Biology 1002B Final: Essential Outcomes

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13 Jun 2018
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Proteins
fundamental aspects of primary, secondary, tertiary structure of proteins.
- Primary sequence: the unique sequence of amino acids forming a polypeptide chain
- Secondary structure: produced by twist and turns of the amino acids determined by hydrogen
bonding (alpha helices or beta sheets)
- Tertiary structure: folding of the amino acid chain to make a 3D shape, the conformation
determines the function of the protein (active site is revealed)
- Quaternary structure: (optional) many polypeptide chains fold together to make a protein
definition of native conformation of a protein.
- the most stable conformation of the protein (lower free energy)
- only the native conformation is 100% functional (Anfensens dogma - used urea)
- only the primary sequence is required to achieve the native conformation
conditions that cause protein denaturation.
- the use of specific chemical or the addition of heat can cause a protein to lose it structure and
therefore its function (denaturation)
role of thermodynamics in protein folding.
- the proteins native conformation is attained because it is driven by thermodynamics, it is
looking for the most stable conformation (lowest free energy)
mechanisms by which protein cofactors are synthesized.
- a cofactor is a nonprotein chemical component that is bound to a protein (pigments)
- called coenzymes or prosthetic groups
- synthesized through biosynthetic pathways
compartments within cells where proteins are synthesized
- proteins are synthesized (translated) on the ribosomes in the ER or the cytoplasm
- if the protein is destined to remain in the cytoplasm, it will be synthesized on cytoplasmic
ribosomes and will not be transported to the membrane
- if the protein is destined to be secreted or transported to the membrane it will be synthesized
on the ER ribosomes to later undergo protein targeting
mechanism by which proteins are localized to specific intracellular compartments.
- vesicles shuttle the proteins from the ER ribosomes to the golgi, then to the plasma
membrane is it is destined to go there
- a signal peptide on the end of the amino acid is recognized & sent to where it is destined,
signal peptide is the first part that gets translated
- the SRP (signal recognition particle) binds to the signal peptide to recruit the protein complex
to the ER, the ribosome deposits the protein into the ER lumen, then the ribosomes are
released (protein targeting)
- nuclear proteins are imported through pores but they keep their tag because they are
constantly being reimported after the nuclear membrane breaks down during cell division
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Thermodynamics and Enzymes
how the first and second laws of thermodynamics can be applied to living systems.
- 1st Law: energy can be transferred or transformed but not created or destroyed
- 2nd Law: the entropy of a system and surrounding will always increase, energy is always
becoming more spread out
- whenever a chemical reaction results in an increase of molecules or a change of state from
solid to liquid or gas, the energy is spreading out over a greater number of molecules
(entropy is increasing)
- energy produced in one biological reaction is used to drive other reactions
how the Free energy (G) change of a system is influenced by changes in entropy and
enthalpy.
- G = ∆H - T∆S, spontaneous if negative
- if entropy increases and enthalpy decreases, the free energy of the system decreases
- if the entropy decreases an enthalpy increases, free energy increases (non-spontaneous)
mechanisms cells use to maintain low entropy.
- cells are thermodynamically open systems because they exchange energy and matter with
their surroundings
- cells need energy to do work (protein synthesis)
- cells maintain low entropy by counter-acting the break down of molecules by carrying out
cellular functions (doing work)
- low entropy because the inside is becoming more ordered when molecules are joined
together to form a complex
role of enzymes in metabolism.
- we need enzymes to get reactions to proceed at temperatures that are conducive to life
because it lowers the activation energy which enables many more molecules to reach the
transition state
- enzymes increase the rate of reactions because it allows more molecules to reach the
transition state
exergonic: a release of free energy (∆G < 0)
endergonic: an absorption of free energy (∆G > 0) - products have more free energy than
reactants
catabolic: the breakdown of molecules to simpler ones, release of energy
anabolic: simple molecules are combined to form complex ones, absorption of energy
transition state: the state where the bonds within one compound
activation energy: the energy required for the reaction to occur
spontaneous: the reaction occurs without the input of energy, ∆G is negative
Bioenergetics (Photosynthesis and Respiration)
fundamental role of cellular respiration and photosynthesis in cell growth (division)
- Cellular respiration is the process by which cells in plants and animals break down sugar and
turn it into energy, which is then used to perform work at the cellular level
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