Biology 1113: Exam 1
Compare and contrast the movement of (1) nucleotides and (2) large proteins through the nuclear pore complex. Which process would you expect to require an input of energy?
(1) Nucleotides are small enough that they would diffuse through the nuclear pore complex along their gradients—a passive process that would not require energy. (2) Large proteins must be escorted through the nuclear pore complex in a directional manner—an active process that requires energy and results in the protein being concentrated inside the nucleus.
Describe key attributes of RNA that make it a candidate for the first living molecule
(1) RNA provides a template that can be copied and can also (2) catalyze the polymerization rxn required for its own replication
how does the molecular structure of cell walls vary between bacteria and archaea
*bacteria*: primary structural component of the cell wall is the modified polysaccharide peptidoglycan. Some bacterial cell walls are also surrounded by an outer membrane consisting of glycolipids *archaea*: cell walls of archaea are highly variable among the different species. BUT peptidoglycan is markedly absent
Hydroxyl groups
- (-OH) hydrogen atom is bonded to oxygen atom which in turn is bonded to carbon skeleton of organic molecule (different than hydroxide ion which is OH-) - act as weak acids - since hydroxyl groups are polar (oxygen has strong attraction for electrons), water is thus attracted to the hydroxyl group. Thus molecules containing hydroxyl groups (like sugars) willl form hydrogen bonds and tend to be soluble/dissolve in water which helps dissolve organic compounds such as sugars - ex. Ethanol (alcohol present in alcoholic beverages)
Structure and Function at the Whole-Cell Level
- An organelle's membrane and its enzymes correlate with its function, and cell structure (e.g. the type, size, and number of organelles) correlates with cell function (cells also differ in size) - Cells are dynamic living things with interacting parts and constantly moving molecules - Ex: cardiac muscle cells in your heart are long/tapered they're filled with protein fibers that slide past one another as the muscle flexes or relaxes to generate the heartbeat. Packed with mitochondria which produce the ATP required for the sliding motion to occur.
Intermediate Filaments
- Anchorage of nucleus and chromosomes, etc - Formation of nuclear lamina which form a dense mesh inside nuclear envelope that anchors chromosomes, defines the shape of the nucleus, and stabilizes the envelope. - Fibrous proteins supercoiled into thicker cables. There are many diff types of protein subunits. NO filament polarity - identical ends, only structural role in eukaryotic cells. ex. Keratins (skin cells, line surfaces inside body) - They provide the mechanical strength required for these cells to resist pressure and abrasion. function like a flexible internal scaffolding to help secure the shape and stability of the cell.
methyl group
- CH3 - can be attached to a carbon or to a different atom - found in DNA, has to do with the methyl group to DNA which affects gene expression (when genes are turned on and when off)
(microfilaments, actin filaments) ATP powered interaction between actin and myosin is basis for
- Cytokinesis: final stage in cell division when the cytoplasm is divided to form two cells. In animals, this accomplished by actin filaments that are connected to the plasma membrane and arranged in a ring. Myosin causes the filaments to slide past one another, reducing the diameter of the ring and pulling in the membrane that eventually fuses to produce two cells. - Cytoplasmic streaming: directed flow of cytosol and organelles that facilitates distribution of materials within some LARGE plant and fungal cells. movement occurs along actin filaments and is powered by myosin - Cell crawling: cellular movement in which the cell produces bulges in membrane that stick to the substrate and are used to pull the cell forward (some animal cells, slime molds, amoebae, etc)
Describe how DNA looks
- DNA is put together like a latter. The antiparallel sugar phosphate backbones make up the ladder's side railing. The nitrogenous bases attached to the sugars that are rotated/paired up via hydrogen bonding forms the inside of the latter that you climb on. - DNA antiparallel strands are twisted together - on the outside of the DNA helix molecule forms 2 types of grooves. The MAJOR GROOVE: the wider of the two. The MINOR GROOVE: the narrower of the two. This groove asymmetry is vital for granting access to proteins that bind to particular base sequences in DNA (ex. Histones)
Example of adhesion and cohesion in nature
- It is important in explaining how water can move from the roots of plants to their leaves against the force of gravity - is also in action in the concave surface (the meniscus) that forms in a glass tube
Actin Filaments (microfilaments)(Smallest diameter)
- Muscle contraction: myosin, motor protein, that converts chemical energy in ATP into kinetic energy of mechanical work. when myosin binds and hydrolyzes ATP to ADP, it undergoes a series of shape changes that extends the "head" region, attaches it to actin, and then contracts to pull itself along the actin filament. These changes cause the actin and myosin to slide past each other. myosin gradually moves toward the plus end of the actin filament - Cell division (cleavage furrow formation) - Structure: two long strands that coil around each other.made of globular protein subunits called actin. Polymerization of individual actin proteins byF noncovalent bonds. Not symmetrical: two distinct ends of an actin filament: the plus end grows faster than the minus end (rate of assembly) - organized into long, parallel bundles or dense, crisscrossing networks in which actin filaments are linked to one another by other proteins: stiffen the cell and define its shape
Why is carbon so special?
- almost all molecules in a living organism (except water) contain carbon - has 4 valence electrons to form 4 strong covalent bonds - can form complex carbon skeletons (long hydrocarbons chains like octane C8H18) (or glucose C6H12O6 which forms a ring structure) - many molecules that contain carbon bonded to other elements, such as hydrogen, are called organic compounds
Amino functional group
- attracts a hydrogen ion (proton) when in solution (picks up H+ from surrounding solution like water in living organisms) - function as bases - found in proteins (together with carboxyl makes an amino acid which is building block)
plasmids (prokaryotes and some eukaryotes)
- both prokaryotes and eukaryotes - small, usually circular, supercoiled DNA molecule that exists separately from cell's main chromosome(s) in prokaryotes and some eukaryotes - contains genes, many cases these genes are not required under normal conditions and help cells adapt under unusual circumstances (like presence of poison). can be considered AUXILIARY (supplemental) genetic elements
What are the main types of protein functions? (CMT- SSD acronym) (https://etext-ise.pearson.com/courses/ball76352/products/2K1R3NIK43P/pages/a74c55191ced6beb2de0d180e273cd84ec2aee5e5?locale=&key=256722764120374528122020 video)
- catalysis - structural - movement - signaling - transport - defense
Carbonyl groups
- consists of a carbon atom joined to an oxygen atom by a double bond - found on molecules such as acetaldehyde and acetone - found in several sugars - polar b/c oxygen has a strong attraction for electrons. If carbonyl group is found at end of carbon skeleton = molecule is called an aldehyde. If it is within the carbon skeleton = molecule is called a ketone.
steroids
- distinguished by the bulky, four-ring fused structure with variable side groups attached - various steroids differ from one another by the functional groups or side groups attached to different carbons in those hydrophobic rings ex. estrogens and testosterone are known for their role as hormones in cell signaling. cholesterol is a steroid (has a polar hydrophilic hydroxyl group attached to the top ring and nonpolar isoprenoid "tail" attached at the bottom)
Chemical equilibrium in solution
- equilibrium favors free monomers over polymers Condensation and hydrolysis represent the forward and reverse reactions of a chemical equilibrium - Look at page 77 diagram Monomer-H + Monomer-OH -> (condensation/dehydration) -> Monomer 1—Monomer 2 + H2O. Monomer in, water out Monomer 1-Monomer 2 + H2O -> (hydrolysis) Monomer 1 + Monomer 2
Eukaryotic Cell Wall
- fungi, algae, and plants, cells have an outer cell wall in addition to their plasma membrane. - Like the cell wall in bacteria and archaea, a eukaryotic cell wall is located outside the plasma membrane and furnishes a durable outer layer that gives structural support to the cell.
What makes water unusual?
- high surface tension - unique polarity - great solvent - liquid water is denser than solid water
Tertiary structure of DNA
- less dependent on primary structure; less variability - 2 forms of Tertiary structure are found in cells: supercoils Supercoils: when DNA becomes wound too tightly/loosely regarding the number of base pairs per helical turn it results in DNA twisting on itself to form compact 3D structure DNA in cells of eukaryotes and archaea form tertiary structures by wrapping around DNA-binding proteins which results in DNA-protein complexes which compact the DNA into movable units during cell division. This also contributes to DNA's ability to sotre and transmit info
nucleoid region function (prokaryotic cell)
- only prokaryotic cells, a dense centrally located region that contains the circular chromosome (DNA) but is NOT surrounded by membrane - genetic info in nucleoid is organized by clustering loops of DNA into distinct domains (not separated from the rest of cell interior by membrane)
Phosphate group
- phosphorous atom is bonded to 4 oxygen atoms; one oxygen is bonded to carbon skeleton. (-OPO3 2-) - carries negative charges on two of the oxygen atoms.. the electronegative oxygen atoms attract electrons to themselves so the phosphate group acts as an acid losing hydrogen ions to the surrounding soln. This dissassociation leaves the group with 2 negative charges (when these groups are transferred from one organic compound to another, the change in charge often dramatically affects the structure of the recipient molecule) - phosphate groups that are bonded together store chemical energy that can be used in chemical rxns in cells - has potential to react with water, releasing energy - found in ATP, the transfer of energy in organic molecuels, nucleic acids
Catalysis
- probably the most important function of proteins b/c of speed supporting life. Enzyme proteins are the most effective catalyst b/c of the variety of reactive functional groups in amino acids Many proteins are specialized to catalyze (speed up chemical reaction), which means to accelerate the rate of a chemical reaction due to a decrease in the free energy of the transition state (activation energy) - an ENZYME: a protein that functions as a catalyst. Ex: carbonic anhydrase molecules in red blood cells that take carbon dioxide from inside cells back to the lungs to be breathed out. Ex: salivary amylase protein in mouth
What is the evidence that amino acids can spontaneously assemble into proteins (W/o help of other cellular factors)?
- researchers have been able to generate stable polymers in the lab by mixing free amino acids with chemical energy and mineral particles. Growing macromolecules are protected from hydrolysis if they cling, or absorb, to a mineral surface. - we have seen amino acids being formed and even polymerized in the hot, metal rich environments of undersea volcanoes - amino acids have linked to form polymers in conditions of cool water IF energy rich carbon and sulfur containing gas is present which is commonly ejected from undersea volcanoes.
What are the properties of water's structure?
- small size - highly polar covalent bonds: each of the covalent O—H bonds in one water molecule is polar due to the difference in electronegativities of hydrogen (+) and oxygen (-). - bent shape/geometry: this shape makes the partial negative charge on the oxygen atom stick out/away from the partial + charges on the hydrogen atoms, giving overall polar nature Resulting in overall polarity ***like polar covalent bonds, when molecules are polar, they carry a partial + charge on one side and a partial - charge on the other
Sulfhydryl groups
- suflur atom bonded to hydrogen atom (HS-) - important b/c sulfhydryl groups can link to one another via disulfide (S-S) bonds which are covalent. This cross-linking helps stabilize some protein structures - ex. Cross linking of cysteines in hair proteins maintains the curliness/straightness of hair (perms = breaking and reforming the cross linking bonds between proteins) - part of the thiols -***ONLY ONE OF THE MENTIONED 7 FUNCTINAL GROUPS THAT IS NONPOLAR
Carboxyl functional group
- when an oxygen atom is double bonded to a carbon atom that is also bonded to an -OH group. The entire assembly of atoms is called the carboxyl group (-COOH) - releases a hydrogen ion (proton) - functions as an acid (has acidic properties b/c covalent bond between oxygen and hydrogen is so polar) 2 electronegative oxygen atoms pull electrons away from the hydrogen atom which weakens the bond between the O-H. Thus, the Hydrogen ion tends to disassociate from the molecule as H+ (donating the hydrogen ions = acidic) molecules that contain these groups are known as carboxylic acids - combine with amino to make an amino acid which is found in proteins. - found in cells in the ionized form with charge of 1-
How Membrane Lipids Interact with Water
- wide array of functions, most prominent function of lipids is their role in cell membranes, even though not all lipids can form membranes. - phospholipids are amphipathic (contain both hydrophilic and hydrophobic regions) ex: cholesterol is amphipathic b/c it has a hydrophilic hydroxyl functional group attached to its hydrophobic 4 carbon rings and isoprenoid tail.
Key points about the peptide bonded backbone of a chain of amino acid residues (bottom page 83 diagram)
1. *R-group orientation*: the side chains of each residue extend out from the backbone which makes it possible for them to interact with each other and with water 2. *Directionality*: in a chain of amino acid residues, there is an amino group (—NH3+) on one end of the backbone and there is a carboxyl group (—COO-) on the other end. The end of the residue sequence that has the free amino group is called the N-terminus, or amino terminus. The end with the free carboxyl group is called the C-terminus, or Carboxy terminus. The amino acid residue sequence is usually written from the N-terminus to C-terminus b/c the N-terminus is the start of the chain when proteins are synthesized in cells. 3. *Flexibility*: the peptide bond itself cannot rotate b/c of its double bond nature. However, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible.
5 types of interactions involving R-groups
1. *hydrogen bonding*: hydrogen bonds form between polar SIDE CHAINS and opposite partial charges either on the PEPTIDE BACKBONE or other R-groups ex: H bond between side chain and carbonyl group on backbone 2. *hydrophobic interactions*: in an aqueous soln, water molecules interact with hydrophilic polar SIDE CHAINS of a polypeptide which forces the hydrophobic nonpolar side chains to glob up/coalesce in the interior of the resulting globular mass. Water molecules surrounding that mass form more H bonds with each other and the polar amino acid residues on the surface of the protein, this increases the stability of their own interactions and the disorder of the rest of the aqueous soln 3. Van der Waal interactions: once nonpolar SIDE CHAINS are forced close to one another by hydrophobic interactions, their association is further stabilized by Van der Waal interactions. A large number of these weak electrical attractions can significantly increase the stability of the protein 4. Covalent bonding: covalent bonds can form between the SIDE CHAINS of two CYSTEINES through a reaction between the sulfhydryl groups. These disulfide ("two-sulfur") bonds are frequently referred to as bridges, b/c they create strong links between distinct regions of the same polypeptide or 2 separate polypeptides 5. Ionic bonding (rare): ionic bonds may from between groups that have full and opposing charges, such as the ionized acidic and basic SIDE CHAINS ionic bonding. This is rare in proteins unless ionized r-groups are located in the interior where there is little water. This is b/c ionized r-groups on the exterior are normally exposed to the aqueous environment and enveloped by a shell of water which prevents them from interacting with one another.
How far apart are the amino acid residues that hydrogen bond in the linear sequence of a polypeptide's primary structure?
1. : α-helix hydrogen bonds form between residues that are just 4 linear positions apart 2. β-pleated sheet: the linear distance between residues may be larger b/c 180° bends in the polypeptide chain bring them close enough together to hydrogen bond ***see page 86 figure 3.8 (b)
All in all, what do functional groups in side chains influence?
1. Chemical Reactivity 2. Solubility (based on if they are polar/charged or nonpolar/uncharged) 3. Size 4. Shape
Describe the four emergent properties of water that allow earth to sustain life
1. Cohesion/Adhesion. Cohesion: water molecules sticking together, holding hands, which creates BIOLOGICAL: surface tension ex. Spiders that walk across water. Cohesion between water molecules allows the surface tension to support the weight of the spider. Ex. Water that forms dome shape on penny. Tons of hydrogen bonding water leads to strong forces which is responsible for belly flopping in pool Adhesion: water interaction with something other than water (hydrogen with something else) BIOLOGICAL: leaf with water droplets. Droplets themselves are held together by cohesion (round sphere shapes). Droplets cling to the leaf by adhesion (hydrogen bonding between hydrogen in water and the leaf's surface) - both work together in helping water get from roots of tree to branches of trees. Adhesion between water and sides of cells that holds them in there. Cohesion between water molecules themselves. So you have water being evaporated, when this happens water molecules hold hands and when one leaves, the other pulls the next up the plant (from the root to other parts of the plant) 2. Denser as a liquid than a solid (expansion upon freezing): as water freezes, molecules move slower allowing for the "locking in" of the hydrogen bonds that lead to formation of low density crystal structure called ice. BIOLOGICAL: allows for ice to float. The water at surface freezes and b/c it is less dense, it will stay at the top. Acts as insulation/barrier so that the water beneath it stays liquid. This is important for wildlife that lives in pond/stream, so that the body of water is not all ice. 3. High specific heat (moderation of temperature): water is able to absorb or release large amounts of heat with only a slight change in its own temp. Ex: you burn yourself on the metal of pan instead of water that is still boiling b/c the specific heat of metal is much less than water. So it absorbs the energy much quicker and increases temp faster. BIOLOGICAL: temperature closer to coast is much cooler b/c water absorbs the heat. The farther inland you get, the warmer it is b/c your away from the water which would have absorbed the heat/insulate/regulate. 4. Versatile Solvent: due to the polarity of water, it is able to interact/form bonds with other ions/ polar molecules. Ex: dissolving salt in water, molecules interact (- of Cl and + of Na, water helps break those apart). BIOLOGICAL: we are made up of a lot of water, so when we discuss the chemical reactions that occur in the body, they are happening in an aqueous environment (water plays a role).
