module 1 Flashcards
what is the definitions of biochemistry?
-the study of life at the molecular level
-the application of the principls of chemistry to explain biology
-the common sets of reactions and principles that underlie all living organisms
-the study of the molecular logic of life
what do all organisms use?
-a common repertoire of building blocks to create common categories of biomolecules (nucleic acids, proteins, polysaccharides, and lipids)
-a common core of essential biochemical processes
what are the four foundations of the living state?
-chemical
-energy
-evolutionary
-genetic
what are the four elements that make up 98% of most organisms?
-carbon
-hydrogen
-oxygen
-nitrogen
-water accounts for much of O and H
what are all known life forms?
-carbon based
what are the readily available elements in the biosphere?
-carbon (from air through plants)
-oxygen (from air)
-hydrogen (from water)
who was fritz haber?
-allowed for 3 billion more people to eat
-created technique to get nitrogen from air and convert into nitrates to use in fertilizer
what was fritz haber’s downside?
-repurposed his method into gunpowder, mustard gas, chemical weapons
-responsible for thousands of soldiers death
-was a jew, later used in concentration camps
-wife committed suicide
what is the availability of nitrogen?
–N in soil limits growth of plants, limits the amount of food we can produce
-naturally occurring N in soil, only enough food for 4 billion people
-
how much are we worth?
-chemicals in body are worth less than a dollar
-sum of parts (tissues, organs, biomolecules) are estimated 45 million dollars
why is carbon so versatile?
-number and variety of chemical bonds it can form
-enables to create wide array of complex molecules
-ex: amino acids, sugars, nucleotides
what is silicon?
-the next best candidate as a chem found for life
-also can form four covalent bonds
-highly abundant in the earth’s atmosphere
why are we based in carbon rather than silicon?
-C to C is stronger than S to S (more stable)
-more energy released on combustion (c to c)
-combustion products of carbon (CO2) are soluble and remain active in the biosphere
-silicon dioxide is insoluble, cant be recycled
why are functional groups unique?
-their size, shape, charge, reactivities, and hydrogen bonding capacity
-the properties of the functional groups determine the structure, function and properties of the biomolecule (anticipate behavior)
why is it important to understand the structure?
-structure dictates function
-do what they do bc of their structures
-allows to predict molecular function, understand complex biology and rationale development of treatments
what is conformation?
-flexible spatial arrangement of atoms within a molecules (can be changed without breaking covalent bonds)
-Ex: piece of paper example
what is configuration?
-fixed spatial arrangement of atoms within a molecule (cannot be changed without breaking covalent bonds)
-conferred by either double bonds or chiral centers
-much more dramatic
-ex: cutting off a finger
what are geometric (cis-trans) isomers?
-have the same chemical formula but differ in the configuration of groups with respect to a non-rotating double bond
-configuration double bond perspective
-can have very diff biological properties
what are cis and trans?
-cis= on this side groups on the same side as the double bond
-trans=across groups on opposite sides of the double bond
what is a chiral carbon?
-has 4 diff substituents attaches: may be arranged in diff ways in space yielding two stereoisomers that differ in their configuration
what is a stereoisomer?
-chemical properties tend to be identical
-biological properties are often distinct
how are stereoisomers diff during chemical reactions vs biochemistry?
-chem= not usually stereo specific
-biochem= stereo specific in terms of chemical reactions
what is contruction?
-biomolecules often constructed exclusively from one stereo isomer
-ex: proteins are built entirely from L-amino acids
what are interactions? (biochem=stereospecific)
-interactions between biomolecules and between biomolecules and small molecules are stereospecific
-reaction with diff receptors change sensation
where does chemistry meet biology?
-synthesis of chemical compounds which have asymmetric carbons result in a mixture of all the chiral forms
-these forms may have different biological activities (therapeutic benefits, pathological side affects differ)
what is an example of how two different chiral forms can cause different effects?
-thalidomide has two chiral forms, one causes birth defects
-Frances Kelsey (canadian physician working for FDA) saved children after she refused approval
how are biomolecules similar to words in a sentence?
-the structure and function of the resulting biomolecules are more complex than their precursor molecules
-the whole is greater than the sum of parts
what are the advantages of constructing biologicals as polymers?
-simplicity: simple and conserved reactions for synthesis and degradation (body has 20000 diff proteins, all from same building blocks)
-recycling: biomolecules can be digested back to component building blocks which are reusable
-diversity: incredibly complex molecules can be generated
what are the four classes of biomolecules?
-proteins
-carbohydrates
-nucleic acids
-lipids
what are proteins?
-linear polymers of amino acids
-20 different amino acids
-carboxyl links to amino group of next amino acid
-aminos link to form linear chains that fold into complex patterns with distinct biological activities
what are polysaccharides?
