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Chapter 7: Cellular Respiration and Fermentation :check:**, Chapter 6:…
Chapter 7: Cellular Respiration and Fermentation :check:
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Glucose metabolism
Glycolysis happen in cytosol
Energy investment
Steps 1-32
ATP hydrolyzed to create fructose-1,6 bisphosphate
Cleavage
Steps 4-5
6 carbon molecules broken into two 3 carbon molecules of glyceraldehyde-3-phosphate
Energy liberation
Steps 6-10
Two glyceraldehyde-3-phosphate molecules broken down into two pyruvate molecules – produces 2 NADH and 4 ATP
Chapter 8: Photosynthesis*
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Photosynthesis powers the biosphere
The biosphere, consisting of Earth's surface and atmosphere, is primarily powered by green plants' photosynthetic power, which replenishes organic molecules and produces oxygen.
Different Trophic levels
Heterotrophs rely on food from their environment, autotrophs create organic molecules from inorganic sources, and photoautotrophs, like green plants and algae, use light for energy.
Chloroplast
a green pigment, is synthesized in mesophyll, where carbon dioxide enters and oxygen exits through stomata.
Chloroplast anatomy
Outer and inner membrane separated by intermembrane space
Pigment molecules are present in a third membrane called the thylakoid membrane.
Thylakoids are made of membrane. Shroud the thylakoid lumen.
Granum – stack of thylakoids
thylakoid membrane and inner membrane is the stroma.
ATP synthesis in chloroplasts occurs through photophosphorylation, a chemiosmotic mechanism, and is driven by the flow of H+ from the thylakoid lumen into the stroma.
Two stages of photosynthesis
Stage1
: Light reactions, occurring in thylakoid membranes, utilize light energy to produce ATP, NADPH, and O2.
Photosystem II
initiates photosynthesis by oxidizing water, generating O2 and H+, and releasing energy in the electron transport chain (ETC), which is used to create the H+ electrochemical gradient.
The light-harvesting complex absorbs photons, transferring energy via resonance. The reaction center, P680*, is unstable, allowing quick energy transfer. The electron is captured and oxidized, producing oxygen gas. Water is used to replace the electron on P680+.
Enhancement Effect
PS1 And PS2 System
PSII is substantially activated by 680 nm light, but not PSI.
PSI is substantially activated at 700 nm, but not PSII.
Stage 2
: The Calvin cycle, which occurs in the stroma, utilizes ATP and NADPH to convert CO2 into carbohydrates.
Photosystem I
plays a crucial role in producing NADPH by adding H+ to NADP+, which depletes H+ from the stroma.
Z scheme
The zag energy curve form illustrates the fluctuating energy of an electron during photosynthesis, with the lowest energy initially in PSII, followed by light exciting the electron in PSII, and then being elevated to higher levels via Photosystem I.
Photosynthetic pigments
: Pigments absorb light energy and reflect others, like leaves which absorb red and violet wavelengths and reflect green ones. The wavelength of light a pigment absorbs depends on the energy needed to boost an electron.
Noncyclic and cyclic electron flow
Cyclic photophosphorylation
: It involves electron cycling, releasing energy to transport H+ into the lumen, driving ATP synthesis, and producing only ATP, with excited PSI electrons returning to PSI.
The
noncyclic
process, starting at PSII and transferring to NADPH, is a linear process that produces both ATP and NADPH in equal amounts.
Synthesizing Carbohydratesvia the Calvin Cycle
Calvin Cycle (aka Calvin-Benson Cycle) [Happen Stroma] CO2 incorporated into carbohydrates. Precursors to other organic molecules,energy storage. Requires massive input of energy.For every 6 CO2 incorporated, 18 ATP and 12 NADPH must be usedProduct is glyceraldehyde-3-phosphate (G3P)Glucose is later made from G3P in separate process
Phase 1 – Carbon fixation
The reaction product, a six-carbon intermediate, is formed when CO2 is incorporated into RuBP using the rubisco enzyme, resulting in the formation of approximately two 3-phosphoglycerate molecules.
Phase 2 – Reduction and carbohydrate production
ATP converts 3PG into 1,3-bisphosphoglycerate, which is reduced by NADPH electrons to glyceraldehyde-3-phosphate (G3P). Only 2 G3P molecules are used for carbohydrates, while 10 are needed for RuBP regeneration.