Describe the replication process of RNA (page 106)
1. Complementary bases pair: to replicate a single stranded RNA, first a complementary copy of the RNA is made. Using the original strand as a template, free ribonucleotides form hydrogen bonds with complementary bases on the template. 2. Copied strand polymerizes: A new strand is polymerized when 3' hydroxyls and 5' phosphates on adjacent nucleotides are linked together via condensation reactions. The product is a doubles stranded RNA molecule 3. Copy and template separate: to arrive at a duplicate of the original single-stranded RNA in step 1 (the template), the hydrogen bonds between the double-stranded product in step 2 must first be broken by heating or by a catalyzed reaction. 4: copy serves as a new template: repeats step 1,2,3. The newly made complementary RNA molecule now exists independently of the original template strand.
If asked to list amino acids in order from most hydrophylic to most hydrophobic, what should you do?
1. Determine what type of R-group the amino acid has: acidic/basic, polar, or nonpolar 2. If the side chain is electrically charged it is the most hydrophilic b/c that means they are ionized (acidic/basic). The most hydrophylic molecules are those that share the most like forces with water. 3. The next strongest like force is uncharged polar. So if it has any oxygens or nitrogens then this will be the next hydrophylic. If you have multiple uncharged polar amino acids, then the one with the most electronegative atoms (O and F) is the most hydrophylic. 4. Nonpolar side chains are the most hydrophobic. If you ahve multiple nonpolar side chains, then the one with the most C—H nonpolar covalent bonds is the most hydrophobic.
When drawing amino acid linkages, steps:
1. Draw the basic general shape of the molecule (NH2-HC-COOH with a double bond between C=O and an R group) 2. Remember that the amino functional group acts as a base so it should be shown as NH3+ (3 hydrogens off the nitrogen). The carboxyl group functions as an acid so it should be written as COO-. (Basically add H+ and erase the H/add -)
When you encounter an organic molecule that is new to you, what are the steps to follow?
1. Examine the overall size and shape provided by the carbon framework 2. Identify the tyes of covalent bonds present based on electronegativities of atoms. Estimate polarity of molecule and amount of potential energy stored in chemical bonds 3. Locate any functional groups and note the properties those groups give to the molecule\\
Describe the types of interactions that stabilize and shape DNA's secondary structure
1. Hydrophobic carbon-nitrogen ring causing double stranded DNA to twist. 2. Hydrogen bonding between complementary base pairs. 3. Van der Waals interactions between tightly packed adjacent base pairs, called base stacking. - the rotated orientation of the interior base pairs in a helix allows the rings of adjacent base pairs to stack on top of one another like coins (4.6b). The nonpolar interior is sandwiched between negatively charged phophate groups of poutward facing backbone which makes double helix hydrophilic overall and thus soluble in aqueous solns (Note that phosphodiester linkages in the backbone is part of primary structure)
Compartmentalization also offers two key advantages in eukaryotic cells
1. Incompatible chemical reactions can be separated - ex. new fatty acids can be synthesized in one organelle while excess or damaged fatty acids are degraded and recycled in a different organelle. 2. Chemical reactions become more efficient - groups of enzymes that work together can be clustered within or on the membranes of organelles instead of floating free in the cytosol. When the product of one reaction is the substrate for a second reaction, clustering the two enzymes increases the speed and efficiency of both reactions. - substrates required for particular reactions can be localized and maintained at high concentrations within organelles. When substrates are used up in a particular part of the organelle, they can be replaced by substrates that have only a short distance to diffuse.
Provide 2 examples of catalytic activities that would have been necessary for ribozymes to replicate in an RNA world
1. Production of nucleotides 2. Polymerization of RNA It is thought that nucleotides were scarce during chemical evolution, so their catalyzed synthesis by a ribozyme would have been advantageous. Catalysis by an RNA replicase would have dramatically increased the reproductive rate of RNA molecules
Describe the process of DNA synthesis
1. Strand separation: DNA strands separate when hydrogen bonds between complementary base pairs are broken. This can happen by adding heat energy or by using enzymes in catalysis reactions 2. Base pairing: each strand of DNA can serve as a template for the formation of a new strand. Free deoxyribonucleotides attach to the 3' ends FIRST of the template strand according to complementary base pairing. 3. Polymerization: As the free deoxyribonucleotides attach to the template strand, their sugar phosphate groups form phosphodiester linkages to create a new strand: the complementary strand. when the new strands polymerize to form a sugar-phosphate backbone, secondary structure is restored. *each copy has one strand from the original DNA molecule and one new strand
Identify two aspects of the structures of cellulose, chitin, and peptidoglycan that correlate with their function as structural molecules.
1. The β-1,4-glycosidic linkages in these molecules result in insoluble fibers that most organisms cannot break down with enzymes. 2. When individual molecules of these carbohydrates align, bonds form between them and produce fibers or sheets that resist pulling and pushing forces.
The Role of Carbohydrates in Cell Identity (identification badge)
1. There is enormous structural diversity in some complex carbohydrates based on monomers and the bonds they can form. 2. complex Polysaccharides act as identification badges (that identifies the type or species of the cell) on the outer surface of the plasma membrane that surrounds a cell. 3. A protein withone or more carbohydrate groups covalently bound is a glycoprotein, and the carbohydrates of glycoproteins are always on the outside of the cell. 4. Glycoproteins are key molecules for cell recognition and cell signaling. 5. Each cell carries a set of glycoproteins on its cell surface, identifying it as part of that body and also identifying its tissue type (nervous, muscle, etc.). 6. The diversity of monosaccharides allows for a virtually unlimited amount of unique glycoproteins to exist, so that each species can have a unique identity. 7. carbs are at the root of sexual reproduction. Wasserman, examined binding of the sperm to the egg during fertilization and demonstrated that sperm only recognize eggs of their own species (no dog and human breeding) - a. Competitive binding added purified egg-surface glycoproteins to sperm. glycoproteins bound to and thus blocked the binding of sperm to eggs. (not of same species) - b. Purified carbohydrates but not proteins caused the block in binding.
phylogeny (evolutionary history) what are organisms divided into?
1. bacteria (prokaryotic) 2. archaea (prokaryotic) 3. eukarya (eukaryotic; included algae, fungi, plants, animals)
Describe four structural differences that could result in different oligosaccharides consisting of two glucose residues and two galactose residues.
1. location of linkages (e.g., 1,4 or 1,6) 2. types of glycosidic linkages (α or β) 3. sequence of the monomers (e.g., two galactose and then two glucose, versus alternating galactose and glucose) 4. whether the four monomers are linked in a line or whether they branch (like the α-1,6)
What distinguishes one monosaccharide from another?
1. location of the carbonyl group (aldehyde vs ketone) page 112 2. total number of carbon atoms present 3. spatial arrangement of atoms (diff of one hydroxyl group between 2 hexose sugars: glucose and galactose) 4. ring forms of the same molecule also have alternative shapes.
How can polysaccharides (carbs) be used? carbohydrate functions
1. they provide fibrous structural materials 2. they mark cell identity 3. they store chemical energy 4. they serve as precursors to other molecules - carbs serve as a building block for more complex molecules (ex. ribose or deoxyribose sugars are carbs that make up RNA and DNA
What do the specific measurements in DNA stand for (page 102)
2.0 nm = the width of the helix 0.34 nm = the distance between bases stacked in a spiral 3.4 nm = the hydrophobic interactions that the bases have with water result in a full helical turn every 10 bases. This is that distance
How many types of amino acids are used to build proteins?
20 amino acids
How many different r-groups are there?
20 different R groups - b/c the only thing that differs between amino acids are the side chains/r-groups.. therefore by saying there are 20 different amino acids that means there are 20 different r groups
Amino acid R-group division (chart on page 82)
3 general types: 1. Charged (since they acidic and basic) [electrically charged; it can form ionic bonds with water] 2. Uncharged polar (due to partial charges on side chain it can form hydrogen bonds with water) 3. Nonpolar
Oligosaccharides
3-10 monosaccharides, "few sugars" - polysaccharides ("many sugars")
What are the 5 prime and 3 prime parts of the sugar-phosphate backbone? (Page 98)
5' end of the nucleic acid: unlinked phosphate, makes sense since RNA and DNA are synthesized/start here in this direction 3' end of the nucleic acid: unlinked hydroxyl group on the carbon sugar. 3' end is where new nucleotides are added to be bound to the unlinked hydroxyl group. Unlinked = meaning the groups are not bonded to another molecule
What parts of an amino acid are joined/separated through condensation/hydrolysis?
A bond forms between the carboxyl functional group of one amino acid and the amino functional group of the other amino acid. (Diagram on page 83) - A hydroxyl group is removed from the carboxyl group of one amino acid and hydrogen is removed from the amino group of the other amino acid, allowing a bond to form between the two groups.
What would happen if the phosphate linkages between nucleotides break?
A break in the sugar phosphate backbone would occur. - this process happens when the RNA molecule folds in a certain way that allows the hydroxyl on the 2' carbon to attack the linkages
phospholipid
A class of lipid having a hydrophilic head (including phosphate group) and a hydrophobic tail (consisting of 2 hydrocarbon chains, either isoprenoids or fatty acids) - major component of the plasma membrane - The phosphate group is also bonded to a small organic molecule that is charged or polar - Phospholipids with fatty acid tails (unbranched) are found in the domains Bacteria and Eukarya. phospholipids with isoprenoid (branched) tails are found in the domain Archaea. the branched out form provides greater membrane stability and protection in the extreme environment
Covalent bond vs ionic bond
A covalent bond forms when outer shell electrons are shared between atoms. (H2) An ionic bond is formed when one or more electrons are transferred from one atom to another. (NaCl)
Macromolecular machines
A group/complex of multiple proteins that assemble to carry out a particular function in cells. - some macromolecular machines contain other types of macromolecules. Ex: the ribosome which consists of several nucleic acid molecules & 50 diff proteins
Monomer
A molecular subunit used to build a macromolecule ("one part") - when a large number of monomers are bonded together, the resulting structure is called a polymer ("many parts")
Substrates (why are enzymes good catalysts?)
A reactant in a chemical reaction that interacts with a catalyst (like an enzyme) - partly why enzymes are good catalysts is b/c they hold substrates in a specific/precise orientation so that they can react
fatty acid
A simple lipid consisting of a hydrocarbon chain bonded at one end to a polar carboxyl functional group (—COOH). - key building blocks of important lipids in organisms Used by many organisms to store chemical energy; a major component of animal and plant fats and phospholipids. - fatty acids are amphipathic and able to assemble into lipid bilayers and form water-filled vesicles.
Ribonucliec Acid (RNA)
A stringle stranded nucleic acid composed of ribonucleotides FUNCTIONS: include catalytic components of ribosomes (+RNA), transporters of amino acids (+RNA), a messages of the DNA code required for protein synthesis (mRNA) - sugar difference: sugar in ribose has an -OH group bonded to the 2' carbon - nitrogeneous base difference of RNA: uses Adenine (A), URACIL (U), Guanine (G), or Cytosine (C)
axoneme
A structure found in eukaryotic cilia and flagella and responsible for their motion; composed of two central microtubules surrounded by nine doublet microtubules (9 + 2 arrangement). - nine doublets of the axoneme originate from a structure called the basal bod: serves as an MTOC for growth of the axoneme doublets.
Primary structure of RNA? What makes RNA more reactive than DNA?
A sugar-phosphate backbone formed by phosphodiester linkages and extending out are a sequence of 4 types of nitrogenous bases (G,C,U,A) Sequence of ribonucleotides. Differs from DNA b/c the sugar in the sugar-phosphate backbone is ribose NOT deoxyribose. And, the pyrimidine base thymine doesn't exist in RNA, instead RNA contains the closely related pyrimidine base uracil SINCE, ribose has a hydroxyl group (-OH) bonded to the carbon at 2' it makes it much more reactive than the hydrogen atom on the 2' carbon of deoxyribose. When RNA molecules fold in certain ways, the hydroxyl group on 2' carbon can attack the phosphodiester linkages between nucleotides which generates a break in the sugar-phosphate backbone. This -OH group makes RNA less stable than DNA.
endomembrane system
A system of organelles in eukaryotic cells that synthesizes, processes, transports, and recycles proteins and lipids. Includes the endoplasmic reticulum (ER), Golgi apparatus, and lysosomes. - grouped b/c the system is continuous or
glycerol
A three-carbon molecule that forms the "backbone" of phospholipids and most fats.
Macromolecules
A very large organic complex molecule composed of many smaller molecules joined together - a molecular subunit used to build a macromolecule is called a monomer ("one part")
Difference between aldehydes and ketones?
Aldehydes contain the carbonyl group (C double bond O) also bonded to hydrogen. These are found at the end of the carbon skeleton. Ketones contain the carbonyl group (C double bond O) bonded to 2 carbons at each end. These are within the carbon skeleton.
Transport proteins
Allow particular molecules to enter and exit cells or carry them throughout the body Ex. Hemoglobin is a popular transport protein Ex. Almost every cells has membrane proteins that control the passage of specific molecuels and ions: like the sodium potassium pump
What causes double stranded DNA to twist into a helix?
Although each base has polar groups that are involved in hydrogen bonding, the bases' carbon-nitrogen rings are mostly nonpolar. Therefore, the "inside" of the latter is nonpolar, meaning it is hydrophobic in an aqueous solution (enviro inside cell) and cause double stranded DNA to twist into a helix to minimize contact between the hydrophobic bases and the surrounding water molecules. (3.4 nm=10 rungs, or inside latter steps, per turn in helical structure)
If you understand this hypothesis, you should be able to predict where amino acids and nucleotides would be placed in Figure 6.9 and explain your reasoning.
Amino acids have amino and carboxyl groups that are ionized in water, and nucleotides have negatively charged phosphates. - Due to their charge and larger size, both of these compounds would be placed below the small ions at the bottom of the permeability scale (<10−12 cm/sec).
what influences protein function in amino acids that don't have functional groups in their side chain?
Amino acids that do not have functional groups in their side chain rarely participate in chemical reactions. So, their influence on protein function depends/stems from their size and shape rather than their reactivity.
Why is protein folding crucial to the function of a completed protein (see picture page 90)
Anfinsen studied a protein called ribonuclease that cleaved (or split) RNA polymers. He broke the hydrogen/disulfide bonds in the protein which unfolded the ribonuclease: this is called denatured. He found that the denatured ribonuclease couldn't degrade/split nucleic acid anymore. - BUT, when the denaturating agents were removed, the ribonuclease spontaneously refolded and was able to function normally again - this CONFIRMS that the primary sequence contains all the info required for protein folding AND that folding (structure) is essential for protein function - also, the process of denaturing (unfolding) a protein is reversible
Defense proteins
Antibodies Proteins called antibodies that attack and destroy viruses and bacteria that cause disease
How does a meniscus form?
As a result of: - Adhesion: at the sides (perimeter) of the surface, partial positive charges on water molecules adhere to the negative charges on the glass, resulting in an upward pull - Cohesion: in the middle (along) of the surface water molecules hydrogen bond to those next to them and below them, this results in an overall (net) lateral and downward pull that resists the upward pull of adhesion
What is the relation between specific heat and polarity?
As molecules increase in their overall polarity (and therefore their ability to form hydrogen bonds), it takes more energy to change their temperature. (B/c more bonds have to be overcome before the temperature can be raised/molecules move faster)
Moderation of temp. How would the coast/inland figure look at night?
At night, it will be warmer at the coast and colder inland. This is because the temps closer to the coast would be close to what they are during the day, there wouldn't be as much fluctuation b/c during the day the body of water has absorbed the heat and at night it releases the heat back into the atmosphere to keep temp in moderate range. When you go inland, you see a larger fluctuation in temperature, as there was nothing to absorb heat during day so it got really hot. Then, at night there is no more sun (source of heat), and no water to release the heat so you see temp drop drastically. So at night in the desert it can get cold because you don't have the water there to moderate it. - this same moderation of temperature occurs in our body. So we don't have huge swings back in forth based on the outside temperature (hot outside vs cold inside house) **ALL DUE TO HIGH SPECIFIC HEAT
Cohesion
Attraction between like molecules. Ex: water is cohesive, meaning that it stays together, because of the hydrogen bonds that form between individual molecules
Adhesion
Attraction between unlike molecules. - usually talked about regarding interactions between a liquid and a solid surface. Ex: water adheres to surfaces that have any polar or charged components
Why is the theory of chemical evolution that monomers polymerize to form the larger and more complex macromolecule not entirely correct?
B/c according to the 2nd law of thermodynamics, a pool of free monomers would not be expecte dot spontaneously self assemble into a polymer. This is because the polymerization reaction takes multiple simple monomers into a single more complex and ordered structure. - this means that polymerization decreases the disorder (entropy) of molecules so it is not energetically favorable.
will a small difference between the structures of carbohydrates, like the spatial orientation of a single hydroxyl group, change the function of the molecule?
