Exam 1

What are carbohydrates?

Commonly referred to as sugars, they are used as fuel and building materials.

What are the three domains of life

Domain bacteria, domain archaea, domain eukarya

What are the three domain of life

Domain eukarya, domain bacteria, domain archaea

The organelle where phospholipids are synthesized

Smooth ER

What is pinocytosis?

Somewhat similar to phagocytosis, but rather than going around large food particles, the process of pinocytosis is essentially taking little tastes of everything going on around the outside of the membrane. A small indent is created on the edge of the membrane and then it lets the extracellular liquid surrounding the cell, including whatever small molecules are present into that area then pinch it off. This process is more about sampling what's going on in the environment, and getting a little taste of it.

What is osmosis?

Special case of diffusion that deals with the movement of water through a semi-permeable membrane. Example shown in lecture, the semi-permeable membrane will let water through, but not sugar. So, rather than sugar moving from one side to the other to reach equilibrium, water moves in the opposite direction to attain equilibrium, moving from area of low concentration to high concentration to balance out the concentration on both sides of the semi-permeable membrane.

What does amphipathic mean?

Special term for molecules that have a hydrophobic portion and hydrophilic portion, like phospholipids

Which of the following membrane activities requires energy from ATP hydrolysis? movement of Na+ ions from a lower concentration in a mammalian cell to a higher concentration in the extracellular fluid movement of glucose molecules into a bacterial cell from a medium containing a higher concentration of glucose than inside the cell facilitated diffusion of chloride ions across the membrane through a chloride channel movement of carbon dioxide out of a paramecium

movement of Na+ ions from a lower concentration in a mammalian cell to a higher concentration in the extracellular fluid (Moving from LOW concentration to HIGH concentration requires energy)

What is a semi-permeable membrane?

A barrier that allows some molecules to pass, and not others. This can happen for a variety of reasons; chemical, etc. In the case of osmosis, it has to do with size.

Identifying general bond types: 1) If N or O are with a C or H? 2) C with H

1) Polar covalent bond 2) Nonpolar covalent bond

What are the two categories of nucleic acids?

DNA and RNA

What nucleotides do DNA and RNA NOT have in common

Thymine & Uracil.. Thymine is found only in DNA Uracil is found only in RNA

What is the mitochondria? What does it do?

"Powerhouse of the cell!" It converts sugar and 02 into ATP/energy currency (through cell respiration) In a lot of eukaryotic cells, it will end with the consumption of oxygen - though this isn't always true.

Three structures found in a plant cell but not an animal cell

1. Cell wall - Plant cells generally have a rigid structure that help offer support and infrastructure to the cells. Plants don't have skeletons, so they have cell walls to offer this support/rigidity. 2. Chloroplasts - This is where photosynthesis happens, this isn't unique to plants, it's also found in algae (like seaweed), but also in other protists, other eukaryotic cells (ancestors of plants). Pretty much found in any photosynthetic eukaryote, NOT found in animals. 3. Large central vacuole - This is the the largest structure in a plant cell (like a nucleus is for an animal cell). The large central vacuole is used for storage (of a variety of things).

What four pieces of evidence most strongly support endosymbiont theory?

1. Mitochondria and chloroplasts have multiple membrane layers, unlike anything else we see in eukaryotes. 2. The fact that they have circular DNA, more similar to what you would find in a prokaryote than a eukaryote. 3. Ribosome more similar to those found in prokaryotes than eukaryotes. 4. The organelles' ability to reproduce independently.

What are two advantages eukaryotic cells gain by having membrane-bound organelles?

1. One is being able to customize microenvironment, or specialized areas to do different functions. By having separate organelles, you can control those microenvironment and those conditions a lot more carefully than you would be able to in a prokaryote. (e.g., lighting a candle in a house with rooms and doors vs. a studio apartment) 2. The other has to do with surface area. Some proteins don't just freely roam around, they have to be attached to a membrane surface in order to do their job/function. By having organelles, the sub membranes can create a greater surface area to attach to. (e.g., art gallery with 4 walls vs. art gallery with 4 walls and random walls that stick out so you have more room to hang art.)

Explain the chemical properties of water that make it essential for life

1.) Density - Water is less dense in its solid form than its liquid form, which is different from other elements. (E.g., gold) This relates to hydrogen bonding and changes to matter going from one state to another. When you go from a liquid state to a solid state for water, the stability of molecules are oriented to maximize hydrogen bonding so that water molecules able to form all four hydrogen bonds. This ends with the molecules positioned in a hexagonal lattice shape, spreading out the solid form to be less dense. The pockets between molecules allows for all four hydrogen bonds to be made, but also explains why the molecules spread out when frozen. (Explains why ice expands when frozen). 2.) Adhesion - Has to do with the fact that water can stick to other polar/charged molecules. (Think about example of string held out 75 degrees from a faucet, water will stick to the string, not just run off the top of the string) 3.) Cohesion - relates to the property that water sticks to itself, hydrogen bonds of water molecules will form hydrogen bonds with other water molecules. (This is how surface tension is possible) 4.) High heat capacity - Is a chemical property that is relates to the amount of energy needed to change the temperature of one kilogram of a substance one degree. When you change temperature, you're causing the molecules to move, breaking the hydrogen bonds faster and faster and becoming more transient. Because there are so many hydrogen bonds, it takes more energy to get the molecules to move faster. 5.) Solvent of life - "Like dissolves like" meaning water can dissolve polar or charged solutions. Things that don't dissolve in water have non-polar bonds, like hydrocarbons.

Compared to a solution of ph 3, a solution of pH 1 is:

100 times more acidic. Because the scale is so wide, the variation in hydrogen ion (H+) concentration changes by ten-fold per movement on the scale. Jumping from 3 to 1 on the pH scale is two spots, so 10^2 = 100 times more acidic

An uncharged atom of sodium has an atomic number of 11 and an atomic mass of 23. How many electrons does this sodium atom have?

11. Atom is uncharged meaning an equal number of protons and electrons. Atomic number is 11, referring to the number of protons in the nucleus.

What is the atomic mass of an atom that has 6 protons, 6 neutrons, and 6 electrons?

12. 6 protons + 6 neutrons.

What is the atomic mass of an atom that has 7 protons, 8 neutrons, and 6 electrons

15, 8 + 7, protons + neutrons

An uncharged atom of boron has an atomic number of 5 and an atomic mass of 11. How many electrons does this boron atom have?

5. Given the atomic number = 5 (implies 5 protons) of an UNCHARGED atom, means that we need 5 electrons to balance the positive charges to make the charge net zero.

What is a polymer? What are the polymer names for the four macromolecule groups covered?

A polymer is a molecule created by linking multiple repetitive units together to form a long chain. Polysaccharide, polypeptide, polynucleotide (or DNA/RNA) Lipids don't have the same basic structure of monomers linked together as carbohydrates, proteins and nucleic acids.

What is the difference between saturated and unsaturated fats?

A saturated fat means that all the bonds in the fatty acid chain are single bonds. An unsaturated fat means that the fatty acid chain can have double or triple bonds. (Can be one or many) These double/triple bonds explain why things like oil are liquid at room temperature compared to butter, which is more solid at room temperature.

What is a solution? Solute? Solvent?

A solution means something dissolved in something else. (E.g., Salt water) A solute is the thing being dissolved (e.g., salt) A solvent is the greater component of the solution, the thing doing the dissolving. (E.g., water)

What is cholesterol?

A steroid found in animals. It is a lipid, but it is not a fat or oil. Like all lipids it does not dissolve well in water. Also quite small which allows for additional functionality. Cholesterol is involved in your membrane. Lots of steroids are involved in communication and cell signaling. Plays a role in membrane fluidity.

What is a cotransporter?

A type of protein that transports two molecules AT THE SAME TIME. See in lecture with the Sucrose-H+ cotransporter.

Ceviche is prepared by marinating fresh raw fish in citrus juice for several hours, until the flesh becomes opaque and firm, as if cooked. How does citrus juice render the seafood safe to eat?

