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2.​ Molecular Biology

​

2. 6 Structure of DNA and RNA

NUCLEOTIDES ​( ´ ω ` )

➔ DNA molecule - ​nucleotides​ (a subunit)

➔ Nucleotides:
◆ Phosphate​ group:
● Acidic
● Negatively charged part of nucleic acids
◆ Pentose​ sugar:
● Deoxyribose/ribose
◆ Nitrogenous​ base
● 1 or 2 rings of nitrogen atoms (purines & pyrimidines)
➔ Backbone​ of alternating sugar & phosphate - gives ​structure
➔ Nucleotides linked together through ​covalent bonds ​ between pentose sugar &
phosphate
➔ Base sequence of ​4 bases

*
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DNA vs. RNA ​＼(＾▽＾)／

DNA RNA
Pentose Sugar Deoxyribose Ribose

Bases ACG​T ACG​U

Strands Double-stranded Single-stranded

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DNA STRUCTURE ​(ﾉ◕ヮ◕)ﾉ*:･ﾟ✧

➔ Forms a ​double helix​ with a ladder structure

➔ Has ​2 strands​ - ​Antiparallel
◆ Opposite directions: ​5’ to 3’ and 3’ to 5​’
◆ Strands linked together by ​hydrogen bonds
➔ Bases:
◆ Purines [Adenine, Guanine]
● Made up of 2 rings (larger)
◆ Pyrimidines [Cytosine, Thymine (DNA), Uracil (RNA)]
● Made up of 1 ring (smaller)
➔ Complementary Base Pairing
◆ C - G = 3 hydrogen bonds
◆ T - A = 2 hydrogen bonds
➔ Bases arranged in triplets - ​codons
➔ Gene​ - section of DNA that ​encodes for proteins
◆ Have unique sequences of bases
◆ Codes for production of unique proteins
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◆ Combination of proteins give unique phenotype

PHOSPHODIESTER BOND ​｡ﾟ( ﾟ^∀^ﾟ)ﾟ｡

➔ Made through ​condensation reactions

2. 7 DNA Transcription, Translation and Replication

DNA REPLICATION ​(´･ ･`)

➔ Replication is ​semi-conservative
◆ New strands are formed from the template strand
◆ Original strand divides, ​free nucleotides​ are added to template strand
◆ Two strands are formed with ​50%​ of the original DNA
◆ Depends on ​complementary base pairing
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➔ Steps:
1. Starts with the ​unwinding of the DNA​ strands by the enzyme ​HELICASE
○ Creates a ​replication fork
2. The enzyme ​PRIMASE​ ​creates an ​RNA primer​ to mark the ​starting point
of the replication
3. The enzyme ​DNA POLYMERASE​ then ​adds DNA bases​ in the​ 5’ to 3’
direction
○ This process is ​continuous​ in the ​leading strand
○ The ​lagging strand​ cannot be replicated in the 5’ to 3’ direction as it
is going in the ​other direction
■ This strand is replicated ​non-continuously:
● PRIMASE​ ​adds an ​RNA primer​ to indicate ​start point
● DNA POLYMERASE​ ​fills in the gaps between the
RNA primers, these short strands are called
OKAZAKI FRAGMENTS
● EXONUCLEASE ENZYMES​ ​then ​removes all RNA
primers​ and ​DNA POLYMERASE​ ​then ​fills in the
gaps​ left behind
4. After the replication of both strands are completed, ​DNA LIGASE​ then
seals​ the new DNA strands together to ​make the helix
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➔ Leading vs. Lagging Strand:

Overview of enzymes:

Enzyme Function

Helicase ➔ Unwinds & separates DNA by

breaking the hydrogen bonds

DNA Primase ➔ Generates a short RNA primer

(~10–15 nucleotides) on each of
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the template strands

DNA Polymerase III ➔ Adds bases to primer​ strand by

reading the code

Exonuclease​ (DNA Polymerase I) ➔ Removes RNA primers

(this is not the name of the enzyme; it’s
just the type of enzyme)

Ligase ➔ Seals sugar-phosphate backbone

To allow for more efficient understanding please watch this video: ​death is
inevitable any form of resistance is futile