Because the molecular structures of glucose and galactose differ, their functions differ. yes. ex: glucose and galactose which differ only by the spatial arrangement of one hydroxyl group) - Glucose is both a source of carbon atoms, used to construct other molecules, and of chemical energy that sustains life. But because molecules interact in precise ways based on their shape, galactose must first be converted to glucose via an enzyme-catalyzed reaction to be used in these same ways. main point: Even seemingly simple changes in structure—like the spatial orientation of a single hydroxyl group—will have functional consequences.
Endosymbiosis theory
Biologists propose that mitochondria and chloroplasts were once free-living bacteria (prokaryotes). They were then engulfed by ancestors of modern eukaryotes but weren't destroyed b/c they had a mutually beneficial relationship
Hydrolysis
Breaks polymers apart by adding a water molecuels - water molecule reacts with the bond that links the monomers together. This separates one monomer from the polymer chain - water in, monomer out
How are ions like calcium, that are released during a signaling event different from the chagnes that occur in prion proteins?
Calcium ions bind to specific proteins to change their folded shape and adopt a functional form which alters cellular activity. In prion proteins that shape changes occurs from protein (bad)-protein(normal)interactions not interactions with other ions.
spongiform encephalopathies
Caused by prions, including mad cow disease. - cows/sheep/goats/humans can be affected and the result is damage to the CNS (brain) - mostly obtained by eating tissues that contain the infectious form of the prion (PrP) - infectious prions are able to propagate by binding to normal/healthy prions which alters its shape into the infectious ones (think like a zombie bite). Shape change = stabilization between prion proteins = linkage of long fibrils that causes cell death - SHOWS HOW A PROTEIN'S FUNCTION DEPENDS ON ITS SHAPE and how the FINAL SHAPE OF A PROTEIN DEPENDS ON FOLDING
Molecular chaperones
Cells contain these special proteins, called molecular chaperones, that help facilitate protein folding. - many molecular chaperons belong to family of molecules called heat shock proteins b/c they are produced in large amounts after cells are exposed to very very high temperatures that cause denaturing (unfolding) FUNCTION: block inappropriate interactions (unfolded proteins) - nonpolar side chains of unfolded polypeptides can spontaneously clump together which disrupts the normal folding process and forms nonfunctional aggregates. The molecular chaperons will then ATTACH to the HYDROPHOBIC PATCHES of the polypeptide and kind of "pinch" them to encourage them before aggregates or groups of them can clump together, they then release them to fold properly after. (Page 91 for pic) - chaperones thus help new proteins and denatured protein fold into the shape specified by their primary sequence
Carbohydrates Can Provide Structural Support
Cellulose and chitin, and peptidoglycan are key structural compounds. - they all form long strands and bonds form between parallel strands. ex: 80 cellulose molecule are cross linked by hydrogen bonds to produce a fiber, multiple cellulose fibers then crisscross to form a tough sheet which is able to withstand pushing and pulling forces. - they are durable. almost all organisms produce enzyme that cleave α-glycosidic linkages (starch/glycogen) BUT only a few organisms have enzymes capable of digesting cellulose, chitin ,or peptidoglycan - their fibers tend to be insoluble due to strong interactions between strands consisting of b-1,4 glycosidic linkages. they don't have water in their fibers so they are resistant to hydrolysis and decay - their indigestible structure makes cellulose important for digestive health. eating plants (dietary fiber) forms a porous/sponge like mass that absorbs/retains water; it adds moisture and bulk that helps fecal material move through intestinal tract more quickly (preventing constipation)
How can folding be infectious? (Prions, PrP)
Certain normal proteins can be made to fold into infectious disease causing agents called PRIONS. These are still proteins and are also called proteinaceous infectious particles. - prion proteins have two differently folded shapes: a normally folded shape and an infectious disease causing shape which can bind normally folded prion proteins and cause them to adopt the infectious shape. The two versions still have the same primary structure, they just have very different folded forms (shapes). Their secondary structure is diff as well as the normal has alpha and the bad one has beta pleated sheets - responsible for mad cow disease- disease in cattle that destroys the CNS
primary difference between channels and carrier proteins is the mechanism of transport
Channels allow movement through a selective pore - like bridges allow people to cross back and forth over a river Carrier proteins selectively pick up a solute on one side of the membrane, then drop it off on the other side. - like a ferry picking up people on one side of a river and then dropping them on the other side.
What creates surface tension?
Cohesion (hydrogen bonds in water) ***adhesion comes into play with cohesion when it comes to water moving through a tree
What is a main component of surface tension?
Cohesion. Surface tension is defined as the cohesive force caused by attraction between the molecules at the surface of a liquid. When water molecules are at the surface, there are no other molecules above them for hydrogen bonding. However, these H bonds do form between surface and nearest neighboring water molecules (next to and below them). This results in tension that minimizes the total surface area. - because of surface tension, light objects (like spiders) do not fall through the water's surface. Water resists the weight of the spider b/c it would increase its surface area and water does not want to do that.
Peptide bonds (further)
Compared to other types of monomer linkages, peptide bonds are unusually stable due to nitrogen donating its pair of unshared valence electrons to the carbon in the C—N which forms a C=N partial double bond (referring to the peptide bond between amino acid molecules) - as a result, a pair of electrons are pushed from the carbonyl (C=O) to the oxygen atom which forms a single bond with an oxygen anion (C—O minus) - all these diff bond configurations oscillate, but the degree of electron sharing is great enough that peptide bonds have some of the characteristics of a double bond. Ex. The peptide bond is PLANAR which limits the movement of the atoms participating in the peptide bond - BASICALLY, the electron sharing between the pair of valence electrons on the nitrogen and the carbon of the peptide (C—N) bond
Hydrocarbons
Compounds composed of only carbon and hydrogen - nonpolar - electrons shared equally in C--H bonds due to similar electronegativities of carbon and hydrogen (no partial charges) - do not dissolve in water
Example of the simplest type of protein with quaternary structure
Contains just two subunits that are identical. The Cro protein found in a virus
What happens when covalent bonds are broken in proteins?
Covalent bonds are also peptide bonds. This means that the peptide bonds that hold amino acid residues together would separate.
central dogmaff
DNA -> RNA -> Protein (flow of genetic info) 1. synthesis of RNA based on info stored in DNA is first step (chromosome in prokaryotes, nucleus in eukaryotes) 2. ribosomes (macromolecular machines) where information stored in RNA can be used to direct synthesis of proteins
Ribbon diagrams
Diagram that shows the backbone of protein structures, (portrays the secondary structures within the overall shape of a protein) - diagrams represent α-helices as coils and β-pleated sheets as 2 arrows side by side in a plane (one pointing up and the other down). The arrow points toward the carboxyl end of the primary structure. Page 86 figure 3.8 (c) - unlike space filling models (page 85 figure 3.6), the ribbon diagram doesn't show the presence of each atom and its volume, only the underlying contours of the protein backbone
differential centrifugation, imaging, live cell imaging
Differential centrifugation: allowed researchers to isolate particular cell components and analyze their chemical composition - Based on breaking cells apart to release the cell components and separating them in a centrifuge. individual parts are purified and studied in isolation IMAGING: simply looking at cells has been most important. - put fluorescing tags or markers on particular cell components and then look at them with sophisticated light microscopes/electron microscopes. Neither of these are able to study how things move from place to place in cell directly, which makes cells seem static when they are actually dynamic LIVE-cell imaging techniques show the dynamicity
osmosis
Diffusion of water through a selectively permeable membrane - occurs only when solutions are separated by a membrane that permits water to cross, but holds back some or all of the solutes - ONLY unbound water molecules are able to diffuse across the membrane during osmosis. Recall that water molecules interact with charged particles and form hydrogen bonds with polar molecules, so if a solute can't cross the membrane, then any associated water molecules are also prevented from crossing - movement is spontaneous - When water moves, the solns on both sides of membrane experience a change in volume and solute concentration (greater the initial diff in solute concentration is, greater the volume change) - opposing forces, such as the pressure resulting from the downward pull of gravity, exert resistance to the directional movement of water.
How Do Proteins Enter the Endomembrane System?
ER signal sequence. begins in FREE ribosomes in the cytosol. *Step 1* Protein synthesis begins on a free ribosome in the cytosol. The ribosome synthesizes the ER signal sequence, using information carried in an mRNA. *Step 2* The signal sequence binds to a signal recognition particle (SRP)—a complex of RNA and protein. The attached SRP causes protein synthesis to stop. *Step 3* The ribosome+signal sequence+SRP complex moves to the rough ER membrane, where it attaches to the SRP receptor. Think of the SRP as a key that is activated by an ER signal sequence. The SRP receptor in the ER membrane is the lock. *Step 4* Once the lock (the receptor) and key (the SRP) connect, the SRP is released and protein synthesis continues through a channel called the translocon. *Step 5* The growing protein is fed into the ER lumen, and the ER signal sequence is removed. - Once proteins are inside the rough ER or inserted into its membrane, they fold into their three-dimensional shape with the help of chaperone proteins. Carbohydrate side chains join them (glycosylation) which results in glycoprotein. - The amino acid sequence is removed when protein synthesis is complete and the protein is released into ER lumen or become integral membrane proteins
How Do Proteins Reach Their Proper Destinations?
Each cargo protein has a molecular tag that directs it to particular vesicle budding sites by interacting with receptors in the trans cisterna. These receptors direct the transport vesicles to the correct destinations.
Lock and key model (Emil Fischer)
Enzymes are the lock; substrates are the keys that fit into the lock and then react - he was right that enzymes bring substrates into a precise orientation that makes rxns more likely - also explained why enzymes only catalyzed one specific reaction (since the orientation of enzyme was specific to the substrate). This enzyme specificity occurs b/c of the types of functional groups in the sites where the substrates bind. - active site: the location in an enzyme molecule where substrates (reactants)bind and react. This is where the clefts (indents) are in the tertiary structure of the enzyme protein. The types of functional groups and their geometry is what causes enzyme specificity. (See page 93)
Explain how the primary and tertiary levels of protein structure relate to enzyme/substrate specificity
Enzymes bind to specific substrates based on the structure of their active site. This active site is formed: when the polypeptide of an enzyme is fully folded into its TERTIARY structure (when the protein is folded into its functional shape). The info required for proteins to fold into their functional state: is in the PRIMARY structure which is also responsible for the specific amino acid residues located in the active site that interact with the substrate
Give examples of monomer/macromolecule/polymerization
Ex. Amino acids are monomers. These polymerize (bonding of many monomers) through condensation reactions to form a protein. The protein is the macromolecule. Ex. Other macromolecules of life include nucleic acids and carbohydrates
Tertiary structure of RNA (page 105)
Ex. pseudoknot structure: 3D structure formed by base pairing between distant regions of already folded RNA molecules (ex. hair pin loops). The unbonded bases on loop part of hair pin falls over and pairs with baess on another part of the single stranded RNA. - As a result, RNA molecules with diff base sequences can have very diff overall shapes and chemical properties. RNA molecules are more diverse in size, shape, and reactivity than DNA molecules - arises when secondary structures fold into more complex shapes Other examples include RIBOZYMES (like the tetrahymena)
Cytoskeleton
Extensive system of protein fibers gives cell its shape and structural stability - involved in moving materials within the cell as well as the cell itself. - organizes all the organelles and other cellular structures into a cohesive whole. - Found in both prokaryotes and eukaryotes, but is much less extensive in prokaryotes
Temperature Affect the Fluidity and Permeability of Membranes
FLUIDITY: phospholipids in the plasma membrane of a cell have a consistency resembling olive oil which allows individual lipid molecules to move laterally within each layer (think: person moving about in a dense crowd) but they rarely flip to other side of bilayer TEMPERATURE: ↑ temperature = ↑ permeability - As temperature drops, molecules in a bilayer move more slowly and become less fluid (moving laterally less). As a result, the hydrophobic tails in the interior of membranes pack together more tightly = less permeable - At very low temperatures, lipid bilayers even begin to solidify. low temperatures can make membranes impermeable to molecules that would normally cross them readily at more moderate temperatures
How do fats and phospholipids differ?
Fats and Phospholipids Differ in the Presence or Absence of a Hydrophilic Region - phospholipids have the glycerol, fatty acids, phosphate, and polar or charged group extending from the top of the molecule. - fats only consist of glycerol and fatty acids
Peroxisomes
Globular organelles which originate when empty vesicles from ER are loaded with peroxisome specific enzymes from the cytosol. Once formed, they do not exchange materials with other organelles so they aren't part of endomembrane system - Centers for reduction-oxidation (redox) reactions. ex. Peroxisomes in liver cells contain enzymes that oxidize ethanol in alcoholic beverages. ex.: glyoxysomes are specialized peroxisomes that are packed with enzymes to oxidize fatty acids to form compound to store energy. These reactions include H2O2 (hydrogen peroxide) which is highly reactive (if it escaped the organelle it could react with and damage DNA, proteins, etc. doesn't happen often though b/c the peroxisome has CATALASE that quickly detoxifies h2o2 to form water and oxygen
Why doesn't heating ice water (solid) cause it to expand like what one would assume? (Since heating = molecules move faster = collide more often = more force)
Heating ice causes the hydrogen bonds between molecules to break which results in the open crystal structure to collapse. ICE: water molecules form a crystal lattice LIQUID: no crystal lattice forms. Hydrogen bonds are constantly being formed/broken, therefore there is much less HB in liquid water than there is in ice. Recall that the HB is what gives ice its crystal structure which means less open space between molecules. As a result, molecules in the liquid phase are packed much more closely together than in the solid phase which means liquid water is more dense than ice.
Water's specific heat and heat of vaporization/ its biological consequences
High specific heat: water molecules must absorb lots of heat energy to break hydrogen bonds and experience increased movement (and thus temperature) High heat of vaporization: water molecules must absorb lots of heat energy to break hydrogen bonds and change water from liquid to gas (water has to absorb a great deal of energy to evaporate) *** these both are critical to the theory of chemical evolution - Water's high specific heat and heat of vaporization tend to resist temperature and phase changes
Why are hydrogen bonds weaker than ionic and covalent bonds?
Hydrogen Bonds are weaker than covalent bonds because they do not involve sharing of electrons, and they are weaker than ionic bonds because they involve the attraction of partial (not full) opposite charges. - An ionic bond essentially donates an electron to the other atom participating in the bond, while electrons in a covalent bond are shared equally between the atoms. (Ionic is usually stronger than covalent)
How does hydrogen bonding occur between the functional groups in the peptide-bonded backbone of a protein? Secondary structures(Page 86 depiction)
Hydrogen bonding between sections of the same backbone is possible ONLY when a polypeptide bends in a way that brings the C=O and H—N groups close together. The polar groups are aligned and from Hydrogen bonds with one another when the backbone bends to form 1 of 2 structures: 1. An alpha (α) helix in which the polypeptide's back bone is coiled (think 3C curl) OR 2. A beta (β) pleated sheet in which segments of a polypeptide chain bend 180° (like curve/half circle) and then fold in the same plane. Think the shape of a track and field where you run the curve and then the straight parts have crimps in them
What is responsible for water having a high capacity for absorbing energy (high specific heat)
Hydrogen bonding. This means that water has a high capacity for absorbing energy.
Which dominates: condensation (dehydration) or hydrolysis?
Hydrolysis dominates - this is b/c it both increases entropy and it is favorable energetically (more free molecules = increased disorder, multiple simple molecules vs one complex molecule) - meaning that polymerization (condensation) would only occur if there is a very HIGH CONCENTRATION of monomers to push reaction to condensation - since equilibrium favors free monomers rather than polymers, a polymer is unlikely to grow much beyond a short cain
Explain thought process of liquid water being more dense than ice.
ICE - the hydrogen bonding in ice is stable (4) - this results in crystal lattice (@0C), ↑ more room between molecules - ↓ less dense as ice WATER - the hydrogen bonding is formed/broken constantly - no crystal lattice, ↓ less room between molecu'es - ↑ dense as liquid * water is most dense @4 degrees celsius.
Why does ice float?
Ice floats b/c liquid water is more dense than solid water - ice serves as a blanket that insulates the liquid below from the cold air above - if water weren't so unusual then Earth's oceans almost certainly would have frozen solid before life had a chance to start.
Polymerization of proteins in early Earth
If proteins were responsible for the start of life early in chemical evolution, then the process of linking amino acids must have occurred in the absence of the cellular factors that are needed (ribosomes, RNA, etc). the key to chemical evolution is also replication
Based on a picture of the structure of an amino acid, how can you tell if it is nonpolar?
If the R-group (side chain) in your amino acid does not have a negative charge (acidic), positive charge (basic), or an oxygen atom (noncharged polar) then you are looking at a nonpolar amino acid Ex. Methionine
Based on a picture of the structure of an amino acid, how can you tell if it is acidic?
If the R-group has a negative charge it is acidic and has lost a proton (gained an electron, -) Ex. Aspartate - the charged side chains (r-groups) can form ionic bonds or interact with water
Based on a picture of the structure of an amino acid, how can you tell if it is basic?