Phase 3 – Regeneration of RuBP
10 G3P are converted into 6 RuBP using 6 ATP
Photorespiration
Rubisco, a carboxylase, can also be an oxygenase, adding oxygen to RuBP and releasing CO2 through photorespiration, a wasteful process in hot and dry environments, particularly when CO2 is low and O2 high. It is preferred in C3 plants.
C4 plants
C4 plants have evolved a mechanism to minimize respiration by making oxaloacetate in the first step of carbon fixation using the Hook-Slack pathway. Leaves have two-cell layer organization, with mesophyll cells releasing CO2 via stomata and bundle-sheath cells releasing CO2 steadily.
CAM plants
which open their stomata at night, convert CO2 into malate, and close them during the day to conserve water, and break down malate into CO2 for the Calvin cycle.
Breakdown of Pyruvate
pyruvate is transported into the mitochondrial matrix
Dehydrogenase-mediated breakdown
Pyruvate, produced through glycolysis in the cytosol, travels through an outer membrane channel and an inner membrane H+/pyruvate synthesizer to reach the mitochondrial matrix.
Pyruvate is converted into an acetyl group and CO2 by pyruvate dehydrogenase, forming NADH. The acetyl group is transferred to CoA, then enters the citric acid cycle.
Oxidative Phosphorylation
create ATP, high energy electrons are extracted from FADH2 and NADH
ATP synthase is responsible for phosphorylation.
The inner mitochondrial membrane's lipid bilayer is impermeable to H+, allowing only protons to pass through ATP synthase, which harnesses free energy to synthesize ATP from ADP through chemical synthesis.
NADH oxidation makes most of the cell’s ATP
NADH oxidation generates an H+ electrochemical gradient, enabling the production of ATP, with a maximum yield of 30-34 molecules per glucose, but rarely reaching the maximum due to its anabolic applications.
ATP synthase
ATP synthase is a rotary machine that converts energy from the proton motive force of the H+ gradient into chemical bond energy in ATP, as confirmed by Racker and Stoeckenius, as it spins.
inner mitochondrial membrane are contained protein complexes and tiny chemical molecules.
redox reactions, accept and donate electrons.
An H+ electrochemical gradient is produced by the movement of electrons
NADH is oxidized to NAD+, with high-energy electrons transferred to NADH dehydrogenase. H+ is pumped into the intermembrane space, and electrons are transferred to ubiquinone. FADH2 is oxidized to FAD, and high-energy electrons are transferred to succinate reductase.
Electrons from ubiquinone travel to cytochrome b-c1, where some energy is used to pump H+ into the intermembrane space, and electrons are transferred to cytochrome c.
Electrons from cytochrome c are transferred to cytochrome oxidase, where energy is harnessed to pump H+ into the intermembrane space, transferring electrons to oxygen, and producing water.
Steps 1-3 generate a H+ electrochemical gradient, which, through ATP synthase, generates ATP from ADP and Pi, utilizing the energy within this gradient.
Citric Acid Cycle
The metabolic cycle involves the entry and exit of molecules, with a series of organic molecules regenerated in each cycle. Acetyl is removed from Acetyl CoA and attached to oxaloacetate to form citrate, releasing CO2, ATP, NADH, and FADH2 in a series of steps.
Connections Among Carbohydrate, Protein, and Fat Metabolism
Other energy-producing molecules like carbohydrates, proteins, and fats also enter the glycolysis or citric acid cycle at different points, increasing efficiency through the same pathways for breakdown.
Anaerobic Respiration and
Fermentation
In oxygen-deficient environments, two strategies can be employed: using substances other than oxygen as final electron acceptors in the electron transport chain, and producing ATP through substrate-level phosphorylation.
E. coli uses nitrate (NO3-) under anaerobic conditions and ATP via chemiosmosis even under aerobic conditions.
Fermentation
Fermentation breaks down organic molecules without net oxidation, which many organisms cannot use as an electron acceptor under anaerobic conditions. Glycolysis, which uses up NAD+ and produces too much NADH, is a dangerous solution. Muscle cells and yeast use pyruvate reduction and ethanol production, respectively, to produce less ATP than oxidative phosphorylation.
