Unit 3

Protein Synthesis

• Biomolecules needed

  • Proteins

    • Long chains of amino acids

    • Come from the food that we eat

    • 20 different amino acids

    • DNA provides the sequence to link Amino Acid in the correct sequence

  • Nucleic Acid

    • Long chains of nucleotides

    • Two Types: DNA and RNA

• Types of nucleic acids

  • DNA (deoxyribonucleic acid)

    • 3 subunits of nucleotide

      • Phosphate

      • Deoxyribose sugar

      • Nitrogenous Bases

        1. Cytosine

        2. Guanine

        3. Adenine

        4. Thymine

    • Double Stranded

  • RNA (ribonucleic acid)

  • 3 subunits of nucleotide

    • Phosphate

    • Ribose sugar

    • Nitrogenous Bases

      • Cytosine

      • Guanine

      • Adenine

      • Uracil

    • Single Stranded

• 6 differences

  • Different bases RNA Ribose sugar, DNA deoxyribose sugar

  • DNA double stranded, RNA single stranded

  • Thymine DNA, Uracil RNA

  • DNA is larger with millions of nucleotides, RNA is small with thousands

  • DNA in nucleous, RNA primarily outside in cytosol

• Types of RNA

  • mRNA: messenger: Code of DNA

  • tRNA: transfer: transport the amino acid to the ribosome

  • rRNA: ribosomal: hooks the amino acid together

• Organelles

  • Nucleus: 

    • Houses the DNA which is the code for proteins

  • Ribosomes: Site of protein synthesis: 

    • Hook the amino acids together in a specific sequence

  • Rough Endoplasmic Reticulum: Highway:

    • Contains ribosomes

    • Transports the amino acid chain to the Golgi 

  • Golgi Apparatus: 

    • Folds, and modifies the amino acid chain into a functional protein

    • Then packages the protein to be sent to do its job.

• Steps of Protein Synthesis

  • Big Picture: DNA → RNA → Protein

    • Occurs in 2 Steps

      • Transcription: DNA → mRNA

      • Translation: RNA → Protein

• Transcription

  • Takes place in Nucleus

  • WHY?

    • DNA can’t leave 

  • How come?

    • Too big

    • Risk of damage = mutations

  • THEREFORE:

    • Make a copy into RNA of the gene

    • GENE = Only a section of the entire DNA Strand

• Steps of Transcription

  • Initiation

    • Enzyme called RNA polymerase binds to the TATA box(an area on the DNA that reads TATATAAT)

    • The DNA unwinds

  • Elongation

    • Complementary RNA nucleotides temporarily bind with coding strand of DNA

      • The complementary DNA strand is a placeholder for when the DNA rewinds

  • Termination

    • POly A tail are the end of the gene sequence RNA polymerase releases

    • pre-mRNA strand unbinds with the DNA

    • DNA rewinds

  • Modification

    • Introns are cut out and exons are spliced together

    • Exons leave the nucleus; now called mRNA

• Translation: mRNA →Protein

  • It needs 3 types of RNA

    • Messenger RNA: mRNA: Made in transcription: Copy of the gene’s DNA

    • Transfer RNA: tRNA: transfers the amino acids to the ribosomes

    • Ribosomal RNA: rRNA: hooks the amino acid together

  • The amino acid comes from the proteins that were eaten and then broken down into amino acid to be absorbed into the bloodstream.

  • Takes place in the cytoplasm

  • It needs the organelles of:

    • Ribosomes: hooks the amino acid together in a chain

    • Rough endoplasmic reticulum: transport the amino acid chain to the golgi

    • Golgi apparatus: folds, modifies, and packages proteins to do their “job”

• Steps of translation

  • Initiation

    • The mRNA binds to the rRNA at AUG

    • The tRNA picks up its specific amino acid (Methionine) from the blood

    • The three mRNA codon determines the first tRNA that binds by complementary codes

      • Remember: 3 mRNA letters = 1 codon = 1tRNA anti-codon

      • So, every 3 letters = 1 aa

  • Elongation

    • A second tRNA binds to the mRNA

    • The two amino acids bond

    • mRNA moves down 3 base pairs (1 codon)

    • First tRNA leaves

  • Termination

    • Elongation occurs until a STOP codon is reached

    • rRNA releases the mRNA, tRNA and amino acid chain

  • Modification

    • Amino acid chain goes to the Golgi to be folded and packaged for its job

• Mutations

  • What is a mutation?

    • Change in the DNA sequence that may ultimately change the amino acid sequence.

  • What causes mutations?

    • UV Radiation

    • Toxins

    • Smoke

    • Viruses

    • Pesticides and fertilizers

  • Effect of mutation:

    • Change in the amino acid chain will change the way it gets folded. If it is not folded correctly then it cannot do its “job”

    • Same amino acid (redundancy built into RNA-aa code) and the same protein is created.

• Types of Mutations

  • Substitute a letter in the DNA sequence.

