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IB Biology Review

Chapters 3, 7, 8, 9
by

Sohyun Kim

on 20 April 2011

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Transcript of IB Biology Review

IB HL BIOLOGY Chapter 3: The Chemistry of Life
Chapter 7: Nucleic Acids and Proteins
Chapter 8: Cell Respiration and Photosynthesis
Chapter 9: Plant Science Chemical Elements and Water 3.1 Definitions:

Elements
pure substances that cannot be broken down further
chemically combine to form compounds

Atoms
particles of elements
combine chemically to form molecule (share electrons)
form covalent or ionic bonds (transfer electrons)

Ions
positively or negatively charged particle Proportions of Elements in Living Organisms:

Oxygen = 65% (2 covalent bonds)
Carbon = 19% (4 covalent bonds)
Hydrogen = 10% (1 covalent bond)
Nitrogen = 3% (3 covalent bonds) Water

1 oxygen + 2 hydrogen
slightly negative oxygen
slightly positive hydrogen
polar molecule

intramolecular force
covalent bond
105 degree angle

intermolecular force
hydrogen bond Photosynthesis 3.8 Cell Respiration 3.7 Enzymes 3.6 Transcription and Translation 3.5 DNA Replication 3.4 DNA Structure 3.3 Plant Structure Chapter Nine Carbohydrates, Lipids and Proteins 3.2 Organic Compounds
produced by living things
include all compounds containing carbon
except hydrogencarbonates, carbonates and oxides of carbon

Inorganic Compounds
all other compounds
less variety than organic Carbohydrates
compounds that contain carbon, hydrogen and oxygen
monosaccharides, disaccharides, and polysaccharides Condensation and Hydrolysis
2 monosaccharides = disaccharide + water
condensation reaction (produce water)
OPPOSITE = hydrolysis reaction (split with water)

glucose + glucose = maltose
glucose + fructose = sucrose
glucose + galactose = lactose Monosaccharides
glucose
fructose
galactose

Disaccharides
maltose
sucrose
lactose

Polysaccharides
starch
glycogen
cellulose Functions in Animals:
glucose = energy; broken to produce ATP
lactose = energy; milk
glycogen = energy storage (short term)

Functions in Plants:
fructose = energy
sucrose = transport and store energy
cellulose = fibre layers provide strength to cell wall Lipids
group of fats
come from animals and oils [from plants]
condensation reaction of glycerol + 3 fatty acids = triglyceride + water
fatty acids = carboxylic acids

saturated fat = no double bonds in carbon chain/ring
unsaturated fat = one or more double bonds in carbon chain/ring Functions
energy storage (long term)
thermal insulation
phospholipid bilayer in cell membrane Proteins
polypeptides = long chains of amino acids

Amino acid
central C atom
4 different groups attached
amine group (NH2)
carboxylic group (COOH)
simple -H group
R group (different in each amino acid) 2 amino acids = dipeptide
condensation reaction
creates a peptide bond between end carbon and N DNA Structure 7.1 DNA Replication 7.3 Transcription 7.3 Enzymes 7.6 Cell Respiration 8.1 Photosynthesis 8.2 DNA Structure 3.3 Proteins 7.5 Levels:
Primary
Secondary
Tertiary
Quaternary Primary Structure
seuqence of amino acids in chain
linear with peptide linkages
characterized by R group Secondary Structure
coils of the chain
hydrogen bonds
fibrous proteins = structural proteins

Examples:
alpha helix structure
beta pleated sheet Tertiary Structure
refers to folding of chain
interactions between R groups
hydrophobic groups cluster inside protein
hydrophilic groups cluster outside
several a.as have sulfur atoms
2 sulfur atoms + enzyme = covalent bond/disulfide bridge
hydrogen bonds also responsible for folding

Globular shape
e.g. hemoglobin, microtubules, enzymes
folding creates active sites where substrates bind Quaternary Structure
combination of different polypeptide chains
kept together by hydrogen bonds, attraction between + and - charges, hydrophobic forces and disulfide bridges

e.g. Heme group (of hemoglobin)
Heme group + 4 polypeptide chains

Conjugated proteins
with prosthetic group
e.g. chlorophyll and enzymes in ETC Functions:

Enzymes
globular proteins
Hormones
some proteins (e.g. insulin)
some steroids
Defense
antibodies/immunoglobulins
globular proteins
defense against antigens
Structure
collagen
fibrous, structural protein
builds tendons and for skin
Transport
hemoglobin
globular conjugated protein
binds to oxygen (due to heme group) Nucleic Acids
stores genetic information
long-chain molecules
building blocks = nucleotides
Two Kinds
deoxyribonucleic acid (DNA) in nucleus
ribonucleic acid (RNA) in cytoplasm

Nucleotides
pentose sugar
phosphate group
nitrogenous base Bases
adenine
cytosine
thymine
guanine
uracil

Purines
adenine and guanine
large two-ring structures

Pyrimidines
cytosine, thymine, uracil
small one-ring structures Linking DNA nucleotides
condensation reaction
phosphate + sugar + base = nucleotide + 2 water
sugar and phosphate = backbone of nucleic acid
covalent bonds between sugar and covalent
hydrogen bonds between bases of strands Structure of DNA
double helix
anti parallel
5' to 3' direction Structure of Nucleosomes
chromosomes are made of DNA, protein and a small amount of chromosomal RNA
DNA has negative charges along the strand
positively charged proteins (histones) are bonded via electrostatic forces
DNA + histone = complex = chromatin

DNA helix + 8 small histone molecules + H1 histone = nucleosome Importance of Nucleosomes
supercoiling helps organize DNA to fit into nucleus
prevents transcription by making the promoter region inaccessible
to start transcription, enzymes will alter the shape of the nucleosome and allow RNA polymerize to attach to the promoter region Nuclear DNA contains:
sequences for genes
sequences that regulate genes
sequences that have no function

Unique genes
a.k.a. single-copy/codable genes
carry our genetic material

Repetitive Sequences
no known function
used for parentage/forensics Exons and Introns
prokaryotes have uninterrupted sections of DNA

eukaryotes have discontinuous DNA
coding sections (exons) interrupted by non-coding intervening sequences (introns) h semi-conservative
one old strand + one new strand
occurs in a 5' to 3' direction (of the new strand)
begins at 3' end of template strand
1. helicase unwinds double helix

Leading Strand
2. RNA primase binds to the old DNA strand
3. DNA polymerase 3 binds free nucleotides to form complementary pairs with covalent bonds
4. deoxyribosenucleoside triphosphate - 2 phophates = deoxyribosenucleotide + 2 ATP

Lagging Strand
5. RNA primer formed via RNA primase
6. deoxyribonucleoside triphophates form hydrogen bonds with organic bases
7. DNA polymerase 3 bind DNA nucleotides to form Okazaki fragments
8. DNA polymerase 1 will remove RNA primer and replace RNA with DNA nucleotides
9. DNA ligase forms bonds the Okazaki fragments to create one strand DNA replication can occur at many points on the eukaryotic chromosome

1. replication bubbles form along DNA helix
2. bubbles grow as forks proceed in opposite directions
3. bubbles join as entire helix is replicated 3 kinds of RNA
rRNA (ribosomal)
mRNA (messenger)
tRNA (transfer) Protein Synthesis
transcription: RNA is produced from DNA template
translation: polypetide is assembled via RNA sequence Transcription
takes place in the nucleus
only one strand of DNA is transcribed (anti-sense)
mRNA has U instead of T
leaves through pores of nuclear envelope into cytoplasm Codons
genetic code is based on 3 nucleotides called codons
20 amino acids in total
more than one combination for each a.a
sequence of codons in mRNA = sequence of a.a in polypeptide Translation
ribosomes attach to mRNA
tRNA carry amino acids and anti-codon will bind to codon on mRNA
peptide bonds formed between amino acids
process stops when a STOP codon is reached (termination NOT coding) One Gene-One Polypeptide
every polypeptide is coded for by one gene
a gene only codes for one polypeptide

hemoglobin has 2 alpha and 2 beta chains
it requires 2 genes

Exceptions
transcription can produce rRNA or tRNA instead of mRNA
these are not translated/produce polypeptides enzyme-controlled process
synthesizing RNA from DNA
5' to 3' direction (of new RNA strand) Sense and Anti-Sense Strand
DNA strand = antisense strand
RNA strand = sense strand