If the R-group has a positive charge it is basic and has gained a proton (lost an electron, +) Ex. Lysine - the charged side chains (r-groups) can form ionic bonds or interact with water
Spontaneous reaction characteristics
If the product has a higher entropy (more disorder) If the product has a lower potential energy (This is why even though condensation reactions in polymerization reduces entropy, the increase in potential energy makes up for it through Activated nucleotides)
Based on a picture of the structure of an amino acid, how can you tell if it is uncharged polar?
If the r-group is uncharged (no + or - indicating that it is basic/acidic) then does it have an oxygen atom or nitrogen? If so, then the highly electronegative oxygen will form a polar covalent bond in the R-group which makes it an uncharged polar - the overall polarity of an R-group is based on the # of highly polar covalent bonds relative to nonpolar bonds Ex. Serine
Evaluate the possibility of hydrogen bonding between nucleotides G—T and A—C
In G—T pair, only one hydrogen bond could form b/c the O—H—O bond repels like partial charges, N—H—N bond repels like partial charges, and the N—H—O is the only one In A—C pair, none could form b/c N—H—N bons are nonpolar.
Explain how the saturation status of hydrocarbon chains affects the physical characteristics of lipids.
In general, unsaturated lipids are more fluid than saturated lipids at a given temperature.
Where is the potential energy in activated nucleotides (like ATP/dATP) stored in?
In the bonds between the phosphates. This energy is then released once the phosphates are removed by hydrolysis (ATP/dATP reacting with water). ATP + H2O —> AMP + Pyrophosphate + energy release AMP = a regular adenine ribonucleoside Pyrophosphate = the 2 phosphate groups removed (this is inorganic b/c it is not attached/bonded to carbon) * this energy release also happens when activated nucleotides (like ATP/dATP) are used as substrates (key in lock and key model) for polymerization of nucleic acids
Electronegativity rule
Increases left to right Increases top to bottom
DNA functions as an information containing molecule
Info is stored in the large sequence of nucleotides. This info is vital for the organism's growth and reproduction
Signaling proteins
Involved in carrying/receiving signals from cell to cell inside the body - usually on the cell's membrane so it can interact with close by cells Ex. Glucagon binding to receptor proteins on liver cells so that enzymes release sugar into bloodstream Ex. Hormonal proteins like INSULIN secreted by pancreas
Channel Proteins Facilitate Diffusion
Ion channels form pores in a membrane which ions can diffuse through from regions of high concentration to regions of low concentration and from areas of like charge to areas of unlike charge (electrochemical gradient) - ions will diffuse in a directional manner if an appropriate channel exist. for Na+ to diffuse there needs to be a specific Na+ ion channel - ion channels are transmembrane proteins
Rank the types of bonds/interactions from strongest to weakest
Ionic bonding Covalent bonding (between nonmetals) Hydrogen
What types of things stay in aqueous solutions?
Ions and polar molecules stay in solution b/c of their interactions with water's partial charges. Ex: Na+ and Cl- from dissolved table salt. The Na+ interacts with the O- in water. The Cl- interacts with the H+ in water. - substances that interact with water in this way are called HYDROPHILIC ('water loving"). Almost any ionic compound and polar molecule dissolve in water b/c of these. Fo
cystic fibrosis and channel proteins
It affects cells that produce mucus, sweat, and digestive juices. - normally their secretions are thin, slippery, and act as lubricants. with someone with CF, secretions are concentrated and sticky, which can clog passageways in organs like the lungs. - cystic fibrosis is caused by defects in a transmembrane protein (CFTR) which allows passage of chloride ions. the reduced rate of Cl- transport was caused the thick mucus in the lungs - WHY? defective CFTR channel prevents Cl- ions from leaving cells surrounding airway passageways, a hypertonic state can't be obtained on airway surfaces which means a hypertonic state can't be obtained on airway surfaces. - the disease results from the mismanagement of osmosis
How do you know which secondary structure will form in a given protein's structure?
It depends on the molecule's primary structure, specifically the identities/types of the amino acid residues in the sequence. - certain amino acids are more likely to be involved in alpha helices than in beta pleated sheets, and vice versa, due to the specific geometry of their side chains. Ex.: proline is rarely found in α-helices b/c of its unusual R-group which bonds to both the central carbon of the residue AND also to the nitrogen of the residue's core amino group (see residue 2 in figure 3.4a). This makes kinks in the peptide-bonded backbone that do not fit well to the shape of an alpha helix.
Why is water so important to life?
It is a great solvent (agent for dissolving or getting substances into solution) due to its unique polarity. The polarity is due to the difference in the electronegativities of hydrogen and oxygen. Ex: sugar molecules in an aqueous solution of coffee. They become separated from one another and interact with water's partial charges instead.
SO did chemical evolution give rise to proteins?
It remains unclear.
What is the nature of DNA's secondary structure
James watson and francis crick presented their model and hypothesized onthe basis of a series of results from other laboratories - they already knew the general structure of nucleotides AND that they polymerized through the formation of phosphodiester linkages. So, watson/crick knew it had a sugar phosphate backbone - the molecule was helical or spiral in nature
Is nucleotide polymerization spontaeous? So, how can it occur in cells? (See video on page 98)
Just like other polymerization rxnws, the joining of nucleotides into nucleic acids decvreases entropy by a lot and it NOT spontaneous. Input of energy is needed to balance in favor of joining the nucleotides - the potential energy of nucleotide monomers is raised by adding 2 phosphate groups to the beginning (5') monophosphates of ribonucleoside or deoxyribonucleoside. This creates nucleoside triphosphates also known as "activated nucleotides". Ex. Activated ribonucleotide is known as adenosine triphosphate or ATP. Ex. Equivalent nucleotide used for DNA synthesis is deoxyadenosine triphosphate (dATP) - when activated nucleotides polymerize, the energy that is released from the condensation reaction compensates for the decrease in entropy which makes it spontaneous
microtube+ATP+vesicle+kinesin
Kinesin: motor proteins that use chem energy of ATP to walk toward + end of microtubule - The discovery of kinesin explained how secretory vesicles could be moved toward the plus end of microtubules, during their transport from the trans-Golgi cisterna to the plasma membrane.
***
Know how each functional group looks like. Chart on page 76
Could chemical evolution result in the production of nucleotides?
Laboratory simulations show that nitrogeneous bases and sugars can be syntehsized readily under conditions that mimic those in early earth oceans - also, minerals in these deep sea vents PREFERENTIALLY bind to ribose sugar concentrating the ribose (sugar found in RNA) from a diverse pool of sugars.
What does life depend on?
Lifeis based on water. - life arose in an aqueous environment - 75% of the volume in a typical cell is water (it's the most abundant molecule in organisms) - you can survive forweeks without eating, but you aren't likely to live more than 3/4 days without drinking
Explain what is primarily responsible for the functional versatility observed in RNA
Like proteins, single stranded RNA molecules will fold into diff shapes that have diff properties. The additional hydroxyl functional group attatched to the 2' carbon (ribose sugar) makes RNA more reactive so it can support catalytic functions
What type of molecule was responsible for the origin of life?
Likely Amino acids. - through experiments studying the waters of prebiotic Earth, amino acids were repeatedly noteworthy - amino acids have also been found in meteorites and in experiments that approx the environment of interstellar space. This coupled together leads researchers to concude that amino acids were present and prob abundant during chemical evolution For the answer to be amino acids for sure, proteins would need to have 3 of the fundamental attributes of life which are info, replication, and evolution
NUCLEIC ACIDS (Picture on page 98)
Macromolecule/polymer made up of monomers called nucleotides. Nucleotides are made up of 3 components: 1) one or more phosphate groups attached to 5 prime carbon 2) five carbon sugar in middle (ribose or deoxyribose) 3) one of several nitrogeous base attached to 1 prime carbon (nitrogen containing). The sugar molecule is the central component of the nucleotide (like the alpha carbon in amino acids)- generally used by cells to store or transmit hereditary information - there are 8 different nucleotides used to build nucleic acids: 4 ribonucleotides (A, U, C, G) and 4 deoxyribonucleotides (A, T, C, G) (after diff sugars and bases are taken into account) - 2 types of nucleic acids: ribonuclic acid (RNA) made up of ribonucleotides and deoxyribonucleic acid (DNA) which is made of deoxyribonucleotides
Carbohydrate
Made up of a carbonyl group (C==O), several hydroxyl groups (-OH), along with multiple carbon-hydrogen bonds (C—H). - The molecular formula of many of these molecules is (CH2O)n where n indicates the number of carbon-hydrate groups (hydrate=water) - the value n = 3 is the smallest sugar - not all CH2O compounds are carbohydrates. Ex: formaldehyde is not a carbohydrate b/c it does not contain a hydroxyl group
Modern cells create how many diff types of proteins?
Modern cells create tens of thousands of distinct proteins, most of which are composed 20 diff types of amino acids. - all 20 of the amino acids (building blocks) have the same common core structure
Theory of chemical evolution
Molecules that were formed in the ocean were protected by water from the excessive heat/sources of energy that could have broken them apart (like sunlight). As a result, the molecules stayed in the ocean and grew in concentration over time which made them more likely to react and continue the process.
Condensation reactions (aka dehydration reactions)
Monomers polymerize through these reactions. - name origin results from the newly formed bonds that occur as a result of the loss of a water molecule. - monomer in, water out (page 77 picture) - rxn in which two molecules (monomers) become covalently bonded to each other thru loss of water - each monomer in condensation reactions contain a hydroxyl group and a hydrogen. Therefore when added to another, water is a product
Can DNA self replicate?
No, DNA can not catalyze the reactions needed to self replicate (it is not spontaneous). The molecule is copied through a series of reactions that are catalyzed by enzymes Dna can't act as an effective catalyst because its structure is so stable/nonreactive so it can't self replicate. Thereofre no support that the first life form consisted of DNA alone
Do amphipathic lipids dissolve in water?
No, their hydrophilic heads interact with water but their hydrophobic tails do not, instead of dissolving amphipathic lipids form one of two structures, micelles and lipid bilayers - form spontaneously in water—no input of energy is required. When amphipathic lipids are dispersed in an aqueous solution, highly organized cages of water form around each of the nonpolar tails. If the tails aggregate to form micelles and bilayers, then only the hydrophilic regions of the lipids are exposed and the water cages will melt. This decrease in water molecule organization results in an overall increase in the entropy of the system.
Is replication of DNA spontaneous?
No, you must add heat (energy) in order for the reaction to take place
Are the shapes of proteins always correlated with their function?
No. - sometimes they are, like in the case of the TATA box which has a groove/space that specifically fits a nucleic acid (molecule of DNA) so that it can regulate gene activity. Or Porin which is doughnut shaped and fits in cell membranes and allows certain hydrophilic molecules to pass through it - however, many proteins found in cells DON'T have overall shapes that are correlated with their functions. Ex. Chymotrypsin protein that has a globular shape which does not tell you much about its function (which is to bind to and cleave/split the peptide bonds of other proteins) **however no matter how large or complex a protein is, its underlying structure can be categorized into 4 basic levels of organization
Nonpolar covalent bond vs polar covalent bond
Nonpolar covalent: electrons are halfway between the two atoms, shared equally. Ex: H2 Polar covalent: electrons are not shared equally (O is mroe electronegative than H), so partial charges exist on the O and H atoms.
Describe a nonpolar molecule in an aqueous solution (hydrophobic interactions)
Nonpolar molecules do not readily dissolve in aqueous solns/don't interact with water which is called hydrophobic ("water fearing") - since the nonpolar molecules don;t interact with water, the surrounding water molecules are forced to form more hydrogen bonds with each other. Thus, the hydrophobic molecules are drawn close to each other to minimize disruption of normal hydrogen bonding between water molecules
Did life arise from a self replicating enzyme? (Was a protein catalyst the first molecule causing life?)
Not likely. To achieve attributes of life, proteins would need to possess information, replicate, and evolve. HOWEVER, the info in proteins is necessary for their function but it does not allow the protein to replicated (use itself as a template to make more). Since it can't replicate, that means it can't evolve.
How do nucleotides (building blocks of nucleic acids) polymerize to form nucleic acids?
Nucleotides polymerize via condensation (dehydration) reactions between hydroxyl on the carbon sugar component of one nucleotide and the phosphate group of another nucleotide - rxn forms a covalent bond between the nucleotides and a molecule of water is released. - bridge formed by the phosphate group between two carbon sugars is called a phosphodiester linkage (aka phosphodiester bond)
SO, what is necessary for monomers to polymerize? (To be linked/bonded together)
Occurs only if there is a very high concentration of monomers to push the reaction toward condensation
How does adding phosphate groups raise the potential energy of a nucleotide?
Phosphates are negatively charged. Like charges repel each other, therefore the bonds between the 3 phosphates are very weak. This makes the potential energy of the bonds higher (the want to break off and make new stronger bonds is higher), repulsive forces. - the energy is released when the phosphates form new more stable bonds with other atoms (through hydrolysis)
Protein is interchangeable with what term
Polypeptide
Endoplasmic Reticulum "inside-formed-network"
Portions of the nuclear envelope extend into the cytoplasm to form an extensive membrane-enclosed factory - ER membrane is continuous with the nuclear envelope - single organelle with 2 regions that are distinct: rough and smooth
What is DNA's primary structure
Primary structure: linear sequence of nucleotides that are linked together by phosphodiester (covalent) bonds, arranged in 5' —> 3'. This has greater variability compared to the other levels Secondary structure: based on complementary base pairing; the 2 antiparallel strands are held together by hydrogen bonds between complementary base pairs Tertiary structure: often includes proteins
What are the levels of protein structure stabilized by?
Primary: peptide bonds Secondary: involve only hydrogen bonds between backbone amino and carbonyl groups Tertiary: form using variety of bonds/interactions between R-groups themselves or between R-groups and the peptide bonded backbone Quaternary: bonds and other interactions between R-groups, and between peptide backbones of diff polypeptides
Autophagy
Process by which damaged organelles and other cytoplasmic components are surrounded by a membrane which fuses with the lysosome to be recycled/digested.
compare contrast flagella in prokaryotes and eukaryotes
Prokaryotic flagella move the cell by rotating like a ship's propeller; eukaryotic flagella move the cell by undulating—they whip back and forth. Eukaryotic flagella are surrounded by the plasma membrane; prokaryotic flagella are not. A prokaryotic flagellum consists of a single helical rod made of flagellin (in bacteria) or other types of proteins (in archaea); a eukaryotic flagellum consists of several microtubules constructed from tubulin dimers.
Is there only one possible shape for a protein?
Protein shape is flexible. - each protein has a specific folded shape necessary for it to perform a function. HOWEVER, most proteins have disordered regions that lack any apparent structure when they are in an inactive state and then when they are prompted by other ions/molecules/chemically modified they adopt their folded/functional form. Thus, proteins are flexible and dynamic when they aren't actively performing their function.
Peripheral membrane proteins
Proteins that bind to membrane lipids or integral membrane proteins without passing through it (only one side of bilayer) - interior and exterior surfaces of the plasma membrane are distinct: the peripheral membrane proteins are diff and the ends of transmembrane proteins differ
What are the macromolecules of life
Proteins, nucleic acids, and carbohydrates - since equilibrium favors free monomers rather than polymers, a polymer is unlikely to grow much beyond a short chain. However, there are multiple diff ways that the macromolecules ay have polymerized early in chemical evolution
Which macromolecule is the most abundant and versatile in life?
Proteins. - they are composed of 20 amino acids with unique side chains. These amino acids polymerize to form protein structures which determine protein function.
Purines vs. Pyrimidines in nucleotides
Purines: adeNINE (A) and GuaNINE (G) (think "GAP") - class consists of DOUBLE rings formed from NINE atoms Pyramidines: Cytosine (C), Uracil (U), Thymine (T) - class consists of SINGLE ringed nitrogen bases formed from SIX atoms **Purines (9 atomsz) are also larger than pyramidines (6 atoms)
Why is liquid water more dense than solid water?
Recall that in ice, each water molecule has 4 hydrogen bonds which forms a regular/repeating lattice structure (crystal). This crystal formation is open and has a relatively larger amount of space between molecules. Having a larger amount of space between molecules = less dense
Why is the order and type of residues in the primary structure of a protein important?
Recall that the R-groups present on each amino acid affect its size, shape, chemical reactivity, and solubility. So, the order of the R-groups present in a polypeptide will affect that molecule's properties and function. - sometimes, even one single change in the sequence of amino acids can result in striking changes in the way that the protein as a whole behaves. Ex.: hemoglobin (oxygen binding protein in red blood cells). In some people, 1 of the 2 polypeptide sequences that make up hemoglobin has a valine instead of a glutamate amino acid residue at the 6th position. This single change causes red blood cells to alter from their normal disc shape to a sickled shape when oxygen concentrations are low. (The change in R-group in valine produces hemoglobin molecules that stick to each other and form fibers when oxygen concen are low, red blood cells that carry these fibers adopt a sickle like shape which get stuck in blood vessels, called capillaries, thereby starving downstream cells of oxygen. This illness is called sickle cell disease.