    • THE FAT RAT SAT = still makes sense

    • THE FAT CAT MAT = does not make sense

  • Insertions: ad a base into the dNA sequence

    • THA EFA TCA TSA T

    • The amino acid would nto make sense

  • Deletions: remove a base in the DNA sequence

    • THE FTC ATS AT

    • The amino acids do not make sense

Photosynthesis

• Law of Conservation

  • Energy cannot be created or destroyed

  • It can be transferred from one form to another

• Photosynthesis

  • The process by which producers convert the energy of sunlight into the chemical energy of glucose

  • Producers: Plants, Algae, and some bacteria.

• Chloroplast

  • Thylakoids: Flat sacs that are stacked together

    • Site of the light reaction

  • Stroma: Fluid space around the thylakoids

    • “Cytoplasm”

    • Site of the dark reaction

• Light Absorption - The role of chlorophyll

  • Pigments absorb the sunlight energy

  • Excites electrons in the pigment molecule

• Electron Transport Chain-The transfer of high energy electrons

  • Excited electrons are passed from one carrier protein to the next

  • Eventually they are passed to NADP+

  • They help to join NADP+ and H+ to bond together to create NADPH

• Oxygen Formation-The bi-product of splitting water

  • Light hits and water splits

    • Replenish the electrons for ETC

    • Generate H+ ions

    • Biproduct: oxygen ( O2 ) is  released out the stomata

• ATP Production-The making of energy

  • Hydrogen ions (H+) diffuse through membrane proteins

  • kinetic energy of Hydrogen used to make lots of ATP

    • ADP + P = ATP

• Light Reaction Summary

  • Need

    • Light

    • Water

  • Made

    • NADPH: moves onto dark rxn

    • ATP: moves onto dark rxn

    • O2: released as a by-product

• Carbon Fixation

  • Needs an enzyme called Rubisco to start the cycle

  • CO2 enters the leaf and initiates the Calvin Cycle (dark rxn).

  • CO2 Joins a 5-carbon compound (RuBP) in the Stroma 

    • 5 carbon and 1 carbon = unstable 6 carbon compound

  • The 6 carbon compound is unstable

    • Immediately split into 2 separate 3-carbon compounds (PGA)

• Reduction

  • ATP and NADPH help power this cycle

    • NADPH - hydrogen donor 

    • ATP - provides energy

  • The PGA (3C) is reduced by NADPH to make G3P

  • G3P is a precursor molecule of Glucose

    • 1 G3P will go on to make glucose, the other 5 will go onto the next step

• Regeneration of RuBP

  • The 5-G3P (3C) that stayed in the cycle

    • They join together to reform RuBP (5C)

• Light Reaction Review

  • 4. Water splits to replenish lost electrons, hydrogen ions and oxygen

  • 5. The kinetic energy of hydrogen diffusion charges ATP synthase to make ATP

  • 3. Formation of NADPH using Hydrogen and electrons

  • 1. Pigment absorb the light energy

  • 2. Electrons are excited and pass through the electron transport chain

• Dark Reaction Review

  • 1. CO2 enters the cycle to make a unstable 6C molecule

  • 5. The other G3P remake RuBP

  • 4. One G3p goes on to make glucose

  • 2. 6C splits into PGA

  • 3. The use of NADPH and ATP turns PGA into G3P

Cellular Respiration

• ATP (Adenosine TriPhosphate)

  • ATP contains more energy than AMP or ADP

    • Each bonded phosphate has high energy electrons to release

      • ADP (adenosine diphosphate)

      • AMP (adenosine monophosphate)

• Glucose compared with ATP

  • Glucose:

    • Stable bonds

    • Lots of Potential Energy

    • Too much energy needed to break the bonds

  • ATP

    • Unstable bonds between the phosphate

    • Less potential energy

    • Doesn’t require energy to break the bonds

• Overview of Cellular Respiration

  • Convert the energy in glucose to the unstable bonds of ATP

  • All living organisms have to perform cellular respiration

    • It occurs in the Mitochondria of eukaryotic cells

    • Prokaryotes = cell membrane

• Cellular Respiration Equation

  • Glucose + Oxygen →Carbon Dioxide + Water + ATP

• Glycolysis

  • Glucose splitting

  • Glucose splitting

  • Occurs in the cytoplasm of prokaryotes and eukaryotes

  • Oxygen independent -It does not matter if oxygen is present or not

• Glycolysis Steps

  • Uses 2 ATP to break glucose into 2 3-carbon molecules

  • The 3-carbon molecules lose H+ and 2e- to NAD+ to make NADH

  • Loss of the hydrogen cause energy to make 2 ATP per each 3-carbon molecule = 4 ATP

  • The final molecule is 2 Pyruvates (3 C)
    

• Summary of Glycolysis

  • Need

    • Glucose

    • 2 ATP

    • NAD+

  • Made

    • 2 Pyruvate

    • 4 ATP

    • 2 NADH

Aerobic Cellular Respiration: Oxygen in the environment

• Pyruvate Oxidation

  • 

  • Pyruvate enters through mitochondrial membrane

  • Going into the matrix(cytoplasm of the mitochondria)

