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UTEP / Biology / BIOL 1305 / What is the lowest level of oxygen that will support life?

What is the lowest level of oxygen that will support life?

What is the lowest level of oxygen that will support life?

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School: University of Texas at El Paso
Department: Biology
Course: General Biology
Professor: Horacio gonzalez
Term: Fall 2015
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Cost: 50
Name: Exam 3 Biology
Description: These notes cover what is going to be on our next exam
Uploaded: 04/09/2018
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15: Cellular Respiration


What is the lowest level of oxygen that will support life?



Overview

- Process by which living cells obtain energy from  organic molecules

- Occurs in the mitochondria

- Primary aim to make ATP and NADH

- Aerobic respiration uses oxygen

o O2 consumed and CO2 released

- Primarily uses glucose but other molecules are also  used

Glucose Metabolism

- This process involved 4 metabolic pathways - ATP is made all along the way, the most in the 4th step

o Glycolysis: break down glucose and turn it into  something else We also discuss several other topics like What month do you breed a mare?

o Breakdown of Pyruvate

o Citric Acid Cycle

o Oxidative Phosphorylation: allows us to produce  the majority of the ATP


How is the citric acid cycle connected to glycolysis?



Glycolysis

- Can occur with or without oxygen

- “splitting sugar”

- occurs in the cytosol

- steps in glycolysis are nearly identical in all living  organisms

- Three phases

o Energy investment (requires input of 2 ATP) o Cleavage (glucose to G3P) If you want to learn more check out What are the main laws of thermodynamics?

o Energy liberation

Cancer Cells Usually Exhibit High Levels of Glycolysis - Many diseases associated with alterations in  carbohydrate metabolism

- Warburg effect: cancer cells preferentially use  glycolysis while decreasing oxidative phosphorylation - Used to diagnose cancers in PET scans

- Glycolytic enzymes overexpressed in 80% of all types of cancers

- May be due to low oxygen levels inside tumors with  overexpression of glycolysis genes in response Breakdown of Pyruvate


How many molecules of atp are produced by each nadh oxidation?



- In eukaryotes, pyruvate is transported into the  mitochondrial matrix  

- Broken down by pyruvate dehydrogenase - Molecule of Co2 removed from each pyruvate - Remaining acetyl group attached to CoA to make  acetyl CoA

- Yield= 1 NADH for each pyruvate  Don't forget about the age old question of What is the meaning of scatterplot?

Citric Acid Cycle

- Metabolic cycle

o Some molecules enter while others leave

o Series of organic molecules regenerated in each  cycle

o Acetyl is removed from acetyl-CoA and attached  to oxaloacetate to form citrate

o Series of steps releases 2Co2, 1 ATP, 3 NADH,  and 1 FADH2

o Oxaloacetate is regenerated to start the cycle  again

Oxidative Phosphorylation  

- High energy electrons removed from NADH and  FADH2 to make ATP

- Typically requires oxygen

- Oxidative process involves electron transport chain - Phosphorylation occurs by ATP Synthase

Oxidation by ETC

- Protein complexes and small organic molecules  embedded in the inner mitochondrial membrane - Accept and donate electrons in a linear manner in a  series of redox reactions

- Movement of electrons generates an H+  

electrochemical gradient

- This provides energy for the next step-synthesizing  ATP If you want to learn more check out When public opinion is not stable, its movements can usually be explained by which of the following?

Phosphorylation by ATP Synthase

- Lipid bilayer of inner mitochondrial membrane is  relatively impermeable to H+

- Protons can only pass through ATP synthase - Harness free energy to synthesize ATP from ADP - Chemiosmosis- chemical synthesis of ATP as a result  of pushing H+ across a membrane

NADH oxidation makes the most of the cell’s ATP - NADH oxidation creates the H+ electrochemical  gradient used to synthesize ATP If you want to learn more check out When and why did the eu develop the european neighbourhood policy (enp)?

- Yield= up to 30-34 ATP molecules

- But rarely achieve maximal amount because: o NADH also used in anabolic pathways

o H+ gradient used for other purposes  

Connections among Carbs, Protein, and Fat Metabolism - Besides glucose, carbohydrates, protein, and fats are also metabolized to produce energy

- Enter into glycolysis or citric acid cycle at different  points

- Utilizing the same pathways for breakdown increases efficiency  

- Metabolism can also be used to make molecules  (anabolism)

Anaerobic Respiration and Fermentation

- For environments that lack oxygen or during oxygen  deficient times

- 2 strategies:

o use substance other than O2 as final electron  acceptor in ETC- anaerobic cellular respiration  o Produce ATP only via substrate-level  

phosphorylation-fermentation  

Fermentation

- Fermentation is the breakdown of organic molecules  without net oxidation

- Glycolysis seems like a natural choice to produce  ATP, but uses up too much NAD+ and makes too  much NADH under anaerobic conditions

- Fermentation is the solution, but the process  produces a lot less ATP

16: Photosynthesis

 Overview

 Plants are phototrophs Don't forget about the age old question of What is the meaning of the information-processing approach?

