Exam 1 right study guide

What is a lipid contained of? Based on this, can it dissolve in water? What about nonpolar compounds?

A lipid contains hydrocarbonds (C-H) and a high percentage of nonpolar C-C bonds. They cannot dissolve in water for that reason, but can dissolve in solvents that are nonpolar themselves (like benzene)

There exsists a saturated fatty acid and an unsaturated fatty acid. What’s the difference?

A saturated fatty acid is one that contains ONLY hydrocarbonds (C-H), while an unsaturated fatty acid will contain C-C bonds, which will make the entire structure form a kink.

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At the top of all saturated/unsaturated fatty acids exist a ____.

polar carboxyl functional group (-COOH)

How can you convert unsaturated lipids to saturated ones? (hint: think about structure)

You can do this by breaking the double bonds and adding hydrogen atoms via the process of hydrogenation.

What are the three most important types of lipids found in our body?

Steroids, fats, and phospholipids.

What does a steroid look like SPECIFICALLY in cholesterol?

A steroid has a four-ring structure with an isoprenoid tail. At the very top is a hydroxyl group.

Look at image, which is cholesterol!

What do fats contain? What can they also be called, why?

All fats have nonpolar molecules composed of three fatty acids that are linked to a three-carbon molecule called glycerol.

They can also be called triacylglycerols or simple triglycerides because of that glycerol molecule.

What is the primary function of fats? Why does this make sense?

They primarily function as energy storage.

This makes sense because of the high-energy bonds in the fatty acid chains. There’s a ton of C-C and C-H bonds compared to the C-O bonds in carbohydrates, meaning they store MUCH more energy (think the quantity here!).

Look at the image. The hydroxyl groups in the carbohydrate are more likely to dissociate in water—not in a lipid though!

How do fats form?

They form through dehydration reactions between a hydroxyl group of glycerol and the carboxyl group of a free fatty acid.

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After a fatty acid reacts to become bigger in a dehydration reaction, how are they joined (aka, after glycerol groups’ hydroxyl group and the carboxyl group react)?

What does the ester linkage provide (what goes in between those two molecules)?

They are joined through an ester linkage between that glycerol and fatty acid molecule, which puts an oxygen atom between them.

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What is a phospholipid composed of?

A phospholipid has a glycerol that is linked to a phosphate group and two hydrocarbon chains of either isoprenoids or fatty acids. The phosphate group is also bonded to a small organic molecule.

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What is the use of a phospholipid?

It functions as a component of the cell membrane (plasma membrane).

Phospholipids have a head and a tail. (omg it’s like the phospholipid bilayer). Is the head polar or nonpolar? What about the tail?

The head is polar and hydrophilic, whie the tails are nonpolar and hydrophobic.

What happens when you put amphipathic lipids (lipids w/ hydrophilic and phobic parts) in water? What two structures form?

When they are placed in water, they do not dissolve because of their hydrophobic tails. Instead, they form either micelles and lipid bilayers.

Micelles are little structures that form when the hydrophilic heads face outward into water. They look like vesicles—small circle.

A lipid bilayer is created when lipid molecules align in paired sheets.

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How are free fatty acids even formed?

They are formed THROUGH micelles (which are like vesicles—a small circle)

What does selective permeability even mean? In a phospholipid bilayer, what substances can cross through easily?

It means that some substances cross a membrane more easily than other substances.

In a bilayer, only small and nonpolar molecules can pass through it since it won’t interact with the hydrophobic, nonpolar tails. Remember that almost anything charged—even ions—cannot cross through well.

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What happens to the phospholipid bilayer, specifically the _____, if the temperature drops?

hydrophobic tails; they will start to move more slowly and then pack more tightly together. This makes it more difficult for any molecule, regardless of polarity or size, to pass through it.

What is the result of cholesterol in terms of permeability? (dont need to say why)

Cholesterol REDUCES the permeability!

What happens when the phospholipid tails contain unsaturated fats?

This will create kinks by the double bonded C=C, producing spaces among the tails. As a result, this reduces the number of van der Waal interactions that keep the tails together, increasing its permeability (allowing more things in).

