chapter 4
DESCRIPTION
Cell Metabolism for Ivy Tech Community CollegeTRANSCRIPT
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Chapter 4, Metabolism
Section 1, Chapter 4
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Cellular Metabolism
• Metabolism = Sum of all reactions in the body
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Anabolism• Synthesizes smaller molecules into larger molecules• Provides materials for growth and repair• Consumes energy
Catabolism• Large molecules decompose into smaller molecules• Releases energy for cellular use
Metabolic reactions are of two types
ATP = energy
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Dehydration Synthesis
• Type of anabolic reaction• Joins triglycerides, polysaccharides, and proteins• Water is formed from dehydration synthesis
Dehydration synthesis joining amino acids together
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Dehydration Synthesis
• Synthesizes polysaccharides from monosaccharides
• Synthesizes proteins from amino acids
• Joins fatty acids to glycerol, forming form fats
• Synthesizes nucleic acids from nucleotides
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Catabolism
• Reverse of Anabolism
• Breaks down molecules
• Releases energy from chemical bonds
• Example: Hydrolysis
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Hydrolysis
• Type of Catabolic reaction• Reverse of dehydration synthesis• Requires water to break bonds
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Hydrolysis
• Decomposes Polysaccharides into monosaccharides & disaccharides
• Decomposes proteins into amino acids
• Decomposes Fats into fatty acids & glycerol
• Decomposes Nucleic Acids into nucleotides
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AnabolismCatabolism
Anabolism & Catabolism are reversible reactions
Enzymes control direction & rate of reactions
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Enzyme Actions
Substrate
• Target molecule of an enzyme• Each enzyme acts on a specific substrate
Enzymes
• Are biological catalyst• They greatly reduce the activation energy required to start
a reaction.
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Enzyme Characteristics
• Most all are Proteins
• Catalyze reactions - Increases the rate of reactions
• Reusable - Not consumed by reaction
• Specificity – Able to “recognize” a specific substrate
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Enzyme Names
• Named for substrate they act upon
• Usually end with ____ ase.
• Examples:• Lipase: decomposes lipids• Protease: decomposes proteins• Nuclease: decomposes nucleic acids• ATP Synthase: synthesizes ATP molecules
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a. Active site
• Region of enzyme that binds to substrate
b. Enzyme-Substrate Complex
• Enzyme temporarily binds to substrate
Enzyme releases product
• Enzyme is reused to join new substrates
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Rates of reactions are limited by:
• The concentration of substrate
• The concentration of enzyme
• The efficiency of enzymes• Some enzymes handle 2-3 molecules per second• Other enzymes handle thousands per second
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Metabolic Pathways• Complex series of reactions leading to a product
• Pathways are controlled by several enzymes
Example: Catabolic pathway for the breakdown of glucose
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• The product of each reaction becomes the substrate of next reaction.
• Each step requires its own enzyme
• “Rate-Limiting Enzyme” • Least efficient enzyme in group • Rate-limiting enzyme is usually first in sequence
Metabolic Pathways
• Enzyme A = Rate-limiting Enzyme
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Negative Feedback in Metabolic Pathway
• Product of reaction often inhibits the rate-limiting enzyme.
• Negative feedback prevents the overproduction of a product.
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Cofactor
• Combines with and activates some enzymes• Exposes the active site of enzyme to substrate
• Cofactors are non-proteins
• Include ions (zinc, iron, copper) and coenzymes
Coenzymes = organic cofactors
• Coenzymes include Vitamins (Vitamin A, B, D)• Reusable – required in small amounts
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Vitamins• Essential organic molecules that humans cannot
synthesize - must come from diet
• Many vitamins are coenzymes
• Vitamins can function repeatedly, so can be used in small amounts.
• Example: Coenzyme A
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Energy for Metabolic Reactions
Energy: is the capacity to change something, or ability to do work.