R-group
Represents the part of the amino acid core structure that makes each of the 20 diff amino acids unique. - these "side chains" vary from just a single hydrogen atom to large structures that contain carbon atoms linked into rings
How biologists study the RNA world
Researchers test the RNA world hypothesis by establishing an environment in the laboratory that selects for ribozymes that catalyze key steps required for an RNA world Ex: David Bartel's team generated an RNA molecule that could catalyze the template directed polymerization needed for RNA replication (an RNA replicase) . Using "natural selection" to target certain characterisitcs of molecules instead of organisms, the team was able to isolate a ribozyme that could add 14 nucleotides to an EXISTING RNA strand Ex. Nucleotides may have been a scarce resource in early Earth conditions, so ribozymes that catalyze the production of RNA nucleotides would be more likely to be copied due to local accumulation of monomers. - starting with a large pool of randomly generated RNA sequences, the researchers selected for RNAs that could catakyze the addition of a uracil base to a ribose sugar. Using the process of natural selection, they purified a ribozyme that could perform this task 1 MILLION times more efficient than the uncatalyzed reaction. Molecular evolution had occurred in the rxn tubes
Dynein
Responsible for bending of cilia and flagella which results in a swimming motion, class of motor proteins that use chem energy of ATP to walk toward the minus end of microtubule - moves vesicles to negative ends of microtubules and for bending microtubules in flagella and cilia
Movement (motor proteins)
Responsible for moving the cell itself or for moving large molecules and other types of cargo inside the cell. Ex. Extending your arm: Proteins actin and myosin slide past each other to flex/extend muscle cells in fingers and arm
An RNA world may have sparked the evolution of life NUCLEIC ACIDS CAN SATISFY 3 OUT OF 5 NECESSARY CHARACTERISTICS NEEDED FOR LIFE
Ribozymes play key roles in the synthesis of proteins. To the point where if the ribozymes were removed from cells, proteins could no longer be made. This means that an RNA mah have preceded proteins. - evolution of protein enzymes would have marked the end of an RNA world, providing means for catalyzing rxns necessary for life to emerge in cellular form, after this 3/5 of fundamental characterisitics of life would have been solidly in place: 1. INFORMATION: proteins/ribozymes would be processing info stored in nucleic acids for the synthesis of more proteins 2. REPLICATION: enzymes and possibly ribozymes would be replicating the nucleic acids that stored the hereditary info 3. EVOLUTION: random changes in the nucleic acids would lead to the synthesis of diff proteins/ribozymes. Selective advantages resulting from some of these changes would allow for the evolution of new functions
How does complementary base pairing direct secondary AND tertiary structures in RNA?
SECONDARY: complementary base pairing between antiparallel regions forms a double helix TERTIARY: base pairing between different regions of an RNA molecule causes it to fold into a more complex tertiary structure **always antiparallel
Compare and contrast secondary/teritary structures in proteins and DNA
Secondary structure of a protein often leads to a more compact tertiary structure when the polypeptide folds on itself Same for DNA! DNA in cells is also normally found in more compact 3D structures - compared to proteins, DNA's teritary structure is less dependent on primary structure and so it is far less variable between different sequences.
exocytosis
Secretion of intracellular molecules (like hormones) that are in membrane bound vesicles, to the outside of the cell by fusion of vesicles to the plasma membrane
How do functional groups affect reactivity in amino acids
Several of side chains (R-groups) contain functional groups (like carboxyl, hydroxyl, sulfhydryl, etc) which participate in chemical reactions (under the right circumstances) Ex. Amino acids with a sulfhydryl group (—SH) in their side chains can form disulfide (S—S) bonds which help link different parts of large proteins. These bonds form naturally between proteins in hair; curly hair has many of these cross links and straight hair has fewer.
What types of carbohydrates are there?
Simple and complex sugars (carbohydrates) - these chains can range in size. When it is just 2 sugars (2 monosaccharide residues) linked together it is called a disaccharide
Monosaccharides
Simple sugars. Are the monomers of carbohydrates - by convention, carbons in a monosaccharide are numbered consecutively starting with the carbon in the carbonyl group
RNA can function as a catalytic molecule (Ribozymes)
Since RNA has a degree of structural and chemical variety, it's capable of forming structure that catalyze chemical reactions. The ribozymes 3D nature is vital to its catalytic activity. - protein enzymes that catalyzed similar reactions as the tetrahymena ribozyme were found to have active sites that were similar in structure. This observation of 2 very different macromolecules demonstrates the critical relation between structure and function - Ribozymes are any RNA molecule that acts as a catalyst to increase the rate of a chemical reaction. They are similar to protein enzymes Ex. Tetrahymena Ribozyme: it catalyzes both the condensation (dehydration) and hydrolysis of phosphodiester linkages in RNA (between ribonucleotides). The folded tertiary structure brings together bases from distant locations in the primary structure to form the active site where catalysis occurs Ex. Ribozymes are responsible for the catalytic activity of ribosomes that polymerize amino acids to form polypeptides (proteins)
If you understand passive transport, you should be able to predict how increasing the temperature would affect the rate of achieving equilibrium in Figure 6.13.
Since temperature is a measure of thermal motion, increases collisions, speed of molecules so increasing temperature would increase the rate of diffusion and thus the rate of passive transport to achieve equilibrium across a membrane.
path of a secretory protein
Step 1: Ribosomes at the rough ER finish the polypeptide as it is moved into the ER lumen. Step 2: Polypeptide folds and is packaged into a vesicle. Step 3: Vesicle is transported to the cis Golgi. Step 4: Protein is processed as it moves through the Golgi apparatus and cargo receptors package it into a transport vesicle. Step 5: Secretory vesicle is transported to the plasma membrane. Step 6: Vesicle fuses with the plasma membrane and releases protein to the outside of the cell.
steps of sodium potassium pump
Step 1: When Na+/K+-ATPase is in the conformation shown here, binding sites with a high affinity for sodium ions are available. Step 2: Three sodium ions diffuse from the inside of the cell, bind to these sites, and activate the ATPase activity in the pump. Step 3: A phosphate group from ATP is transferred to the pump. When the phosphate group attaches, the pump changes its shape in a way that opens the ion-binding pocket to the external environment and reduces the pump's affinity for sodium ions. Step 4: The sodium ions exit the protein and diffuse to the exterior of the cell. Step 5: In this conformation, the pump has binding sites with a high affinity for potassium ions facing the external environment. Step 6: Two potassium ions from outside the cell bind to the pump. Step 7: When the potassium is bound, the phosphate group is cleaved from the protein and its structure changes in response—back to the original shape with the ion-binding pocket facing the interior of the cell. Step 8: In this conformation, the pump has low affinity for potassium ions. The potassium ions exit the protein and diffuse into the interior of the cell. The cycle then repeats.
How do proteins have so many functions
Structure gives rise to function. - the variability in protein size (# of amino acid residues linked) and shape (triple helix collagen that form long cable like fibers shows shapes of proteins can widely differ; the TATA box which has a groove/space for a molecule of DNA to fit which then regulates gene activity which shows that SOMETIMES shape is related to function) as well as chemical properties of the amino acid residues is responsible for the diverse set of functions that proteins perform in cells - in overall shape, proteins are the most diverse class of molecules known
What was the significance of the formation of the Earth's first ocean?
Substances are most likely to come into contact with one another and react when they are solutes (meaning when they are dissolved in a solvent like water). The formation of the Earth's first ocean was a turning point in chemical evolution b/c it gave the process a place to happen. - the reactions that were responsible for chemical evolution (like those occurring inside your body) depend on direct/physical interaction between molecules)
Predict what type of organelle would be dominant in cells of your immune system that consume and digest bacterial cells.
Such cells would likely have many lysosomes to digest and recycle components that are consumed, such as bacteria.
Protein
Term used to describe any chain of amino acid residues - in formal use, refers to the completed (often functional) form of the molecule - most proteins are large enough to be considered polypeptides, some are only functional when multiple polypeptide subunits interact with one another
Why can't DNA catalyze the reactions needed to self replicate by itself? (Instead of needing enzymes, etc)
The DNA double helix is highly structured, regular, symmetric, held together by phosphodiester linkages, hydrogen bonding, hydrophobic interactions, etc. The molecule also does not have many exposed functional groups that can participate in chemical rxns which makes DNA stable and resistant to degradation. This makes DNA an ideal molecule for housing information, its structure is consistent with its function - even when researchers find intact DNA from fossils that are thousands of years old, the molecules have the same sequence of bases as the organism had when it was alive HOWEVER, this also makes it bad at catalysis, the structure of DNA is too stable and nonreactive to catalyze any reaction compared to the wide variation in R-groups of amino acids and the crazy amount of shapes found in proteins
Specific heat
The amount of energy required to raise the temperature of 1 gram of a substance by 1 degree celsius.
What do the carbon atoms in an organic molecule do?
The carbons atoms furnish a skeleton/blueprint that gives the molecule its overall shape
How do amino acids behave in water
The combination of the amino and carboxyl functional groups is key to how the amino acid behaves - amino acids will ionize. The concentration of protons at the pH of 7 causes the amino group to behave as a base and attract a proton to form NH3+. The carboxyl group will behave as an acid as the 2 highly electronegative oxygen atoms pull the electron away from the hydrogen atom which makes the C—O bond weaker and more able for the group to lose a proton to form COO+ (from COOH) - NH2 becomes NH3+ and COOH becomes COO+. These charges are important b/c 1. They help amino acids stay in solution where they interact with one another and other solutes 2. They affect the amino acid's chemical reactivity
electrochemical gradient
The combined effect of an ion's concentration gradient and electrical (charge) gradient across a membrane that affects the diffusion of ions across the membrane.
ester linkage
The covalent bond formed by a condensation reaction between a carboxyl group and a hydroxyl group. Ester linkages join fatty acids to glycerol to form a fat or phospholipid. - when two atoms (one of them carrying a double-bonded oxygen, often a carbonyl group) are linked together by an oxygen
Glycosidic linkage
The covalent bond formed by a condensation reaction between two sugar (monosaccharide) monomers (—O—) - joins the residues of a polysaccharide - 2 types: alpha-1,4 glycosidic linkage and beta-1,4 glycosidic linkage. Numbers refer to the carbons on either side of the linkage, indicating that the linkages are between Carbon-1 and Carbon-4 of glucose ring. Carbons are same but Geometry is different as alpha refers to hydroxyls oriented below the glucose ring plane. Beta refers to the hydroxyl being above the plane. - main difference between glycosidic linkages and the linkages of peptide/phosphodiester is that their linkages form between the same locations in their monomers which gives the proteins and nucleic acids a standard backbone structure. HOWEVER, glycosidic linkages form between hydroxyl groups which vary in number (at least 2 in every mono). So the location and geometry of glycosidic linkages vary widely among diff oligosaccharides and polysaccharides. They are similar to proteins/nucleic acids thought b/c the structure/function depends on the type of monomers involved
Heat of vaporization
The energy requires to change 1 gram of water from a liquid to gas
Describe some ways that the various types of carbohydrates you ate during breakfast today are being used in your body right now.
The energy-storage molecules, like starch, are being hydrolyzed to release glucose. Disaccharides like the lactose in milk would be hydrolyzed to release glucose and galactose. These sugars may be further broken down to produce ATP and raw materials for building other molecules, such as glycolipids and glycoproteins. The insoluble cellulose that makes up dietary fiber does not get broken down, but it will help retain water and support the digestion and passage of fecal material.
Natural selection
The evolutionary process by which individuals (in this case molecules) with certain characteristics reproduce more frequently than others. - once the first self replicating molecules evolved, chance errors in the copying process created variations that would go through natural selection (where molecules with certain characteristics were more likely to reproduce). At this point, chemical evolution was over and biological evolution was off and running.
How many polypeptides are in each of the levels of protein structure?
The first 3 levels of protein structure involve only single polypeptides - some proteins contain multiple polypeptides that interact to form one single functional structure (whole)
Primary structure of proteins
The first level of protein structure; the specific unique/distinct sequence of amino acids that make up a protein. - a protein's primary structure is fundamental to its function. It is also fundamental to the higher levels of protein structure - concluded by Frederick Sanger (12 yrs of studying). He was the first to determine the amino acid sequence of insulin (hormone regulating sugar concentrations in blood). - with 20 types of amino acids available and chain lengths of up to tens of thousands of amino acid residues, the number of primary structures that are possible is basically limitless (20^n diff combos of amino acid residues for a polymer possible with a given length of n). Ex: a chain of just 10 amino acids has 20^10 possible sequences, over 10,000 billion variations.
Evaluate hypothesis that life began as RNA molecule
The first living molecules had to (1) provide a template that could be copied and (2) catalyze polymerization rxns that would link monomers into a copy of that template. - since RNA can do both, most people think that the first life form was an RNA (1) RNA also contains a sequence of bases that act like letters in a sentence, so it can function as an information carrying molecule. This info stored in RNA can be used to make copies of itself via complemetnary base pairing. (2) The fact that a ribozyme could catalyze the formation of a phosphodiester bond/linkage
Quaternary Structure of proteins
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits. - individual polypeptides are held together by many of the same bonds/interactions found in the tertiary level of structure - if only 2 subunits are in the quaternary structure it is referred to as a dimer ("two-parts"). When the two polypeptide subunits are identical, they are called homodimers; heterodimers when they are non-identical - if there are 4 subunits/polypeptides then it is called a tetramer ("four-parts"). Ex. Hemoglobin contains 2 identical copies of an alpha helix subunit and 2 identical copies of a beta pleated sheet subunit (see page 88)
What defines the chemical behavior in organic molecules?
The functional groups. The chemical behavior of the compound (the types of reactions that it participates in) is dictated by !groups of H-, N-, O-, P-, and S- atoms that are bonded to one of the carbon atoms in a specific way! - the number and types of functional groups attached to a framework of carbon atoms imply a great deal about how that molecule is going to behave
Each of the hydrogen bonds in an alpha helix or a beta pleated sheet is weak relative to a covalent (peptide) bond. So how come secondary structures are highly stable?
The large number/amount of hydrogen bonds in these secondary structures makes them highly stable. As a result, they increase the stability of the overall molecule and helps define its shape. *HOWEVER* for overall shape and stability, the tertiary structure of a protein is even more important!!!
Amino acid
The most important type of amino- and carboxyl- containing molecules are the amino acids (they contain both amino group and a carboxyl group) - picks up H ions from surrounding soln so this amino group acts as a base. - NH2. Consists of a nitrogen atom bonded to 2 hydrogen atoms and to the carbon skeleton - amino acids can be linked together by covalent bonds that form betwen amino and carboxyl groups
What does it mean to say that protein structure is heirarchical
The order and type of amino acids in the primary structure is responsible for the secondary structures, which then fold up to form tertiary structure. Quaternary structure (if present) is based on interactions between tertiary structures of the polypeptide subunits
What forms the primary structure of a nucleic acid?
The order of the different nucleotides - always written in the 5' -> 3' direction (remember 5' = where it starts, phosphate. 3' = where it ends, carbon sugar)
What interaction is between the oxygen and hydrogen of water MOLECULES
The partial + charge on hydrogen atttracts the partial - on oxygen. This weak electrical interaction is an example of a HYDROGEN BOND. - Hydrogen bonding occurs between hydrogen and usually nitrogen, oxygen, flourine
How many bonds can one solid water (ice) molecule make?
The partial charges on water molecules can form up to four hydrogen bonds. The oxygen can form two; each hydrogen can form one.
Sugar phosphate backbone (see pic on page 98)
The phosphodiester linkage between the phosphate group of one nucleotide and the sugar of another nucleotide - the sugar-phosphate backbone in nucleic acids is analagous to the peptide bonded backbone in proteins - ***think of it like this: what is the only thing that changes from monomer to monomer (amino acid residue to residue)? The R-groups. Therefore, what links the similar parts of the rest of the monomers? Peptide bonds. Therefore it is called a peptide bonded backbone What is the only thing that changes from ribonucleotide to ribonucleotide (or deoxynucleotide to deoxynucleotide)? The nitrogeneous base. Therefore, what links the similar parts of the rest of the monomers? Phosphodiester linkages. Therefore it is called a sugar phosphate backbone (b/c that is was a linkage is)
How do R-groups affect solubility?
The polarity and charge (nature) of the R-groups affects the solubility of an amino acid in its natural environment (which is the aqueous interior of the cell) - both POLAR and ELECTRICALLY CHARGED r-groups interact readily with water and are *hydrophilic*. These dissolve easily in water - nonpolar r-groups lack the charged or highly electronegative atoms that would form hydrogen bonds with water. These r-groups are hydrophobic (not interacting with water). Hydrophobic r-groups tend to coalesce in aqueous solution (clump)
Polymerization
The process of linking (bonding) monomers together
Why causes amino acids to have different properties?