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What happens when the phospholipid tails contain saturated fats?

This will create fewer spaces (since no kinks) in the atmosphere and produce MORE van der Waal interactions. The forces that hold them together will therefore increase, making the membrane denser and decreasing its permeability (allowing less things in).

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Can certain polar molecules cross the membrane easily without using energy?

Yes, but they have to small small and uncharged.

What is diffusion?

This is the spotaneous (automatic) movement of molecules and ions.

How does a concentration gradient form? And how does it work? Finally, what KIND of transport is that?

It forms when there is a difference in SOLUTE concentration. THey will move from higher concentrations to areas of lower concentrations.

this kind of transport is called passive transport.

When the concentrations inside and outside the cell are at equilibrium, will movement just stop? Why?

It will NOT stop because particles are still colliding with each other in random directions, causing movement.

What is osmosis? When does this occur?

This is the movement of water across the lipid bilayer.

This only occurs when solutoins of different solute concentrations are separated by a membrane that PERMITS water to cross. KEYWORD PERMITS.

For example, osmosis might happen when water can cross through a membrane but the solutes themselves cannot.

What is the direction of water during osmosis?

Water will move from areas with LOW solute concentration to areas of HIGH solute concentration to get a perfect balance of solute concentration.

How can a protein fit within the lipid biplayer?

It can fit in based on its structure. It’s possible to have polar and charged amino acids be at the ends of the protein, with the nonpolar strands being lodged in the middle.

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Label from top to bottom:

Peripheral membrane protein, integral membrane protein, peripheral membrane protein.

How can you remove a protein(s) from the phospholipid bilayer?

You can do this by using detergents, which is a small amphitpatic molecule that can form micelles and ARE water soluble (unlike amphipathic lipids).

When detergents are added to the solution surrounding the lipid biplayer, the hydrophobic tails of the detergent molecule interact with the hydrophobic tails of the lipids and of the transmembrane proteins. As a result, the membrane becomes displaced and forms water soluble detergent-protein complexes that can be isolated.

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How might ions travel through the lipid bilayer? How?

They will usually travel through the membrane using ion channels, which form pores (openings) in a membrane. They will travel from regions of high concentration to regions of low concentrations and from areas from like charge to unlike charge.

What is an electrochemical gradient?

This is a gradient that considers both the concentration of ions and their respective charges.

PLEASE look and read image

What is a carrier protein? What is the best studied example and what is its carrier protein?

These proteins selectively pick up a solute on one side of the membrane, then drop it off on the other side.

The best studied example is the glucose carrier protein, since it takes glucose so long to diffuse through passive transport. The carrier protein is called GLUT-1.

How does the GLUT-1 carrier protein work? Does it require energy?

It works by binding to a glucose molecule (6-carbon sugar), then causing a conformational change (aka an induced fit). As it binds, the protein moves in a way that moves the sugar through the hydrophobic region of the membrane, then releasing it on the otherside.

It does not require energy because it all takes place through diffusion (concentration gradients).

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What is the type of transport that moves molecules AGAINST the concentration gradient? What usually provides the energy for this?

This is called active transport. ATP usually provides this energy!

How does Na⁺/K⁺ ATPase work for sodium? FIRST, give the name you’re familiar with :)

This is the sodium-potassium pump.

First, the pump will look for sodium ions when there is a high affinity (or desire). After the sodium ions bond, a phosphate group form ATP binds to the protein, making it—the protein—change shape. As the protein changes shape, it will push the sodium ions to the outside of the cell here potassium ions lie.

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How does Na⁺/K⁺ ATPase work for potassium? FIRST, give the name you’re familiar with :)

This is the sodium-potassium pump.


for potassium, the protein will have two potassium ions bond to the pump. WWhen this happens, the phosphate group is taken OUT of the protein, allowing the pump to return to its ORIGINAL shape and releasing the potassium ions into the INSIDE of the cell.