they are complementary to each other
except RNA has uracil instead of thymine

mRNA = codons
tRNA = anticodons Transcription in Prokaryotes
involves promoter region
RNA polymerase can function in both directions
RNA nucleotides forms hydrogen bonds with DNA strand
ribonucleoside triphosphate will attach with a covalent bond to 3' hydroxl group of growing strand = ATP Mature mRNA
the entire section of DNA is transcribed into mRNA
introns need to be removed via splicing with splicesosomes
a phosphate cap is added to the 5' end and an adenine poly A tail will be added to the 3' end for protection and stability 7.4 Translation tRNA
clover shape
amino acids bind to 3' end in a 2 step process
catalyzed by its own tRNA-activating enzyme

1. a.a. react with ATP (activation)
2. a.a. binds to acceptor stem of tRNA

20 different amino acids = 20 different tRNA-activating enzymes
CCA at 3'form covalent bond with approprate amino acid = condensation reaction
during translation, bond between tRNA and a.a is broken
amino acid forms peptide link with polypeptide chain Initiation (in prokaryotes)
tRNA + amino acid + ATP ---> activated tRNA-amino acid complex + AMP

rRNA will recognize and attach to ribsomal binding site on mRNA near 5' end
small subunit will slide along mRNA until AUG is found
start codon is AUG so anti-codon = UAC (methionine)
large subunit joins complex Elongation
tRNA will bind to A site
anti-codon will bind to mRNA strand codons
amino acids will bond with peptide links
move along the A, P and E sites Termination
stop codons on mRNA are found near 3' end
when A site reaches this sequence, a protein release factor will arrive
break bond between polypeptide chain and last tRNA by hydrolysis
polypeptide is released from ribosome which will dissociate into subunits Distribution of Ribosomes
depends on function of the protein they make
proteins to be used inside cell = ribosomes found throughout cytoplasm
proteins to be exported or used by lysosomes = endoplasmic reticulum
enter lumen of RER, move to Golgi Apparatus and packaged into vesicles globular protein molecule
accelerates specific chemical reactions
biological catalysts
does not alter equilibrium
active site is region on enzyme's surface where the substrate attaches to during a reaction Enzyme-Substrate Specificity
lock and key model
substrate fits into active site as a key fits a lock

induced fit model
enzyme can alter its shape to fit the substrate Factors Affecting Enzyme Activity
temperature
pH
concentration of substrate Denaturation
structural change in a protein
results in loss of its biological properties

high temperatures and extreme pH can denature a protein
change of active site will cause loss in function Metabolic Pathways
chains and cycles of enzyme-catalyzed reactions
e.g. photosynthesis and cellular respiration Inhibition
molecules (inhibitors) can reduce rate of enzyme-controlled reaction

Competitive Inhibitors:
similiar to structure of substrate molecule
binds to active site of enzyme and prevents substrate from binding
increase substrate concentration to reduce effect

Non-Competitive Inhibitors:
binds to enzyme NOT on the active site
shape of active site changes and substrate cannot fit Allostery
kind of non-competitive inhibition
allosteric enzymes are made of 2+ polypeptide chains
activity is regulated by compounds (not substrates) called allosteric effectors
two types: allosteric activators (speed up) and inhibitors (slow down)

End Product Inhibition
end products of metabolic pathway can act as allosteric inhibitors
presence of high concentration of end-product
inhibit production on one of the enzymes somewhere in pathway
= no more endproduct will be produced

Allosteric Inhibition
molecule can bind to allosteric site of enzyme
change shape of active site so substrate cannot bind to it controlled release of energy from organic compounds in cells to form ATP
can take place with or without oxygen

Glycolysis
first stage
glucose ---> 2 pyruvate + ATP
located in cytoplasm
does NOT require presence of oxygen Anaerobic Cell Respiration
no oxygen present
glycolysis still occurs
pyruvate is converted into another substance

yeast cells: pyruvate ---> ethanol + CO2
human cells: pyruvate ---> lactate Aerobic Respiration
oxygen is present
pyruvate produced in cytoplasm will move to mitchondria
pyruvate broken down to CO2 and H2O Glycolysis
takes place in the cytoplasm
2 pyruvate for every glucose

