Biochem ppt 1 - Lecture notes 1 PDF

Title Biochem ppt 1 - Lecture notes 1
Author Hannah Massengale
Course  Biochemistry I
Institution University of Southern Mississippi
Pages 16
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Summary

Lecture 1 notes
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Description

1/24/18 PPT

I.

BIOCHEMISTRY I – Structure and Catalysis

FOUNDATIONS OF BIOCHEMISTRY (Biological)

- Biochemistry is a science dealing with the chemistry of living matter - Living matter is characterized by: 1. High Complexity 2. Capable of using energy to do work 3. Sensing and responding to surrounding 4. Self-replication and evolution ***All life obeys the same chemical and physical Laws! -Fundamental features that identity life: 1. Life is self-sustaining and organized 2. Life is made of cells 3. Life is information-base 4. Life adapts and evolves.

1. Life is Complex (Meaning living organisms have) - Internal structures with defined functions - Large number of different compounds - Macromolecules that are capable of highly specific interaction

Biochemistry = study of molecules of living organism’s structures, mechanisms, and chemical processes

Biomolecules = molecules from living systems (all organic molecules) structures, mechanisms, and chemical processes

4 major biomolecules: Proteins, Nucleic acids (DNA, RNA), Sugars (saccharides), and Lipids (diverse molecules)

There are 3 domains of life: Living organisms are divided into three domains

Bacteria (Eubacteria) Living organisms

Archaea (Archaebacteria) Eukarya (Eukaryotes)

LUCA: stands for Last Universal Common Ancestor

COMMON FEATURES OF LIVING ORGANISMS: (specificity is KEY) - High level of chemical complexity and organization systems for extracting, transforming, and using energy. - Defined functions of molecules and structures (complexes) - Sensing and responding to surroundings - Precise reproduction and self-assembly - The ability to change (slowly) for adaptation

1.1 CELLULAR FOUNDATIONS (1)

Cell – the structural and functional unit of life / universal building block of life -

Living organisms are made of cells Simplest living organisms are single-celled Larger organisms consist of many cells with different functions Not all cells are the same

Genome – complete set of genes

1.3Cellular Foundations b. cell size Microorganisms – 1-2 micrometers Eukaryotes - 5-100 micrometers The lower limit – defined by minimal volume required to hold minimal number of molecules (mycoplasma estimated 200nm or 0.2 micrometers The upper limit – defined by diffusion (estimated 100 micro meters)

1.4Cellular foundations c. three domains of life: differences in cellular and molecular level define three distinct domains of life

Bacteria/ Eubacteria

Aerobic Anaerobic No nucleus

Archaea/ Archaebacteria Live in extreme environment

Eukarya/ Eukaryotes – with nucleus

Electron flow = energy

Why is O2 important to us?

1.6 Cellular Foundations **Organisms can be classified by energy and carbon sources

1.7 Cellular Foundations

Bacterial, Plant, and Animal Cells are different - The internal structure and properties of cells from organisms indifferent kingdoms are different - E.coli – a model organism for prokaryotes is the most studied organism

1.9 Cellular Foundations e. Eukaryotic cells – complex (nucleus, organelles, cytoskeleton) Subcellular organelles can be isolated by centrifugation

 Have nucleus by definition - protection for DNA; site of DNA metabolism - selective import and export via nuclear membrane pores - some cells become anuclear (red blood cells)  Have membrane-enclosed organelles - Mitochondria for energy in animals, plants and fungi - Chloroplasts for energy in plant - Lysosome for digestion of un-needed molecules  Spatial separation of energy-yielding and energy consuming reactions helps cells to maintain homeostasis and stay away from equilibrium

f. Cytoskeleton (10) defining cell shape and dynamics Actin filaments cytoskeleton filaments

microtubules intermediate filaments

**Assembled and disassembled from simple protein subunits** Endocytosis Exocytosis

Transport in/out by membrane fusion/fission

Living Systems Extract Energy plants Sunlight is the energy source for:

green bacteria Cyanobacteria

Fuels (organic matter) is energy for:

animals Most bacteria

-Energy input is needed in order to maintain complex structures and be in a dynamic steady state, away from the equilibrium. *****Which means  there needs to be a dynamic equilibrium or else the organism will not be alive. Static equilibrium = death.

