BIOL 112 Midterm

What force is involved in hydrophobic interactions

vander walls

what is the formula for polysaccharides?

Cn(H2O)n-1

How does water move up trees?

Cohesion and adhesion forces form a column in the xylem and move water up.

Why is water denser then ice?

The Hydrogen bonds create extra space between the IMFs when freezing making more space and higher volume.

Which molecules dissolve in water

All polar molecules and water.

Why is water very good at facilitating reactions?

It is a really good solvent.

What are Buffers?

Make an overall solution resistant to pH change, as they react with both bases and acids.

What do buffers show and prove?

the Law of mass action: Addition of reactants accelerates the reaction to the right. Likewise, the removal of products accelerates to the right.

What types of compounds act as buffers? Why?

Weak acids:

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Weak acids do not fully disassociate in solution. For example, when acetic acid (CH3COOH) is dissolved in water, it dissociates into hydrogen ions (H+) and acetate ions (CH3COO-):

CH3COOH + H2O ⇌ H3O+ + CH3COO-

\n The acetate ions act as a conjugate base and can combine with any additional hydrogen ions that may be introduced into the solution, thus neutralizing the added acid. Similarly, if a strong base (such as NaOH) is added to the solution, the acetate ions will react with the hydroxide ions (OH-) to form water and a new weak acid:

How do you make a buffer act in both directions?

If you want to make a buffer that buffers in both directions, you have to add equal amounts of weak acid and its conjugate base to reach the half-equivalence point of the titration curve.

What are the 6 main functional groups in this course?

Amino

Carbonyl

Carboxyl

Phosphate

Hydroxyl

Sulfhydryl

What all living things share? Whats the significance?

Macromolecules are made the same in all living things and are present in all living organisms. This means organisms can acquire energy by eating other organisms.

What is a condensation reaction?

formation of a polymer linked by covalent bonds, releasing one water molecule with each monomer added. This reaction is anabolic, requires energy input. Examples are DNA replication, protein synthesis, making of starch.

What is a hydrolysis reaction?

Breaking of covalent bonds with the help of water to transform a polymer into its constituent monomers. This reaction is catabolic, releases energy. Example: digestion of food molecules for energy generation.

What is ATP hydrolysis? Does it gain or release energy? What does it due? Anabolic or catabolic. Does it require energy or is spontaneous?

releases energy. Covalent bond formation in a polymer. Requires energy. Catabolic reaction that allows ATP to be used as chemical energy.

What is the longest protein/polypeptide?

Titin = 33 000 Amino Acids

What is an important part of determining protein function?

The folding of the polypeptide, this is largely determined and influenced by the sequence of polypeptides.

What are the 3 types of amino acids? What determines this?

The R- side chain determines it:


1. Non-Polar Amino Acids
2. Polar Amino Acids
3. Electrically charged amino acids

Explain one main reason why buffers are important in the blood in relation to proteins

Ionized amino acids in a Low or High pH environment can begin to receive and donate protons. This leads to changing charge and thus chaining their function and stability.

What are the main sections and parts of the peptide bond?

Carboxyl + amino group

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OCN

What do all proteins start and end with?

All start with an amino group and end with a carboxyl group

Are peptide bonds rigid? What does this mean? Can they rotate?

As the polypeptide backbone consists of single covalent bonds, it is pretty flexible (rotation about the single bonds is possible, full rotation for the C-C bond, less so for the N-C bond).

What determines the secondary structure of a protein?

The pattern and areas of hydrogen bonding determine the shape and structure of the protein

What is the arrangement of R chains and hydrogen bonds in secondary structures? Does this contribute to the secondary structure?

Alpha helix: R chains point outwards (away from the helix)

* Hydrogen bonds form in the direction of the helix

Beta-sheet: R chains away from the plane (upward and downward)

* Hydrogen bonds form within the plane of the sheet

Describe ribbon diagrams of secondary structures

What is unique about proline?

The side chain is covalently bonded to both the C and the N atom of the peptide backbone. This generates a kink in the peptide because the ring prevents free rotation of the N-C bond. Also, the backbone hydrogen bond cannot form, because the backbone N lacks a hydrogen. Therefore, formation of secondary structures (alpha helix, beta pleated sheet) is impossible. A proline is often the last amino acid of an alpha helix.

What happens to amino acids at neutral pH

They become ionized

What reaction occurs in peptide bond formation

Peptide bond formation (a condensation reaction) occurs between the carboxyl group of one amino acid and the amino group of the next amino acid generating a peptide backbone consisting of NCCNCCNCCNCC repetitions (in this example there are four amino acids covalently bonded.