 Energy within light is captured and used to synthesize  carbohydrates

 Co2 is reduced, H2O is oxidized

 Occurs in chloroplasts

 QUESTION: answer: Both 2 and 3 (non-spontaneous &  endergonic

 The Chloroplast

 Stomata are the site of gas exchange and transpiration  Mesophyll tissue is composed of cells containing chloroplasts  Thylakoids contain chlorophyll and are organized into  photosystems  

 Stroma contain many of the enzymes necessary to produce  organics  

 RXNS that harness light energy  

 Light is a type of electromagnetic radiation

 Travels as waves, which can have short or long wavelengths  Also behave as particles of light called photons   Shorter wavelengths have more energy  

 Pigments absorb light of different wavelengths   Non-Cyclic Electron Pathway

 Light energy absorbed by photosystem II antenna complex  and passed from molecule to molecules until it reaches the  reactions (chlorophyll a)

 Excited electron is captured by primary electron acceptor  H2O is oxidized to produce H+ and O2 (released)  Excited electron travels down the ETC and, in doing so,  

releases energy that is used to convert ADP to ATP via a  process known as photophosphorylation  

 Light energy absorbed by photosystem I antenna complex  and passed from molecule to molecules until it reaches the  reaction center

 Excited electron is captured by primary electron acceptor   Electrons traveling along the ETC and hydrogen from step 3  (the oxidation of water) are used to convert NADP+ to  NADPH

 ATP and NADPH generated in this process are used in dark  reactions (Calvin cycle)

 Calvin Cycle- “Dark Reactions”

 CO2 is 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 used

 12 NADPH can be oxidized to help us produce more ATP  Product is glyceraldehyde-3-phosphate (G3P)

 Glucose is later made from G3P in a separate process  Phase 1: Carbon Fixation

 Co2 incorporated into RuBP using rubisco

 Reaction product is a short-lived, 6C molecule that is  almost immediately cleaved to produce 2 molecules of  3PG

 Phase 2: reduction and carbohydrate production  6 ATP are used to convert 3PG into 1,3-BPG

 NADPH electrons reduce 1,3-BPG to G3P

 2 molecules of G2P used to produce carbohydrates  Phase 3: regeneration of RuBP

 10 molecules of G3P are converted into 6 RuBP and 6 ATP

17: DNA Replication (I)

 Griffith’s Bacterial Transformation  

 Late 1920s- Frederick Griffith was working with  Streptococcus pneumoniae bacteria

 2 strains of S. pneumoniae  

 strains that secrete capsules look smooth and infections  are virulent (lethal) in mice

 Strains that do not secrete capsules look rough ad  infections are benign in mice

 The capsule creates a protective “coat” around the bacteria,  so they survive in the blood  

 DNA as the genetic material: the research of Hershey and  Chase

 1952: studied a T2 virus that infects E. coli  

 Phage coat is made entirely of protein

 DNA found inside capsid  

 Hershey and Chase

 What does the phage inject into the bacteria –DNA or  protein?

 H & C tagged each component with a radioactive label   S labels proteins

 P labels DNA

 The fraction containing cell contents was identified as  containing radiolabeled DNA, hence DNA was found to be the genetic material  

 Question: Answer: 3. Radiolabeled P was isolated among the  cell fraction containing infected E. coli, indicating the presence  of DNA in that cell fraction  

 Nucleic Acid Structure

 Levels of DNA structure

 Nucleotides- the building blocks of DNA and RNA  Strand- a linear polymer strand of DNA or RNA

 Double helix- the 2 strands of DNA

 Chromosomes- DNA associated with an array of different  proteins into a complex structure

 Genome- the complete complement of genetic material in  an organism

 DNA

 Formed from nucleotides

 Nucleotides composed of 3 components:  

 Phosphate group

 Pentose sugar

∙ Deoxyribose  

∙ DNA= deoxyribose nucleic acid

 Nitrogenous base

∙ Purines – adenine guanine  

∙ Pyrimidines- cytosine, thymine  

 RNA

 Formed from nucleotides

 Nucleotides composed of three components:

 Phosphate group

 Pentose sugar

∙ Ribose

∙ RNA= ribonucleic acid

 Nitrogenous base

∙ Purines- adenine, guanine

∙ Pyrimidines- cytosine, uracil  

 Strands

 Nucleotides are covalently bonded

 Phosphodiester bond- phosphate group links two sugars  Backbone- formed from phosphates and sugars  Bases project away from backbone

 Written 5’ to 3’, such as 5’-TACG-3’

 Solving the structure of DNA

 In 1953, James Watson and Francis Crick proposed the  structure of the DNA double helix using a simple, ball and  stick model

 This was an improvement upon Linus Pauling’s prediction  that DNA was a triple helix

 Rosalind Franklin’s X-ray diffraction results were crucial  evidence, suggesting a helical structure with uniform  diameter  