Common forms of energy: HeatLightSoundChemical energyMechanical energyElectrical energy
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Energy cannot be created or destroyed. Only transferred from one form to another
Fuel (chemical energy) +
Oxygen
= Kinetic Energy + CO2 + H2O
Think of a combustion engine
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Cellular Respiration
• Cell Respiration: is the transfer of energy from food to make available for cellular use
• Energy is stored in the electrons of food molecules
• Oxidation: “controlled burning” of food molecules to release their energy
• Cellular respiration requires enzymes
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Cellular Respiration
Glucose (C6H12O6) + 6O2 → Energy for ATP + H2O + CO2
ATP
Energy from foods such as glucose is used to make ATP
End of Section 1, Chapter 4
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Chapter 4, Metabolism…continued
Section 2, Chapter 4
Mitochondria
Mitochondria
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Cellular Respiration
Glucose (C6H12O6) + 6O2 → Energy for ATP + H2O + CO2
ATP
Energy from Chemical bonds
Energy forATP synthesis
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Adenosine Triphosphate (ATP)Currency of Energy for cells
AdenosineTriphosphate
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Adenosine Diphosphate (ADP)
AdenosineDiphosphate
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ADP +
Phosphate+
Energy
ATP
hydrolysis
ADP
Energy released by hydrolyzing 3 rd phosphate group
Products:
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Cell respiration regenerates ATP
Phosphorylation of ADP resynthesizes ATP
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ATP provides energyFor metabolic reactions
Cell RespirationRegenerates ATP
Figure 4.8
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Cell Respiration
Anaerobic• No oxygen required• Yields little energy• Yields 2 ATP per glucose
Aerobic• Requires oxygen• Much greater energy yield• Up to 38 ATP per glucose
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glycolysis
Acetyl CoA synthesis
Citric Acid Cycle
Electron Transport Chain
4 Reactions of Cell Respiration
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Glycolysis
• Series of 10 reactions
• Breaks down glucose into 2 Pyruvic Acid molecules
• Occurs in Cytoplasm of Cell
• Anaerobic Reaction (no oxygen required)
• Yields • 2 ATP (net gain) per glucose• 2 NADH molecule• 2 Pyruvic Acid molecules
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• 2 Phosphates are added to end of glucose • Glucose is a 6-carbon sugar
• Primes glucose for further reactions
• Consumes 2 ATP
GlycolysisStep 1. Phosphorylation of glucose
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GlycolysisStep 2. Lyse glucose
Glucose (6 carbon)
Pyruvic Acid(3 Carbon)
Pyruvic Acid(3 Carbon)
2 NADH4 ATP
• 6-Carbon glucose is split into 2 3-carbon Pyruvic Acid molecules• Produces 4 ATP total • Produces 2 NADH molecules
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Glycolysis
+ 2 ATP net gain
- 2ATP consumed
+4 ATP produced
Products of Glycolysis• 2 ATP• 2 Pyruvic Acids• 2 NADH (electron carriers)
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PRODUCTION OF NADH & FADH2
1. NAD+ + 2H
• NADH
1• F
ADH
2
2
• NADH & FADH2 carry electrons from food to electron transport chain• The transport of electrons provides energy for ATP synthesis
2 electrons attached to hydrogen
NADH + H+HH+
2. FAD + FADH22H
NADH & FADH2 carry electrons to the electron transport chain
2 electrons attached to NADH
2 electrons attached to FADH2
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Products of Glycolysis• 2 ATP• 2 NADH (electron carriers)• 2 Pyruvic Acids
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Pyruvic Acid(3 Carbon)If Oxygen is
available
If no Oxygen is available
(anaerobic)
Aerobic Pathway
AnaerobicPathway
Fate of pyruvic acid depends on oxygen availability
Oxygen required to accept electrons from
NADH & FADH2
No oxygen to receive electrons from NADH
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AnaerobicPathway
NAD
2 electrons
Pyruvic Acid + Lactic Acid + NAD+H
Without Oxygen, NADH donates its electrons to pyruvic acid
Lactic Acid is formed as waste
This regenerates NAD+, which is used again for glycolysis
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AnaerobicPathway
Anaerobic Respiration• Inefficient reaction; yields only 2 ATP • Consumes a great deal of glucose• Quick source of energy; for intense exercise
End of Section 2, Chapter 4
Once oxygen is available:Lactic Acid is converted back to glucose by the liver
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Aerobic Respiration
Section 3, Chapter 4
mitochondria
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If Oxygen is available, pyruvic acid can continue through aerobic respiration inside the mitochondria
Pyruvic Acid(3 Carbon)
Aerobic Pathways Include:1. Acetyl CoA synthesis2. Citric Acid Cycle3. Electron Transport Chain (ETC)
Mitochondria
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Mitochondria• Powerhouse of cell• Synthesizes ATP• 2 layers
– Outer Membrane– Inner Membrane
• Cristae • highly folded inner membrane• Greatly increases surface area for reactions
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Synthesis of Acetyl CoA
Pyruvic Acid is converted into Acetyl CoA
Acetyl CoA = substrate for Citric Acid Cycle
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Synthesis of Acetyl CoAPyruvic Acid(3 Carbon)
Acetic Acid(2 Carbon)
CO2
(waste)
CoA
Acetyl CoA
(Enters Citric Acid Cycle)
(coenzyme A)
1 carbon is lost as CO2
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Products from Acetyl CoA Synthesis
• 1 molecule of CO2
• Acetyl CoA
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Citric Acid Cycle
Acetyl CoA + Oxaloacetic Acid → Citric Acid(2 carbons) (4 carbons) (6 carbons)
Citric Acid is converted back to Oxaloacetic acid through a series of 8-9reactions
Citric Acid = Start molecule of cycle
Oxaloacetic acid = end molecule of cycle
Begins when Acetyl CoA combines with Oxaloacetic Acid to form Citric Acid.
