Cell Bio Exam 1: Intro And Cell Chemistry

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purpose of organelles

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compartmentalize functions

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lipid bilayer is made up of

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polar heads and non polar fatty acyl tails

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cells are made of

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atoms and molecules, basically carbon/hydrogen/nitrogen/oxygen

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makes up 77% of a cell

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water (70%), inorganic ions (1%, Na+, Cl-, K+, H2PO4-), and small molecules (6%, amino acids, nucleotides, fatty acids, sugars)

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about 23% of a cell is made up of

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monomers polymerized to macromolecules

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amino acids polymerize into

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proteins

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nucleic acids polymerize into

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DNA/RNA

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monosaccharides polymerize into

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polysaccharides

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fatty acids polymerize into

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lipids/membranes

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polymerization of macromolecules is drive by

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covalent bond formation (i.e., phosphodiester bonds link nucleotides in DNA and RNA molecules)

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covalent bonds

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share electrons

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bond strength

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covalent bonds strong, difficult to form and break. Non covalent bonds are weaker

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non covalent bonds

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ionic bonds, hydrogen bonds, van der waals bonds, thermal energy.

individual non covalent bonds are weak and easily broken. But, many together are strong.

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Van der Waals

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transient dipole moment creates transient partial charge that attracts other electrons. Responsible for non-polar interactions. Key for membrane formation, non polar membrane core

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hydrogen bonding

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partial charging molecules.

sets up cytoplasm/nucleasm. all aqueous compartments.

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ions dissolve in the cytoplasm because

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a shell of water molecules forms ionic interactions around them. Ions into solution. Forms hydrogen or ionic bonds.

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proteins that are soluble in the cytoplasm...

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Have polar amino acids on their surface. The AAs form hydrogen bonds with water.

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hydrophobic lipids

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Do not readily dissolve in water. Nonpolar hydrophobic molecules do not have partial charges since electrons areequally shared in covalent bonds between carbon and hydrogen (fats, oils, sterols).

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water cannot readily form hydrogen bonds with

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hydrophobic molecules

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Nucleus

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Large membrane bound organelle in eukaryotes

Nuclear Envelope: double membrane that surrounds nucleus, outer membrane continuous with ER, both membranes perforated with nuclear pore complexes

Nucleolus: where rRNA synthesis and processing occurs, where ribosome subunits are assembled, large structure

Chromosomes: DNA arranged in structure

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Rough Endoplasmic Reticulum

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interconnected membrane structures connected to nuclear envelope. Has ribosomes, synthesis and processing of secreted and membrane proteins

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Ribosomes

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large complex made up of several different rRNA molecules and up to 83 proteins. Large and small subunits. The engines of translation (protein synthesis)

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Peroxisomes

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contains enzymes for degrading fatty acids and amino acids by reactions that generate H2O2 which is converted to oxygen and water by catalase

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Smooth Endoplasmic Reticulum

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interconnected membrane structures connected to nuclear envelope. Does not have ribosomes. Functions in lipid synthesis.

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Golgi Apparatus

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flattened, interconnected membrane bound compartments (cistern) in eukaryotes. Function in processing and sorting of proteins and lipids destined for other cellular compartments or for secretion

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Lysosome

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internal pH of around 4.5 and contains hydrolytic enzymes. Functions in degradation of materials internalized by endocytosis and of cellular components in autophagy

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Mitochondrion

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Two phospholipid bilayers, contains DNA and produces much of the ATP for eukaryotic cells. Has invaginations called cristae that extend from the outer membrane to the center.

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Cytoskeletal Elements

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provides organization and structural support to the cell, allows for movement of organelles/chromosomes/the cell itself

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Plasma Membrane

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membrane surrounding cell that separates it from the environment. Has phospholipid bilayer and associated membrane lipids and proteins

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adenosine triphosphate

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ATP. Important for capture and transfer of free energy. Hydrolysis of each of the two phosphoanhydride bonds releases a large amount of free energy that can drive cell processes

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adenosine diphosphate

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ADP. One of the products of ATP hydrolysis by ATPases

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enzymes

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a protein that catalyzes a reaction

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nucleotides

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Nucleoside (purine or pyrimidine + ribose or deoxyribose) with one or more phosphate groups linked to the 5' carbon of the sugar

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transcription

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one strand of a DNA molecule is used as a template for the synthesis of a complementary strand of RNA by RNA polymerase

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RNA polymerase

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enzyme that copies one strand of DNA (template strand) to make the complementary RNA strand

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messenger RNA

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mRNA. Produced by transcription of DNA by RNA polymerase. Specifies primary structure of a protein.

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translation

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ribosome-mediated assembly of a protein whose AA sequence is specified by the nucleotide sequence in a mRNA

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ribozymes

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RNA with catalytic activity. Function in RNA splicing and protein synthesis

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endocytosis

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uptake of extracellular material by invagination of the plasma membrane (several types)

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autophagy

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Eating oneself. Cystolic proteins and organelles are delivered to the lysosome, degraded, and recycled.

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phagocytosis

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large particles (like bacteria) are internalized by eukaryotes

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vacuole

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membrane limited plant organelle that stores water, ions, and small nutrients and may have a degradative function like lysosomes of animal cells

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chloroplasts

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Plant organelle that has a double membrane and contains internal chlorophyll containing membranes (thylakoids). Where the light absorbing reactions of photosynthesis occur

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amphipathic/amphiphillc

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both hydrophobic AND hydrophillic

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ionic bonds result from

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the electrostatic attraction between positive and negative charges of ions

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exergonic

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energy releasing reaction, products have lower energy than reactants, spontaneous

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endergonic

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energy consuming reaction, products have higher energy than reactants, non spontaneous

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Gibbs free energy

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DeltaG = Gproducts - G reactants

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If DeltaG is negative

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exergonic spontaneous reaction

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If DeltaG is positive

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endergonic non spontaneous reaction

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entropy

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measure of disorder

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enthalpy

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energy of the system

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aerobic

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oxygen dependent

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catabolism

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degradation

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oxidation

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loss of electronss

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reduction

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gain of electrons

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NAD+

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an electron carrier that is reduced to NADH

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FAD

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electron carrier reduced to FADH2

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first law of thermodynamics

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energy not created or destroyed, just changes form

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second law of thermodynamics

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events proceed from higher free energy to lower free energy. the amount of disorder in the universe always increases.

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example of second law

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A closed system (CELL), with polymeric molecules requires an input of energy to remain ordered (LOW ENTROPY)

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example of first law

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light energy---->chemical energy---->mechanical energy

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ATP hydrolysis is

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the breaking of a covalent phosphoanhydride bond between gamma and beta phosphate.

An IMPORTANT reaction thatreleases energy. DG=-7.3kcal/mol

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Reactions with +DG occur in cells all the time

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Reaction coupling: Endergonic reactions coupled with exergonic reactions like ATP hydrolysis using a transiently phosphorylated intermediate.

Reaction embedding: In pathways, product of first endergonic reaction is consumed in next step to keep ratio of reactant to product above equilibrium constant.