Acid pH denatures proteins by disrupting their hydrogen bonds. When we went over the levels of protein structure, hydrogen bonds play a role in both secondary, tertiary, and quaternary levels of protein structure. If you can break up hydrogen bonding, you're destroying most levels of protein structure and taking it back down to its nearly primal level, just an unfolding of sequence of amino acids, at which point it's not going to be functioning. So when you put things in a different pH than it is designed to live in, all proteins (like all living things) are evolved to function in a specific environment, including things like temperature and pH. When you change the pH by adding citrus, you're changing hydrogen iono concentration. In an acidic pH, you're increasing the hydrogen ions that are present, and that's adding a bunch of positive ions into the environment where the protein is not designed to function in, and that's going to start interfering with those hydrogen bonds. All cooking is doing the same thing, breaking up protein structure, denaturing proteins in meat/tissue of the animal, making it easier to eat, and denaturing proteins in any potential contaminants that could have grown on the food.

Match each nucleotide to the nucleic acid molecule it can be found in: Adenine, Cytosine, Guanine, Thymine, Uracil

Adenine - DNA & RNA Cytosine - DNA & RNA Guanine - DNA & RNA Thymine - DNA only Uracil - RNA only

What nucleotides do DNA and RNA have in common?

Adenine, Guanine, and Cytosine

Why does a meniscus form on the surface of the water in a graduated cylinder?

Adhesion & Cohesion, the water molecules are going to cling to each other across the middle, and then cling to the walls of the graduated cylinder. You get this stretching that causes the dip in the middle.

What property/properties of water allow water to travel up trees?

Adhesion and cohesion

What is the basic structure of an amino acid?

All amino acids have the same basic structure: a central carbon (called alpha α carbon), off of the α carbon there is an amino acid group on one side which is a Nitrogen (N) with two Hydrogens (H), a carboxyl group on the other side, Carbon (C) double bonded to an Oxygen (O) and an OH, and a Hydrogen (H) in the third bond, and opposite the hydrogen is the R group/side chain, which varies from amino acid to amino acid. The bottom part (the amino group, the alpha carbon, and the carboxyl group) of the chain will always be the same for amino acids; the backbone of amino acids. The variable is the side chain (R group)

What are the similarities between prokaryotic and eukaryotic cells?

All cells have ribosomes (responsible for making proteins), all cells have a cell membrane, phospholipid bilayer (separating the inside of the cell from the outside). They also share a lot of physiological and lifestyle features, both are living things, and they have to produce energy, they have to grow/develop, and be able to divide and reproduce. -Something that is really variable that is found in some prokaryotes and in some eukaryotes is the cell wall. Most prokaryotes have it but not all of them, there are quite a few that don't. In eukaryotes, some have it, some don't (animal cells don't, plants and fungi generally do).

What is the composition of a nucleotide?

All polynucleotides follow this structure; The backbone is composed of a negatively charged phosphate group, a five-carbon (pentose) sugar and a nitrogenous base (the variable portion).

What happens at the secondary level of protein structure?

Called secondary protein structure; This is where the primary chain structure folds into two distinct shapes (the alpha helix or the beta pleated sheet). The shapes are held together by hydrogen bonds BETWEEN THE AMINO ACIDS**

What are the 5 types of nucleotides?

Called the five basic nitrogenous bases Adenine (A), Cytosine (C), Thymine (T), Guanine (G), and Uracil (U).

What are the polymer names for nucleic acids?

Can be referred to as polynucleotide, generally referred to ask DNA or RNA.

Electronegativity ranges:

Anything greater than > 2.0 difference = Ionic bond Anything < 0.5 = non-polar covalent bond (small difference, equal sharing) Anything between 1.7 to 0.5 = polar covalent bond.

You lead a team characterizing a new type of cell discovered in an animal system. While looking at the microscopic images of the cell, you notice that the ER in these cells have a much higher level of ribosomes than have been seen in other cells. What can you hypothesize about the role of these cells?

Anytime a cell has more of something than average, that usually indicates that that's the primary job. Mentioned earlier, liver cells have a lot of smooth ER because that's responsible for detoxifying things like alcohol and contaminants. In plant cells the cells that are in leaves are responsible for photosynthesis, so there are tons of chloroplasts, whereas other tissues don't. If you have a bunch of ribosomes, you know that ribosomes are responsible for producing proteins, so that's probably what the cell is doing. By saying that this cell has a lot of ribosomes, that means that the proteins are probably being secreted, and that it's designed to make a bunch of proteins and then shooting them out into the environment through transport vesicles.

What is the difference between passive and active transport?

As long as the molecule is moving along the concentration gradient (from HIGH concentration to LOW concentration) it doesn't require energy.. If you want to move the molecule AGAINST the concentration gradient (from LOW concentration to HIGH concentration), that requires energy.

Hydrogen bonds occur when:

As the molecules are moving around each other (either as a liquid, gas, or moving solid) you end up for a brief time with the positive and negative ends of the molecule oriented toward each other. The bond breaks once they are no longer oriented toward each other.

What is the fluid mosaic model?

Basic idea comes down to two components: it's fluid, and it's mosaic. Mosaic - has to do with the fact that there isn't just a phospholipid bilayer, there are also proteins, molecules (like cholesterol), carbohydrates, a mixture of a bunch of different molecules. Fluid - They're all in motion. The phospholipids in the membrane are constantly shifting around (think about water on the surface of a lake or ocean); the phospholipid bilayer can even flip around from top to bottom, drifting around. The vast majority of proteins also move around, a little slower though (think buoy). This isn't true for all proteins, like anchoring proteins). But receptors and other enzymes on the surface also drift around. Fluid membrane where the membrane is constantly in a low state of motion.

How are polymers made and broken down?

Building a polymer occurs with a dehydration reaction to synthesize a polymer to make the connection in the link. Breaking down a polymer is done through hydrolysis (hydro=water, lysis=cutting)

Match the appropriate term: Carbohydrate polymer - Carbohydrate monomer - Carbohydrate linking bond -

Carbohydrate polymer - Polysaccharide Carbohydrate monomer - Monosaccharide Carbohydrate linking bond - Glycosidic Linkage

What is cellulose?

Cellulose is a polysaccharide found in plants. It differs from starch as it is a structural polysaccharide. It helps support the rigid structure of plants, and allows plants to grow vertically and hold itself up. It's not branched like starch or glycogen. Instead, it's repeating monomer units forming straight lines that are held together by hydrogen bonds

What does cholesterol do to membrane fluidity?

Cholesterol reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification. Because it is a lipid, it's nonpolar meaning it can form hydrophobic interactions and help make the membrane more viscous at moderate temperatures. When the temperature starts getting colder and lower, the structure is slightly irregular compared to the hydrophobic tails, so at lower temperatures it hinders solidification, keeping things more fluid. Acts as a buffer and stabilizes the ideal viscosity.

Evidence for the endosymbiont theory for mitochondria/choroplasts.

Circular mitochondrial/chloroplast DNA that differs from other eukaryotes, more similar to prokaryotes. Independent reproduction Ribosomes in mitochondria/chloroplasts differ than the ribosomes found in other organelles Multiple membrane layers

What amino acid can form disulfide bonds?

Cysteine

What amino acid is capable of forming disulfide bonds?

Cysteine, the Sulfur Hydrogen R-Group/side chain allows for really unique interactions.

Is DNA soluble in water? What does it tell you about its polarity?

DNA is soluble in water, which implies that the solution (DNA) is either polar or charged.

What domains of life are eukaryotic?

Eukaryotes cover the domain Eukaria, which encompasses a lot of the things you're used to interacting with on a daily basis, things like plants, animals, fungi, all of which are multicellular.

The reactive properties or chemical behaviors of atoms depend on...

Electrons in the outer electron shell of the atom.

Describe Primary Protein Structure

Essentially how the protein builds itself into its shape. Proteins start as just a simple polypeptide chain, and they have to fold themselves into a functional three-dimensional shape, composed of the small components joining together to form the whole structure. The first step, or primary protein structure consists of the sequence of amino acids that are held together by peptide bonds into a linear chain. The sequence is really important, the order of the amino acids that are in the chain largely determine/influence how the chain is going to fold into the 3-d structure that determines the functionality of the protein. This forming doesn't happen in just one step, what happens is the chains (which are small segments) take on certain shapes in making the secondary structure, and it is the secondary chain that starts to fold into the bigger full-on structure.