Glucose + 2ADP + 2Pi + 2NAD+
------------------------------------>
2 Pyruvate + 2 ATP + 2 NADH + 2H2O + 2H+

1. phosphorylation (x2)
ATP is used to add phosphate group to glucose
produce hexose biphosphate (6C2P)
2. lysis reaction
produce 2 triose phosphate (3CP) or G3P
3. combined oxidation phosphorylation
DHAP ---> G3P
reduction of NAD+ to NADH
4. phosphorylation
does not require ATP
produce triose biphosphate
attach inorganic phosphate to triose phosphate
5. formation of ATP
ADP ---> ATP Mitchondria
large organelles found in eukaryotic cells Pyruvate Oxydation
link reaction
pyruvate transported to mitochondrial matrix

Pyruvate + CoA + NAD+ -----> Acetyl CoA + CO2 + NADH + H+ Krebs Cycle
Acetyl CoA will combine with C4 to become C6
will be decarboxylated twice ---> C5 + CO2 ---> C4 + CO2

each cycle will input one acetyl CoA
produce one CoA molecule and 2 CO2
also produce 3NADH + 3H+, 1 FADH2 + 1 ATP glycolysis:
glucose ---> 2 pyruvate + 2 ATP + 2NADH + 2H+

link reaction:
pyruvate ---> acetyl CoA + CO2 + NADH + H+

krebs cycle:
acetyl CoA ---> ATP + 2 CO2 + FADH2 + 3NADH + 3H+ Electron Transport Chain
NADH and H+ and FADH2 give electrons to electron carriers in inner membrane
electrons move through membrane
passed in a series of redox reactions
H+ are pumped from matrix into intermembrane space
creates concentration gradient
drives H+ back into the matrix through ATP synthase
energy will combine ADP and inorganic phosphate ---> ATP light energy converted into chemical energy
carbon dioxide and water are needed
presence of sunlight and chlorophyll are needed
produce glucose and oxygen Light
sunlight is white light made of all colors
different colors = different wavelengths
ultraviolet has shortest wavelength, infrared has longest wavelength on the visible spectrum Chlorophyll
most plants are green
color due to presence of pigment chlorophyll
found in chloroplast
main photosynthetic pigment
reflects green light and absorbs other colors Absorption by Chlorophyll
appears to be green
absorption spectrum shows the % absorption to wavelength Stages
light dependent
light independent Factors of Rate of Photosynthesis
chlorophyll requirement
temperature requirement
CO2 requirement
light requirement occurs in chloroplasts
cells in palisade layer have large number of chloroplast Light Reactions
light dependent and light independent stage Light Dependent
light energy splits water molecules into H+, O2 and e-
oxygen = waste = leaves chloroplast
H+ and e- will be used to produce ATP and NADPH

location = membrane of grana (stacks of thylakoid membrane)

non-cyclic photophosphorylation
cyclic photophosphorylation Non-Cyclic Photophosphorylation

photoactivation of photosystem 2
light absorbed by photosystem 2
excites some electrons to leave normal position
electrons taken by electron acceptor X
= chlorophyll 'a' molecule with positive charge
chlorophyll a+ will induce lysis of water

electron transport
electrons passed through # of electron carriers
in membrane via oxidation-reduction reactions
end up in photosystem 1

photoactivation of photosystem 1
light absorbed by PS1
electrons move away from nucleus
leave chlorophyll a molecule and taken by electron acceptor Y
passed on to NADP+ which combines with H+ to form NADPH
Chl a+ of PS1 receives electrons from electron carrier chain
becomes uncharged Chl a molecule Cyclic Photophosphorylation
electrons from PS1 go to electron acceptor Y
does NOT produce NADPH
returns to PS1
produces ATP
will not be able to enter Calvin cycle Light Independent Reactions
ATP (provides energy) and NADPH (provides reducing power)
Calvin Cycle takes place in the stroma of the chloroplast
three molecules of CO2 are combined to form G3P
RuBP is CO2 acceptor and is catalyzed by RuBisCo
GP reduced to triose phosphate (need NADPH)
RuBP is regenerated from triose phosphate (need ATP) Structure of Chloroplast
electron carriers are fixed in membrane of grana thylakoid
thylakoid membrane has a large surface area = many light-dependent reactions can occur at the same time
H+ ions are actively moved across thylakoid membrane into lumen of grana, which will be affected by [H+] due to small volume
Calvin cycle occurs in stroma of chloroplast
pH of stroma is around 8 In order for Saleem to reach Bombay and discover Mary, one final battle for supremacy must take place. Picture Singh, who claims to be world’s greatest snake charmer, takes his meager savings and travels to Bombay to assert his title. There can only be one greatest, according to Picture Singh, and he is willing to sacrifice everything to prove it. He succeeds in proving his skills, but only after he literally descends into a world of darkness, and nearly destroys himself in the process. Picture Singh’s victory is ultimately a defeat, or a ladder that becomes a snake. Even in its final moments, life proves to be ambiguous and full of ironies.