GENES ​(・∀・)ノ

➔ A gene is a​ section of DNA​ that is​ transcribed into RNA

➔ Sections of a gene:
◆ Promoter:
● Non-coding sequence responsible for ​initiation of transcription
● Binding site​ for RNA polymerase
◆ Coding Sequence:
● Causes DNA to​ unwind and separate​ after being bound to promoter
● Region that is ​transcribed by RNA polymerase
◆ Terminator:
● RNA polymerase will continue to transcribe the DNA until it reaches
a ​terminator sequence
➔ Antisense vs. sense:
◆ Antisense strand (template strand)​ - transcribed into RNA
◆ Sense strand (coding strand) ​- not transcribed into RNA
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➔ Amino acid sequence of polypeptide is determined by mRNA according to

genetic code

DNA TRANSCRIPTION ​(ﾉ>ω<)ﾉ :｡･:*:･ﾟ’★,｡･:*:･ﾟ’☆

➔ Transcription
◆ The​ synthesis of mRNA​ copied from DNA base sequences by​ RNA
polymerase
◆ Occurs along the ​antisense strand
◆ Free nucleotides exist in the cell which line up opposite their
complementary base partner
◆ Transcription occurs in a ​5’ → 3’​ direction
◆ Nucleosomes​ control transcription
➔ Overview of transcription:
1. Initiation:​ RNA polymerase binds to the promoter and causes the
unwinding and separating of the DNA strands
2. Elongation:​ RNA polymerase moves along the coding sequence,
synthesising RNA in a 5’ → 3’ direction
3. Termination:​ ​When RNA polymerase reaches the terminator, both the
enzyme and nascent RNA strand detach and the DNA rewinds
4. In eukaryotic cells, the mRNA undergoes​ post-transcriptional modification:
a. Capping​ by adding a ​methyl group to the 5’-end​ to protect it against
degradation by exonucleases
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b. Polyadenylation​, which is adding a ​poly-A-tail to the 3’-end​ and it

facilitates its export from the nucleus
c. Splicing​ which is the​ removal of non-coding sequences called
introns​. It increases the number of different proteins an organism
can produce

DNA TRANSLATION

➔ Ribosome:
◆ Made up of:
● Protein​ (for stability)
● Ribosomal RNA​ (for catalytic activity)
◆ Consists of:
● Small subunit​ - contains an mRNA binding site
● Large subunit​ - contains three tRNA binding sites:
○ an ​aminoacyl (​A​)​ site, a ​peptidyl (​P​)​ site and an ​exit (​E​)​ site
◆ Can be found free floating in cytosol or bound to rough ER
◆ Differ in size according to prokaryotes (70S) and eukaryotes (80S)
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➔ Transfer RNA (tRNA)

◆ Folds into a clover-leaf structure
◆ 4 key regions:
● The acceptor stem​ (3’-CCA) carries an amino acid
● The anticodon​ associates with the mRNA codon (via
complementary base pairing)
● The T arm​ associates with the ribosome (via the E, P and A binding
sites)
● The D arm​ ​associates with the tRNA activating enzyme
(responsible for adding the amino acid to the acceptor stem)
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➔ Steps:
1. Initiation
a. Involves the ​assembly of the three components​ that carry out the
process (mRNA, tRNA, ribosome)
b. First, the small ribosomal subunit binds to the 5’-end of the mRNA

and moves along it until it reaches the start codon (AUG)

c. Next, he appropriate tRNA molecule bind to the codon via its
anticodon (according to complementary base pairing)
d. Finally, the large ribosomal subunit aligns itself to the tRNA
molecule at the P​ ​site and forms a complex with the small subunit

2. Elongation
a. A second tRNA molecule pairs with the next codon in the ribosomal

A site
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b. The amino acid in the P site is covalently attached via a peptide

bond (condensation reaction) to the amino acid in the A site

c. The tRNA in the P site is now deacylated (no amino acid), while the

tRNA in the A site carries the peptide chain

3. Translocation
a. The ribosome moves along the mRNA strand by one codon

position (in a 5’ ​→ 3’ direction)

b. The deacylated tRNA moves into the E site and is released, while

the tRNA carrying the peptide chain moves to the P site

c. Another tRNA molecules attaches to the next codon in the now

unoccupied A site and the process is repeated

4. Termination
a. Involves the ​disassembly of the components​ and the release of a
polypeptide chain
b. Elongation and translocation continue in a repeating cycle until the