What is membrane synthesis?

Explains where the cell membrane comes from - they come as part of the endomembrane system. The vast majority of organelles in the cell have an interconnected ability to move things around through vesicles The membrane, like all other molecules in the cell, eventually wear out and needs to be replaced. In the ER, there is lipid synthesis happening in the sER, and basic structure of the bilayer will be synthesized there. In the rER, ribosomes are creating the proteins that need to be integrated in the membrane, and they are directly injected into the membrane. Then everything goes through the golgi (mail center), maybe gets some modifications (like carbohydrate attachments), and is sent through another vesicle that will fuse with the cell membrane. That vesicle then becomes part of the overall membrane. Anytime there is transportation of molecules from organelle to organelle, you're introducing new molecules (new replacements) to the membrane.

The monomer unit of a lipid is a fatty acid

False, lipids do not have the same monomer/polymer structure as the other three macromolecules covered in class.

T/F - Microtubules are organelles that provide support for cell structure

False, not an organelle.

T/F, in plant cells, you want them to exist in isotonic solutions.

False, this is only true for animal cells. In plant cells, it's different because of the presences of a cell well. If you put a plant in a hypertonic solution (high concentration outside, low concentration inside), the same shriveling will happen, except the cell wall is rigid and won't move, so externally the cell wall will stay the same, but the inside of the cell will be plasmolyzed. This happens because parts of the membrane are anchored to the cell wall, giving a weird stretched structure inside the cell wall. Just as bad for plant cells as it is for animal cells. Remember, hypotonic exists when there is high concentration inside the cell, and low concentration outside, and isotonic is equal concentrations on the inside and outside of the cell. Plants maintain their physiology as a hypotonic situation. Plants maintain the environment around them, when the fluid surrounding their cells are at a lower concentration of solute than inside their cells (lower outside, higher inside); this is so that water is constantly rushing in. This puts the cells in their target state, providing plants with upright support. (E.g., think about the pressure of a balloon inside of a box, pumped to the max size that the box will allow. It won't pop because you can't pump in more air, because it will have reached its capacity with the cell wall.) When plants are in an isotonic state, the plant will become flaccid. The cell wall stays rigid, but without the pressure of constant water coming in, the plant will lose that pressure that holds them upright, and they will start to droop. This is what happens when plants start to wilt. Also explains why plants recover quickly if they're re-watered after not wilting for too long. It doesn't require plants to regrow anything, it's due mainly to water moving around inside the cells.

T/F all eukaryotes are multicellular.

False. While plants and animals are pretty much exclusively multicellular, like fungi, most are multicellular, but there are a few things that are unicellular. There are additional members of the eukaryotic family that are unicellular (things like seaweed). There are also other unicellular eukaryotes that are known collectively as protists. Protists is a catch-all term, for something that is technically a eukaryote, but isn't a plant, animal or fungi; this includes things like seaweed and algae. Fungi, most are multicellular, but there are a few that are unicellular. Protists, there are many that are unicellular, there are some that are multicellular.

T/F there is a cotransporter in the Sodium/Potassium (Na+/K+) pump discussed in lecture.

False. This is not a cotransporter because the transportation of the sodium and potassium happened sequentially, not at the same time.

Is FAT soluble in water? What does it tell you about its polarity?

Fat is not soluble in water. It's mostly a hydrocarbon so it will not dissolve in water as it cannot form hydrogen bonds with water molecules.

What is the typical pattern for electron-distribution?

First ring/orbital has a maximum of two electrons Second orbital can max out at 8 electrons Third orbital can max out at 8 electrons

What were the types of vacuoles covered in lecture? What are their function?

Food vacuole - product of phagocytosis * When you use phagocytosis to surround the food or large materials to bring it into the cell Contractile vacuole - pumps out of cells *Seen inside eukaryotes, especially those in freshwater environments. For cells that need to constantly pump water back out of their cell. Central Vacuole - Large storage organelle found in plant cells *Is a large storage organelle, found in plant cellls. Plants are a product of their environment, and they can't control what they take in or what's going on in their environment. So, if the plant is growing near toxic chemicals (like lead, arsenic, etc.) some of that will get into the plant. Sometimes the plant is able to break it down or get rid of it, bbut other times they just shove it into the central vacuole where it can't do damage to the plant. It can also be used to store food molecules, excess nutrients, and excess molecules. The cell has tight regulation over what goes in, and what comes out.

What characterizes steroids?

Four fused rings at its core.

What is a functional group? What does it do?

Functional groups are different classifications of atoms and arrangements that you can add onto another molecule. By adding functional groups you can shift the polarity of the overall molecule, depending on the size of the molecule and how much you add to it.

For each molecule below describe the ability/rate of diffusion through the cell membrane and why. Glucose RNA O2 CO2 H20 Na+

Glucose - is polar, which will make it difficult to diffuse through the hydrophobic membrane layer. RNA - is (negatively) charged, due to the negative phosphate group in the backbone. It is also relatively big, so it will have a hard time diffusing throuogh the membrane. O2 and CO2 are both small, nonpolar molecules, so they will easily diffuse through the hydrophobic membrane. H2O is polar, so it cannot easily diffuse through the hydrophobic membrane. *Does have rare and minor leakage across, but this is a result of the motion of the bilayer and water molecules, not common. Na+ is a charged ion, so it will not easily diffuse through the membrane.

What is glycogen?

Glycogen is a polysaccharide found in ANIMALS, used for energy storage. Glycogen is very extensively branched, which allows for the cramming of as much sugars as possible into a compact space. As energy is used up, it can be broken off the chain. Primarily found in muscle cells and in the liver. Energy from glycogen is used for quick bursts of big requirements of energy.

What is the bond that holds together monosaccharide units?

Glycosidic linkage

How does adhesion and cohesion function?

Hydrogen bonds

What are the 4 essential elements most common in the composition of most animals (including humans).

Hydrogen, Nitrogen, Carbon, Oxygen

What is hydrolysis?

Hydrolysis is the chemical break down of a polymer with the addition of a water molecule. Hydro=water, lysis = cutting

What is the difference between hydroxide and hydronium?

Hydroxide (OH-) is an anion, or has a negative charge that comes from the transfer of a hydrogen ion. Hydronium (H+) has an extra hydrogen ion, making it a cation..

What type of solution has a lower concentration of solutes outside than in the cell?

Hypotonic Solution

What are the four interactions that can occur in the tertiary protein structure?

IF polar side chains - you can get hydrogen bonding of the R group/side-chains. *** (This is different than the secondary protein structure, the bonds are between the side-chains NOT the amino acid backbone). if you have two nonpolar amino acid side chains next to each other, you can get a HYDROPHOBIC interaction. This is where the hydrophobic molecules essentially squish tightly together to minimize how much water they have to interact with, creating as little surface area for water at the edges. When you have a acidic/negative side chain interacting with a basic/positive sidie chain, you can get IONIC bonds forming. The last interaction occurs between CYSTEINE amino acids; the Sulfur Hydrogen side-chain allows for disulfide bridges, which are a type of covalent bond that is incredibly sturdy.

What can form hydrogen bonds?

If something is polar, it can form hydrogen bonds. Also, if something is charged and can interact with the positive components of the water, then it dissolves, allowing hydrogen bonds. (i.e., salts, sodium chloride ions).

What is a isotonic solution? (Blood cells)

If the concentration of solutes inside and outside the cell are roughly equal, then there will be equilibrium, where some water is going into the cell and some water will be leaving the cell, and the cell will be in its normal state.

What is a hypotonic solution? (Blood cells)

If the concentration of solutes inside the cell is greater than the concentration of solutes outside of the cell, water will try to move from the outside and rush into the cell. The water will try to reach equilibrium, which can lead to the cell bursting or lysing.

How do we know that the membrane is fluid. (Hint: Labeled plasma membrane experiment)

In an experiment, labeled plasma membrane proteins in a mouse cell and a human cell with different markers, after fusion they observed the markers. After an hour, they found that the proteins were mixed, with markers from both the mouse cell and the human cell. If the membrane wasn't fluid, we would have seen a cell with human proteins on one half and mouse markers on the other half, but it looked fused, but not intermixed. P This idea provides the idea for the fluid mosaic model.

