Princeton MCAT Biology Review

What does the structure of an amino acid contain?

**pg41

• Alpha amino group (NH2)

• Alpha carboxyl group (COOH)

• Variable R Group [side chain]

• Tetrahedral carbon with H attached

What type of bond is a peptide bond?

How is a peptide bond formed between two amino acids? (2 things)

**pg42

Covalent bond

1)• Formed between a-carboxyl group of one amino acid and the a-amino group of another amino acid.

2)• Water is lost in the formation process

In the oligopeptide Phe-Glu-Gly-Ser-Ala, which residue has a free a-amino group, and which residue has a free a-carboxyl group?

Phenylalanine has a free amino group and Alanine has a free carboxyl group because all the other amino acids are hitched together in peptide bonds

What is proteolysis/ proteolytic cleavage?

What is the protein involved?

Hydrolysis of a protein (The chemical breakdown of the protein due to a reaction with water)..... A specific means of cleaving peptide bonds (cleaving the peptide bond adjacent to a specific amino acid)

Protein involved is a proteolytic enzyme or protease

What type of bond is a disulfide bridge?

What does it connect?

Can it connect between two different polypeptide chains?

How/ why does this happen?

**pg43

Covalent bond

Connects two cysteine groups

Yes

Cysteine has a reactive thiol group (SH) in its side chain

What is cysteine called once the residues become disulfide-bonded together?

Cystine

What is denaturation and what compound is used to denature?

By what extreme processes does denaturation occur

Denaturation is disruption of the protein's shape using urea to break the hydrogen bonds without breaking the peptide bonds.

Urea disrupts the hydrogen bonding by pH, temperature, and tonicity extremes (changes in salt concentration)

Describe the primary structure of a protein and name the bond that characterizes it

A linear amino acid sequence that is characterized by the peptide bond

Describe the secondary structure of a protein and name the bond that characterizes it

Hydrogen bonding between the backbone NH and CO groups that folds the polypeptide chain

What are the common shapes for a secondary structure of a protein?

alpha helix and beta pleated sheets

What are the two types of beta pleated sheets? List and describe

Parallel - Strands run in the same direction

Anti-parallel - Strands run in opposite directions

Describe the tertiary structure of a protein and list the two interactions that are happening

R-groups interact with each other

R-groups interact with water

Folding into globular proteins happens

If a single polypeptide folds once and forms a beta-pleated sheet with itself, would this be a parallel or antiparallel beta-pleated sheet?

It would be antiparallel because on participant in the beta-pleated sheet would have a C to N direction, while the other would be running N to C

Which of the following may be considered an example of tertiary protein structure?

I. van der Waals interactions between two Phe R-groups located far apart on a polypeptide

II. Hydrogen bonds between backbone amino and carboxyl groups

III. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide

I. because of interactions between R-groups

CAN BE III. because disulfide bridges between two cysteine R-groups is still an interaction between two R-groups

NOT II. because hydrogen bonds are made during secondary structure

What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?

Quaternary means are bonds that form between chains that aren't linked by peptide bonds

Tertiary disulfides are bonds that form between residues in the same polypeptide

Describe the quaternary structure and name the four ways of interaction that it can have

Interactions between polypeptide subunits

1. van der Waals forces

2. Hydrogen bonds

3. Disulfide bonds

4. Electrostatic interactions

What is the term for a single polypeptide chain that's part of a larger complex

Subunit

What is the principle energy source for cellular metabolism ?

Carbohydrates

What is oxidation?

The process that breaks carbohydrates down into carbon dioxide

What is a monosaccharide?

What is another name for it?

What is the general chemical formula?

A single carbohydrate molecule

simple sugar

CnH2nOn

What are five metabolically important monosaccharides?

What do they look like?

**pg47

1. Fructose

2. Glucose

3. Ribose

4. Deoxyribose

5. Galactose

**see pg 47 for illustrations

What is a glycosidic linkage?

A covalent bond between two sugar molecules that is formed during a dehydration reaction

What is a disaccharide?

What are three common disaccharides?

Two monosaccharides joined with a glycosidic linkage

1. maltose

2. sucrose

3. lactose

What type of glycosidic linkage can mammals digest?

And what type can they generally not digest?

alpha glycosidic linkages

beta glycosidic linkages

What two sugar molecules make up sucrose?

What does it look like?

**pg47

Glucose and fructose

What two sugar molecules make up lactose?

What does it look like?

**pg47

Glucose and galactose

What are the three physiological roles of lipids?

