop codon
sequence.
・New nucleotide is added to the 3’ end of growing chain by RNAP similar
polypeptide
to the DNA polymerase in DNA replication.
③Termination
・Transcription stops at the end of the stop signal.
When RNAP comes to the stop signal, it releases both the DNA
template and the new RNA strand.
(in eukaryotic cells, RNAP adds nucleotides to the mRNA after it
passes the stop signal)
Transcription does not require primer, but needs several proteins to initiate.
In prokaryotes, transcription and translation are coupled.
→ribosomes bind to the 5’ end of the growing mRNA and initiate translation before the mRNA is fully
transcribed. Usually degradation of the 5’ end of mRNA begins even before the polypeptide is complete.
The half-life (the time it takes for half the molecules to be degraded) of mRNA in prokaryotes is only about 2
minutes.
36. Transcription in eukaryotes
In prokaryotes, mRNA is translated as it is transcribed from DNA.
However, this cannot occur in eukaryotes because eukaryotic chromosomes are confined to the cell nucleus, and
protein synthesis take place in the cytosol.
Before it is translated, eukaryotic mRNA is transported through the pores in the nuclear envelope and into the
cytosol.
Before mRNA is transported from nucleus, posttranscription occurs. (→see under)
5’ cap and poly-A tail are considered that they help export the mRNA from the nucleus, stabilize against
degradation in the cytosol, and facilitate initiation of translation.
Eukaryotic mRNAs are much more stable than prokaryotic one. Their half-lives range from 30 minutes to as
long as 24 hours.
The average half-life of a mammalian cell is about 10 hours.
Pre-mRNA
Start codon
①A DNA sequence containing both exons and introns
Stop codon
5’
is transcribed by RNA polymerase to make
3’
G
pre-mRNA.
exon
②Pre-mRNA is capped by the addition of a modified base
intron
5’
3’
G
A
(7-metylguanosine cap) to its 5’ end.
A
③A poly-A (adenine) tail is added to the 3’ end.
mature-mRNA
3’
5’
G
A
A
④Splicing (removal of introns and exons are spliced
nucleus
together).
cytosol
⑤The mature mRNA is transported through the nuclear
3’
5’
G
A
envelope.
A
37. Translation
The conversion of information provided by mRNA into a specific sequence of amino acids in a polypeptide chain.
This process requires tRNA and ribosomes.
①Initiation
Initiation factors bind to the small ribosomal subunit.
The small ribosomal subunit with initiation factors binds to mRNA
Small rebosomal subunit
in the region of start codon (AUG).
Start codon
3’
5’
The initiator tRNA binds to the start codon, and one of the initiation
factors is released.
The large ribosomal subunit binds to them, remaining initiation
mRNA
factors are released, the initiation complex is complete.
Initiation factor
MET (fMET in bacteria)
Initiator tRNA
Large ribosomal
subunit
P site
A site
E site
5’
3’
3’
5’
Initiation complex
②Elongation
Cyclic process in which amino acids are added one by one to the growing polypeptide chain.
Proceeds in the 5’ → 3’ direction along the mRNA.
Polypeptide chain grows from its amino end to its carboxyl end.
3 sites on the ribosome.
A site → tRNA with new amino acid
P site → tRNA with polypeptide
E site → site for exit
①The polypeptide chain is covalently bonded to the tRNA that
Amino acids
AminoacyltRNA
Carries the amino acid most recently added to the chain.
This tRNA is in the P site of the ribosome.
P
E
A
5’
3’
Aminoacyl tRNA binds to codon in A site
GTP → GDP
Amino acids
②An aminoacyl tRNA binds to the A site by complementary basepairing between the tRNA’s anticodon and the mRNA’s codon.
E
P
A
5’
3’
Peptide bond formation
③The growing polypeptide chain detaches from the tRNA in the
P site, and becomes attached by a peptide bond to the amino
Acid linked to the tRNA at the A site.
E
P
A
5’
3’
Translocation toward 3’ end of mRNA
GTP → GDP
④In the translocation step, the ribosome moves one codon toward
the 3’ end of mRNA.
As a result, the growing polypeptide chain is transferred to the
E
P
P site.
A
5’
3’
Uncharged tRNA in the E site exits the ribosome.
Back to ①, and these cycles are continued.
③Termination
Termination occurs when the ribosome reaches one of the three stop codons (UAA, UAG, UGA).
The A site binds to a release factor.
Release factor triggers the release of the completed polypeptide chain and dissociation of the translation
complex.
Release factor
①When the ribosome reaches a stop codon, the A site binds to
a protein release factor.
E
P
A
5’
3’
Stop codon (UAA, UAG, UGA)
Polypeptide
chain is
released
②The release factor hydrolyzes the bond between the
polypeptide chain and the tRNA.
A
E
It causes the release of the polypeptide chain from the tRNA
P
in the P site.