The properties of amino acids vary b/c their R-groups vary.
selectively permeability
The property of a membrane that allows some materials to pass through while keeping others out, or letting some substances pass more easier than others. - controlling what passes between interior and exterior environment is a key characteristic of cells ex. small nonpolar molecules such as oxygen (O2) move across bilayers quickly. small molecules that are polar but uncharged (H2O) rate of transport decreases Larger polar molecules cross membrane slower (glucose cross lipid bilayer 10,000 times slower than H2O) small but charged ions (Na+, K+) do not effectively cross lipid bilayers without "help" from membrane proteins (w/o proteins = 1 billion times slower than H2O)
Secondary structure of proteins
The second level of protein structure; generated by interactions between functional groups, specifically carboxyl and amino, in the peptide bonded backbone - secondary structures are distinct shaped sections of the linear amino acid residue sequence that are stablized by HYDROGEN BONDING that occurs between the oxygen on the carbonyl functional group (C=O) of one amino acid residue and the hydrogen on the amino group (N—H) of another. the oxygen in carbonyl is highly electronegative, holds a partial - charge while the hydrogen in the amino group has a partial positive charge b/c it is bonded to nitrogen which has a high electronegativity - the regular local patterns of coils or folds of a polypeptide chain.
what happens if the hydrogen bonds between secondary structures (alpha/beta) are broken?
The secondary structure would unfold (either the "curl"/alpha helix, or the "crimp"/beta pleated sheet)
Give an example of how the spatial orientation of glycosidic linkages affects the structure function and durability of carbs
The structural differences between maltose and lactose is that The beta glycosidic linkages lactose cause the glucose ring to be flipped whereas maltose consists of alpha gylcosidic linkages. - The functional consequence of this is that the enzymes used to hydrolyze maltose will not cleave lactose. Instead, lactose is cleaved by lactase (enzyme humans stop secreting after childhood). W/o this protein, many become lactose intolerant (no dairy products)
Tertiary structure of proteins
The third level of protein structure; the overall, three-dimensional shape of a protein/polypeptide due to interactions between amino acid residues that are brought together as the backbone bends and folds in space. - amino acid residues that interact with one another are usually far apart in the linear sequence. - form using variety of bonds/interactions between R-groups themselves or between R-groups and the backbone - if you were to look at a picture of these, it would look like a group of secondary structures (either alpha or beta) together (see page 88)
Are there more molecules of water in a given volume of liquid or solid water?
There are more molecules of water in a given volume of liquid water than there are in the same volume of solid water - this is b/c water is denser as a liquid than as a solid
Water;s high heat of vaporization biological consequences
This is the reason why sweating is effective in cooling the body down after a hot day. The water molecules in sweat must absorb a great amount of energy (heat) from the body before they evaporate. Therefore, you lose heat in the form of energy changing liquid water to gas phase to evaporate. * also critical to theory of chemical evolution
Polymerization of monosaccharides (sugars)
Through condensation reaction between 2 hydroxyl groups resulting in a covalent connection (—O—) which is called a glycosidic linkage - hydrolysis therefore cleaves the linkages (monomer out, water in)
Propose a hypothesis to explain why toxins like nicotine, cocaine, and caffeine are stored in vacuoles instead of the cytosol.
Toxins are stored in membrane enclosed vacuoles to prevent them from contacting and damaging components of the cytosol or other organelles in the cell.
Microtubules
Tubulin dimers polymerize in a polar head-to-tail fashion via noncovalent bonds to form thin chains called protofilaments that, in turn, interact with one another to form hollow tubes. protofilaments always align in the same orientation, microtubules also exhibit polarity. α-tubulins at one end (the minus end) and β-tubulins at the other end (the plus end). - assembled from subunits consisting of two closely related proteins, α-tubulin and β-tubulin, that exist under normal conditions as stable protein dimers - Originate from a structure called the microtubule-organizing center (MTOC), plus ends of microtubules grow outward radiating thruout cell. centrosome serves as MTOC center for cell's cytoskeleton - Microtubules are best known for their role in separating chromosomes during mitosis and meiosis - ***If microtubules are prevented from forming, the network-like configuration of the ER collapses and the Golgi apparatus breaks up into vesicles.*** - movement of materials elsewhere in the cell. For instance, the movement of vesicles from the rough ER to the Golgi apparatus requires microtubule tracks.
Density of water compared to other states
Unlike most substances, water is denser as a liquid than as a solid - MEANING, there are more molecules of water in a given volume of liquid water than there are in the same volume of solid water, or ice - when you fill an ice tray with water and put it in the freezer, the water expands as ice
pulse chase experiment
Used to track protein movement: mark a population of molecules at a particular interval (the pulse, Expose experimental cells to a high concentration of a modified amino acid for a short time.proteins synthesized during that interval will be radiolabeled.) and then follow their fate over time (the chase, The time following the end of the pulse is referred to as the chase. The proteins synthesized during the chase period will NOT be radiolabeled.) - think adding a small amount of dye to a stream and then following the movement of the dye to track the pattern of water flow. - pulse labeled proteins can then be tracked (even during chase)
RNA's versatility
VERY versatile, many functions. - RNA is a nucleic acid that folds into complex 3D shapes like proteins - their structural flexibility allows them to have many functions. Ex: RNA is an intermediate (messenger RNA) between DNA and protein as it transmits the info needed to synthesize proteins/polypeptides (catalyzes the synthesis of proteins, regulates production of mRNA from DNA, etc)
DNA strands form an antiparallel Double Helix
W and C constructed physical models that led them: - 2 strands of DNA side by side with sugar phosphate backbones on outside and nitrogenous bases on the inside. In order for the bases to fit within the 2.0nm width, it must be a purine-pyrimidine pair - this purine-pyrimidine pairing allows hydrogen bonds to form between complementary bases. Adenine forms 2 hydrogen bonds with thymine. Guanine forms 3 hydrogen bonds with cytosine. This 3rd bond makes G/C bond stronger than A/T - ANTIPARALLEL strands: describes the opposite orientation of nucleic acids strands that are hydrogen bonded to one another, with one strand running in the 5'-3' direction and the other 3'-5' direction. This happens so that the bases on opposite strands are flipped 180 degrees relative to each other. - antiparallel strands were predicted to to be twisted together to form double helix (this was hypothesized after all the above info)
How does water interact with polar molecules and ions?
Water interacts with polar molecules via hydrogen bonding Water interacts with ions via similar electrical attractions
What is one important consequence of water being able to hydrogen bond with molecules next to and below them, but not above them?
Water resists any force that increases its surface area. Specifically, any force that depresses a water's surface meets with resistance. This resistance makes the surface of water act like an elastic membrance. Water's elastic membrance is stronger than other liquids because of hydrogen bonds - water's extraordinarily high surface tensions explains why it is better to cut the water's surface with your fingertips when you dive into a pool, rather than doing a belly flop. (Surface tension=energy it takes to increase a liquid's surface area)
What happens when you break hydrogen bonds associated with water?
Water vaporizes. - This is associated with the heat of vaporization
Who discovered complementary base pairing? Who revealed the major role of DNA?
Watson and Crick - complementary base pairing explained the equal purine-pyrimidine ratios that Chargaff noted - they revealed the role of DNA as a library of information. In cells, information consists of a sequence of nucleotides where the 4 nitrogenous bases are like letters, when put together they have meaning like words
What information specifically did watson and crick use from others
Watson and Crick's model was a hypothesis based on a series of results from other laboratories (they themselves did not do experiments) 1. Erwin Chargafff estabilished 2 rules: 1) number of purines in a DNA molecule is equal to the number of pyrimidines and 2) the DNA molecule has an equal number of T/A and it has an equal number of C/G 2. Rosalind Franklin and Maurice Wilkins bombarded DNA with X-rays (X-ray crystallography) and observed how it scattered the radiation, they then calculated the distances between groups of atoms in DNA. This showed 3 distances that were repeated over and over (2.0, 0.34, 3.4 nm) so they inferred DNA had a regular repeating structure. The pattern of x ray scattering suggested that the molecule was spiral in nature
Did RNA replicase come before ribonucleotides? Or other way around
We know that RNA may have preceded proteins. Therefore, this means that ribonucleotides likely came before RNA replicase. (RNA replicase is an enzyme that can produce RNA from an RNA template)
Protein folding is often regulated
We know that the function of a protein depends on its shape, so controlling when the protein is folded in its activated form ultimately regulates the protein's activity. Ex. Proteins involved in cell signalling are regulated in when they are folded to the activated state. They are usually disordered and don't complete their folding until after binding to other molecules/ions that are only present during a specific signalling event. This results in the protein to fold into an ordered and active conformation which controls cellular activities.
Van der Waal interactions (dispersion)
Weak electrical interactions that occur b/c the constant motion of electrons gives molecules small asymmetry in charge that changes with time. When nonpolar molecules get extremely close, the minute partial charge on one molecule induces an opposite partial charge in the nearby molecule which causes an attraction (very weak relative to other bonds). - once hydrophic molecules are close to one ankther, their association is further stabilized by these weak electrical attractions. A large number of van der waal interactions can significantly increase the stability of clustered hydrophobic molecules.
Energy Stored in Glucose is Used to Make ATP
When a cell needs energy, glucose is broken down and some of the released energy is captured through synthesis of the nucleotide adenosine triphosphate (ATP) (CH2O)n+O2+ADP+Pi→CO2+H2O+ATP - the chemical energy stored in bonds of C—C and C—H in the carbohydrate is released as new C═O bonds are formed in CO2. The excess energy is transferred to a new bond that links a 3rd phosphate group to ADP to form ATP - The energy in ATP drives reactions that are responsible for everything from polymerization to muscle movement.
Residues
When amino acids are linked by peptide bonds into a chain, they are individually called residues to distinguish them from other free amino acid monomers
alpha and beta forms of glucose differ in ...
When sugars form a ring structure, the position of the newly formed hydroxyl group (e.g., at C-1 in glucose) can be placed in one of 2 spatial arrangements (below or above the plane of the ring) - The two forms exist in equilibrium, but beta glucose (hydroxyl above ring) is more common because it is slightly more stable than alpha glucose (hydroxyl below ring)
Bond Saturation and Membrane Permeability
When unsaturated hydrocarbon tails are packed into a lipid bilayer, kinks created by double bonds produce spaces among the tails - spaces reduce van der waals interactions that help hold the hydrophobic tails together, weakening the barrier to solutes. - MORE PERMEABLE when they contain many short, kinked, unsaturated hydrocarbon tails Packed saturated hydrocarbon tails have fewer spaces, and more van der Waals interactions - As the length of saturated hydrocarbon tails increases, forces that hold them together also increase, making the membrane even denser. - LESS PERMEABLE when they contain long, straight, saturated hydrocarbon tails
Do alpha helices/beta pleated sheets/DNA double helix/RNA hair pin loop secondary structures form spontaneously?
Yes
Do proteins spontaneously fold into their tertiary or quaternary structures? What has more entropy, a folded or unfolded protein?
Yes - an unfolded protein has a much higher entropy, but folding is spontaneous b/c chemical bonds/interactions release enough energy to overcome the decrease entropy and thus increase entropy in surrounding environment. Resulting in less potential energy and more stability than unfolded molecule
Does the structure of dna allow it to be replicated?
Yes, DNA's primary structure serves as a template for the synthesis of a complementary strand meaning that DNA contains the info required for a copy of itself to be made
If you understand the basis of electrochemical gradients, you should be able to add another arrow to Figure 6.21 indicating the electrochemical gradient for chloride ions. (page 137)
Your arrow should point from below to above the membrane. There is no concentration gradient for chloride, but the upper side has a net positive charge, which favors the import of negative ions like chloride
gate channel proteins (voltage gated channel proteins)
a channel protein that opens and closes in response to a specific stimulus, such as the binding of a particular substance or a change in voltage across the membrane - PASSIVE, FACILITATED DIFFUSION ex. The channel gate (at the bottom of the pore) changes shape based on the voltage across the membrane. The channel filter (blue residues at the top of the pore displaces water molecules that normally surround the K+ ions in an aqueous solution before ions pass through the pore - controlled by proteins that can change shape to open or close the channel in response to various signal
concentration gradient
a difference in solute concentration across space ex: like a membrane - net movement from regions of high concentration to regions of low concentration - Diffusion down a concentration gradient is a SPONTANEOUS process b/c there is an increase in entropy - Once the molecules or ions are randomly distributed throughout a solution, an equilibrium is established. (movement does not stop across membrane due to constant random motion, BUT there is no longer a net movement of solutes across the membrane because they are equally likely to move in any direction)
carrier proteins
a transmembrane protein that facilitates diffusion of a small molecule (ex. glucose) across a membrane by a process involving a reversible change in the shape of the protein
Cholesterol Affects Membrane Permeability
adding cholesterol molecules to artificial membranes dramatically reduces their permeability - WHY? Cholesterol is located in the membrane with its hydrophobic steroid rings buried deeply in the hydrocarbon tails of the phospholipid. bulky cholesterol rings force the phospholipid tails closer to each other, increasing their packing density which causes the membrane to be less permeable
Secondary Active Transport
aka cotransport transport of ion/molecule in a defined direction (often against its gradient) made possible by the transport of ANOTHER ION/MOLECULE being moved along its gradient - ATP is not directly used to power transport. For example, glucose wants to go inside cell (against concentration gradient). Na+ is naturally more concentrated on outside of cell. The charge on the outside is also more positive. Therefore, Na+ electrochemical gradient is BOTH wanting it to go down the gradient (membrane permeability does not allow for the free facilitated diffusion of ions, so active transport is needed). Glucose takes advantage of this and uses the Na+ potential energy to transport it against glucoses' concentration gradient (uses stored energy from electrochemical gradient of sodium) HOW? - cotransport protein in gut cells use Na+ gradient created by the sodium potassium pump to import glucose against chemical gradient. Na+ ions bind to cotransporter = shape changes so glucose can bind = Na+ ions and glucose travels inside cell. note that Na+ is moving down its gradient and glucose is moving against its gradient. once they are dropped off inside cell, protein's original shape returns - this is how glucose in food you eat is actively transported in body
cytoplasm (both prokaryotes and eukaryotes)
all the contents of a cell bounded by the plasma membrane, excluding the nucleus (in eukaryotes)
transmembrane proteins (integral membrane proteins)
any membrane protein that spans the entire lipid bilayer - ends of transmembrane proteins differ - The Hydrophobic Region of an Amphipathic Protein Can Be Anchored into a Lipid Bilayer
lipid
any organic substance that does not dissolve in water, but dissolves well in non polar organic solvents. lipids include fatty acids, fats, oils, waxes, steroids, and phospholipids - lipids do not possess a shared chemical structure. therefore lipids are not polymers since they don't have the same subunits - insoluble in water due to high proportion of C—C and C—H bonds relative to polar functional groups - dissolve in solvents that are non polar (benzene, C6H6) - significant hydrocarbon component - the type of bond between carbons in hydrocarbon chains is a key factor to structure/function (un/saturated) - three of the most important types of lipids found in cells: steroids, fats, and phospholipids. - many lipids are amphipathic, very important b/c it is responsible for the plasma membrane
bacterial prokaryotes vs archaeal prokaryotes difference in phospholipid bilayer
bacterial phospholipids: consist of fatty acids (saturated/unsaturated and carboxyl group) bound to glycerol archaeal phospholipids: use highly branched isoprenoid chains (methyl groups) bound to glycerol - they also differ in structure of hydrocarbon chains AND types of linkages used to join hydrocarbon tails to glycerol heads ****ARCHAEAL MEMBRANE IS MORE STABLE in extreme environments that are inhabited by certain species in this domain
Receptor-Mediated Endocytosis
begins when particles outside the cell bind to receptors on the plasma membrane. Then, the plasma membrane folds in and pinches off to form an endocytic vesicle. These vesicles then drop off their cargo in an organelle called the early endosome. proton pumps in the membrane of this organelle acidifies its lumen, causing the cargo to be released from their receptors. (cargo receptors are then repackaged into vesicles and returned to the plasma membrane) - As proton pumps continue to lower the early endosome's pH, it matures into a late endosome (pre-lysosome). Acid hydrolyses from Golgi apparatus are dropped off here to turn it into a lysosome. - mannose-6-phosphate tag would make the final location of a protein be the lysosome
When does hydrogen bonding occur? (Hydrogen bonding is generally weak)
between polar molecules where an H atom is directly bonded to an N, O or F atom. - so hydrogen bonds can form between water molecules and polar solutes (like the H+ in water and the O- in glucose C6H12O6)
Plasma Membranes Define the Intracellular Environment
biological membranes combine the selective permeability of the lipid bilayer AND the specificity of proteins involved in passive/active transport to create an internal environment that is different from the external one. - likely that early cells were able to create this internal environment so that it was advantageous to life - cells that were efficient in selectively transporting proteins that are required for survival/replication across membrane are favored by natural selection (would dominate population). cellular life had begun
How Does Lipid Structure Affect Membrane Permeability?