What does cholesterol do to the cell membrane at moderate/high temperaturse?

Increases the viscosity of the membrane

What is the gap between membrane layers called?

Intermembrane space

Describe the three types of chemical bonds and provide examples of each

Ionic bond (i.e., NaCl) The sodium ion gives away one valence electron to the chlorine atom, completing the outer shell of both the sodium atom and the chlorine atom. *This also creates ions meaning that both atoms have a charge, Na loses an electron so it has a positive charge (more protons than electrons) and Cl gains an electron so it has a negative charge (more electrons than protons) Ionic bonds form crystals. covalent bond - occurs when there is a SHARING of electrons (rather than giving away) E.g., h2, 02, h20, * Polar covalent bonds - when there is UNEQUAL sharing of electron, resulting in a dipole. * Nonpolar covalent bonds - when sharing is EQUAL, meaning there is no dipole Hydrogen bond are bonds between two atoms within a molecule. Hydrogen bonds are relatively weak (compared to ionic and covalent bonds). They occur when molecules are moving around each other (either in a liquid, gas, or solid in motion) where for a brief time, the positive and negative ends of the molecules are oriented to each other. Once they are no longer oriented toward each other, the bond will break.

Ionic bond formation occurs when

Ionic bonds form when there is a give-and-take of electrons from one atom to another

What are the four types of interactions that make up protein structure

Ionic bonds, polypeptide bonds, hydrogen bonds and disulfide bridges/bonds.

What is an ion? What are the types of ions?

Ions are atoms with a charge. Cation - positively charged ion Anion - negatively charged ion

Define isotopes and how they are useful

Isotopes are variation in the number of neutrons in an atom/element. There can't be changes in the number of protons in a given element, because changing protons (either increasing or decreasing) would change the entire element. You can, however, change the number of neutrons to get different isotopes of that same element. E.g.,: Carbon atomic # = 6 Carbon-12 will have 6 protons, and 6 neutrons Carbon-13 will have 6 protons (same), and 7 neutrons (6+7=13) Carbon-14 will have 6 protons (same), and 8 neutrons (6+8=14) They can be useful because depending on what you do (either adding or taking away neutrons) can create unique properties and unique instabilities (radioactivity). i.e: Carbon-14 is radioactive, as it destabilizes. It can be used for carbon dating.

Why is there huge variety in what organisms look like?

It comes down to their structure. Structure relates to function. Animals, plants, micro-organisms all have different goals/purposes, interactions with their vastly different environments. Evolutionary feedback loops that dictates your shape/function. Limited to functions based on the shape you are/structure you exist in. OVER TIME with evolution, new structures can develop and shift to provide new functions

How does the mitochondria differ from other organelles?

It has a more complex structure than a lot of the other organelles we've discussed. *One of the unique components is that it has a two membrane layer, whereas other organelles usually have one membrane. (Consists of a smooth outer membrane and a more convoluted/complex inner membrane) Like other organelles, mitochondria have ribosomes and DNA, but their ribosomes and DNA look unique compared to those found in other eukaryotic cells. The DNA is circular rather than linear, and the ribosomes in mitochondria resemble the ribosomes found in prokaryotes more than eukaryotes. Their reproduction/division is independent from the rest of the cell; which differs from the other organelles covered (nucleus, ER, golgi)

What is the nucleus?

It houses the cell's genetic information (DNA). It is a membrane-bound organelle, found in eukaryotic cells that houses the genetic information. The nucleus's primary job is to protecting the DNA (the blueprint of everything that goes on in a cell). Any changes or mutations to the DNA can cause severe effects for survival and function of the cell. It tightly regulates what has access to the DNA.

What happens in the third level of protein structure, what is it called?

It is called the Tertiary Protein Structure This is where the three-dimensional structure starts to form. The structures formed in the seconary structure stage are now oriented toward/around each other, folding the chain into a 3-d structure that gives the protein its function. At this level, there are four different interactions that can help influence/hold together the structure/function. These interactions depend on the side-chains/R group. The type of interactions depend on the amino acids and what's next to each other.

What is the Golgi apparatus?

It is known as the transport hub/mail center of the cell. Anything that needs to go from one location to another goes to the Golgi first, where it will be redirected to the end location. It modifies proteins, sorts and packages materials into vesicles. Sometimes a protein is made in the ribosome but it isn't ready, the Golgi will sometimes add extra bits (sugar, cut off little pieces, etc.) The Golgi is responsible for a lot of fine modification of proteins that can sometimes be needed. It has a receiving side, faced towards the nucleus, and a shipping side, facing out towards the membrane.

What is the cytoskeleton?

It provides support and motility to the cell. It has long protein chains that provide support.

What property of water best describes the ability of water to clean our clothes?

Its ability to act as a solvent. Anything that is polar or charged, on our skin or clothing will wash out relatively quickly because it will dissolve in the water. You need soaps when you're dealing with more complex with non-polar things like greases, fats, and oils, Soap has surfactants which are able to break up fats, oils, lipids, that can then be washed away with the water.

What is endosymbiont theory?

Its the best hypothesize for why mitochondria and chloroplasts came to be, since they're unique compared to other organelles. General idea is that they historically were purely prokaryotes, since eukaryotes are a step-up evolutionarily/more advanced. Over time, the plasma membrane bled in and took on a structure that protected and surrounded the dNA, forming the nucleus, our earliest eukaryotic ancestors. Eventually the membrane between the nucleus and plasma membrane slowly evolved different features like the ER and the golgi. One of these eukaryotic cells engulfed an aerobic bacteria (able to do aerobic cellular respiration), and that bacteria had a double membrane system (common for bacteria). Usually bacteria are broken down and digested to use for nutrients, but for some reason, something went wrong and this bacteria survived and lived inside the larger eukaryotic cell, which is where the idea of endosymbiont originated. Over many thousands of years, those cells were reproduced and the bacteria survived inside the eukaryotic cells, which became to lose functionality, so it didn't keep producing the same molecules/function the same was, as it relied on on the host cell to provide certain resources and nutrients. This evolutionarily, led to the specialization where mitochondria can't be a free-living bacteria. Some time down the line, after the ancestral eukaryote, there is now a functional mitochondria. This same process happened in chloroplasts, but with a photosynthetic bacteria, which led to the reliance organelle rather than a free-living organism, leading to ancestral photosynthetic eukaryotes.

Describe the directional nature of nucleotides

Like amino acids, there is a directional nature. Since it is a repeating pattern, one end has the phosphate group (called the five-prime end) and the other end with the sugar (called the three-prime end).

Which macromolecule group can't form polymers?

Lipids

What is the basic structure of a lipid?

Lipids have a glycerol (three-carbon chain) backbone with varying hydrocarbon (fatty acid) chains, held together by ester linkages.

What are lipids?

Lipids include fats and oils. They also have large hydrocarbon portions. They are hydrophobic molecules that don't form true polymers. Lipids are mostly defined by the fact that they're large molecules that are in the cell that are hydrophobic. (Water fearing.) The other three macromolecule classes are hydrophilic (water loving)

Select the option that would decrease membrane fluidity at moderate temperatures. Longer fatty acid chains More cholesterol More unsaturated fatty acids More saturated fatty acids

Longer fatty acid chains More cholesterol More saturated fatty acids

What organelle carries digestive enzymes?

Lysosomes

Protein has four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt folding. Mercaptoethanol dismantles proteins by disrupting disulfide bonds. Urea breaks down all hydrogen bonds in the protein. Heat can potentially disrupt all intermolecular interactions in a protein. What levels of structure would be disrupted by these agents and why?

Mercaptoethanol would disrupt proteins in the tertiary and quaternary protein structure Urea would disrupt proteins in the secondary, tertiary, and quaternary protein structure levels. Hydrogen bonding occurs between the side chains in the secondary protein structure, in the tertiary protein structure it would disrupt bonding between the side-chains in the alpha helix and beta pleated sheets, and in the quaternary level, it could disrupt bonding between subunit polypeptides. Heat, if hot enough, could potentially break down bonds at every level.

What is the golgi apparatus?

Modifies proteins, storing and packaging into vesicles, ships stuff around the cell.