  1. Pyruvate loses a CO2 (waste-respired)and is now a 2C molecule called Acetyl

  2. NAD+ removes another H+ & 2e-

     • Leave as NADH

  3. Joins with Coenzyme A

     • Now call the molecule Acetyl CoA

• Summary of Pyruvate Oxidation

  • Need

    • Pyruvate(3-C)

    • NAD+

    • CoEnzyme A

  • Make

    • Acetyl CoA(2-C)

    • NADH

    • CO2

• Krebs Cycle

  • 

  • Acetyl CoA joins a 4C startup molecule to make a 6C molecule

  • This cycle completes by harvesting Hydrogens from the 6C molecule

    • NAD+ and FAD2+ remove H+ from the 6C to make NADH and FADH2

  • Removal of the Hydrogen cause ATP to be produced

    • 2 pyruvates = 2 times = 2 ATP

  • The 6C loses 2 CO2 to remake the initial 4C molecule

• Summary of the Kreb Cycle

  • Need

    • Acetyl CoA

    • NAD+ and FAD+

  • Make

    • CO2 waste

    • NADH and FADH2

    • 2 ATP

• Electron Transport Chain

  • 

  • Occurs on the Cristae (membrane inside the mitochondria)

  • Needs Oxygen to be the final electron acceptor, without it the cycle shuts down

    1. NADH and FADH2 drop off the Hydrogen at the membrane

    2. Various proteins transport Hydrogen across the membrane and H loses electrons to the proteins

    3. These electrons filter through proteins known as the ETC

    4. The hydrogen flows back through a special protein(ATP Synthase) that will turn to make ATP = 32-34 ATP

    5. The Hydrogens and electrons are ultimately picked up by O2 to make water (waste)

• Summary of Electron Transport Chain

  • Need

    • NADH

    • FADH2

    • O2

  • Make

    • H2O

    • 32 ATP

Anaerobic Cellular Respiration

• Alcoholic Fermentation

  • No oxygen is in the environment

  • In cytoplasm

  • Plants and Yeast

  • Pyruvate loses a CO2 and add back the H

    • CO2 is let out of the cell = bubbles, bread rise

    • Hydrogen comes from the NADH molecule made in glycolysis

  • The final molecule is a 2C Ethanol

  • 0 ATP

• Lactic Acid Fermentation

  • No oxygen in the environment

  • Animals and bacteria

  • Pyruvate adds back hydrogen lost in glycolysis

  • End product is 3C lactic acid

    • Builds up in muscle and makes them sore

  • 0 ATP

Comparison

• Anaerobic Cellular Respiration

  • Happens in cytoplasm

  • Less ATP produced

  • Also known as fermentation

    • Lactic acid fermentation

    • Alcholic fermentation

• Aerobic Cellular Respiration

  • Happens in mitochondria

  • More ATP produced

• Anaerobic and Aerobic Cell Respiration always starts with Glycolysis

Cell Cycle

• Reasons for Cell Division

  • Growth

  • Replace dead or damaged cells

  • Reproduction for single celled organisms

  • Maintain proper surface area to volume ratio

• Two forms of DNA

  • Chromatin: Uncoiled DNA that allows for the genes to be copied in protein synthesis

  • Chromosomes: coiled DNA that make it easier to transport and less likely to get damaged

• Cell Cycle

  • Three stages to the cell cycle:

    1. Interphase: Cell is doing normal cell functions and preparing for mitosis (Chromatin)

    2. Mitosis: the cell is dividing from one parent cell into 2 identical daughter cells (Chromosomes)

    3. Cytokinesis: Splitting of the cytoplasm

• Interphase

  • Three Stages

    • G1: Growth: Cell is doing normal cell functions like

      • Protein synthesis

      • Cell Respiration

      • Passive and Active Transport

    • S: Synthesis of DNA: DNA Replication

      • The DNA Splits

      • Each strand serves as a template to add DNA nucleotides

      • As the nucleotides are added the parent and daughter strands wind together

    • G2: Growth: Continued growth and Replication of cell organelles

• Prophase

  • Chromatin condenses into chromosomes in their replicated sister chromatid state

  • Nuclear membrane breaks down

  • Centrosomes make spindle fibers that attach to the centromere

• Metaphase

  • The spindle fibers move the sister chromatids to the center of the cell

• Anaphase

  • The spindle fiber shorten pulling the sister chromatids apart to the opposite sides of the cell.

• Telophase

  • Spindle fibers breakdown

  • Nuclear membrane rebuilds around the chromosomes

  • Chromosomes uncoil into chromatin

• Cytokinesis - Animal

  • The cell membrane pinches inward seperating the cytoplasm and cell into 2 identical cells

• Cytokinesis - Plant

  • A new cell wall is built along the center of the cell.