How do we classify ends of an amino acid?

An amino acid always starts with an amino group \[N-terminus\] and ends with a carboxyl group \[C-terminus\]).

What is interacting during hydrogen bond interaction in secondary structures?

First, hydrogen bonds form within the polypeptide backbone between the O of a carboxyl group and the H of an amino group. This can give rise to exactly two secondary structures that form very quickly after a polypeptide has been made: the alpha-helix and the beta-pleated sheet. Note that these hydrogen bonds do not involve the side chains at all!

Do all Amino Acids fold into secondary structures?

NO

What interactions occur that determine the tertiary structure of a protein? 4 things

SIDE CHAIN INTERACTIONS:


1. Hydrogen bonds
2. Hydrophobic + van der Waals interactions
3. Disulfide bonds
4. Ionic bonds

What are coiled coils? Which kind of proteins are arranged like this?

When 2 alpha helices have hydrophobic amino acids at every 4th position. This creates a band of hydrophobicity

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Fibrous structural proteins consist mainly of alpha helices arranged as coiled coils, such as keratins in hair and feathers.

What is a quartenary structure?

when multiple polypeptide structures come together

Is denaturing a protein reversible? What does this show?

Yes! to a certain extent! This is evidence that the primary structure is sufficient for protein folding, or in other words, all the information about protein folding and function is encoded by the primary structure.

What is the most important interactions in tertiary structures? How does it work?

Hydrophobic interactions:


1. stretches of uncharged amino acids will fold toward the interior of the protein (away from water)
2. stretches of charged and polar amino acids fold toward the exterior of the proteins (toward the water).

Which parts of the protein formation process requires energy and which parts dont?

Primary structure formation requires energy, secondary + tertiary structure happens spontaneously

What is protein turnover? How long is it typically?

Replacement of older proteins with new ones: Minutes to weeks (average 2 days)

What are chaperones?

Chaperone proteins help proteins to fold properly after synthesis or after stress related unfolding.

What are Nucleotides made of?

5 carbon sugar

nitrogenous base

phosphate group

What are the 4 kinds of nucleotides in DNA and RNA

DNA:

Adenine

Guanine

Thymine

Cytosine

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RNA:

Adenine

Guanine

Uracil

Cytosine

What are the functions of DNA and RNA

1. Cell Signalling
2. Energy storage as monomers

What are the 2 kinds of nitrogenous bases?

Purines:

Guanine , Adenine

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Pyrimidines:

Cytosine, Uracil/thymine

what is the difference in structure in DNA vs RNA

Uracil is replaced by thymine in DNA.

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DNA lacks the hydroxyl group at the carbon-2 (deoxyribose)

How do nucleotides polymerize? In what direction is this?

Condensation reactions!!!

Phosphodiester bonds (these happen by condensation reactions). The 3’ hydroxyl group forms a covalent bond with the 5’ phosphate group of the incoming nucleotide.

The DNA/RNA molecule polymerization starts with the 5’ phosphate group and ends with a 3’ hydroxyl.

Describe the molecules and where they bond in a nucleotide

Phosphate group bonded to the 5’-carbon sugar

Nitrogenous base bonded to 1’-carbon sugar

Where are phosphate binded to in nucleotides?

5’carbon

Which is larger purines or pyramindines?

Purines

What are phosphodiester linkages?

3’ and 5’ carbons of nucleotides are joined by this bond.

Where are new nucleotides added?

3’ side. attach to unlinked 3’ carbon

Which nitrogenous bases bond? What kind of bond holds them together in the double helix?

Purine - pyramidine bonds

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A hydrogen bond is used to hold nitrogen bases together

Is DNA a reactive moleucle? why is this important?

DNA is a very inert and non-reactive molecule as this protects our genetic material and information safe.

Describe the Double Helix configuration: Describe the grooves

* DNA is made of two antiparallel strands held together by hydrogen bonds between the bases
* Purine bases can only pair with pyrimidine bases, and \n more specifically, guanine (G) with cytosine (C), and adenine (A) with thymine (T).
* G-C forms three hydrogen bonds, and is therefore more stable than A-T, which forms two hydrogen bonds.

What are the major and minor grooves in the sugar phosphate backbone? Why are these important?

In the major groove, the two sugar-phosphate backbones are more widely spaced allowing DNA-binding proteins to recognize the bases in the interior.

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This is very important for transcription factors, restriction enzymes etc. **which recognize a unique DNA sequence.**

What is special about RNA? How does it work?

It can catalyze chemical reactions as it can fold into complicated structures that are similar to enzymes and proteins.