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For potassium ions to get into the inside of the cell, what needs to happen beforehand?

sodium ions needed to have left the cell. Otherwise, there’s no way the potassium ions could’ve binded.

Why are electrochemical gradients so crucial toward the function of a cell? After you answer this, explain how that process works… (also, does it use ATP)

They are essential because they make it possible for the cell to engage in secondary active transport (cotransport).

Cotransport is when the cell uses the energy released by the sodium-potassium pump to drag a SECOND substance (like glucose/amino acid) across the membrane, even going AGAINST its natural concentration gradient. IT DOES NOT use ATP and relies on the concentration gradient created by other pumps.

Is it possible for glucose to be moved AGAINST its concentration gradient? How?

It is possible, but only through cotrasnport (secondary active transport). This occurs when sodium ions move back into the cell, driving glucose across the membrane against its gradient.

What is the monomer of a protein? How many of them are there?

amino acid; 20

What is the structure of an amino acid?

A hydrogen atom, NH₂ as the AMINO functional group, COOH (carboxyl functional group), and a distinctive R-group (side chain)

In an amino acid, what is the central carbon also known as?

It is known as the alpha carbon, where all of the four bonds (that make up the structure of the amino acid) bond around.

Label the image from left to right with the black covers first, then answer the pink one last (be specific with that!)

Also, is this ionized or non-ionized?

Amino group, R-chain, Carboxyl Group, Alpha carbon.

This is NON-ionized!

What happens when an amino acid is put into water? (say why)

The amino acid will ionize. Since water has a pH of 7, the amino group (NH₂) will act as a base, attracting a proton to form (NH₃⁺). Additionally the carboxyl group will donate a proton, forming COO^-

Why are the charges on the functional groups (name them and give their charge) of an amino acid so important? (two reasons)

amino group (positive since it gains a proton), carboxyl group (negative since it loses a proton).

It is so important that they have charges because they help amino acids STAY in an aqueous solution, where they can interact with one another and with other solutes. Additionally, the affect the amino acid’s reactivity to perform reactions.

What is the importance of the R-chain on an amino acid?

This r-chain is what characterizes a specific amino acid (remember there’s 20).

NOTE: YOU NEED to know whether they are polar, nonpolar, acidic, basic, which one forms a disulfide bond based on a picture of them!

Peptide bonds are between (what kind of macromolecule)? Are they stable or unstable AND WHY?

two amino acids. They are usually stable because the nitrogen can sporadically (it goes back and forth) donate its pair of unshared valence electrons to the carbon in the C-N bond, forming a C=N double bond. When this happens, a pair of electrons are pushed FROM the carbonyl (C=O) ot the oxygen atom, forming a single bond with an oxygen anion (C—O^-). This gives the peptide bond flexibility!

TLDR; think of resonance because that’s the big picture here!

What is the directionality of an amino acid chain? (be relatively specific here)

It will usually start at the N-terminus (NH₃⁺) and then end at the carboxyl group (COO^-)

When you have many amino acids binded together, but fewer than 50, what is the chain called? What about one with more than 50?! And finally, why don’t we just called it a protein?

An oligopeptide (or simply a peptide lol). More than 50 is called a polypeptide!

We don’t just call it a protein because a protein refers to the complete, fully functional form of the molecule. They usualy contain multiple polypeptides!

What kind of R-groups would be willing to dissolve in water (or are considered hydro_____)? What about ones that don’t dissolve in water; what do they do instead?

hydrophilic;

The r-groups that fit this category are ones that are both polar and electrically charged.

The ones that don’t dissolve in water are non-polar and don’t have highly electronegative atoms capable of forming hydrogen bonds with water. Instead of dissolving, they usually group up with each other in an aqueous solution.

What amino acid is a really special one? Why?

The special one is methionine, because it does not have a negative charge, a positive charge, or an oxygen atom. It’s a nonpolar amino acid!

What is the primary structure of a protein characterized as?

The primary structure usually contains the unique SEQUENCE of amino acids. There’s over 10,000 billion variations!!!

Why is the order and type of amino acid so important in the primary structure of a protein?