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Acetyl CoA(2 carbons)
Oxaloacetic Acid(4 carbons)
+
Citric Acid(6 Carbons)
Oxaloacetic acidis regenerated
2CO2
(waste) Citric Acid Cycle
8-9 reactions
FAD
FADH2
3NAD+3 NADH
2 ATP
2ADP
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• 2 ATP• 3 NADH = transports electrons to ETC• 1 FADH2 = transports electrons to ETC
• 2 CO2
Products of Citric Acid Cycle
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Electron transport chain (ETC)
• Occurs on inner membrane of mitochondria• ATP synthase (enzyme): phosphorylates ADP → ATP• Involves a chain of 3 enzymes (protein complexes)• Produces 32-34 ATP per glucose• Requires Oxygen to accept electrons
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Enzyme Complexes in ETC• Transport Complex Proteins
– 3 Membrane proteins on inner membrane of Mitochondria
– NADH & FADH2 transfer electrons to complex proteins
– Electrons are passed from one complex to the next complex
– Transfer of electrons releases energy to power ATP Synthase
• ATP Synthase– Phosphorylates ADP into ATP– Powered by Transport Complex Proteins
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½ O2(final electron acceptor)
NADH
2 electrons
Complex I
Complex II
Complex III
ATP SynthaseADP + PATP
NAD+(reused)
2H+
energy
energy
energy
+ H2O
ETC
Without Oxygen to accept electrons, ETC would grind to a halt!
Decreasing energy
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Products of Electron Transport Chain• H2O
• 32-34 ATP
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Lipids & Proteins can also be broken down
for ATP synthesis
Most common entry point to aerobic respiration is into citric
acid cycle as acetyl coA
Summary of catabolismof proteins, fats, & carbohydrates
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End of Section 3, Chapter 4
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DNA Replication & Protein Synthesis
Section 4, Chapter 4
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DNA RNAtranscription
Proteinstranslation
Pathway of Protein Synthesis
DNA Replication (DNA Synthesis)
DNA DNACopy of original
replication
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Definitions
Gene = portion of DNA that encodes for one protein
Genetic code = 3 letter DNA sequence that encodes for 1 amino acid
Genome = complete set of genetic instructions for an organism
Human genome = 46 chromosomes in diploid pairs
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Properties of DNA 1. double-stranded nucleic acid2. sugar phosphate backbone3. sugar = deoxyribose4. contains nitrogenous bases (B)5. stabilized by hydrogen bonds6. antiparallel strands (opposite directions)
Strand 2Strand 1
Antiparallel Hydrogen bonds
backbonebackbone
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Adenine & Guanine = Purines • 2 organic rings
Thymine & Cytosine = Pyrimidines• 1 organic ring
4 nitrogenous basesAdenine (A) Thymine (T)Cytosine (C) Guanine (G)
Properties of DNA
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Complementary Base Pairs
Purine pairs with Pyrimidine:
Adenine pairs with ThymineGuanine pairs with Cytosine
A & T = complimentary base pairG & C = complementary base pair
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C A C C T G GOriginal DNA strand:
Complimentary strand: G T G G A C C
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H-bonds stabilizecomplimentary
base pairs
DNA is twisted into adouble helix
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Overview of DNA Replication
• Occurs during S-phase
• Original DNA strand is used as a template to synthesize a new complimentary DNA strand.
• Catalyzed by DNA Polymerase – Synthesizes new DNA strand
• Semi-Conservative – One strand of the replicated DNA is new, the other is the original molecule.