What is a monomer?

Monomers are the individual links in a chain.

What range do most plant and animal cells fall into (size)?

Most plant and animal cells and bacteria cells fall into the 100 micron range, usually visible with light microscopes.

What is active transport? What are two examples from lecture of active transport?

Moving a solute against its concentration gradient (from LOW concentration to HIGH concentration), always requires some form of energy. Most commonly ATP. This is done when you want really high concentration on one side of the membrane. Na+/K+ Pump Proton Pump

Can basic hydrocarbons dissolve in water?

No, hydrocarbons can't form hydrogen bonds, so it will be excluded by water.

What kind of bond is a carbon-carbon bond?

Non-polar covalent bond because it's the same item twice.

What bond is in a carbon-hydrogen bond?

Non-polar covalent bond because they have very little difference in their electronegativities This means that the whole molecule is nonpolar. Meaning it won't dissolve well in water.

An amino acid whose side chain contains oxygen but no charge would most likely be classified as...

Nonpolar

What types of bonds are found in hydrocarbons?

Nonpolar covalent bonds

What are hydrocarbons?

Nonpolar organic molecules made of hydrogen and carbon.

What is an aquaporin?

Specific water channel protein that allows water to freely diffuse in and out of the cell, most eukaryotic cells have these because they need to maintain water balance of the cell.

What are the amino acid categories (and the characteristics)?

Nonpolar side chains - hydrophobic, almost entirely carbon and hydrogen. Formed by non-polar covalent bonds, hence non-polar side chains. The side chains do not want to interact with water, hence hydrophobic. Polar side chains - Hydrophilic meaning they can form hydrogen bonds with water, held together by polar covalent bonds. Acidic (negatively charged) side chains - Oxygens on the end, in certain conditions and environment (depending on the pH of the environment) generally negatively charged/acidic. Basic (positively charged) side chains - Nitrogen interactions in side chain creating potential positive charges. Water can form hydrogen bonds with charged molecules, so these side chains will interact with water.

What can and cannot freely move through a membrane?

Nonpolar things can move freely across; Polar or charged things can't move through the hydrophobic region of the membrane without assistance (things like water, which has polar bonds, or charged things like a sodium ion).

What is the monomer for nucleic acids?

Nucleotides

Human pancreatic cells obtain O2 and molecules like glucose, amino acids, and cholesterol from their environment. They also release CO2 as a waste product and secrete digestive enzymes in response to hormonal signals. Describe how each of these are accomplished.

O2 and CO2 - are both small and nonpolar, so they will easily diffuse through the membrane. Amino acids - are polar (polar backbone), so they will require active transport to get through the membrane. Cholesterol is nonpolar, so it will easily diffuse through the membrane. Digestive enzymes are proteins, so they can't get through the membrane on other proteins. Secretion of digestive enzymes would be done through the endomembrane system through transport vesicles. Enzymes are produced in the rER and sent through transport vesicles to the golgi, where it will be redirected to the membrane to be diffused and secreted.

Is OIL soluble in water? What does it tell you about its polarity?

Oil is not soluble in water. It's a hydrocarbon, so it does not dissolve in water because it cannot form hydrogen bonds with water molecules.

How does the nucleus control what can enter and exit?

On the surface of the nucleus there are nuclear pore complexes, which are a group of proteins that help control what can enter and exit. This is one of the most regulated transport systems in the cell, allowing only the most important things in and out.

What are the differences between prokaryotes and eukaryotes?

One of the main differences is that prokaryotes are generally smaller than eukaryotes. (Most prokaryotes are somewhere between 1 to 10 micron, whereas most eukaryotic cells are somewhere between 10 to 100 microns.) Structural differences: -One of the major differences, the name sake difference, eukaryotes have a nucleus (a membrane bound structure, a phospholipid membrane that forms a nucleus where the DNA is stored). In prokaryotes, you have what is called a nucleoid, which is essentially just packaged DNA. -Eukaryotes have membrane-bound organelles, where each of the organelles have different structures with a visible difference between mitochondria, endoplasmic reticulum (ER), and Golgi; different structures and different functions. Prokaryotes don't have separate membrane-bound organelles, prokaryotes have a lot of the same proteins, a lot of the same function, they're just localized regionally instead of within membranes. One last big difference between prokaryotes and eukaryotes is their DNA itself; - Eukaryotic DNA is generally kept in multiple linear chromosomes - Prokaryotic DNA is circular, and there's usually only a single one, there can sometimes be other DNA found in prokaryotes, but they're not considered genome or chromosomes.

Properties of Life (7 categories)

Order, evolutionary adaptation, response to the environment, reproduction, growth & redevelopment, energy processing, regulation

What domains of life are prokaroytic?

Prokaryotes include all of domain bacteria and domain archaea. These are PREDOMINANTLY unicellular, but there are certain situations where they'll work together to form a larger structure, but prokaryotes are broadly able to survive independently as a single cell.

What components make up DNA?

Pentose sugars, phosphate groups, and nitrogenous bases.

What bond holds together polypeptides?

Peptide bonds are covalent bonds between amino acids creating polypeptides.

Which method of transport can move the largest molecules? Pinocytosis Receptor Mediated Endocytosis Channel Proteins Ion Pumps Phagocytosis

Phagocytosis

What is phagocytosis?

Phagocytosis is the process through which the cell membrane will stick out a little bit on the surface and create an indented area that will surround a large food particle, pinch-off, and then pull it in so that it becomes a food vacuole, eventually to be broken down through fusion with a lysosome.

What are the major components of the cell membrane?

Phospholipid bilayer, membrane proteins, cholesterol and carbohydrate chains.

What are phospholipids?

Phospholipids are a modified lipid that makes up the cell membrane. Still composed of glycerol, and a negatively charged phosphate group, giving the phospholipid polarity and charge which allows for interactions with water molecules. Amphipathic meaning molecule that has hydrophobic portion and hydrophilic portion. Has a hydrophobic region (called the hydrophobic tails) and a hydrophilic region called the hydrophilic head (has the glycerol, phosphate, choline area) These two regions allow for the formation of the phospholipid bi-layer, where the hydrophobic tails face each other on the inside, and the hydrophilic heads stick out on the outsides.

Eukaryotic Cells - Animals vs. Plants

Plant and animal eukaryotic cells are similar, have a lot of same structures and functions but there are also distinct differences. Plant cells have a few additional structures, being plant cells, and plants needing extra functionalities that animals don't.

What types of bonds would be found between a nitrogen atom and a hydrogen atom within a molecule

Polar covalent bond

Difference between polar covalent and nonpolar covalent bonds?

Polar covalent bonds have unequal sharing of electrons. The result of the electron spending more time in one atom than another leads to a slight positive charge on one side of the molecule and a slight negative charge on the opposite side. This is called a dipole. Non-polar covalent bonds have an equal sharing of electrons, hence no formation of a dipole.

The hydrogen atoms of a water molecule are bonded to the oxygen atoms by ____ bonds, whereas neighboring water molecules are held together by ____ bonds.

Polar covalent; hydrogen

What is the polymer term for proteins?

Polypeptide,

How are polypeptides bonded?

Polypeptides have a front end and back end. The front end is the amino group/N-terminus (composed of Nitrogen) and the back end is the carboxyl/C-terminus end (composed of Carbon double bonded to oxygen) The front of the chain is called the N-terminus, the end of the chain is called the C-terminus.

A strong acid is added to a protein structure causing the pH to drop in the solution. What levels of protein structure would be disrupted?

Primary - Not disrupted Secondary - Disrupted Tertiary - Disrupted Quaternary - Disrupted

What are the two broad categories that break apart cells (and essentially all living things)?

Prokaryotes and eukaryotes

What are the difference between prokaryotes and eukaryotes?

Prokaryotes do not have a nucleus but eukaryotes do. Prokaryotes are generally smaller than eukaryotes Eukaryotes have membrane-bound organelles but prokaryotes don't. Prokaryotes have circular DNA while eukaryotes have more linear DNA Prokaryotes are usually unicellular and eukaryotes are usually multicellular (USUALLY).