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This is because the nucleotide bases in the same strand can bond together (this cant happen in DNA) and thus more folding can occur.

What is the stem loop structure?

mRNAs carry them, they help regulate the mRNA.

What are the two main sections of metabolism?

**Anabolic:** Linking simple molecules to make them more complex. These are energy storing and require energy input.

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**Catabolic:** Break down complex molecules into simpler ones. This releases energy.

Do cells always need to acquire energy from environemnt?

yes

What drives energy conversions?

It is NOT the energy content as,

**First Law of Thermodynamics:**

During any conversion of energy, the total initial energy equals the total final energy

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But it is the tendency of energy to become evenly distributed or dispersed over time.

What is the second law of thermodynamics? How is it significant chemical reactions.

Energy spontaneously disperses from being localized to becoming spread out (entropy increases).

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chemical reactions only occur if energy disperses in the universe. **The dispersing energy is the driving force for energy conversions.** energy trasnformations always result in a higher probability (more disordered).

What is Free energy?

the amount of energy released to drive a reaction.

What are the 2 ways a cell can release free energy (drive a reaction)?

1. with a chemical reaction creating disorder in the cell (e.g. digesting a polymer). This is a change in entropy in a closed system, called Δ S. Note, Δ S does not refer to the overall change of entropy in the entire universe.
2. with a chemical reaction releasing heat (enthalpy = Δ H ), which generates disorder/disperses energy in the surrounding environment. In this case, the entropy outside the closed system increases

What are the 4 types of reactions!

1. Heat is released (negative Δ H ) and disorder is increased (positive T ΔS): this reaction is always spontaneous (exergonic), because Δ G is always negative: −Δ H −(T Δ S).
2. Heat is released (negative Δ H ), but disorder decreases (negative T ΔS): −Δ H − ( −T Δ S ) =− Δ H+ T Δ S For example, in protein folding, heat is released, because favorable ionic bonds and other side-chain interactions occur, but the disorder decreases, because you get a nicely folded protein; because S depends on temperature, this process occurs only below a certain temperature; above a certain temperature, T ΔS becomes bigger than \\n Δ H , and the overall Δ G positive, therefore no protein folding above, say 50 degrees
3. Heat is used (positive Δ H ), but disorder increases (positive T ΔS): + Δ H−(+ T Δ S) spontaneous above a certain temperature, e.g. dissolving NaCl in water. You can try this experiment at home: simply \n dissolve two teaspoons of salt in a glass of water: Heat is sucked away from the environment, that’s why the glass gets cold; heat is needed to break the strong crystal bonds; it’s the generation of disorder that drives the reaction
4. Heat is used and disorder decreases: never spontaneous (endergonic): + Δ H−(−T Δ S). Therefore, anabolic reactions can ONLY occur by coupling them to exergonic reactions to make the overall Δ G negative!

What happens at chemical equillibrium?

The rates of the forward and reverse reactions take place at the same rate therfore delta G =0

is delta G constant in a reaction

NO, it changes as the reaction proceeds.

How is energy stored in a cell?

ATP, ATP hydrolysis is an exergonic process which is used to drive endergonic reactions such as making a polymer.

Why are there different delta G values for ATP hydrolysis inside and out of the cell?

Because there is a huge concentration difference between ATP and ADP.

Why is ATP so useful?

because its delta G is intermediate between what you gain in respiration and what you expend in anabolism

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ATP is an intermediate between catabolism and anabolism because the energy of catabolic reactions is used to drive anabolic reactions and the energy used for chemical reactions is stored in ATP.

What can delta G predict?

the direction of a reaction can be predicted, but not the rate of the reaction.

What is the activation energy?

In a chemical reaction, Ea is the energy needed to put the molecules into a transition state.

What is a catalyst?

any substance that speeds up a chemical reaction without being used up

What can enzymes/catalysts only work on?

exergonic reactions. DELTA G DOES NOT CHANGE

Describe the model of enzyme action?

1. substate Initiation: reactants bind to the active in a specific orientation, creating the complex
2. Transition state facilitation: interactions between the substrate and enzyme lower the Ea. (enzyme shape is changed)
3. Termination: Products have lower affinity for active site and are released. Enzyme goes back to original orientation.

What are the 3 main ways enzymes lower Ea of reactions?

\*\*The charged environment is a good example of why pH is so important, a diff pH would change the charge of the environment and alter the shape of the enzyme.

What are cofactors?

small organic or metal ions that are not amino acids are associated more less tightly with the enzyme

What is a saturated system (enzymes)?