Chapter 6: Energy, Enzymes, and Metabolism
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Energy and Chemical Reactions
Energy, the ability to promote change or perform work, comes in two forms: Kinetic Energy, associated with movement, and Potential Energy, due to structure or location, including chemical energy.
Laws of Thermodynamics
The First Law of Thermodynamics, also known as the "Law of Conservation of Energy," states that energy cannot be created or destroyed but can be transformed into another type.
The Second Law of Thermodynamics states that energy transfer between forms increases a system's entropy, reducing the energy available for organisms to promote change.
Change in free energy determines direction of chemical reactions
Total energy is calculated by combining usable and unusable energy. Energy transformations increase entropy, which is unusable for work. Free energy (G) is the amount of energy available for work.
H = G + TS
The equation for enthalpy, free energy, entropy, and absolute temperature in Kelvin (K) is: H = enthalpy, G = free energy, S = entropy, and T = absolute temperature in K.
Spontaneous reactions
The spontaneous breakdown of sucrose to CO2 and H2O in a sugar bowl is not necessarily fast but can be slow, depending on the free energy change (ΔG). If negative, the process is exergonic and spontaneous.
ΔG = Δ H – T Δ S
Exergonic energy is released through a spontaneous reaction, with a negative free energy change (ΔG) at the zero point.
Endergonic reactions are not spontaneous and require the addition of energy to drive them, as indicated by ΔG>0.
Hydrolysis of ATP
Cells use ATP hydrolysis to drive reactions
An endergonic reaction can be coupled to an exergonic reaction, resulting in spontaneous reactions if the net free energy change for both processes is negative.
The reaction, with a kinetic energy of -7.3 kcal/mole, promotes product formation, which is utilized for various cellular processes.
Enzymes and Ribozymes
A spontaneous reaction is not always fast, as catalysts speed up the rate of a chemical reaction without being consumed, enzymes are protein catalysts in living cells, and ribozymes are RNA molecules with catalytic properties.
Activation energy
The reaction requires initial energy input, allowing molecules to reach bond rearrangement and achieve a transition state. Common methods to overcome activation energy include large amounts of heat and enzymes.
Enzymes lower activation energy by straining bonds, positioning reactants, changing local environment, and directly participating through very temporary bonding.
Other enzyme terminology
Enzyme-substrate complex
Active site – location where reaction takes place
Substrates The enzyme (hexokinase) binds to (ATP and glucose).
Enzymes exhibit high substrate specificity, using a lock and key metaphor for binding. The interaction also involves conformational changes, resulting in a highly specific and induced fit phenomenon.
Enzyme reactions
Saturation occurs when most active sites are occupied by the substrate, with Vmax indicating the velocity of reaction near its maximum rate.
Michaelis constant (KM) is a measure of substrate concentration, with higher KM enzymes requiring higher substrate concentration, which isinversely related to the affinity between enzyme and substrate.
Inhibition
Competitive inhibition occurs when a molecule binds to an active site, inhibiting the substrate's binding ability, resulting in an increase in the current KM and the need for more substrate.
Noncompetitive inhibition reduces Vmax without affecting Km, as the inhibitor binds to the allosteric site, not the active site.
Other requirements for enzymes
:Prosthetic groups are small, permanently attached molecules to enzymes, while cofactors are temporary inorganic ions that temporarily bind to enzymes, and enzymes are organic molecules that remain unchanged post-reaction.
Overview of Metabolism
Metabolic pathways involve chemical reactions coordinated by specific enzymes, including catabolic, anabolic, and endogenous pathways, which must be coupled to exergonic reactions.
Catabolic reactions
Reactants are broken down, used for recycling building blocks and energy to drive endergonic reactions, with energy stored in intermediates like ATP and NADH.
Two ways to make ATP
Substrate-level phosphorylation is a process where enzymes directly transfer phosphate from one molecule to another molecule.
Chemiosmosis is a process where energy stored in an electrochemical gradient is utilized to produce ATP from ADP and Pi.
Redox reaction
Electrons are removed from one molecule and added to another through oxidation, which involves the removal of electrons, and reduction, which involves the addition of electrons.
NADH
Molecules like NADH, adenine dinucleotide, are used to create energy intermediates, which can be used to make ATP and donate electrons during synthesis reactions.