It is because every R-group affects the overall protein’s size, shape, reactivity, and solubility. So if something is just slightly incorrect or flipped (like a different amino acid), then the entire protein could be messed up, like in the example of hemoglobin, where a change on the amino 6 group makes it sickle cell disease.

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What is the second structure of a protein characterized by? (be specific on where hydrogen bonding occurs!)

ALSO, say what this results in?

The secondary structure contains the interactions between funtional groups in the peptide-bonded backbone. They are largely formed of hydrogen bonding that occurs between the oxygen on the carbonyl group of one amino acid and the hydrogen on the amino group of another.

This will result in either an alpha-helix or beta-plated sheet (look at image)

You don’t need to know the specifics, but how do we know whether an alpha-helix or beta-plated sheet will form?

We will usually know based on the molecule’s primary structure, specifically the amino acid sequence(s). Certain amino acids, like proline, are rarely found in alpha-helices because of its unusual R-group.

How is it that hydrogen bonds give shape to an alpha or beta shape of a protein (secondary structure) if the hydrogen bond is SO much weaker to a covalent bond?

It’s mainly because of the NUMBER of hydrogen bonds that occur on both the alpha and beta shape. As a result, they make the secondary structure really stable and define its shape.

What are the characteristics of the tertiary structure of a protein? (five specifics; this is the hardest flashcard)

The tertiary structure is characterized by its three-dimensional shape, which happens from the interactions between the R-groups OR between the R-groups and their backbone. There are five important interactions that build to this 3D shape:

• hydrogen bonding - between the polar side chains and/or the backbone.

• hydrophobic interactions - between water molecules interacting with the hydrophilic polar side of a polypeptide, forcing the hydrophobic ends to group together

• Van der Waal interactions - when nonpolar chains are close to one another, they can bring each other together for a temporary amount of time

• covalent bonding between the side chains of TWO CYSTEINES via disulfide bonds. This is a VERY strong linkage that gives to shape

• Ionic bonding betwen groups tha thave full and opposite charges, like the ionized acidic and basic chains
  
  

Go from left to right filling that in:

alpha-helices; beta-plated sheets

What are the characteristics of the quaternary structure?

This structure includes multiple polypeptides, which might be the same or different. When the two polypeptide subunits are identical, they are homodimers; heterodimers when they are non-identical.

You can also have a mix of homo/hetero dimers of the quaternary strucutre includes MULTIPLE polypeptides (e.g., 40).

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The first three stages of protein structure only involve _____?

SINGLE polypeptides

In a primary structure, what stablizes the polypeptide? What about in secondary? Tertiary? Quaternary?

Primary - Peptide bonds stablize it

Secondary - Hydrogen bonding between groups ALONG the peptided-bonded backbone

Tertiary - Bonds and other interactions (those 5) between R-groups or between R-groups and the peptide-bonded backbone

Quaternary - Bonds and other interactions between R-groups and between peptide backbones of DIFFERENT polypeptides.

Look at image (top to bottom like this card)

How might a protein be denatured? How might one guess if they’re denatured by simply looking at the protein?

A protein can be denatured if it is put into compounds that break the hydrogen bonds and disulfide bonds, which give the protein by default a unique condensed structure.

Them unfolding is a sign of denaturing!

What is the name of the special protein(s) that help proteins fold? How does this work?

They are called molecular chaperones. Essentially, they assist in the folding of a protein by attaching to the hydrophobic parts of the nonpolar side chain of polypeptides to prevent aggregates from forming, THEN, they will release them to fold properly.

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Since protein folding can be so critical to its function, how is it regulated?

It is regulated by molecular chaperons and won’t fold UNLESS it binds to other molecules/ions during a signaling event (this is where molecular chaperons are apparent).

What is the reactant in a catalyzed reaction? Additionally, why are enzymes such effective catalysts?

The reactant in a catalyzed reaction is the substrate. Enzymes are so good because they can hold the subtrate in a precise orientation that allows them to react in reactions.

Where do substrates bind on the enzyme? And what happens?