From the statements below, which are true differences between prokaryotic cells and eukaryotic cells? Prokaryotes have cell walls and eukaryotes do not Prokaryotes have circular chromosomes and eukaryotes do not Prokaryotes are generally smaller than eukaryotes Eukaryotes have ribosomes and prokaryotes do not Prokaryotes have membrane-bound organelles, eukaryotes do not Eukaryotes have a nucleus, prokaryotes do not Prokaryotes are unicellular and eukaryotes are multicellular

Prokaryotes have circular chromosomes and eukaryotes do not Prokaryotes are generally smaller than eukaryotes Eukaryotes have a nucleus, prokaryotes do not

For each function, identify the organelle responsible: Protecting genetic information - Producing membrane integrated proteins - Lipid synthesis - Producing ATP - Stores calcium - Transportin/sequestering digestive enzymes -

Protecting genetic information - nucleus Producing membrane integrated proteins - Rough ER Lipid synthesis - Smooth ER Producing ATP - mitochondria Stores calcium - Smooth ER Transportin/sequestering digestive enzymes - lysosomes

Match the terms: Protein polymer - Protein Linking Bond - Nucleic acid monomer -

Protein polymer - Polypeptide Protein Linking Bond - Polypeptide bond Nucleic acid monomer - nucleotides

What are proteins?

Proteins are the most complicated group of macromolecules we discussed. They have a wide variety of function, as well as complex and intricate structures. Different functions include enzymatic proteins, defensive proteins, storage proteins, transport proteins, hormonal proteins, receptor proteins, contractile & motor proteins, and structural proteins.

Describe and diagram the basic structure of atoms

Protons and neutrons make up the central nucleus, protons have a positive +1 charge and mass of 1, neutrons have a neutral (0) charge and a mass of 1. Electrons orbit around the outside, and generally have a mass of zero and a negative -1 charge. The electron shell keeps individual atoms from merging and separate from other atoms. It creates a cloud that repulses it from other atoms.

A patient has had a serious accident and lost a lot of blood. In an attempt to replenish body fluids, distilled water, equal to the volume of blood lost, is transferred directly into one of his veins. What will be the most probable result of this transfusion?

Pure water has a lower concentration of solutes compared to the concentration in blood cells. This will mean that the water will try to rush into the blood cells, leading to bursting/lysed cells, and eventually to death of the person. When people are hooked up to IVs in the hospital, they are hooked up to sterile saline solutions that have equal concentration/isotonic to human blood to prevent this problem.

What is receptor-mediated endocytosis?

RME is a line between phagocytosis and pinocytosis. It is triggered when a specific molecule is present. There will be a region on the surface of the plasma membrane that is coated with receptor proteins (coat proteins). The receptors wait until their specific signaling molecule binds to them. Only when the specific molecule has bound to the receptor will that area indent and pinch off to form a vesicle. RME is a very specific, targeted form of the transport process, only when a certain molecule is present (depending on the specific receptor) will it occur. It is more targeted than phagocytosis and pinocytosis, although it requires more energy investment because it has to pull all of the receptor proteins and coat proteins.

Uses of radioisotopes

Radioactive isotopes can be used for... Carbon dating In medicine - some scans use radioactive elements that decay relatively quickly to look for blockages in blood vessels and pathways.

What is a dipole?

Results in the electron spending more time with one atom of a covalent bond than the other. This leads to a slight negative charge on one side of the molecule and a slight positive charge on the opposite side of the molecule. NOTE: NOT a full charge shift, just a slight charge.

What are ribosomes?

Ribosomes are large complexes of protein and RNA that synthesizes proteins; responsible for making every protein in the cell, regardless of its function. Ribosomes are not organelles, they don't have a membrane. Ribosomes consist of complexes of two different things: - Made up of a bunch of proteins, as well as some RNA molecules. (RNA molecules are referred to as ribosomal RNA or rRNA). - All ribosomes are made of two subunits, a larger subunit, and a smaller subunit. (Made up of a complex or proteins and RNA interacting with each other.)

Is salt soluble in water? What does it tell you about its polarity?

Salt is soluble in water, which implies that it is either polar or charged. NaCl is charged, which means it can form hydrogen bonds with water molecules.

What interactions/forces hold together structures in the quaternary protein structure?

Same interactions as the tertiary level; hydrogen bonds, ionic bonds, hydrophobic bonds and disulphide bonds.

Uranium is a metallic element that is used in nuclear reactors and nuclear weapons. The vast majority of uranium found on Earth is in the form of uranium-238, an isotope with a mass number of 238, while the uranium that is used for nuclear reactors and weapons is uranium-235, an isotope with a mass number of 235. What is the atomic difference between uranium-235 and uranium-238?

Since they're both uranium, they both have the same number of protons (Given by atomic number 92) There is a difference of three neutrons between the two isotopes.

What is starch?

Starch is a polysaccharide found in plants. It is used for energy storage in plants, since plants don't have fat storage. It has a similar structure to glycogen, but it's not as extensively branched. Plants use their starch storage throughout the night when the sun is down. When the sun is back up during the day time, through photosynthesis, plants replenish their starch reserve.

What are the difference between DNA and RNA?

Structurally, there are three key differences between DNA and RNA. 1.) Sugar; DNA (Deoxyribose Acid) and RNA (Ribonucleic Acid) both have a pentose/five-carbon sugar, with one difference where DNA has one less oxygen (hence, deoxy). 2) The types of nitrogenous bases seen in DNA and RNA. - In DNA and RNA, we see Adenine (A), Cyotosine (C),and Guanine (G). - In DNA only, we see Thymine (T) - In RNA only, we see Uracil (U) 3) Third big structural difference is that DNA is almost always double-stranded, and it forms a double helix structure; one strand will have the backbone and nitrogenous bases, paired together with another strand with a backbone and nitrogenous bases, bonded together by hydrogen bonds. RNA is usually single stranded, and the structure is more variable, but RNA usually folds up on itself, forming complex 3-d structures, more variable than what you'll see in DNA. ** This is because RNA has more functions, whereas DNA's only function is to store genetic information, RNA plays roles in transmitting genetic information but in a variety of different ways.

Is SUGAR soluble in water? What does it tell you about its polarity?

Sugar is soluble in water, so I assume it is polar.

How are the atomic number and atomic mass different?

The atomic number of an element is equal to the # of protons, the atomic mass is equal to the # of protons + neutrons. The atomic number is the identifier, if this number changes, then the entire element changes. Neutrons and electrons can vary though. When you shift electrons, you are creating ions (giving the atom a charge). When you shift neutrons, you are creating an isotope of the element.

What is diffusion?

The basic principles that due to the random movement of molecules, leads to the general principle of molecules moving from areas of HIGH concentration to areas of LOW concentration. Molecules randomly bounce around and eventually end up in equilibrium. (Think spraying a perfume, concentration of smell 1 min vs. 10 minutes after spraying) In a solution with multiple solutes, the movement of molecules will be independent of each other. Both solutes will work towards equilibrium.

What type of bond holds nucleotides together?

The bond is called a phosphodiester bond, which is a type of covalent bond.

Which of the following statements is a reasonable explanation for why unsaturated fatty acids help keep a membrane more fluid at lower temperatures? Unsaturated fatty acids have a higher cholesterol content, which prevents adjacent lipids from packing tightly. The double bonds block interaction among the hydrophilic head groups of the lipids. The double bonds form kinks in the fatty acid tails, preventing adjacent lipids from packing tightly. Unsaturated fatty acids are more nonpolar than saturated fatty acids.

The double bonds form kinks in the fatty acid tails, preventing adjacent lipids from packing tightly.

What is the endoplasmic reticulum?

The endoplasmic reticulum (ER) comes in two forms; rough ER and smooth ER. The rough ER (rER): 1. Bounds ribosomes 2. Glycoprotein synthesis 3. Distribute transport vesicles 4. Synthesize membrane The smooth ER (sER): 1. No ribosomes 2. Synthesizes lipids 3. Metabolizes carbs 4. Detoxifies drugs (there is a lot of smooth ER in the liver, used to detoxify alcohol) 5. Stores calcium ions.

What does it mean if a fat is unsaturated?

The fatty acid tails have double/triple bonds.

What is an electrochemical gradient?