Solar energy – the ultimate source of biological Energy: -Solar energy is important because it allows for life on Earth. Photosynthetic cells take use solar energy in combination with the CO2 and H2O heterotrophic cells dispose of and in turn, they put out O2 and Carbohydrates. ^^THIS IS A DYNAMIC EQUILIBRIUM

Molecular logic: Chemistry

We will look at chemistry behind accelerating rxns, organization of metabolism and signaling, and storage and transfer of info.  Cells build supramolecular structures

< 1nm

10x nm

100/1000x nm

um

Monomers  Polymers  Supramolecular  Cells

Molecular Interactions

EXAMPLE: Amino acid  Protein  Chromatin Nucleotide  DNA  Chromatin

Glucose  Cellulose  Cell Wall

*Monomer and polymer have STRONG COVALENT bonds *Supramolecular structures and cells have NON-COVALENT bonds These are weak individually, but strong collectively

CHEMICAL FOUNDATIONS

-Biomolecules are carbon-based.

But why? C is only element that can form multiple carbon-carbon bonding in mass chains.

(He said a tip when adding stuff together is to remove the H2O.)

-Elements H, O, N, P, and S are common -Metal ions also necessary for metabolism (K+, Na+, Ca++, Mg++, Zn++, Fe++) - Together about 30 elements essential for life

a) Biomolecule are organic molecules (C- containing)

b) Cells contain a universal set of small molecules

-Cytosol has 1000 types of small molecules: Amino acids/Nucleotides, sugars and its phosphorylated forms/Sugars and its phosphorylated forms/Carboxylic acids - polar or charged (dipole moments due to polarity)

-Central metabolites= involved in major pathways (essential) -Secondary metabolites = small molecules, specific for certain cell types or organisms -Metabolome – complete set of small molecule metabolites

C)Macromolecules- major components in a cell

Monomer – single unit Oligomer – 2 or more monomer units

Polymer – really large # of monomers Nucleic Acids – 2 types: (DNA, genome, info rich) & (RNA, versatile funct.) Polysaccharides – starch, glycogen, cellulose Lipids – NOT POLYMERS. Made of long chain fatty acid and polar heads. -All lipids are non-covalently interacting

D) Configuration vs Conformation

-Configuration – same chemical bonds but different fixed spatial arrangement, can’t change from one to other without breaking (hand over hand example) -Conformation – spatial arrangement that can change without breaking bonds. - CIS and TRANS usually

*usually double bonds prevent movement of an atoms around its axis* Cis and trans have different physical and chemical properties E) Biomolecules are stereospecific - stereospecificity is important bc proteins and certain molecules have to go in a certain way a pen cant go through a hole of it goes in long ways so it has to be parallel with a hole in order to go in

Interactions can be D or L: D = ribose, deoxyribose in RNA/DNA L = amino acids in proteins

 Macromolecules have unique binding pockets

 Only certain molecules fit well and can bind  Binding of chiral biomolecules is stereospecific

IF AN ENZYME BINDS THE L-FORM, IT DOES NOT BIND THE D-FORM AND VICE VERSA

PHYSICAL FOUNDATIONS

a. Organisms are not at a static equilibrium state - Molecules, ions, and energy in a dynamic state (give and take) b. Organisms extract energy, matter – open states - Not a closed system - We interact with our environment - Energy- nutrients such as sugar, fat, sunlight - Matter – nutrients, CO2, water c. The flow of electrons = energy

- Food oxidation (glucose  CO2) - CO2 reduction (photosynthetic organisms) - Electron rich molecules – energy rich (reduced state) - OIL RIG d. Creating and maintaining order needs work and energy - ΔG = ΔH –TΔS (Thermodynamics) - G = free energy (energy to do work) - H = enthalpy (heat) - T = temperature (K) - S = entropy (disorder) -G = spontaneous...


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