They bind on the active site, which is very specific FOR that substrate. After binding, the active site will slightly shift to lock in that substrate called an induced fit.

What are the three fundamental characteristics of life that NUCLEIC ACIDS satisy? What about carbohydrates?

Nucleic acids fulfill 3/5: information, replication, and evolution.

Carbohydrates fufill 1/5: energy

What are all of the characteristics of a carbohydrate? (aka what do they contain)

Carbohydrates contain monomers called monosaccharides, small polymers called oligosaccharides, and the large polymer called polysaccharides.

Tricky question, but what is the molecular formula of a carbohydrate?

They usually have the molecular formula of (CH₂O)_n where n is the number of carbon-hydrate groups.

What kind of functional groups make up a carbohydrate? (also say what bonds)

They are made up of a carbonyl group, several hydroxyl groups, and many carbon-hydrogen bonds.

NOTICE, to be considered a carbohydrate YOU MUST have these characteristics ALONG with (CH₂O)_n.

How might monosaccharides be different from each other? (talk about grouping)

They can be different based on the functional groups they have. The carbonyl group can be found either at the end of the molecule, forming an aldehyde sugar (aldose) or within the carbon chain, forming a ketose.

LOOK AT THIS IMAGE

Are sugars polar molecules? Why?

They are considered polar molecules because of the carbonyl group along with the multiple hydroxyl groups they have. They can be easily dissolved in aqueous solutions.

What is a 3-carbon sugar called? A 5-carbon? A six-carbon?

triose; pentose; hexose

What is a second reason monosaccharides differ from each other? (talk about atom)

Also, does this mean their function differs? They’re both sugars at the end of the day, right?

They differ based on their atom arrangement. For example, the placement of a hydroxyl group might affect the type of sugar it is (like glucose vs galactose).

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Since they don’t resemble the exact same molecular structure, their functions WILL DIFFER. EX: glucose and galactose look almost the same, but galatocse need to be converted via enzyme-catalyzed reaction to glucose before being used to construct other molecules (like glucose).

Mannose is a six-carbon sugar that is similar to glucose, except for the orientation of the hydroxyl group on the second carbon. Draw the structural formula of mannose, and circle carbon number 2 and the hydroxyl group.

PLEASE make an effort to draw this. It isn’t hard at all.

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Try to draw the structural formula of a three cabron sugar (C₃H₆O₃) in a linear form and then draw three DIFFERENT sugars that illustrate three ways monosaccharides differ from one another (they all still have the exact same number of carbon, hydrogne, oxygen!)

PLEASE make an effor to draw variations of these—I can almost guarantee this will be on the test.

How do monosachharides polymerize? What does it result in?

They polymerize when a dehydration reaction occurs between two hydroxyl groups, resulting in a glycosidic bond.

The opposite of this is a hydrolysis reaction, which breaks that bond.

What is the difference between a glycosidic bond and the following bonds: peptide bonds, phosphodiester bonds (start by talking about how these bonds form)

Remember that peptide and phosphodiester bonds form between the same locations in their monomers, giving both proteins and nucleic acids their standard backbone structure.

In carbohydrates, glycosidic linkages form between hydroxyl groups, but different hydroxyl groups can participate in the bond. Therefore, monosaccharides can be linked in different positions (such as 1→4 or 1→6) and orientations (α or β sheets), allowing carbohydrates to form linear or branched structures.

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Identify the bond here:

glycosidic bond (or linkage)

What are the two most common glycosidic linkages?

One is called the alpha-1 4-glycosidic linkage

The other is called the beta-1 4-glycosidic linage.

NOTICE: the numbers refer to the carbons on either side of the linkage. So on one end, it’ll start on the 1’ and end on the 4’ carbon.

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Is this an alpha or beta linkage, how do you know?

This is an alpha linkage because the glycosidic bond points in the same direction as the hydroxyl groups.

Is this an alpha or beta linkage? How do you know?

This is a beta linkage because the glycosidic bond points in the opposite directino of the hydroxyl groups.

Is this an alpha or beta glucose? Why?