ribosome reaches a stop codon

c. Codons recruit a release factor that signals for translation to stop
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d. The polypeptide is released and the ribosome disassembles back

into its two independent subunits

CODONS AND THE GENETIC CODE ​∠( 」∠)＿

➔ The ​genetic code converts base sequences​ on mRNA into an ​amino acid
sequence
➔ Codon​ = sequence of three bases
➔ There are 64 possible codons
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➔ Each amino acid is carried by a ​tRNA​; it contains 3 complementary base

anti-codons
➔ The genetic code is ​universal
➔ Genetic code is ​transferable between species
➔ This ability is used to make human insulin in bacteria

2. 8 Cell Respiration

DIE MITOCHONDRIEN ​°˖✧◝(⁰▿⁰)◜✧˖°

➔ Structure

Structure Adaptive Functions

Outer mitochondrial membrane ➔ Separates contents of

mitochondrion from the rest of the
cell
➔ Creates compartment with ideal
conditions for aerobic respiration

Inner mitochondrial membrane ➔ Contains electron transport chain &

ATP synthase
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➔ Carries out oxidative

phosphorylation

Intermembrane ➔ Protons pumped into space by

electron transport chain
➔ Very small space; a high proton
concentration can be easily be
formed in chemiosmosis

Matrix ➔ Fluid inside mitochondrion

➔ Contains enzymes for krebs cycle
and link reactions

Cristae ➔ Tubular / shelf-like projections of

inner membrane
➔ Increases surface area for
oxidative phosphorylation

Mitochondrial ribosome & genetic ➔ Speeds up the coding of new

information proteins required within the
mitochondria
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ENERGY CONVERSION ​ ( )

➔ Cells require energy​ for:

◆ Synthesizing large molecules (DNA, RNA, proteins)
◆ Pumping molecules/ions across membranes by active transport
◆ Moving things around the cell (chromosomes, vesicles, protein fibres in
muscle cells that cause contraction)
➔ Adenosine Triphosphate (ATP)
◆ A ​high energy molecule​ that functions as an ​immediate power source for
cells
◆ Contains ​3 covalently bonded phosphate groups
● Store potential energy in their bonds
◆ Phosphorylation​ makes molecules less stable
● Hence ATP is a readily active molecule which contains high energy
bonds
◆ When ATP is hydrolysed (forms ADP + Pi), the ​energy stored is released
◆ Key functions:
● Energy currency​ of the cell
● May transfer released phosphate group to other organic molecules,
making them less stable
◆ Synthesised from ADP using energy from solar energy and oxidative
processes
➔ Anaerobic respiration
◆ Incomplete breakdown of glucose for a ​small yield of ATP​ (no oxygen)
➔ Aerobic respiration
◆ Complete breakdown of glucose for a ​large yield of ATP​ (with oxygen)
➔ Aerobic vs. Anaerobic:
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Anaerobic Aerobic

Reactants Glucose Glucose + Oxygen

Combustion Incomplete Complete

Energy yield Low (2 ATP) High (36 - 38 ATP)

Products Animals: Lactic acid CO​2​ + H​2​O

Yeast: Ethanol + CO​2

Location Cytoplasm Cytoplasm & Mitochondria

Stages Glycolysis Glycolysis

Fermentation Link reaction
Krebs cycle
Oxidative phosphorylation

➔ By staggering the breakdown, the energy requirements are reduced (activation

energy can be divided across several steps)

➔ Released energy is ​transferred to activated carrier molecules​ via ​redox reactions
➔ Redox reactions:
◆ Reduction: gain of electrons/hydrogen or loss of oxygen
◆ Oxidation: loss of electrons/hydrogen or gain of oxygen

GLYCOLYSIS ​⊂(´• ω •`⊂)

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➔ Harvests pyruvate by oxidizing sugar