Anabolic reactions
Biosynthetic reactions generate large or smaller molecules not found in food, requiring energy inputs from intermediates like NADH or ATP.
Regulation of metabolic pathways
Gene regulation involves turning genes on or off, while cell regulation involves cell-signaling pathways like hormones, and biochemical regulation involves feedback inhibition to prevent over accumulation of products.
High final product concentration binds to enzyme 1 and causes conformational change, inhibiting the enzyme's conversion of initial substrate into intermediate 1.
Recycling of Organic Molecules
Large molecules have a short half-life, which is the time it takes for 50% to be broken down and recycled, requiring efficient use and recycling by all living organisms.
The genome's expression enables cells to adapt to environmental changes, producing RNA and proteins when needed and breaking down when not, mRNA degradation conserves energy for unnecessary proteins, and removes faulty copies.
mRNA degradation
Exonucleases are enzymes that remove nucleotides from the end of a DNA molecule, while exosomes are multiprotein complexes that utilize exonucleases.
Proteasome
Ubiquitin tags are a complex that breaks down proteins using protease enzymes, allowing cells to degrade improperly folded proteins and rapidly degrade proteins to respond to changing cell conditions.
Lysosomes
Lysosomes are organelles that break down proteins, carbohydrates, nucleic acids, and lipids, with endocytosis taking up these substances, and autophagy recycling worn-out organelles.
Chapter11: Nucleic Acid Structure, DNA Replication, and Chromosome Structure :
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Nucleic Acid Structure
DNA
Chapter 12: Gene Expression at the Molecular Level
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Overview of Gene Expression
Gene function can be viewed at two levels: the molecular function of the protein product and the trait conferred by the gene, both of which are interconnected in determining traits.
Modern understanding
The "one gene, one enzyme" hypothesis is modified to include other categories of cellular proteins, such as hemoglobin, which consists of multiple polypeptides working together for a single function, unlike enzymes.
Central dogma
Transcription
:Produces a transcript (RNA copy) of a gene
This messenger RNA (mRNA) specifies the amino acid sequence of a polypeptide
Gene
DNA sequences are organized units that enable DNA segments to be transcribed into RNA, resulting in a functional product (GENE expression). Other genes code for RNA itself, such as Transfer RNA (tRNA) which converts mRNA into amino acids, and Ribosomal RNA (rRNA) part of ribosomes.
The promoter is a signal that indicates the start of transcription
The transcribed region contains information that specifies an amino acid sequence.
The terminator signifies the conclusion of transcription.
The regulatory sequence serves as a binding site for regulatory proteins, which play a crucial role in regulating the rate of transcription
**1. Initiation**
Step of recognition. The RNA polymerase in bacteria recognizes the promoter region due to the presence of sigma factor.
When DNA strands split close to the promoter to create an open complex, the stage is finished.
2.Elongation
RNA polymerase produces RNA synthesis uses an RNA template, also known as a coding strand. There is no usage of noncoding strands combined 5' and 3'.Thymine was replaced by uracil.
3.Termination
Termination sequence is reached by RNA polymerase.
causes the freshly formed RNA transcript and polymerase to separate from DNA
Translation
:Process of synthesizing specific polypeptide on a ribosome using the mRNA template
Additionally, RNA processing is a procedure that occurs in eukaryotes when pre-mRNA is converted to active mRNA.
The genetic material, consisting of genes, serves as the blueprint for an organism's traits. Structural genes code for polypeptides, which function as proteins within the cell. The structure and functionality of cells are determined by proteins' actions.
Eukaryotic transcription
RNA polymerase, a type of transcription factor, has basic features similar to prokaryotes but with more proteins in each step. It transcribes mRNA, nonstructural genes for rRNA and tRNA, and requires 5 general transcription factors.
RNA Processing
Bacterial mRNAs can be translated immediately, while eukaryotic mRNAs require processing into mature form. Introns are transcribed but not translated, while exons are found in mature mRNA. Splicing removes introns and adds tails and caps.
Splicing
Introns are present in many eukaryotic genes, with most structural genes having one or more. Spliceosomes, composed of snRNPs, precisely remove introns. Alternative splicing can produce different products, and rRNA and tRNA are self-splicing ribozymes that catalyze reactions.
