Advanced Cell Biology. Lecture 7

Home , Hydrogen carrier

Alexey Shipunov

Minot State University

January 27, 2012 Advanced Cell Biology. Lecture 7

Outline

Questions and answers

Nucleic acids Structure Other nucleic acids

Macromolecules in cells

Cells and energy Advanced Cell Biology. Lecture 7

Outline

Questions and answers

Nucleic acids Structure Other nucleic acids

Macromolecules in cells

Cells and energy Advanced Cell Biology. Lecture 7

Outline

Questions and answers

Nucleic acids Structure Other nucleic acids

Macromolecules in cells

Cells and energy Advanced Cell Biology. Lecture 7

Outline

Questions and answers

Nucleic acids Structure Other nucleic acids

Macromolecules in cells

Cells and energy I TAACCTTCG

I DNA

Advanced Cell Biology. Lecture 7 Questions and answers

Previous ﬁnal question: the answer

Write a sequence complementary to ATTGGAAGC Is it from DNA or RNA? Advanced Cell Biology. Lecture 7 Questions and answers

Previous ﬁnal question: the answer

Write a sequence complementary to ATTGGAAGC Is it from DNA or RNA?

I TAACCTTCG

I DNA Advanced Cell Biology. Lecture 7 Nucleic acids Structure

Nucleic acids Structure Advanced Cell Biology. Lecture 7 Nucleic acids Structure Hydrogen bonds in complementary strands Advanced Cell Biology. Lecture 7 Nucleic acids Structure Double helix

I DNA form helical structure where phosphate and sugar form “envelope” and bases form a “core”

I Two grooves: major and minor Advanced Cell Biology. Lecture 7 Nucleic acids Structure DNA double helix Advanced Cell Biology. Lecture 7 Nucleic acids Structure DNA double helix from top Advanced Cell Biology. Lecture 7 Nucleic acids Structure Sequences, ends, abbreviations

I Since nucleotides are complementary, it is usually only one strand listed

I Each strand has 3’ (–OH) and 5’ ends (phosphate) Advanced Cell Biology. Lecture 7 Nucleic acids Structure 3’ and 5’ ends Advanced Cell Biology. Lecture 7 Nucleic acids Structure Abbreviations for nucleic acids components Advanced Cell Biology. Lecture 7 Nucleic acids Structure Abbreviations for nucleotide sequences Advanced Cell Biology. Lecture 7 Nucleic acids Structure Nucleotides and UV light Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids

Nucleic acids Other nucleic acids Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids ATP

I ATP (adenosine-triphosphate) is coenzyme (ferment helper), derivative of ribose, adenine and three phosphoric acids

I Contain two highly energetic bonds Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids ATP Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids ATP movie

ATP movie Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids NADP

I NADP, nicotinamide adenine dinucleotide phosphate is a coenzyme, derivative of adenine

I Typically, used as hydrogen carrier

I Has a medical name “vitamin B3” Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids NADPH Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids Other nucleotide coenzymes

I FAD, ﬂavin adenine dinucleotide, vitamin B2

I CoA, coenzyme A, vitamin B5 I Both are extremely important for cell respiration Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids FAD Advanced Cell Biology. Lecture 7 Nucleic acids Other nucleic acids CoA Advanced Cell Biology. Lecture 7 Macromolecules in cells

Most frequent macromolecules

I Polymer molecules generate most of cell dry weight (30% of total weight)

I Proteins are 15%, nucleic acids 7%, lipids and polysaccharides 2% each Advanced Cell Biology. Lecture 7 Macromolecules in cells

Noncovalent bonds, conformations and binding

I Non-covalent bonds are responsible from shaping of macromolecules

I Almost every macromolecule has different shaping variants—conformations

I Intermolecular binding is also due to noncovalent bonds Advanced Cell Biology. Lecture 7 Macromolecules in cells

Types of noncovalent bonds

I Hydrophobic forces

I Van der Waals attractions: due to ﬂuctuation of electric charges

I Electrostatic, including hydrogen Advanced Cell Biology. Lecture 7 Macromolecules in cells