➔ Main organic compound is ​sugar​ but lipids and proteins can be used as well
◆ Lipids are not preferred because they are harder to transfer and digest
◆ Proteins are not preferred because they release potentially toxic
nitrogenous waste when broken down
➔ Occurs in the ​cytosol
➔ A hexose sugar (6C) is converted into 2 molecules of pyruvate (3C)
➔ Steps:
1. Energy investment phase
a. Phosphorylation:
i. A hexose sugar is phosphorylated using 2 ATP
ii. Molecule is less stable; prevents diffusion out of cell
b. Lysis
i. Hexose bisphosphate (6C) split into 2 triose-phosphate (3C)
2. Energy payoff phase
a. Oxidation:
i. Hydrogen atoms removed from each 3C via oxidation to
reduce NAD​+​ to NADH (+ H​+​)
ii. 2 molecules of NADH are produced in total
b. ATP formation:
i. Some of the energy released is used to synthesise ATP
directly (substrate level phosphorylation)
ii. 4 ATP is generated in total (2 ATP per 3C)
+
➔ Net total = ​2 pyruvate + 2 ATP molecules + 2 NADH + H​
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➔ Aerobic respiration:
◆ Pyruvate is​ transported to the mitochondria​ for further breakdown
(complete oxidation)
➔ Anaerobic respiration (fermentation):
◆ Pyruvate is not broken down any further ​(incomplete oxidation)
◆ Remains in cytosol​ and is converted to ​lactic acid (animals)​ or ​ethanol +
CO2 (plants and yeast)
◆ Reduced hydrogen carriers are oxidised via aerobic respiration to restore
available stocks of NAD​+
◆ In the absence of oxygen, glycolysis will quickly deplete available stocks

of NAD​+​, preventing further glycolysis

◆ Fermentation of pyruvate​ involves a ​reduction reaction​ that oxidises

NADH (releasing NAD​+​ to restore available stocks)

LINK REACTION ​C= C= C= C= C=┌(;・ω・)┘

➔ Transports pyruvate into mitochondria

➔ Pyruvate (3C)​ is converted into ​Acetyl-CoA
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◆ Pyruvate is oxidized by NAD​+​, thus producing NADH

◆ The oxidized pyruvate (3C) is then decarboxylated by carboxy-lyases
(enzymes that catalyze decarboxylation) enzymes and loses one carbon
atom, thus forming acetyl
◆ CoA binds with the acetyl, giving the final product of Acetyl-CoA
◆ Happens twice​ since there’s 2 pyruvates
● End products = 2 pyruvates and 2 NADH
➔ Please do watch this video as it is very understandable: ​isnt link that guy from
zelda lmao

KREBS CYCLE ​(◕‿◕✿)

➔ Takes place in the ​matrix

➔ Acetyl-CoA becomes​ 3 NADH + 2 ATP + 1 FADH
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◆ End products: 2 ATP + 6 NADH + 2 FADH + 4 CO​2 ​ (2 krebs cycle per

glucose molecule since it makes 2 Acetyl-CoA)
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For more complete info regarding cycle of krebs please do watch this very nice
video​: ​krebby patty secret formula

ELECTRON TRANSPORT CHAIN ​(ノωヽ)

➔ Happens in the ​inner membranes​ of mitochondria

➔ Steps:
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◆ NADH goes to ​an electron receiver​ and gets ​oxidized

◆ The released electron is ​absorbed by the electron acceptor
◆ The oxidizing of the NADH also ​yields protons​, which are pumped and
moved to the intermembrane space​ using energy yielded from every time
the electron moves to a different receptor
◆ This process is basically repeated for FADH except that the FADH
receptor is not a channel, reducing the number of available spots for
proton pumping, reducing the amount of protons in the intermembrane
space
◆ When electrons reach the last electron protein channel, it moves back into
the matrix and associates with molecular oxygen, making ​oxygen the final
electron receiver,​ this makes it ready to form​ water
◆ The ​accumulation of protons ​in the intermembrane space causes a
concentration gradient​ which means that the protons will ​naturally flow
back to the matrix​ through the only channel available, the ATP synthase
◆ The protons passing through the ​ATP synthase spins its rotor parts,
providing it with ​energy​ to bind ADP with a phosphate ion, thus producing
ATP
◆ The protons then react with oxygen to form water

ATP synthase
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Electron transport chain