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DNA Replication
A C T A A T A A C G G A T
A T T G C C T AT G A T T
Hydrogen Bonds
C T A G
G A T C
Original DNA strand
sugar phosphate backbone
Strand 1
Strand 2
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DNA Replication
A C T A A
T A A C G G A T
A T T G C C T A
T G A T T C T A G
G A T C
Step 1. Hydrogen bonds break, and strands separate
Replication bubble
DNA Polymerase
DNA Polymerase
Step 2. DNA Polymerases attach to open strands
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H bonds continue to break
DNA Replication
A C T A A
T A A C G G A T
A T T G C C T A
T G A T T C T A G
G A T C
Step 3. DNA Polymerase adds new bases
Replication bubble
A T T G C C
A TAGGC
T A
AT
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DNA Replication
A C T A A T A A C G G A T
A T T G C C T AT G A T T C T A G
G A T C
Step 3. DNA Polymerase adds new bases
A T T G C C
A TAGGC
T A
AT
C T A G
AATCA T T T
TTAGT
C
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DNA Replication
A C T A A T A A C G G A T G A T C
A T T G C C T A C T A GTTAGT
A T T G C C T AT G A T T C T A G
A TAGGCATAATCA T T T C
2 Complete DNA moleculesEach with 1 original strand & 1 new strand
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The two DNA molecules separate during mitosis
End of Section 4, Chapter 4
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Section 5, Chapter 4
Transcription & Translation
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Transcription
RNA synthesis from DNA template
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RNA molecule
1. single-stranded nucleic acid
2. sugar phosphate backbone
3. sugar = ribose
4. Uracil (U) replaces Thymine (T)U & A = complimentary base pair
Properties of RNA
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76
3 RNA Molecules
• Transfer RNA (tRNA):• Translates a codon of MRNA into an amino acid • Carries amino acids to mRNA• Anticodons on tRNA are complimentary to codons of mRNA•
• Ribosomal RNA (rRNA):• Provides structure and enzyme activity for ribosomes
• Messenger RNA (mRNA):• Transcribed from DNA in nucleus
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mRNA Molecules
Messenger RNA (mRNA):
•Delivers genetic information from nucleus to the cytoplasm
• Single polynucleotide chain
•Formed beside a strand of DNA
• RNA nucleotides are complementary to DNA nucleotides (exception – no thymine in RNA; replaced with uracil)
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DNA
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DNA mRNA
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Transcription
1. Synthesis of messenger RNA (mRNA) from DNA template
2. Occurs in nucleus
3. Only 1 of the DNA strands is transcribed
4. Transcription is catalyzed by RNA Polymerase
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A C T A C T A A C G G A T
A T T G C C T AT G A T G C T A G
G A T C
Step 1. RNA Polymerase attaches to DNA strands& breaks Hydrogen bonds
Strand 1
Strand 2
RNAPolymerase
DNA strands
Transcription
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A C T A A
T A C C G G A T
A T G G C C T A
T G A T T
C T A G
G A T C
Step 2. Strands Separate
Replication bubble
Step 3. RNA Polymerase synthesizes mRNAusing DNA strand as a template
A UG G C CU A C U A GRNAPolymerase
mRNA
Transcription
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A C T A A
T G A T T
Step 4. RNA Polymerase releases mRNA & DNA resumes original structure
T A C C G G A T G A T C
A T G G C C T A C T A G
A UG G C CU A C U A G
mRNA
RNAPolymerase
Transcription
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A C T A A
T G A T T
Step 5. mRNA is undergoes further processing & leaves nucleus
T A C C G G A T G A T C
A T G G C C T A C T A G
A UG G C CU A C U A G
mRNA
Transcription
DNA strands
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A UG G C CU A C U A G
Properties of mRNA
• Codon = 3 letter sequence that encodes for an amino acid • All mRNA begin with AUG “Start Codon”
Start Codon
mRNA
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Examples of CodonsNote: • Codons are redundant - Each amino acid corresponds to more than one codon
• e.g. UCU, UCC, and UCA all encode for Serine
•Start Codon (AUG) initiates translation
•Stop Codons terminate translation
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The codon sequence of mRNAdetermines the amino acid sequenceof a protein.
Figure 4.23
Protein Synthesis
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Translation =
Synthesis of proteins, using mRNA as template
1. Occurs on Ribosomes in cytoplasm
2. transfer RNA (tRNA) transports amino acids to mRNA
3. anticodons on tRNA align with codons on mRNA
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tRNA
1. Anticodon
2. Amino acid binding site
Clover-leaf shape RNA with 2 important regions
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Ribosomes
• Small particle of protein & ribosomal RNA (rRNA)
• Ribosomes have 2 subunits• Small subunit binds to mRNA• Large subunit holds tRNA & amino acids
• Small subunit has 2 binding sites for adjacent mRNA codons
• Ribosomes link amino acids by peptide bonds
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large subunit
small subunit
Binding sites with codons
anticodons
Peptide bond forming
Ribosomes
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1. mRNA binds to the small subunit of a Ribosome.
2. The ribosome ‘reads’ the mRNA sequence
3. tRNA brings amino acids to the ribosomes, aligning their anticodons with mRNA codons
4. The Ribosome links the amino acids together
5. Polypeptide chain lengthens
Sequence of Translation
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Translation- Figure 4.24Anchors polypeptide.
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Translation
tRNA released
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TRANSCRIPTION
TRANSLATIONFigure 4.23
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After translation Chaperone proteins fold protein into its configuration
Enzymes may further modify proteins after translation = post-translational modification• Phosphorylation – adding a phosphate to the protein• Glycosylation – adding a sugar to the protein
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End of Section 5, Chapter 4