“Abracadabra” proves a fitting title for the novel’s final chapter, since the chapter is as much about the continued presence of magic as anything else. As Aadam Sinai’s first word, it suggests that, despite everything that has happened—the wars, the tragic deaths, and the chaotic political turmoil—the next generation of midnight’s children retain the magic of potential, and the ability to change the world. In Aadam’s mouth, it becomes a word of defiance, accumulated over the months of silent listening that marked the first three years of his life. A sense of cautious hope pervades the last chapter. Saleem is set to marry Padma, and in her strong body, he sees a flicker of hope that his own, cracked body might somehow be preserved. Perhaps, armed with Padma and with love, he won’t disintegrate and be consumed after all.

Despite all the changes and exiles he has undergone, Saleem ends up almost exactly where he began: at a house on Methwold’s Estate, his son in the care of Mary Pereira, just as he was once in her care himself. Saleem has succeeded in telling his story, thereby preserving it for his son, just as fruit gets preserved for chutney. That initial optimism is tempered, however, by Saleem’s final prophecy, which spills out in a stream of consciousness. Imagining his future, Saleem sees himself falling apart on his birthday and crumbling into millions of specks of dust, just as his grandfather Aadam crumbled into dust in his time. Saleem’s birthday is, of course, the anniversary of his nation’s independence. Crumbling into dust becomes a symbolic act of both exhaustion and unity. Having given everything he has within him—not only through his life, but through the telling of his story as well—Saleem can surrender himself, dissolving into a metaphor for his nation, as he crumbles into as many pieces of dust as there are people in India. "I fell victim to the temptation of every autobiographer, to the illustion that since the past exists only in one's memories and the words which strive vainly to encapsulate them, it is possible to create past events simply by saying they occurred." (443) "I was heading abracadabra abracadabra into the heart of a nostalgia which would keep me alive long enough to write these pages (and to create a corresponding number of pickles)..." (450) "Once again an abracadabra, an open-sesame: words printed on a chutney-jar, opening the last door of my life...I was seized by an irresistible determination to track down the maker of that impossible chutney of memory..." (456) "Abracadabra: not an Indian word at all, a cabbalistic formula derived from the name of the supreme god of teh Basilidan gnostics, containing the number 365, the number of the days of the year, and of the heavens, and of the spirits emanating from the god Abraxas. 'Who,' I am wondering, not for the first time, 'does the boy imagine he is?'" (459) "Tonight, by screwing the lid firmly on to a jar bearing the legend Special Formula No. 30: 'Abracadabra', I reach the end of my long-winded autobiography; in words and pickles, I have immortalized my memories, although distortions are inevitable in both methods. We must live, I'm afraid, with the shadows of imperfection." (459) "One day, perhaps, the world may taste the pickles of history...they possess the authentic taste of truth...they are, despite everything, acts of love." (461) "Yes, they will trample me underfoot, the numbers marching one two three, four hundred million five hundred six, reducing me to specks of voiceless dust, just as, all in good time, they will trample my son who is not my son, and his son who will not be his, and his who will not be his, until the thousand and first generation, until a thousand and one midnights have bestowed their terrible gifts and a thousand and one children have died, because it is the priviledge and the curse of midnight's children to be both masters and victims of their times, to forsake privacy and be sucked into the annihilating whirlpool of the multitudes, and to be unable to live or die in peace." (463) abracadabra (ăb"rukudăb'ru) [key], magical formula used by the Gnostics to invoke the aid of benevolent spirits to ward off disease and affliction. It is supposed to be variously worn as a protective charm
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