bond saturation hydrocarbon chain length
sandwich model (1935)
cell membranes were made like a sandwich in which hydrophilic proteins coat both sides of a pure lipid bilayer, like bread of sandwich
Extracellular Matrix
cells of animals lack a cell wall, but are often supported by a more diffuse mixture of secreted proteins/polysaccharides that form the extracellular matrix - provides cells with structural support and may be used to attach cells to one another. - Rods/fibers run through this stiff matrix made of polysaccharides/proteins
Structure of amino acids
central carbon: carbon atoms have a valence of 4 meaning they can form up to 4 covalent bonds. In all 20 amino acids, a central carbon atom (referred to as the alpha carbon) bonds covalently to 4 other atoms or groups of atoms: 1. H— a hydrogen atom 2. NH2- an amino functional group 3. COOH— a carboxyl functional group 4. A distinctive "R-group" (referred to as a "side chain")
Polypeptide
chain of amino acids
most prominent structure inside prokaryotic cell
chromosome: gene carrying structure that has a large DNA molecule associated with proteins located in NUCLEOID - prokaryotic cells contain ONE CIRCULAR chromosome. to fit into the cell, the DNA double helix coils on itself with aid of enzymes to form a compact supercoiled structure - DNA molecule contains information (encoded in nitrogenous bases), and the proteins give the DNA structural support. - chromosomes contain DNA, which contains genes that code for RNA (1st step in central dogma) genes: segments of DNA that have info for building functional RNAs, some may be used to make polypeptides (proteins)
What Happens Inside the Golgi Apparatus?
cisternae at various stages of maturation contain different suites of enzymes - dynamic. New cisternae constantly form at the cis face of the Golgi apparatus, while old cisternae break apart at the trans face, to be replaced by the cisternae behind it.
emergent properties of water
cohesive behavior, ability to moderate temperature, expansion upon freezing, versatility as a solvent - meaning these properties emerge as the interaction of multiple of water molecules (due to the hydrogen bonding between molecules)
fats
composed of three fatty acids (hydrocarbon and carboxyl) that are linked to a three-carbon molecule called glycerol - also called triglycerides - fats form when a dehydration reaction occurs between a hydroxyl group of glycerol and the carboxyl group of a free fatty acid joined by an ester linkage - since fatty acids are not linked into chains, they are not considered monomers, and thus fats are not polymers. - energy storage is the primary role of fats due to large number of high energy bonds in the fatty acid chains. FATS STORE MORE ENERGY THAN CARBOHYDRATES ratio of C—C and C—H bonds, high potential energy to C—O bonds, low potential energy is much greater in fats than in energy storage carbohydrates. fats can store about twice as much - If the glycerol-linked fatty acids are polyunsaturated, the resulting triglycerides are liquid at room temperature
Evaluate the claim that polysaccharides are superior to proteins (see Chapter 3) as markers of cellular identity.
correct, carbohydrates have the potential for greater structural variation than proteins. WHY? 1. Glycosidic linkages between sugar monomers can vary more in location and geometry than can peptide-bond linkages between amino acid residues, which are completely standardized. 2. The different monosaccharide monomers vary extensively in their size, the position of the carbonyl group, the orientations of hydroxyl groups, and the presence of modifications in the polymerized forms (e.g., modified sugar residues in chitin and peptidoglycan).
Phosphodiester linkage
covalent bonds that join adjacent nucleotides between the -OH group of the 3' carbon of one nucleotide and the phosphate on the 5' carbon of the next - see page 98. Phosphate connecting/in between 2 carbon sugars ****when phosphodiester linkages join ribonucleotides together, the polymer formed is RNA. When the linkages join deoxyribonucleotides together, the polymer formed is DNA******
lipid bilayer
created when lipid molecules align in paired sheets. hydrophilic heads in each layer face the surrounding solution while the hydrophobic tails face one another inside the bilayer. In this way, the hydrophilic heads interact with water while the hydrophobic tails interact with one another. - Phospholipids, which have bulkier nonpolar regions consisting of two hydrocarbon tails, tend to form bilayers. usually called phospholipid bilayers
cytoskeleton
dense and complex network of fibers that helps maintain cell shape by providing structural support. cytoskeleton is dynamic. Its fibrous proteins move and change to alter the cell's shape, shift its contents, and even move the cell itself. - 3 major types of cytoskeletal elements in eukaryotic cells: actin filaments, intermediate filaments, and microtubules.
What does the tertiary structure depend on?
distant structure interactions of r-groups; ionic bonding, H bonds, Van der Waals, hydrophobic packing, and disulfide bridge formation (covalent bonding) occurs - depends partly on the presence of secondary structures (like alpha helices and beta pleated sheets), thus it depends on both primary and secondary structures
Carbohydrates store and provide chemical energy in cells. What aspect of carbohydrate structure makes this function possible?
energy in light is transformed into chemical energy, the energy is then stored in sugars. ex: plants harvest energy in sunlight and store it in bonds of carbohydrates by process of photosynthesis. (CO2 + H2O + sunlight) --> (CH2O)n +O2 1. electrons in the C═O bonds of CO2 and C—O bonds of carbs are held tightly due to oxygen's high electronegativity = relatively low potential energy 2. electrons in the C—H bonds of carbs shared equally due to similar electronegativity of C and H = bonds are weaker = relatively high potential energy 3. electrons in (C—C) bonds of carbs are shared equally = relatively high potential energy high potential energy = more storage capability of chemical energy THUS: carbs store much more chemical energy than CO2 (b/c C—C and C—H bonds have much higher potential energy than C—O bonds AND participating atoms have low electronegativities/share electrons equally) - carbs are valuable as fuel in cells, PE in bonds is released when they are broken and new stronger bonds are formed
eukaryote size
eukaryotic cells are much larger, on average, than bacteria and archaea. - advantage: for many species of unicellular eukaryotes, this size difference allows them to make a living by ingesting bacteria and archaea whole - disadvantage: As a cell increases in diameter, its volume increases more than its surface area (surface-area-to-volume ratio). surface is where the cell exchanges substances with its environment, the reduction in this ratio decreases the rate of exchange: Diffusion only allows for rapid movement across very small distances.
nucleus function
eukaryotic chromosomes are enclosed within a membrane-bound compartment. each chromosome occupies a distinct area, but is very concentrated at the edges and loosely packed in the interior. - 1st step of central dogma: synthesis of RNA from information encoded in DNA - nucleolus: inside nucleus, responsible for making and processing RNA molecules that assemble into large/small ribosomal subunits (makes ribosomes) - administrative center for information storage and processing - nuclear envelope: nucleus is enclosed by a unique double membrane structure. there are pore like openings in the envelope. - nuclear lamina: inside surface is linked to fibrous proteins that form a lattice like sheet. stiffens/roughens the double membrane and maintains organelle shape.
Recycling Material in the Lysosome
existing proteins must first be digested in the lysosome (proteins do not readily pass through membranes) 3 pathways: Receptor-mediated endocytosis and phagocytosis (bring material in and surrounding it w/ lipid bilayer from plasma membrane (ends) and autophagy. All have same function: Molecules are hydrolyzed and the products are transported across the lysosomal membrane into the cytosol for recycling
Oligopeptide
fewer than 50 amino acids linked together by peptide bonds - ("few-peptides") or aka simply a *peptide*
cell wall (prokaryotes and eukaryotes)
fibrous layer found outside plasma membrane of most bacteria, archaea, and eukaryotes - it contains a high concentration of solutes, it is hypertonic relative to outside environment, therefore water moves in the cell via osmosis= cell's volume increases. this pressure is resisted by a stiff cell wall. - Bacterial and archaeal cell walls are a tough, fibrous layer that surrounds the plasma membrane (protects the organisms, gives shape/rigidity). in prokaryotes, the osmotic pressure that pushes the plasma membrane against the cell wall has a force similar to the pressure in an automobile tire. - molecular structure of cell walls differs between bacteria and archaea
polyunsaturated
foods that contain lipids with many double bonds - advertised as healthier than foods with saturated lipids - may help protect the heart from disease
ribosomes (both prokaryotes and eukaryotes)
found throughout the cell interior. not unusual for cell to have 10,000+ ribosomes - function: protein synthesis (they make proteins) - complex structures made of large and small subunits. each Ribosome Is made up of RNA and protein molecules - primary structures of RNA/protein components are diff in bacteria/archaea (function/size is same)
Determine if free fatty acids and fats are amphipathic, and explain why or why not.
free fatty acids: amphipathic fats: not amphipathic (1) Free fatty acids are amphipathic because their hydrocarbon tails are hydrophobic but their carboxyl functional groups are hydrophilic. (2) In fats, the charged carboxyl groups of fatty acids are converted to ester linkages. This change reduces the difference in polarity across the molecule, making it more uniformly nonpolar. As a result, fats are not considered amphipathic.
ribosomes function
freely scattered throughout the cytosol (fluid) and on surface of rough ER (millions) - complex macromolecular machines that use info in RNA to manufacture proteins - ribosomes are NOT compartments inside a cell so they are not classified as organelles - Proteins manufactured by free ribosomes either remain in the cytosol or are imported into other organelles, such as the nucleus
glycolipids and glycoproteins
glycolipid: any lipid molecule that is covalently bonded to one or more carbohydrates glycoprotein: any protein with one or more covalently bonded carbohydrates, typically oligosaccharides - key in cell-cell recognition/signalling. each human cell has carbs on its surface that identify it as part of you body. ex: blood type determined by type of carb on surface of blood cells - some carbs are attached to membrane components like these lipid and proteins and project outward from the cell surface into the surrounding environment. they are usually short
Secondary structure of RNA (page 104)
hair pin loops (many other secondary structures are possible) - purine and pyrimidine bases (G-C and A-U) undergo hydrogen bonding with complementary bases on the SAME STRAND, rather than forming H bonds w/ complementary bases on a different stand like DNA. (Other base pairs can occur in RNA besides the g/c a/u) - within strand base pairing works b/c bases on one part of an RNA strand fold over and align with bases on another part of the same strand, the 2 sugar-phosphate strands are antiparallel. In this way, hydrogen bonding between complementary bases results in a helical structure that resembles a double helix of DNA (remember RNA structure forms from one single nucleic acid strand instead of 2). - another way of saying it: the key is when bases on one part of the strand fold over and align w/ ribonucleotides on another segment of the same strand, the two sugar-phosphate strands are antiparallel resulting in a stable double helix... if the section where the fold occurs includes a large # of unbonded bases, then a stem-and-loop structure called a hairpin forms - the hair pin loops form spontaneously. The bases are brought together by hydrophobic interactions and are stabilized by hydrogen bonding/base stacking interactions
glycogen
highly branched storage polysaccharide in animals stored in the cells of liver and muscle tissues in humans. it is broken down by enzymes into glucose monomers which are processed to supply energy. - HELIX polymer of α-glucose. very similar to amylopectin but its α-1,6 glycosidic linkages occur more frequently (1 out of 10 glucose subunits) - more branches provide more ends for enzymes to release glucose when your body needs it
RNA world hypothesis
hypothesis that RNA both stored genetic information and catalyzed its own replication. Also, that RNA emerged before DNA and proteins during chemical evolution.
Photosynthetic Species Have Internal Membrane Complexes (prokaryotes)
in BACTERIA that perform photosynthesis, there are multiple membranes that pass through the internal region of the cells. - internal membranes provide an extensive SURFACE AREA that allows more photosynthetic reactions to occur and thus INCREASES the cell's ability to make FOOD. - the photosynthetic membranes observed in bacteria are infoldings of plasma membrane and they contain enzymes/pigments required for rxns that turn energy sunlight into chemical energy stored in sugars to occur - sometimes, membrane-bound vesicles pinch off as the plasma membrane folds in. other times, flattened stacks of photosynthetic membrane remain connected to the plasma membrane
why was transmission electron microscope so important? (1931)
it changed our view of prokaryotes dramatically. - this microscope passes a beam of electrons through extremely thin sections of cells so that we can see their internal structure - finest resolution
Membranes and Chemical Evolution
it is likely that the primary importance of the first lipid bilayers was to act as a container for replicating the first "living" molecule (thought to be RNA) - Ribonucleotide monomers would need to be available for these RNAs to replicate, these are only able to pass through/diffuse across bilayers made from fatty acids, NOT phospholipids - Protocells: hypothetical pre-cell/simple vesicle-like structures that harbor nucleic acids and replicating macromolecules
what is usually the form of monosaccharides? linear chains or ring structures Can the Same Monosaccharide Exist in More Than One Form?
it's actually rare for sugars consisting of five or more carbons to exist as linear chains In aqueous solution, they spontaneously form ring structures when the carbonyl group reacts with a hydroxyl group on another carbon. - sugars therefore exist in both linear and ring forms (linear just being more rare)
cytoskeleton (both prokaryotes and eukaryotes)
long, thin filaments in cytoplasm of prokaryotes which serve many roles . ex. in bacteria, they are essential for cell division to take place - in eukaryotic cells: network of protein fibers in cytoplasm that are involved in cell shape, support, locomotion, and transport of materials within cell - prokaryotic cells have similar but much less extensive network of fibers
starch
major form of stored carbohydrate for later use in plant - mixture of 2 storage polysaccharides: amylose and amylopectin which both use α-glucose monomers joined by glycosidic linkages - HELIX shape caused by angle of the bonds which makes the chain of glucose residues coil into a helix - amylose is unbranched while amylopectin is branched at α-1,6 (glycosidic linkage between C-1 and C-6) - branching occurs at a bout one out of every 30 glucose residues in amylopectin
Polymer
molecules composed of many monomers; makes up macromolecules - "many parts"
active transport
movement of ions/molecules across a membrane in a single direction, often against a gradient (not always) - requires energy (ex. hydrolysis ATP) and assistance of a transport protein (ex. pump) ex. The Sodium-Potassium Pump In cells, ATP often provides the energy for active transport by transferring a phosphate group (HPO42−) to an active transport protein called a pump. Recall that ATP contains three phosphate groups, and that phosphate groups carry two negative charges. When a phosphate group is transferred from ATP to a pump, its negative charges interact with charged amino acid residues in the protein. As a result, the pump's potential energy increases and its shape changes.
How Do Molecules Enter the Nucleus? (nuclear localization signal, NLS)
nuclear pores do not select proteins based on their size alone, they use a short amino acid sequence that marks a protein for delivery into the nucleus - Often use special transport proteins that function like trucks that haul cargo into or out of the nucleus through the nuclear pore complex, depending on whether they have an import or export zip code - Nuclear proteins contain a "zip code", a molecular address tag, that allows them to travel through the nuclear pore complex. These proteins are synthesized by ribosomes that are free in the cytosol, and the zip code allows them to pass into the nucleus - Nucleoplasmin: strictly found in the nucleus that, when injected as whole, quickly enters nucleus. Used enzymes (proteases) to cleave nucleoplasmin into 2 pieces (core/tail) and inject them into diff cells. tail=rapidly traveled from cytosol into nucleus. core=were not allowed to pass and remained in cytosol. Found that a specific amino acid residue section of polypeptide had to be present to direct the protein to the nucleus
Deoxyribonucleic acid (DNA)
nucleic acid composed of deoxyribonucleotides FUNCTION: stores genetic information and is replicated using proteins STRUCTURE: double helix with 2 intertwined strands connected by noncovalent bonds - the sugar in deoxyribose (deoxy = lacking oxygen) has only an H at the 2' carbon instead of an -OH - difference the nitrogeneous bases of DNA are: Cytosine, Guanine, THYMINE, or Adenine
glucose carrier
one protein that specifically increases membrane permeability to glucose (sugar) is Glut-1 - when glucose binds to GLUT-1, it changes the shape of the protein in a way that moves the sugar through the hydrophobic region of the membrane and releases it on the other side. - GLUT-1 FACILITATES DIFFUSION by allowing glucose to enter the carrier from either side of the membrane dictated by its concentration gradient.
facilitated diffusion
passive movement (diffusion) of a substance across a membrane with the assistance of transmembrane carrier proteins or channel proteins
what is responsible for the differences in permeability?
pattern of permeability is explained by hypothesis that charged substances and polar molecules above a certain size are more stable dissolved in water—a polar environment—than they would be in the nonpolar interior of membranes.
What type of bond forms between amino acids?
peptide bonds form between the carboxyl functional group of one amino acid and the amino functional group of another amino acid molecule. The electron sharing between the C—N gives the peptide bobnd characteristics of a double bond. - the C—N peptide bond is a type of nonpolar covalent bond resulting from the condensation/dehydration reaction - during the condensation reaction, a water molecule is removed and the carboxyl group becomes a carbonyl functional group (C double bond O) and the amino group simply becomes (N—H) in the end.
Artificial Membranes as an Experimental System
phospholipids are added to an aqueous solution and agitated, causing them to form vesicles, small bubble-like structures consisting of lipid bilayers surrounding a small amount of aqueous sln, these are called LIPOSOMES (as they are artificially generated by mixing amphipathic lipids with aqueous soln) - hydrophobic tails are shielded from water while hydrophilic heads remain in contact with water on the inside or outside of the vesicle another artificial membrane is PLANAR BILAYER which is constructed across a hole in a glass or plastic wall separating two aqueous solutions. scientist used these two membranes in concern of permeability (tendency to allow a given substance to pass through it)
Phagocytosis
plasma membrane of a cell surrounds a smaller cell or food particle and engulfs it, forming a structure called a phagosome. structure is delivered to a lysosome, where the phagosome and lysosome membranes fuse and the contents of the phagosome are digested.