18: DNA Replication II 

1) An Overview of DNA Replication

a) Late 1950s­ 3 different models were proposed for DNA replication i) Semiconservative Model

ii) Conservative Model

iii) Dispersive Model

b) Newly­made strands are “daughter strands”

c) Original strands are “parental strands”

2) Conservative Mechanism

a) DNA replication produces 1 double helix with both parental strands  and the other with 2 new daughter strands

3) Dispersive Mechanism

a) DNA replication produces DNA strands in which segments of new  DNA are interspersed with the parental DNA

4) Semiconservative Mechanism

a) DNA replication produces DNA molecules with 1 parental strand and  1 newly made daughter strand

5) Molecular Mechanism of DNA Replication

a) Origin of replication provides an opining called a replication bubble  that forms two replication forks 

b) DNA replication proceeds outward from fork

c) Prokaryotes (bacteria) have a single origin of replication d) Eukaryotes have multiple origins of replication 

6) Steps of DNA Replication

a) DNA topoisomerase (gyrase) relieves tension ahead of replication  fork 

b) DNA helicase binds to DNA and travels 5’ to 3’ using ATP to separate strand and move fork forward

c) Single­stranded binding proteins (SSBPs) attach to parental strands  to prevent them from rejoining 

7) Steps of DNA Replication

a) Primase lays down an RNA primer to which new bases can be added b) DNA polymerase III binds to DNA and travels 5’ to 3’ adding  dioxynulceotid triphosphates (dNTPs) as it moves 

c) DNA polymerase I removes original RNA primer and replaces it with  DNA

8) Leading Vs Lagging Strand

a) An issue arises from the fact that DNA polymerase must synthesize  in a 5’ to 3’ direction but replication is bidirectional

9) Leading Strand

a) DNA synthesized in one long molecule because DNA polymerase III  is moving toward the 5’ end of the parental DNA strand 

10) Lagging Strand

a) DNA synthesized in short, non­continuous Okazaki fragments  because DNA polymerase III is moving toward the 3’ end of the  parental strand 

11) Telomeres 

a) Series of short nucleotide sequences repeated at the ends of  chromosomes in eukaryotes

b) Have a 3’ overhand that makes it impossible for DNA polymerase to  bind (and therefore there is no complementary strand to this  overhang)

c) As individual ages, telomerase “weakens,” leading to shortening of  telomeres

d) High levels of telomerase found in cancers 

19: Transcription

1) Overview of Gene Expression

a) We can look at gene function at two levels:

i) Molecular function of the protein product

ii) Organism’s conferred by the gene

b) Two levels are connected­ the molecular function affects the structure and function of cells to determine the trait

2) Beadle and Tatum­ Linking Genes to Proteins

a) They worked on N. crassa, common bread mold 

b) Minimum requirements for growth

i) Carbon source (sugar), inorganic salts, biotin

c) Wild­type N. crassa can grow on the minimal media containing basic  requirements for growth

d) Mutant strains unable to grow unless supplemented with specific  substances (vitamins or amino acids)

e) Hypothesis: “one gene, one enzyme”

f) Each mutant was plated, and it was discovered that each single  mutation required the addition of a single type of vitamin

g) Conclusion­ supports one gene, one enzyme hypothesis 3) Modern Understanding

a) A modern interpretation of the “one gene, one enzyme” hypothesis b) Enzymes are only one category of cellular proteins­ genes also  encode other proteins

c) Also, some proteins are composed of several polypeptides that work  together for one function

i) Ex: hemoglobin is composed of 4 polypeptides

d) “one gene, one polypeptide”

4) Central Dogma

a) Transcription

i) Produces a transcript (RNA copy) of a gene

ii) This messenger RNA (mRNA) specifies the amino acid sequence  of a polypeptide

b) Translation

i) Process of synthesizing a specific polypeptide on a ribosome  using the mRNA template

c) Eukaryotes have an intervening step called RNA processing where  pre­mRNA is processed into active mRNA

d) Some genes do not encode polypeptides­ an RNA is the first  functional produce

i) Structural RNAs 

ii) Regulatory RNAs

5) Transcription

a) Gene:

i) An organized unit of DNA sequences that enables a segment of  DNA to be transcribed into RNA and ultimately results in the  formation of a functional product

ii) Other genes code for RNA itself as a product

(1)Transfer RNA (tRNA)­ translates mRNA into amino acids (2)Ribosomal RNA (rRNA)­ part of ribosomes 

6) Three stages of transcription

a) Initiation

i) Recognition step

ii) In bacteria, sigma factor causes RNA polymerase to recognize the promoter region

iii) Stage is completed when DNA strands separate near promoter to  form open complex 

b) Elongation

i) RNA polymerase synthesizes RNA

ii) Template strand of DNA used for RNA synthesis

(1)This is the strand of DNA presented in the 3’ to 5’ direction iii) mRNA is synthesized in the 5’ to 3’ direction

iv) Uracil substituted for thymine 

c) Termination

i) RNA polymerase reaches termination sequence

ii) Causes both the polymerase and newly­mad RNA transcript to  dissociate from DNA

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