-made of sugars
-monosaccharides linked together to form linear or branched polymers
-biological roles include structural, energy storage, and cellular recognition
-linked through glycosidic linkages
-form branch points (can form more than 1 covalent bond)
what are nucleic acids?
-linear polymers of nucleotide building blocks (5 building blocks for DNA and RNA)
-involved in all aspects of storage and utilization of genetic information
-linked through phosphodiester bonds
what are lipids?
-are aggregates (rather than defined polymers) of building blocks
-serve in energy storage, formation of membranes and signaling
-not joined through covalent bonds (only 1)
-use non-covalent forms which allows freedom of rotation
what are prokaryotes?
-small (1 nano meter in diameter), simple, single cell organisms (bacteria)
-rapid growth, quick adaptations to changing environmental conditions
-a single compartment, the nucleoid, which contains nucleic acid. Other biomolecules (proteins, etc) in a complex, organized mix
what are eukaryotes?
-large, complex cells (100 nanometers)
-make up multi-cellular organisms
-organelles (mitochondria, nucleus, etc) to support specialized functions
-differentiation of cells to unique and specialized cell types
how many euk and pro cells do we have in our bodies?
-30 trillion euks
-100 trillion pros
why are pros critical for our health?
-bacteria in the gut helps digest food and maintain a functional immune system
-our second brain (the gut), including the microflora, may impact mental health, obesity and intelligence
what are some ways to influence the microbiota?
-diet
-pro and prebiotics
-fecal transplants
what is a major challenge of biochemistry?
-studying molecules in isolation simplifies experiments but may be at the expense of biological significance
-experiements which are siccessful in vitro often fail in vitro
what are the two experimental appraoches?
-in vitro: studies the behavior of molecules outside the context of the cell and organism
-in vivo (in the living) : studies occur within the complexity of the cell or organism
how expensive is the energy we use in one day?
-to purchase all the ATP from our body in one day would be about 4.5 million dllars
what can cellular energy conversion be considered in the context of?
-laws of thermodynamics
what is the first law of thermodynamics?
-in any physical or chemical change, the total amount of energy in the universe remains constant, although the forms of the energy may change
-can’t be created nor destroyed
how are cells related to the first law of thermodynamics?
-cells are highly effective transducers of energy, converting the energy of metabolized nutrients, or the energy of the sun, into work, heat, or the generation of complex biomolecules
what is the second law of thermodynamics?
-the tendency in nature is toward ever greater disorder: the total entropy (disorder) of the universe is continually increasing
-however, living systems and their biomolecules require a high degree of organization
what is free energy?
-willard gibbs developed the theory of energy change during chemical reactions
-free energy of any closed system can defined as:
Free energy: G=H-TS
Free energy change: change of G=change of (enthalpy)-(temperature)(change in entropy)
-enthalpy (H)= reflects the number and kinds of bonds
-entropy (S)= the degree of randomness
-temperature= in degrees kelvin
what does free energy mean?
-change in G >0: non-spontaneous process, needs input of free energy to proceed, endergonic
-change in G<0: spontaneous process, releases free energy which cane be used to do work; proceeds until equilibrium is reached, exergonic
-change in G=0: system is at equilibrium, there is no change in free energy in the system
how does energy coupling link to reactions in biology?
-cells can drive thermodynamically unfavorable reactions by coupling energy requiring (endergonic) to energy releasing (exergonic) reactions
-if the sum of the free energy changes is negative, then the overall process is exergonic
what is the central role of ATP in metabolism?
-energy extracted to the form of adenosine triphosphate (ATP) which serves as a common energy current
-ATP serves as the link between catabolic reactions and anabolic (building things up) reactions
what does the perpetuation of life requires that genetic information be:
-stored in a stable form
-expressed accurately in the form of gene products
-reproduced with minimal errors
for many organisms, DNA provides:
-the instructions for forming all other cellular components
-a template for production of identical DNA molecules to be distributed to the progeny when a cell divides
what is the central dogma of biochemistry?
DNA ->RNA -> proteins
transcription->translation
what is the structure of DNA?
-two complimentary strands
-each strand is a linear polymer of four different types of building blocks
-it is a linear sequence within the strands that encodes information
what does amino acids have to do with genetic foundations?
-the nucleotide sequence of genes dictates the sequence of amino acids incorporated into the corresponding protein
-the amino acid sequence of the proteins dictates the structure->dictates its biological activity
how does the changes in hereditary instructions allow evolution?
-random changes in genotype can result in a change in phenotype
-of this change offers a survival advantage, it will be selected over time
-fuel for evolution