5’
3’
Stop codon (UAA, UAG, UGA)
③The remaining parts of the translation complex dissociate
E
P
A
5’
H O
H2N C C O
R
3’
3’
5’
Loop 2
※tRNA
Connection between the mRNA and polypeptide by having
Loop 3;
aminoacyla triplet codon (anti codon).
tRNA
3 loops
loop1 → anti codon (complementary to the codon in mRNA) synthetase
loop2 → for attachment to the ribosome
Loop 1;
anticodon
loop3 → for aminoacyl-tRNA synthetase (use 2 ATP (ATP → AMP ＋ 2Pi))
38. Comparison of eukaryotic and prokaryotic cell functions
→ see 9
→ compare 35 and 36
There are 3 types of RNA polymerase in eukaryotes, but only 1 type of RNA polymerase in prokaryotes.
RNA polymeraseⅠ; rRNA in big subunit of the ribosome
RNA polymeraseⅡ; mRNA
RNA polymeraseⅢ; tRNA, and rRNA in small subunit of the ribosome
39. Mutations
Types of mutations range from disruption of a chromosome’s structure to a change in only a single pair of
nucleotide bases.
Mutations that affect the base sequence of the DNA are;
(1)Base substitution → 1 base is changed to another (A ⇔ G (purine), C ⇔ T (pyrimidine))
①Silent mutation
1 base is changed, but the codon codes the same amino acid. Therefore no change in the amino acid
sequence and final product (protein).
Ex. TCC (the codon in mRNA is AGG which codes Arginine) → (C is changed to T)
→ TCT (the codon in mRNA is AGA which still codes Arginine)
②Missense mutation
1 base is changed, and the codon codes the wrong amino acid.
Ex. sickle cell anemia (the codon coding Glutamic acid (ionic) is changed to another codon coding
Valine (hydrophobic), and causes a change in the shape of hemoglobin)
③Nonsense mutation
1 base is changed, and the stop codon is created.
Ex. GCT (the codon in mRNA is CGA which codes Arginine) → (G is changed to A)
→ ACT (the codon in mRNA is UGA which is the stop codon)
(2)Frameshift mutation
①Insertion
1 or 2 nucleotides are inserted into the DNA, altering the reading frame.
As a result, a new sequence of amino acids is created downstream of the insertion site.
②Deletion
1 or 2 nucleotides are deleted from the DNA, also altering the reading frame.
40. Mitosis
The division of cell nucleus resulting in 2 daughter nuclei, each with the same number of chromosomes as the
parent nucleus. Cytokinesis usually overlaps the telophase.
4 phases
①Prophase
Early prophase
・nuclear envelope begins to disappear.
・nucleolus disappears.
・long fibers of chromatin become evident and begin to
condense as visible chromosomes.
(each chromosome is duplicated in S phase, composed of
a pair of sister chromatids)
Late prophase
・chromosomes continue to shorten and thicken.
centromere
Kinetochore
(protein)
2 chromatids
(a pair of sister chromatids)
・mitotic spindle begins to form.
②Metaphase
・chromosomes aligned on the metaphase plate.
(equatorial plane)
・mitotic spindle is complete
3 types of microtubules in mitotic spindle
1
①kinetochore microtubules
→ attach to kinetochore on the chromosomes, and to
centrosome (in animal cells, each centrosome contains
2
2 centrioles).
3
Centrosome is also called MTOC
(microtubule－organizing center).
②astral microtubules
→ anchor the centrosomes to the
③pole to pole microtubules
→ fixation of the mitotic spindle
poles.
③Anaphase
・Anaphase begins as the sister chromatids separate.
・The new separate chromosomes move to opposite poles,
using the spindle microtubules as tracks.
(once the chromatids are separated, each chromatid is called
chromosome)
・ Anaphase ends when all the chromosomes have reached
the poles.
④Telophase
・Anaphase begins as the sister chromatids separate.
・The new separate chromosomes move to opposite poles,
using the spindle microtubules as tracks.
(once the chromatids are separated, each chromatid is called
chromosome)
・ Anaphase ends when all the chromosomes have reached
the poles.
Cleavage furrow
41. Meiosis
42. Comparison of mitosis and meiosis
43. Lactose operon model
An operon is a group of key nucleotide sequences including an operator, a common promoter, and one or more
structural genes that are controlled as a unit to produce messenger RNA (mRNA). Operons occur primarily in
prokaryotes and nematodes(線虫).
Control of operon genes is a type of gene regulation that enables organisms to regulate the expression of various
genes depending on environmental conditions. Operon regulation can be either negative or positive. Negative
regulation involves the binding of a repressor to the operator to prevent transcription.
Repressor gene
Operon
Promoter Operator
・Repressor protein is translated and binds to the operator in
normal condition. (glucose (+) , lactose(－))
Structural
・When the allolactose (isomer of lactose) presents in the nucleus,
Operon
Repressor gene
Structural
gene
Promoter Operator
DNA
Z
Y
A
allolactose binds to the allosteric site of repressor protein.
・Thus, prepressor protein detaches from operator.
Allolactose
RNA-polymerase can bind to promoter.
Promoter Operator
DNA
・After detaching of repressor from operator,
Operon
Repressor gene
Z
Structural
gene
Y
A
transcription
RNA- polymerase
translation
Z
Y
A
・The structural genes「Z」
「Y」
「A」on DNA are now transcribed
and translated.