This is a beta glucose because the hydroxyl groups point on the opposite sides of each other.

Is this an alpha or beta glucose?

This is an alpha glucose because the hydroxyl groups point in the same direction as each other.

How do animal cells store energy? Plant cells?

Animal cells store energy in the form of glycogen, while plant cells store energy in the way of starch.

Describe the chemical structure of starch (just say the type of monosaccharide and how they’re joined together)…

Starch is made up of alpha-glucose that is joined by glycosidic linkages. Most fo them are between the C-1 and C-4 carbons, and the angle of these bonds forms a helix.

What are the two types of polymers that make up starch? (say the bonding too)

One of them is a molecule called amylose, which contains only alpha-1 4-glycosidic linkages. The other is amylopectin, which happenes ONCE out of 30 alpha 1 6-glycosidic linkages.

How is glycogen different from starch?

The only difference comes from the branching structure in amylopectin. It happens in about 1 of every 10 glucose subunits, whereas it’s 1 out of every 30 in starch.

What is the cell wall made out of? After you say that, be specific with it!

The cell wall is made out of cellulose, which is a polymer made from beta-glucose monomers joined by beta-1 4-glycosidic linkages.

How is cellulose different from starch? (talk about shape)

It is different based on the orientation. It has a flipped orientation, making it look like a linear molecule rather than the helix in starch. This allows cellulose to form strong fibers reinforced by hydrogen bonds. This is what gives the cell wall support!!!!


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What is chitin? How is it different from a cell wall?

This is a polysaccharide that stiffens the cell walls of fungi.

It is different from a cell wall beacuse it does not consist of glucose residues but instead has a nitrogen based group joined by Beta-1 4 glycosidic linkages.

What is the bacterial cell wall called? What does its structure look like? Also, what are the parallel strands joined by?

It is called peptidoglycan. It’s structure is very complex and has a long backbone of NAG and NAM (N-acetylmuramic acid) that alternate with each other and are linked by B-1 4 glycosidic bonds. It also has a short amino chain that is attached ot the C-3 carbon of NAM.

The parallel strands are joined by peptide bonds!

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What is one of the basic functions of carbohydrates? Give an example and say what the sugar is itself…

One basic function of a carbohydrate is to serve as the building block for more complex molecules. For example, the nucleotides tha tmake up RNA and DNA polymers have a ribose or deoxyribose sugar! The sugar itself is a monosaccharide!

How might carbohydrates interact to give membrane a certain shape?

They might end up attaching to lipids and proteins to then project outward from the cell surface into the surrounding environment.

What is a glycolipid? What about a glycoprotein?

A glycolipid is a lipid that has been covalently bonded to a carbohydrate (called glycosylated). A glycoprotein is a protein that has been covalently linked to a carbohydrate.

Fill in the blank, going from the top half (then work left to right), then the very bottom:

Oligosaccharide, glycolipid, glycoprotein.

Is an oligosaccharide the same thing as a glycolipid? Why

It is not the same thing. A glycolipid contains a carbohydrate COMPONENT, which can be an oligosaccharide, but it still contains lipid portions. It’s only covalently bonded to a carbohydrate.

What enzyme is responsible for catalyzing the hydrolysis of an alpha-glycosidic linkage in glycogen molecules? What about in starch?

phosphorylase; amylase

Answer question

Only the second and third option.

The first one is incorrect because it’s really DEOXYribonucleotides that are added to a DNA strand.
The fourth one is incorrect because complementary base pairing happens between nitrogenous bases, NOT sugars.

In a general scope, PLEASE read the answers carefully. Like really carefully, because if you got this wrong, you’re just selling. It’s mistakes—you know this!

Answer question:

It is the fourth option.

Remember the three components of a nucleotide. We know the 1’ carbon is attached ot the nitrogenous base and that the 5` carbon is attached to the phosphate group.

Remember that the bonds between a sugar and a nitrogenous base is an N-glycosidic bond (the N is nitrogen).


The first option is wrong because it’s NOT oygen that attaches the base to the sugar. It’s nitrogen!