Capping
Modified guanosine, attached to the 5' end, is necessary for mRNA to exit the nucleus and bind ribosome.
Poly A tail
The addition of 100-200 adenine nucleotides to the 3' end of a gene increases stability and lifespan in the cytosol but is not encoded in the gene sequence.
Translation and the Genetic Code
Genetic code is the sequence of bases in an mRNA molecule, read in groups of three nucleotide bases or codons. Most codons specify a specific amino acid, while degenerate code can specify the same amino acid multiple times.
Bacterial mRNA has a 5' ribosomal-binding site, with a typical polypeptide of a few hundred amino acids, and stop codons (UAA, UAG, or UGA) for termination or nonsense.
Reading frame
Start codon defines reading frame
Met –Gln -Gln -Gly -Phe -Thr
5’ –AUAAGGAGGUUACG(AUG)(CAG)(CAG)(GGC)(UUU)(ACC) – 3’
When a U is added, the reading frame is shifted, and the codons and amino acids listed change.
5’ –AUAAGGAGGUUACG(AUG)(UCA)(GCA)(GGG)(CUU)(UAC)C – 3’
Three RNA nucleotides make up the mRNA codon.
U of RNA is replaced by T of DNA.
The third RNA nucleotide in the tRNA molecule is called the anticodon permits tRNA binding to the mRNA codon
The Machinery of Translation
Translation of mRNA and tRNA ribosomes requires numerous parts, resulting in significant energy usage in most cells.
tRNA
Different genes encode different tRNA molecules, with tRNASer carrying serine. Common features include a cloverleaf structure, anticodon for mRNA to ribosome, and an acceptor stem for amino acid binding.
Aminoacyl-tRNA synthetase
The aminoacyl-tRNA synthetase catalyzes the attachment of amino acids to tRNA, resulting in charged tRNA or aminoacyl tRNA, and its ability to recognize appropriate tRNA is known as the "second genetic code."
The aminoacyl-tRNA synthetase binds to a specific amino acid and ATP, activates it through AMP covalent binding, releases pyrophosphate, and the correct tRNA binds to the synthetase, causing the amino acid to be covalently attached to the tRNA.
Ribosomes
Prokaryotes have one type of ribosome, while eukaryotes have distinct ribosomes in different compartments. Cytosolic ribosomes, composed of large and small subunits, are exploited by antibiotics to inhibit bacterial ribosomes.
Ribosome shape determined by rRNA includes distinct sites for tRNA binding and polypeptide synthesis, with P site representing peptide, A site representing aminoacyl, and E site representing exit.
The Stages of Translation
Initiation
The assembly of mRNA, the first tRNA, and ribosomal subunits requires the assistance of ribosomal initiation factors and energy input through GTP hydrolysis
Two eukaryotic differences in initiation include mRNAs having a guanosine cap at 5' end, recognized by cap-binding proteins, and a more variable start codon position, often using the first AUG codon.
Elongation
Aminoacyl tRNA binds to the A site by codon/anticodon recognition, using elongation factors to hydrolzye GTP for energy. Peptidyl tRNA is in the P site, while aminoacyl tRNA is in the A site.
Peptide bond formation occurs between amino acid at A site and growing polypeptide chain. Polypeptide is removed from tRNA at P site and transferred to amino acid at A site through peptidyl transfer reaction, catalyzed by rRNA (ribosome) as a ribozyme.
The ribosome moves towards the 3' end of mRNA, shifting tRNAs from P and A sites to E and P sites, and the next codon is at the A spot, causing uncharged tRNA to exit.
Termination
The translation ends when a stop codon, UAA, UAG, or UGA is found in the A site, which is recognized by release factors.
The polypeptide is attached to a tRNA at the P site and a stop codon at the A site, where a release factor binds to the stop codon, releasing the polypeptide.
which are composed of phosphate group, pentose sugar, and deoxyribose, and a nitrogenous base, with pyrimidines (Adenine, Guanine, Cytosine, Thymine).Formed from nucleotides (A, G, C, T)
Nucleotides are the building blocks of DNA and RNA, while strings are linear polymer strands. Double helix strands are two strands. Chromosomes are DNA linked to proteins, and the genome is the complete genetic material in an organism.