When all the active sites are occupied. A further increase in substrate wouldnt result in an increase in rate. This is the maximum speed. This varies from enzyme to enzyme

What are the 2 types of enzyme inhibition?

**Competitive:** Enzymes can be regulated competitively, with the regulator binding the active site.

**Allosteric:** The regulator binding somewhere else on the enzyme (allosteric = other site)

Why is allosteric inhibition more efficient?

Less inhibitor molecules are required (you need more competitor molecules than substrate molecules \n for effective competitive inhibition, but you only need more allosteric regulators than enzymes, because nothing else binds at the allosteric site).

What is the formula for carbohydrates?

CnH2nOn

What are Optical Isomers?

a group is attached in different ways to the same carbon atom. The optical isomer is the mirror image of the first molecule. THESE ARE STILL NOT THE SAME MOLECULE, THE COVALENT BONDS ARE DIFFERENT

Give an example of an optical isomer?

Glucose and galactose

What is the structure of glucose?

In solution, straight-chain glucose forms another covalent bond to become the ring form of glucose. Because this converts C-1 from a symmetric to an asymmetric carbon atom (C-1 in the ring form has four different groups \n attached to it, versus 3 in the straight chain form), you can get two glucose Isomers, alpha- and beta- glucose.

How are polysaccarides held together? Explain Maltose, starch and cellobiose and cellulose form.

Glycosidic linkages:

* these occur between the C-1 of one sugar with an OH group of the second sugar
* alpha 1,4 linkages create maltose and eventually starch
* Beta 1,4 linkages gives rise to cellobiose which becomes cellulose

Explain how maltose and eventually Starch is formed. What is the orientation of the CH2OH groups?

alpha 1,4 glycosidic linkage creates maltose

Multiple 1,4 linkages in a row becomes Starch

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CH2OH groups are all on the same side, bending the polymer resulting in a spiral shape.

Explain how Cellobiose is formed

* Beta 1,4 glycosidic linkages
* multiple of these linkages creates cellulose
* The second glucose group is flipped and thus the CH2OH groups are on opposite sides making a very symmetrical and straight molecule.

Explain the difference in structures between starch glycogen and cellulose?

Cellulose:

* Parallel strands joined by hydrogen bonds.

Glycogen:

* Highly branched Helices

Starch:

* Amylose: unbranched helices
* Amylopectin: branched helices

What is the one thing all lipids have in common?

They are insoluble in water

What is the structure of fats and oils?

three fatty acid bonded to a glycerol connected by covalent bonds.

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They are ampiphillic, carboxyl is polar and non-polar is tails

What are some of the essential roles of lipids?

* energy storage (fats and oils)
* cell membranes (phospholipids)
* Capture of light (carotinoids)
* Hormones steroids and vitamins
* electrical insulation of nerves

What holds the glycerol and fatty acids together in fats?

Ester linkages:

* form via condesation reactions
* 3 fatty acids to one glycerol

What is the structure of phospholipids?

What are unsaturated and saturated fatty acids? How does this relate to boiling points, cell membranes and fish?

Double bonds:

* some of them cause kinks in the chain, therefore they cannot be packed as closely together as saturated fatty acids.
* This is why butter is solid at room temp (only straight tailed fatty acids)
* And why oils are liquid.
* unsaturated fatty acids in lipid bilayers increase fluidity and permeability of the membrane.
* Fish and plants adjust the amount of double bonds in phospholipids to keep membrane fluidity stable over a wide variety of temperatures.

What is the delta G of the membrane assembly?

Negative enthalpy and free energy. Thus making it a self-assembling process.

How are integral proteins inserted into the membrane? How do they move?

* inserted by means of 1 or more alpha helices. However this only works if all amino acids making up the alpha-helix are hydrophobic as their side chains are pointing outwards interacting with the lipids. (Hydrogen bonds are along the length of the alpha helix.
* They only move laterally. Cannot move vertically

What is freeze fracture? Why is it used?

Splits membranes into two lipid leaflets.

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freezing tightly binds phospholipids to surrounding water molecues by hydrogen bonds, whereas the two leaflets are only held together by van der waals

What is the function of membranes?

* serve as a barrier and to selectively transport molecules the cell needs or wants to get rid of.

What can enter and not enter the cell membrane on their own?

CAN:

* gases like oxygen and small polar molecules like water

CANT:

Large charged molecules and ions not at all

What is diffusion?

the passive mixing of substances resulting in net transport along the concentration gradient.

How do individual molecules move through membranes?

Brownian motion!!! Random walk and proportional to the square root of time.