The gradient refers to the concentration difference across the membrane. One side has a higher concentration than the other. Chemical gradient (like example in class; refers to Hydrogen, a chemical element) Electrical gradient because it creates a charge difference. Anytime you make an electrochemical gradient, you're creating a strong disparity in charging concentration in one side of the membrane over the other. You can use this as power.

Tay-Sachs disease is a human genetic abnormality that results in cells accumulating and becoming clogged with very large, complex, undigested lipids. Which cellular organelle must be involved in this condition?

The lysosome - normally these large complex undigested lipids would be a food vacuole. The lysosomes would come fused with that and break it down. However, in Tay-Sachs, that function doesn't happen and these lipids slowly build up in the cell, eventually leading to cell death, and death of the individual.

What are lysosomes? Why do we need them?

The lysosomes is a structure in the cell that is responsible for digesting or breaking down large molecules and structures within the cell. We need lysosomes so that instead of just releasing digestive enzymes into the cytoplasm, where they can't tell the difference between old and good mitochondrias, they're just going to float around freely breaking down everything. Lysosomes help maintain breaking down only the things you want, minimizing the potential off-target damaging effects of having these digestive enzymes free floating in the cell.

What organelles are similar in having a two membrane structure

The mitochondria and chloroplasts in plant cells both have multiple membrane structures.

What is the monomer name for proteins?

The monomer in a protein is an amino acid.

What is the main difference between glycogen, starch, and cellulose

The polysaccharide chain branching.

why do ionic bonds form crystals?

The reason you get crystals from the forming of ionic bonds is that they want to maximize only having the opposite charge around them. The structure of crystals come from the interaction between positive and negative ions.

In chloroplasts, what is the area between the inner membrane and the thylakoid membrane?

The stroma.

Biology is...

The study of life

How does hydrogen bonding occur in water molecules?

The unequal sharing of electrons between the two hydrogen and one oxygen atom that make up a water molecule leads to a polar covalent bond (with a dipole). There is a slight positive charge on the hydrogen side of the molecule and a slight negative charge on the side of the oxygen. The slight positive charge of the hydrogen side of a water molecule will attract the slight negative oxygen side of other water molecules, leading to hydrogen bonds between the two water molecules. NOTE: IN the molecule, between hydrogen and oxygen is a polar covalent bond. BETWEEN THE TWO WATER MOLECULES is a hydrogen bond between the slightly charged sides of different water molecules.

If the atomic number of uranium is 92, how many neutrons does an atom of uranium-235 have in its nucleus?

There are 143 neutrons in the atom. Atomic number implies that there are 92 protons in the atom. 235-92 = 143 neutrons

How many different (common) amino acids are there?

There are 20 different types of common amino acids, with additional rare ones that are in certain oroganisms.

Why do isotopes matter?

There are some processes that rely on radioactivity There are some variation, some cellular processes that rely on different isotopes of things.

What are the two primary reasons that lysosomes will be used?

There are two primary reasons that lysosomes will be used: 1. One is food vacuoles - important for process of PHAGOCYTOSIS. Process where the small indent or bleb can form on the surface of a cell membrane around a large food particle (large chunk of carbohydrate, nucleic acid, or protein) that is too big to be transported through normal small methods, but has a lot of useful nutrients. The lysosome will fuse with the membrane vesicle, digestive enzymes will then have free access to the large food particle, break it down into smaller pieces, and once that's done it can be deactivated and those nutritional components/breakdown products (amino acids, monosaccharides, etc.) can then be accessed and utilized by the cell. 2. The other thing that lysosomes will do is break down worn-out organelles, especially things like mitochondria. Mitochondria are very active, and due to processes that they're doing in the molecules they're exposed to, they do wear out relatively rapidly compared to other organelles, and they sometimes need to be broken down into constitutive components so that they can be recycled and rebuild the new resources to make new mitochondria. This occurs when the mitochondria is surrounded by a membrane vesicle, and a lysosome will fuse with it and release digestive enzymes to break down the worn out mitochondria into smaller structures/constitutive pieces, the process is called AUTOPHAGY.

How are amino acids categorized?

They are categorized by their different side chains, which relate to the different properties associated to their chemistry and bonding.

Where can ribosomes be found?

They can be found in two different places within the cell: - Free ribosomes are found in cytosol, floating freely around the cell. Lots of ribosome don't need to be in a specific place to do their job, they just need to be available in the cytoplasm to do their function. Free floating ribosomes will produce free-floating proteins. - Lots of proteins need to be embedded into a cell membrane, either attached to the surface or sticking all the way through to do their job. If a ribosome needs to be carefully localized to do its function, or attached to a membrane, it will produce ribosomes that are actually bound to the ER membrane; these ribosomes are physically tethered to a membrane which makes it easier for them to insert proteins into the membrane/associated region.

What are chloroplasts? What makes it unique?

They convert light and water into sugar through photosynthesis for plants. It has a third set of membranes called the thylakoids which plays a big role in photosynthesis. It has three membrane layers, the inner and outer membranes are smooth, and the thylakoid membrane is more complex/has a lobe structure. Has a lot of features similar to those found in the mitochondria, it also has its own ribosomes and DNA that are circular rather than linear. They also reproduce independently, their division and separation is separate/not regulated by the cell cycle like the other organelles.

A solution of pH 5 would have a higher concentration of H+ than a solution with pH 8

True, more H+ means more acidic (closer to 0 on pH scale).

What are nucleic acids?

They store and transmit genetic information; DNA is responsible for storing genetic information RNA is responsible for transmitting genetic information

What are cytoskeleton made up of?

They're all made of protein structures like microtubules (look like corkscrewing large tube structure proteins), microfilaments (actin forms this tubing twist, like a braid), and intermediate filaments (very large, tightly coiled fiber structures.)

Why are lipids hydrophobic?

They're mostly hydrocarbons so they are nonpolar/cannot form hydrogen bonds with water molecules.

How are molecules released outside of the cell?

This can be done by sending a transport vesicle from the Golgi to the plasma membrane where it will fuse and whatever components contained within that vesicle will be released. This is a common procedure, this is how digestive enzymes are released into your stomach acid, it's how neurotransmitters work in your brain and in your synapses. This ability to release large molecules into the environment is through transport vesicles.

What is the endomembrane system?

This is a somewhat interconnected group of organelles including the NUCLEUS, the ER, the GOLGI APPARATUS, and a couple other organelles. It's responsible for producing materials and moving them around the cell, doing a variety of different functions.

Why are disulfide bonds unique?

This is a type of covalent bond that can form between cysteine in the tertiary protein structure. This is the strongest type of interaction at this level of protein structure. It's extremely hard to break. Heat and basic chemical reactions can easily break up hydrogen, hydrophobic, and ionic bonds fairly easily, but in order to break a disulfide bond you have to add in specific and strong chemical agents, which is a fairly difficult process. These bonds are usually found in sturdy amino acids (like antibodies, some of the sturdiest proteins we have).

What happens in the quaternary protein structure?

This is the last level of protein structure. Not all proteins have a quaternary structure. Some proteins are functional on their own, once they've folded into their 3-d form they can go out and do its job. This happens when multiple polypeptide chains (in their 3-d form) interact with one another in order to function. Some proteins have a lot of subunits, some have two, it varies depending on the type of protein.

Define; electronegativity

This is the tendency of an atom to pull electrons towards itself. The types of bonds formed between atoms largely depend on the electronegativity difference between the atoms. If there is a low difference (where atoms have equal pull - either high pull or low pull, but equal) no one's going to lose the tug-of-war and you'll get a nonpolar covalent bond. If one atom has a really strong pull and another has a really weak pull leading to a big difference, that's when you get an ionic bond. In the middle of these two scenarios, when THERE IS a tug-of-war that isn't won, but definitely leaning toward one side over the other, is when you get a polar-covalent bond.

What property of water causes the cracks in the pavement in cold climates?

This relates to water's density. When water solidifies, it expands (due to the molecules locking into a lattice-like structure) which then causes the cracks in concrete.

T/F Ribosomes are found in all cells?

True. Ribosomes are found in all cells, eukaryotic or prokaryotic. Although they do vary significantly. They look different, have different functions, and have different sizes depending on whether its in a eukaryote or prokaryote. There is even variation within groups, especially in the RNA molecules (one of the main things used to sort or analyze taxon, how closely related two bacterial strains are to each other on an evolutionary timescale is by looking at the variation in ribosomes).