Polypeptides
polymers that contain 50 or more amino acids - ("many-peptides")
Rough ER
portion of the endoplasmic reticulum dotted with ribosomes PROTEIN MANUFACTURING CENTER - membrane forms a network of flattened sacs and tubules - rough ER synthesizes proteins that move into interior of organelle (lumen) which is where manufactured proteins undergo folding/processing - they then either stay in the rough ER or they are packaged into vesicles/transported as cargo to other organelles, plasma membrane, cell exterior, etc. these proteins have many differing functions
smooth ER
portion of the endoplasmic reticulum that is free of ribosomes LIPID PROCESSING CENTER - synthesizes lipids. smooth ER contains enzymes to do these reactions (sometimes removes toxic molecules) - functions as storage for calcium ions (Ca2+) that can be released to cell
Mitochondria
primarily responsible for supplying ATP in eukaryotic cells - Has multiple chromosomes called mitochondrial DNA (mtDNA) independent of nuclear chromosomes. Contains genes that encode RNAs for mitochondrial ribosomes (smaller than usual ones) which produce mitochondrial proteins. (Most of the proteins found in mitochondria are produced from ribosomes in the cytosol and imported into the organelle.) - Has 2 membranes. Outer membrane: defined organelle's surface - Inner membrane forms a series of sac like cristae. The inner membrane has a solution called mitochondrial matrix. the foldings in inner membrane increase surface area allowing more ATP to be made. enzymes/molecular machines that synthesize ATP are in inner membrane or matrix. The chemical energy in carbs/fats is used to produce ATP
peptidoglycan
primary structural polysaccharide in bacterial cell walls - most complex of polysaccharides out of the 5. has long backbone formed by NAG and N-acetylmuramic acid (NAM) which alternate with each other. they are linked by b-1,4 GLYCOSIDIC linkages - short chain of amino acids is attached at the C-3 carbon of NAM (every other monomer) which allows for the formation of peptide bonds between adjacent strands 4. PEPTIDE bonds play a similar role to the H-bonds of chitin and cellulose by providing structural polysaccharides that are long, straight, parallel strands bound to each other, making these polysaccharides strong and stable.
What are the levels of organization in proteins
primary structure, secondary structure, tertiary structure, quaternary structure
hydrogenation
process of converting unsaturated lipids to saturated lipids by breaking double bonds and adding hydrogen atoms
flagella and fimbriae in prokaryotes
prokaryotes interact with their environment via these structures which grow from the plasma membrane prokaryotic flagella is made out of diff proteins at cell surface. functions are the same—to rotate a long rigid filament that propels the cell through water. fimbriae more numerous than flagella, often distributed over the cell's entire surface, these are not involved in cell motility, but their ability to glue bacteria to the surface of tissues makes them crucial in establishing many infections. bacteria: flagella and fimbriae are common on bacterial surfaces Archaea: flagella and appendages similar to fimbriae, but they are structurally distinct from those found on bacteria.
Moving from the ER to the Golgi Apparatus
proteins are transported in vesicles that bud off from the ER and move to the cis face of the Golgi apparatus. - Proteins inside rough ER fold into 3D shape with help of chaperone proteins - hypothesis Supported by differential centrifugation to isolate/characterize vesicles which contained pulse labeled proteins
If amphipathic lipids are responsible for the lipid bilayer of a cell membrane, how do proteins fit in? Can a protein be amphipathic too?
proteins consist of amino acids, which have side chains (can be highly nonpolar to highly polar/charged) therefore, a protein could have a series of nonpolar amino acid residues in the middle of its primary structure flanked by polar or charged amino acid residues - nonpolar residues = in the interior of a lipid bilayer. polar or charged residues = surrounding water, stable alongside the polar lipid heads - The Hydrophobic Region of an Amphipathic Protein Can Be Anchored into a Lipid Bilayer. proteins can form openings and function as a selective passageway across a lipid bilayer due to structure of secondary/tertiary proteins being almost infinite - proteins were often just as common, in terms of mass, as phospholipids in/on plasma membrane
Structural proteins
proteins that form an organism's physical attributes. Make up things like fingernails and hair, muscles, ligaments, tendons, silk of spides, hair of mammals and form the internal skeleton of individual cells. - structural proteins keep red blood cells flexible and in their normal disc like shape
lysosomes
recycling center found in animals - contain 40 diff enzymes for hydrolyzing diff types of macromolecules (proteins, lipids, carbs etc). the monomers that result from hydrolysis get sent out the lysosome via transport proteins in its membrane. Once in the cytosol, they can be used as sources of energy or building blocks for new molecules. - digestive enzymes are called acid hydrolyses b/c at acidic conditions (pH 5.0) they use water to break up macromolecules into monomers. in the cytosol the pH is 7.2 so the acid hydrolyses are less active - proton pumps in lysosomal membrane maintain acidic pH in the lumen (interior) of the lysosome by importing hydrogen ions
saturated fatty acid
referring to lipids in which all the carbon carbon bonds are single bonds - relatively high melting points compared to unsaturated - if hydrocarbon chain does not contain a double bond, it is saturated with the max number of hydrogen atoms that can attach to carbon skeleton
unsaturated fatty acid
referring to lipids in which at least one carbon carbon bond is a double bond - double bonds produce links in hydrocarbon chains and decrease the compound's melting point
Systems for Studying Membrane Proteins
separate proteins from membranes using detergents (small amphipathic molecule that can form micelles, water soluble unlike amphipathic lipids) - When detergents are added to the solution surrounding a lipid bilayer hydrophobic tails of the detergent molecule interact with the hydrophobic tails of the lipids and transmembrane proteins. result: membrane phospholipids are separated into water-soluble detergent-protein complexes - three broad classes of proteins that affect membrane permeability were found: channels, carriers, and pumps
nuclear envelope
separates the nucleus from the rest of the cell; supported by an internal fibrous nuclear lamina and bounded by two membranes. - makes and assembles the subunits needed for ribosome synthesis which are then taken to cytosol for protein synthesis (rRNA (ribosomal RNA) are manufactured in nucleolus bind to proteins to create ribosomes. mRNA carries info needed to manufacture proteins.) - - Nuclear pore complex: 30 proteins form an opening in the nuclear envelope connecting the inside of the nucleus with the cytosol (outer nuclear membrane) and allowing the free diffusion of small molecules and ions; regulates transport of RNA and proteins - Chromosomal DNA does NOT travel thru here. RNA synthesized from DNA is exported through nuclear pore complexes to cytosol
Sugars
simple carbohydrates, provide chemical energy in cells - presence of carbonyl group/multiple polar hydroxyl groups means that sugars are very reactive/hydrophilic which means it is polar and forms hydrogen bonds with water and are easily dissolved in aqueous solns
why are there so many diffferent monosaccharides
so many aspects of their structure are variable: aldose or ketose placement of the carbonyl group, the number of carbons, and the different arrangements of hydroxyl groups in space. - Ring forms of the same molecule also have alternative shapes. - These variations give each monosaccharide a unique structure and function.
sperm attaches/binds to eggs via what
sperm binds to the carbohydrates of egg surface glycoproteins when they attach to egg cells - the carbohydrate part of the egg glycoproteins (made up of carb and protein) is essential for recognition and attachment. when sperm were mixed with purified carb alone, they were unable to attach to eggs as they were able to detect it. while when mixed with purified protein, they were not inhibited and still attached to eggs.
diffusion
spontaneous movement of molecules/ions from one region to another, often from a net movement from a region of high concentration to low concentration to make the cell interior and exterior environments more similar. - substances located on one side of a lipid bilayer can move to the other side spontaneously
5 carbohydrate polymers:
starch, glycogen, cellulose, chitin, peptidoglycan all the macromolecules are joined by a-1,4 or b-1,4 glycosidic linkages - small changes in structure can have huge changes in function
Isoprenoids
steroids and fat-soluble vitamins - entirely of carbon atoms bonded to hydrogen atoms - has branches of methyl groups (-CH3) - wide range of functions: from pigments and scents to vitamins and precursors of sex hormones, important building blocks for more complex lipids
vacuoles
storage center in cells of plants, fungi etc (eukaryotes not animal cells though) - vacuoles of plant/fungal cells are large, up to 80% of cell's volume - ions are stored at such high concentrations that they draw water into the vacuole (increase volume) which pushes the cytoplasm and plasma membrane against cell wall. responsible for wilted green plants regaining rigid structure after water is added to soil - creates internal pressure characteristic of plants - some vacuoles contain hydrolyses to digest and recycle macromolecules, can be classified as the plant equivalent of lysosomes of animal cells
bacterial organelle
storing calcium ions; holding crystals of the mineral magnetite, which function like compass needles to help cells swim in a directed way; and concentrating enzymes responsible for synthesizing complex carbon compounds from carbon dioxide.
chitin
structural polysaccharide in fungi and animals, it stiffens their cell wall - most important component of external skeletons of insects and crustaceans - similar to cellulose, but has NAG (N-acetylglucosamine) these NAG monomers are joined by b-1,4 glycosidic linkages. - FLIPPED due to geometry of the bonds. NAG subunits in chitin also form hydrogen bonds between adjacent strands to produce a stiff protective armor
cellulose
structural polysaccharide in plants. primary building material for cell walls in plants and algae - monosaccharide involved: glucose residue - polymer made from b-glucose monomers joined by b-1,4 glycosidic linkages - FLIPPED, each glucose residue in the chain is flipped in relation to the adjacent residue. flipped orientation (1) generates a linear molecule rather than helix in starch (2) permits multiple hydrogen bonds to form between adjacent parallel strands, interacting cellulose fibers give plant cells structural support
Golgi apparatus
system of membranous compartments (cisternae) which are flattened sacs that stack on top of each other like pancakes - most proteins that leave rough ER pass through this - Golgi apparatus has a distinct polarity/sideness. cis surface is closest to nucleus (receives vesicles containing rough ER products) and trans surface is pointed towards the plasma membrane (ships them out to other organelles or the cell surface) - "bubbles" on either side of a Golgi stack. These are membrane-bound transport vesicles that carry proteins or other products to and from the organelle.
If you understand what forces contribute to osmosis, you should be able to predict whether or not the concentration of a solute before reaching equilibrium would be the same across the membrane after reaching equilibrium. Explain your answer.
the concentration will be different after reaching equilibrium. - the side that had a higher concentration of solutes in the beginning will have a higher one after reaching equilibrium. - why? pressure from the downward pull of gravity will push water molecules back to the left, against continued transport of water toward the higher solute concentration. - this opposing force prevents the solns separated by the membrane from achieving the same concentration
passive transport
the diffusion of a substance across a membrane without the INPUT of energy - it happens because of energy already present in an existing gradient. it still requires energy but it is naturally supplied.
cytosol
the fluid portion between the plasma membrane and membrane enclosed organelles - only a fraction of the total cell volume in eukaryotic cells
cell morphology
the overall shape and appearance of an organism and its component parts - eukaryotic cells have a membrane-bound compartment called a nucleus, and prokaryotic cells do no
Enzymes Hydrolyze Energy-Storage Polysaccharides (starch/glycogen) to Release Glucose
these molecules are efficient energy storage molecules b/c they polymerize via α-glycosidic linkages instead of the b-glycosidic linkages in structure - alpha-linkages in storage polysaccharides are readily hydrolyzed by enzymes to release glucose (structural resist this) - phosphorylase: enzyme that breaks down glycogen by catalyzing hydrolysis of α-glycosidic linkages between glucose residues - amylases: enzyme that can break down starch by catalyzing hydrolysis of the α-glycosidic linkages between glucose residues ex. digest the starch that you eat, secreted by salivary/pancreas in mouth/small intestine - glucose subunits are produced by hydrolysis of glycogen and starch. glucose is broken down and released energy synthesizes ATP that can be used in the cell. glycogen/starch is like a Hershey's bar that you can break off whenever you need a boost
what links phospholipids together
they are NOT linked. van der Waals interactions allow nonpolar molecules to stick together
micelles
tiny spherical aggregates created when the hydrophilic heads of a set of lipids face outward and interact with the water, while the hydrophobic tails interact with each other in the interior, away from the water. - tend to form from free fatty acids or other simple amphipathic lipids with single hydrocarbon chains
organelles
tiny structure inside a cell that carries out a specific function within the cell that are often membrane bound - "Little organs" - Bacteria do not contain membrane-bound organelles
channel proteins
transmembrane protein that forms a pore in a cell membrane, which may open or close in response to a signal. the structure of most channels allows them to admit just one or a few ions/molecules - PASSIVE, FACILITATED DIFFUSION - Key side chains in the interior of the pore function as a filter (only water molecules as they're capable of interacting with all of the functional groups in side chain in a precise manner which excludes all other substances that may be associated w/ H2O ex. aquaporin: facilitates movement of water (osmosis) across membrane. - amino acid residues that line a channel's pore are hydrophilic relative to the residues facing the hydrocarbon tails of the membrane - increases rate of transport of water which is important for absorption of water in your gastrointestinal tract.
The Sodium Potassium Pump
transmembrane protein that uses energy of ATP to move sodium ions out of the cell and potassium inside, normally against their electrochemical gradient. aka Na+/K+-ATPase (part of the name refers to the ions that are transported, ATP=adenosine triphosphate is used, and -ase identifies the molecule as an enzyme) - 3 Na+ out for every 2 K+ in, this makes outside of membrane more positively charged relative to inside. - sodium-potassium pump converts energy from ATP to an electrochemical gradient across the membrane that favors a flow of anions (negative ions) out of the cell and a flow of cations (positive ions) into the cell.
carbon sugars naming
trisoes = 3 carbon sugars pentose = 5 carbons hexose = 6 carbon sugar, ex: glucose in bloodstream bloodclaat
prokaryotic cell
unicellular, cell that does not have a nucleus or other membrane-bound organelles. - bacterial and archaea cells (phospholipid components of archaea/bacterial membranes have diff structures) - there is diversity among the millions of species that we once thought was very uniform includes: ALL have at least one chromosome, a plasma membrane, and many ribosomes sometimes: chromosome, cytoplasm, plasmid surface appendages that allow bacteria to stick to surfaces plasma membrane: acts as a selective barrier allowing passage of oxygen, nutrients, and waste cell wall: a rigid structure outside plasma membrane that surrounds/supports/protects cell nucleoid region: houses cell's DNA, containing genes that control the cell ribosomes: where proteins are synthesized capsule: sticky belly like protective layer outside cell wall flagellum: structure that propels the cell
How does bond saturation affect hydrocarbon structure?
van der Waals interactions allow nonpolar molecules to stick together - If the lipids are mad of straight chains (saturated) many of these interactions will form along the chain which allows the lipids to pack together tightly to form a solid. ex. butter solid at room temp (relatively high melting point) - If the hydrocarbons are bent (unsaturated, double bond carbon) they will have fewer of these interactions, move freely, and form a liquid. ex. oils = highly unsaturated lipids are liquid at room temp
how does the type of bond between carbons in hydrocarbon chains affect structure/function in lipids (just like subtle differences in orientation of hydroxyl (—OH) groups can lead to dramatic effects in structure/function of sugars)
when 2 carbon atoms form a double bond, the attached atoms are found in a plane (ethylene). when attached by single bond, it is 3D tetrahedra (ethane) - carbon atoms are locked into place and cannot rotate freely as single bonded C—C can. as a result, cis bonds (certain double bonds between carbons) produce a "kink" in an otherwise straight hydrocarbon chain
Why does water have a high specific heat?
when a source of energy hits the water, hydrogen bonds must be broken first before the heat can be transferred/water molecules begin moving faster.
Chloroplasts
where sunlight is converted to chemical energy during photosynthesis (sugar manufacturing centers) - Surrounded by double membrane. Contains copies of circular chromosome and ribosomes. Grow and divide independently of cell division - Has thylakoids which are sac like structures throughout the interior of organelle that have pigments/enzymes/machines in their membrane. Thylakoids are arranged in interconnected stacks called grana - Stroma, fluid filled space surrounding grana contain enzymes that use chemical energy to produce sugars
fluid mosaic model (1972)
widely accepted hypothesis that cellular membranes consist of proteins embedded in a fluid phospholipid bilayer - membranes are a dynamic and fluid mosaic of phospholipids and different types of proteins. - HOW? Freeze fracture electron microscopy; steps involve freezing and fracturing the membrane before examining it with a scanning electron microscope, SEM, allows researchers to split cell membranes and view the middle of the structure - the picture showed pits and mounds studding the inner surfaces of the lipid bilayer which are the locations of membrane proteins (mounds=proteins that remained attached to one side of the split lipid bilayer pits=are the holes they left behind) - these observations were consistent with the fluid-mosaic model but NOT the sandwich model
Predict how the structure of cellulose would change if all of the β-1,4-glycosidic linkages were changed to α-1,4-glycosidic linkages.
α-glucose residues would all be oriented the same (no longer flipped across the glycosidic linkages) and the molecule would coil into a helix. - The hydrogen bonds that were present between adjacent β-glucose polymers would no longer occur with the α-glucose polymer, so multi-strand fibers would not be formed