RNA
Nucleotides, composed of phosphate group, pentose sugar, and ribose, form RNA. Nutrines are Adenine and Guanine, while pyrimidines are Cytosine and Uracil.
Nucleotide numbering system
Sugar carbons range from 1' to 5', with a base attached to 1' carbon on sugar and a phosphate attached to 5' carbon on sugar.
Strands
Nucleotides are covalently bonded through a phosphatediester bond, with a backbone formed from phosphates and sugars. Bases project away from the backbone, written 5' to 3'.
Base-pairing
Erwin Chargoff's analysis of DNA base composition across various species consistently demonstrated that adenine (A) equals thymine (T), and cytosine (C) equals guanine (G).
Chargoff's rule maintains consistent width by pairing A with T and G with C
The structure of complementary DNA strands, which are 5'-3' and 3'-3', and antiparallel strands, which are 3'-5'.
An Overview of DNA Replication
In the late 1950s, three DNA replication models were proposed: semiconservative, conservative, and diffuse, with newly-made strands referred to as "daughter strands" and original strands as "parental strands."
1.The semiconservative mechanism in DNA replication involves producing DNA molecules with one parental strand and one newly created daughter strand
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*2. Conservative mechanism: Producing one double helix with both parental strands and the other with two new daughter strands.
3. Dispersive Mechanism: DNA replication involves the creation of DNA strands where new DNA segments are interspersed with the parental DNA.
Molecular Mechanism of DNA Replication
The origin of replication creates a replication bubble, forming two replication forks, and DNA replication proceeds outward from these forks, with bacteria having a single origin.
Eukaryotes have multiple origins of replication
DNA helicase
Binds to DNA and travels 5’ to 3’ using ATP to separate strand and move fork forward
DNA topoisomerase
Relives additional coiling ahead of replication fork
DNA polymerase is single-strand binding proteins
Keep parental strands open to act as templates
Features of DNA polymerase
DNA polymerase cannot start synthesis on a bare template strand and requires a primer, which is created from RNA and replaced with DNA later, working only 5' to 3'.
RNA primers are converted to DNA by DNA polymerase III. DNA primase returns to the fork's opening and creates a second primer for lagging strand RNA.
DNA polymerase III transcribes RNA primers into DNA. DNA primase makes a second primer for lagging strand RNA by going back to the fork's opening.
DNA ligase creates a covalent link between the first and second Okazaki fragments in the lagging strand. An additional Okazaki
A fragment is produced. The main thread keeps becoming longer.
Leading strand
DNA is synthesized as a single long molecule, with DNA primase producing a single RNA primer, and DNA polymerase adding nucleotides in a 5' to 3' direction.
Lagging strand
DNA is synthesized 5' to 3' as Okazaki fragments, which consist of RNA primers and DNA.
In both strands
DNA polymerase removes RNA primers from both strands and replaces them with DNA, while DNA ligase joins adjacent DNA fragments.
DNA replication is very accurate
Three mechanisms for accuracy in DNA repair include stable hydrogen bonding between A and T and G and C, the active site of DNA polymerase unlikely to form bonds if mismatched pairs are present, DNA polymerase proofreading to remove mismatched pairs, and other DNA repair enzymes.
Telomeres
In eukaryotes, a series of short nucleotide sequences at chromosome ends is a unique form of DNA replication found in telomeres, where the 3' overhang lacks a complementary strand.
The DNA polymerase enzyme struggles to copy the 3' end of a strand, causing chromosomes to become shorter. This problem necessitates the creation of upstream primers, as the telomerase enzyme attaches numerous DNA repeat sequences to chromosome ends.
Telomere shortening is linked to cellular senescence, reducing telomerase function as organisms age. 99% of human cancers have high telomerase levels.
Molecular Structure of Eukaryotic Chromosomes
Eukaryotic chromosomes, composed of chromatin and DNA-protein complex, are discrete units of genetic material, ranging from hundreds of millions of base pairs to 1 meter in length.
Radial loop domains interact with 30-nm fibers and nuclear matrix, with each chromosome in discrete territories. Compaction level is not uniform, with heterochromatin and euchromatin types.
Cell division
Cells prepare to divide, chromosomes become more compacted, with euchromatin being less compact and hetrochromatin being more compact, and metaphase chromosomes being highly compacted.
Montasir Alam Chowdhury 202205154
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