What is the difference between a monosaccharide, disaccharide and a polysaccharide?

Unique to carbohydrates, disaccharide is the term for two monomer units for carbohydrates. The monomer term for carbohydrates is monosaccharide. Anything with more than two units in a polymer for carbohydrates is called a polysaccharide.

What type of fatty acid makes the cell membrane more fluid?

Unsaturated fatty acid

What does the cell membrane consist of?

Very complex structure. Has the phospholipid bilayer, cholesterol, cytoskeletal elements that crisscross across the inside of the cell to provide the cell structure, especially in animal cells/cells that don't have a cell wall. Extracellular matrix made up of proteins and carbohydrates, providing a scaffolding for cells to attach to. Has glycoproteins, glycolipids, integral, and peripheral proteins, among many.

What happens when a solution gets more Hydronium (H+)?

When a solution gets more hydrogen ions (H+ goes up), the solution becomes more acidic, and the pH level goes down (towards 0 on a scale of 0-14)

What happens when a solution gets more hydroxide (OH-)?

When a solution gets more hydroxide (OH-) ions, the solution becomes more basic, and the pH level goes up towards 14 (on a range of 0-14)

What is facilitated diffusion?

When molecules cant get through the membrane on their own, one of the ways they can get through is through facilitated diffusion. In facilitated diffusion, there is some sort of protein that allows the molecule to diffuse along its concentration gradient. **Diffusion is always going to be the movement of molecules from an area of HIGHER concentration to an area of LOWER concentration DOESN'T require energy. The molecules just move in the direction of the concentration gradient to get equilibrium of solutes in the solution.

What are two effects of the proton pump?

When protons are moved from inside of the cell to ooutside the cell, two things happen: 1. Changing of hydrogen ion (H+) concentration, putting more H+ outside the membrane. This makes the environment outside more acidic and the inside more basic. 2. Also creating a charge difference. When pumping more charges out of the cell than inside, this creates an environment where the outside is more positively charged than the inside of the cell.

What is a hypertonic solution (Blood cells)

When the concentration of solutes outside of the cell is greater than the concentration of solutes inside of the cell. This will cause water to try to move from low-concentration to high concentration, rushing out of the cell, leaving the cell shriveled and dehydrated, and potentially leading to the cell dying. (e.g., this is why you don't drink salt water, the salt ions in salt water will have a higher concentration of solutes, drawing water out from your blood cells, leaving you dehydrated).

Covalent bonds occur:

When two atoms are sharing electrons (rather than giving away electrons). When sharing electrons, things are not necessarily going to be equal. Sometimes it is, sometimes it isn't. It depends on the strength of the pull on the electron. Some atoms have a stronger pull of electrons than others that lead to a tug-of-war, sometimes leading to an inequality where electrons spend more time in one atom than another. In the case of h20, oxygen has much stronger pull on electrons than hydrogen does.

Why do weak hydrogen bonds matter?

While one hydrogen bond by itself may be weak, they can happen in really large numbers. When they occur in large numbers, they have a lot of power. E.g., if you have 1 million water molecules, then you can form 4 million hydrogen bonds with other water molecules. This additive power gives them a lot of power. This gives water the properties that make it really unique. This comes into play with the polarity of molecules, how molecules interact with water, why oils/fats do not dissolve in water when sugars or salts can dissolve quickly.

What exists within the nucleus?

Within the nucleus, the DNA isn't just loose like a big ball of string, but carefully packaged into a structure called CHROMATIN. It's composed of DNA strands and protein complexes that help to package and organize the DNA, the DNA string is wrapped around and packages the larger chromatin structure. However tight or loosely the chromatin is packaged depends on the structure and function of the specific DNA. There is another substructure in the nucleus, not an organelle, but a densely packed functional region called the NUCLEOLUS, which is the area responsible for the production of ribosomes.

You are preparing a saline solution that is isotonic to red blood cells (0.9% NaCl) but the red blood cells burst when added to the solution. Which is the most likely explanation for this result: You accidentally made a solution that is hypertonic to red blood cells You accidentally made a 0.09% NaCl solution. You accidentally made a 9% NaCl solution The red blood cell membranes are impermeable to water You successfully made a solution that was isotonic to red blood cells

You accidentally made a 0.09% NaCl solution.

How can you make hydrocarbons dissolve in water?

You can take basic hydrocarbon molecules and starting adding things to them, making changes to them that will alter the molecule's properties making it soluble in water. You can add charges or polar-covalent bonds by adding functional groups to make the hydrocarbon water soluble.

Shapes in Secondary Protein Structure

alpha helix; a tight spiral, where the amino acids are turned into a coil beta pleated sheet; is more like a ribbon, takes the polypeptide chain and lays it flat (like a quilt/ribbon)

Which of the following molecules dramatically increases the rate of diffusion of water across cell membranes? aquaporins gated ion channels ATP the sodium-potassium pump

aquaporins

An animal cell membrane will be most fluid at room temperature if it contains: a.) more cholesterol b.) longer chain fatty acids c.) More unsaturated fatty acids d.) More saturated fatty Acids e.) All of the above

b. More unsaturated fatty acids When talking about fluidity, this means we need to disrupt the structure. Disrupting the regularity of the membrane and the interactions as much as possible. Unsaturated means that there are double and triple bonds in the fatty acid chains, double/triple bonds disrupt the structure, ending with a bend/kink in the tail (rather than one that is linear). If the tails are linear, it makes it easier for the fatty acid chains to settle. The tail creates this disrupted structure which does not allow them to solidify.

Which treatment would increase the rate of sucrose transport into a plant cell? a.) Decreasing extracellular sucrose concentration b.) Decreasing extracellular pH c.) Decreasing cytoplasmic pH d.) Adding a substance to increase membrane permeability of pH

b.) Decreasing extracellular pH To get the sucrose cotransporter to work faster, we want to make the electrochemical gradient stronger by adding H+ hydrogen ions to the outside. This would make the sucrose-H+ cotransporter take in more sucrose. We need to make the outside more acidic (adding more H+) ions, making the pH lower. If you bring the hydrogen ion concentration up, you make the pH lower, and increase the power of the cotransporter/electrochemical gradient.

In RME (Receptor-mediated endocytosis), receptor molecules are initially localized on the outer surface of the plasma membrane. Where do the receptors end up following endocytosis? a.) On the inside of the plasma membrane b.) On the inside surface of the vesicle c.) On the outside surface of the vesicle d.) On the inside surface of the golgi e.) On the outside surface of the golgi

b.) On the inside surface of the vesicle We start with receptors on the outer surface of the plasma membrane. The membrane then pinches in to form a vesicle, so that means once the vesicle is formed, the receptors are on the inside surface of the vesicle. The inside of the vesicle matches what is outside the plasma membrane.

Which of the following are found in plants, animals, and bacterial cells? a.) mitochondria b.) ribosomes c.) chloroplasts d.) endoplasmic reticulum

b.) ribosomes - If you are a cell, you need ribosomes to make proteins. The other three are all membrane-bound organelles found in eukaryotic cells but not prokaryotes.

All lipids: a) Are made of glycerol and fatty acid b) Contain nitrogen c) Have low energy content d) Do not dissolve well in water or e) Are acidic when mixed with water

d) Do not dissolve well in water. This is the characteristic trait for lipids. a) does not work because glycerol and fatty acids make up SOME but not all lipids, like steroids.

The result of changing the pH surrounding a protein

disruption of the protein structure due to interference with the hydrogen bonds

Bonds where one atom steals electrons from another

ionic bonds

According to the fluid mosaic model, a membrane is composed of a single layer of fluid phospholipids between two layers of hydrophilic proteins is composed of a fluid bilayer of phospholipids with embedded proteins is composed of a fluid bilayer of phospholipids between two layers of hydrophilic proteins is composed of a mosaic of fluid polysaccharides and proteins

is composed of a fluid bilayer of phospholipids with embedded proteins

An organism with a cell wall would most likely be unable to take in materials through facilitated diffusion active transport phagocytosis Osmosis

phagocytosis