Binding with noncovalent (electrostatic) bonds Advanced Cell Biology. Lecture 7 Cells and energy

Metabolism

I Metabolism is the sum of all chemical reactions in living organism

I Catabolism is the part of metabolism responsible for degrading complex molecules

I Anabolism is the opposite part Advanced Cell Biology. Lecture 7 Cells and energy

Metabolism Advanced Cell Biology. Lecture 7 Cells and energy

Second law of thermodynamics

I Thermodynamic deﬁnition (Rudolf Clausius): No process is possible whose sole result is the transfer of heat from a body of lower temperature to a body of higher temperature.

I Simplistic deﬁnition: In isolated system, disorder is always increasing

I To revert initial order, energy should be spent

I Generally speaking, entropy is a measure of disorder (better—measure of randomness) δQ I In strict sense, entropy is dS = T , where Q is amount of heat and T —absolute temperature (constant) Advanced Cell Biology. Lecture 7 Cells and energy

Entropy Advanced Cell Biology. Lecture 7 Cells and energy

Triumph of entropy: “post-apocalyptic world” Advanced Cell Biology. Lecture 7 Cells and energy

Entropy explained: energy tube Advanced Cell Biology. Lecture 7 Cells and energy

Different forms of energy

I Mechanical energy: potential and kinetic

I Heat energy

I Electromagnetic energy

I All forms are inconvertible; and ﬁrst law of thermodynamics says that energy never disappears, it only changes its form Advanced Cell Biology. Lecture 7 Cells and energy

Photosynthesis

I The way of transforming light energy to energy of chemical bonds

I The schematic description is: light energy + CO2 + H2O → sugars + O2 + heat energy I Part of anabolism Advanced Cell Biology. Lecture 7 Cells and energy

Cellular respiration

I Almost opposite process

I Schematic description: sugars + O2 → CO2 + H2O + chemical energy (ATP) I Part of catabolism Advanced Cell Biology. Lecture 7 Cells and energy

Oxidation and electron transfer

I Cellular respiration is based on oxidation, taking electrons off

I Converse reaction is reduction; together they are redox reactions

I For organic molecules, typical oxidation sequence is: carbohydrates → alcohols → aldehydes → organic acids → CO2 Advanced Cell Biology. Lecture 7 Cells and energy

Enzymes and energy of activation

I Most of processes need the energy of activation

I Enzymes could lower activation barriers Advanced Cell Biology. Lecture 7 Cells and energy

Energy of activation Advanced Cell Biology. Lecture 7 Cells and energy

Catalysis movie Advanced Cell Biology. Lecture 7 Cells and energy

Enzyme terminology: catalysis and substrate

I Enzyme binds with substrate,

I then catalyze conversion of substrate into product,

I and returns untouched to the initial state Advanced Cell Biology. Lecture 7 Cells and energy

Catalysis terms Advanced Cell Biology. Lecture 7 Cells and energy

Enzyme performance

I Two numbers are using for measuring enzyme performance: Vmax and KM I Vmax is maximal available reaction rate I KM is the concentration of substrate when the rate is Vmax/2 Advanced Cell Biology. Lecture 7 Cells and energy

Enzyme performance How living organisms are working against the second law of thermodynamics?

Advanced Cell Biology. Lecture 7 Cells and energy

Final question (3 points) Advanced Cell Biology. Lecture 7 Cells and energy

Final question (3 points)

How living organisms are working against the second law of thermodynamics? Advanced Cell Biology. Lecture 7 Cells and energy

Summary

I The second law of thermodynamics is about increasing entropy

I All metabolic reactions need energy Advanced Cell Biology. Lecture 7 Cells and energy

For Further Reading

A. Shipunov. Advanced Cell Biology [Electronic resource]. 2011—onwards. Mode of access: http: //ashipunov.info/shipunov/school/biol_250

B. Alberts et al. Essential Cell Biology. 3rd edition. Garland Science, 2009. Chapter 2, Chapter 3: 58–100.