Here is video for most efficient understanding comrades: ​electron bzz bzz chain

2. 9 Photosynthesis

PHOTOSYNTHESIS ​(⊃｡•́‿•̀｡)⊃━✿✿✿✿✿✿

➔ Synthesis of organic compounds​ from​ inorganic molecules​ in the ​presence of

sunlight / using light energy
➔ An example of ​energy conversion
➔ Requires ​photosynthetic pigments
◆ Can be separated using chromatography
➔ Can only occur in certain organisms (plants, bacteria, fungi)
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➔ In plants, this occurs in ​chloroplasts

➔ Equation:

LIGHT SPECTRUM ​✺◟( • ω • )◞✺

➔ The electromagnetic spectrum​: range of all possible frequencies of

electromagnetic radiation
➔ Colours are ​different wavelengths of white ligh​t and range from red (~700 nm) to
violet (~400 nm)

PIGMENTS ​(　’ω’)旦~~

➔ Chlorophyll:
◆ Green pigment found in ​photosynthetic organisms
◆ Responsible for ​light absorption
◆ Absorbs most strongly blue, reflects most strongly green
➔ Absorption spectrum
◆ Indicates ​wavelengths of light absorbed​ by each pigment
➔ Action spectrum
◆ Indicates ​overall rate of photosynthesis​ at each wavelength of light
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➔ Strong correlation between cumulative absorption spectra of all pigments and

action spectrum

LIGHT AND DARK REACTIONS ଘ​ (੭ˊ ˋ)੭* ◌ੈ✩‧₊˚

➔ Two step process:

◆ Light - dependent reaction:​ converts light energy into chemical energy
(ATP)
◆ Light - independent reaction: ​uses chemical energy (ATP) into synthesize
organic compounds

➔ Reaction Steps
◆ L
​ ight Dependent (Step 1)

● Light absorbed by chlorophyll, excites electrons,​ produces ATP

​

● Light absorbed by water, splits (photolysis) ​produces oxygen and

hydrogen
◆ Light Independent (Step 2)
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● Light absorbed by chlorophyll, produces ATP

​

● Light absorbed by water, splits (photolysis) produces oxygen and

hydrogen
● Hydrogen and ATP used in light independent, oxygen released
from stomata as waste
● ATP and hydrogen (carried by NADPH) transferred to sight of light
independent
● Hydrogen combined with CO2, forms complex organic compounds
​

(carbohydrates, amino acids)

● ATP provides energy to power anabolic reactions, fix carbon
molecules together

CALVIN CYCLE ​∑d(°∀°d)

1. Step 1: Carbon Fixation

a. Begins with ribulose biphosphate (RuBP), a 5C compound
b. The enzyme rubisco catalyses the attachment of a CO​2​ molecule to RuBP
c. The resulting 6C compound is unstable and breaks down into 2 3C GP
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d. 1 cycle = 3 RuBP + 3 CO​2 →

​ 6 GP (glycerate-3-phosphate)
2. Reduction of GP
a. GP is converted into triose phosphate (TP) using NADPH and ATP
b. Reduction by NADPH transfers hydrogen atoms to the compound, while

the hydrolysis of ATP provides energy

c. 6 NADP + 6 ATP needed to form 6 TP
3. Regeneration of RuBP
a. One TP molecule from the 6 TP produced may be used to form half a
sugar molecule
b. Two cycles are required to produce a single glucose monomer
c. The remaining five TP molecules are recombined to regenerate stocks of

RuBP (5 ​× 3C = 3 × 5C)
d. Requires energy derived from the hydrolysis of ATP
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CHLOROPLAST ​☆*:.｡.o(≧▽≦)o.｡.:*☆

➔ Responsible for photosynthesis

➔ Contains ​membrane sacs (​thylakoids​) ​and ​arranged into stacks (​Grana​)
◆ Membrane sacs ​contains chlorophyll​ and site of light dependent
reaction
➔ Surrounding fluid matrix (​Stroma​)
◆ Contains carbon fixating enzymes and site of light independent
reaction
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Video video paling enak buat di pelajarin:

DNA REPLICATION YG 3D 3D ITU
DNA TRANSC AND TRANSL
MITOCHONDRIA STRUCTURE - 1:08
MITOCHONDRIA STRUCTURE JG BUT INDIAN
CHLOROPLAST STRUCTURE
CALVIN CYCLE
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