1. triglycerides (fats) store energy in adipose cells

2. phospholipids form a barrier between the intracellular and extracellular environments in cellular membranes

3. Cholesterol is a building block for hydrophobic steroid hormones

What are some characteristics of lipids?

Hydrophobic

lipophilic

non-polar

What is a fatty acid?

How long is a typical chain?

How many carbons are synthesized at a time and from what?

Fatty acids made in human cells are ______ numbered

Long unsubstituted alkanes that end in COOH

14-18 carbons long

2 carbons are synthesized at one time from acetate

even-numbered

What is a saturated fatty acid

Does not contain a double bond

What is an unsaturated fatty acid and what is the formation of its bonds typically in?

Contains one or more double bonds and are almost always in Z or cis formation.

How does the shape of an unsaturated fatty acid differ from that of a saturated fatty acid?

An unsaturated fatty acid is bent or kinked at the cis double bond

If fatty acids are mixed into water, how are they likely to associate with each other?

The fatty acids will form lipid droplets when mixed with water.

Specifically, the long hydrophobic chains will minimize contact with water and will thus expose the carboxyl groups to the aqueous environment

What happens during micelle formation and what causes it?

hydrophobic interaction is the force that drives the tails into the center of the micelle when free fatty acids interact with an aqueous solution

What is another name of triacylglycerol?

What is the purpose of this molecule?

Triglyceride

The storage form of the fatty acid

How is a triacylglycerol formed?

Three fatty acids are esterified to a glycerol molecule

What is a glycerol and what is its formula?

What is its purpose?

a 3-carbon triol with the formula of OHCH2--CHOH--CH2OH

contains 3 hydroxyl groups that can be esterified to fatty acids

What is esterification and how does it pertain to triacylglycerols?

The reaction of an alcohol with an acid to produce an ester and water

The alcohol is the glycerol and the acid is the fatty acid R group that is being attached

What is a lipase?

An enzyme that hydrolyzes fats

What is more efficient in storing energy molecules? Fats or carbohydrates? and Why? Be specific about the reasons why.

Fats

Packing: their hydrophobicity allows fats to pack together much closer than carbohydrates because carbohydrates carry a great amount of water-of-solvation, meaning water molecules hydrogen bonded to their hydroxyl groups

Energy content: No matter what you dissolve it in, fat has more energy carbon-for-carbon than a carbohydrate.

What stabilizes the lipid bilayer membrane?

van der Waals forces

Would a saturated or unsaturated fatty acid residue have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?

Saturated fatty acids. (make the membrane more solid)

Unsaturated fatty acids have a bent shape that prevents as much contact with neighboring groups to form van der Waals interactions

What are the structural determinants of fluidity and how does each one affect fluidity?

Degree of saturation: the more saturated, the less fluid

Tail Length: the longer the tail, the less fluid

Amount of cholesterol present: low temperatures, more fluid

high temperatures, less fluid

What is a terpene?

What is its general formula?

Simple hydrocarbon that is a member of a broad class of compounds built from isoprene units. Can be linear or cyclic.

(C5H8)n

What is the formula for an isoprene unit and what kind of bond does it contain?

C5H8

Contains a double bond

What is the name of the terpene that contains 2 isoprene units?

3?

4?

6?

Monoterpene

Sesquiterpene

diterpene

triterpene

What do all steroids have in common and what is it based on?

All steroids have the basic tetracyclic ring system based on the structure of cholesterol

**structure on pg 53

What are terpenoids?

Functionalized terpenes that are functionalized with other elements such as O, N, S, etc.

What are two common types of steroid hormones?

Testosterone = androgen/ male sex hormone

Estradiol = estrogen/ female sex hormone

What is a nucleotide? Be specific.

Nucleotides are the building blocks of nucleic acids (RNA and DNA)

1 nucleotide is made up of:

1) a ribose or deoxyribose sugar group

2) a purine or a pyrimidine

3) one, two, or three phosphate units attached to carbon five of the sugar ring

What does ATP stand for and what is it?

What types of organisms does it apply to?

Adenine triphosphate

Universal short-term energy storage

Plays a central role in cellular metabolism

RNA precursor

Energy stored in their phosphoanhydride bonds can later be used to process cellular processes as well as synthesizing glucose or fats (long-term energy storage)

Applies from bacteria to humans. Some viruses may carry ATP but can't make their own

* Freestanding Practice Question*

Why is ATP known as a "high energy" structure at neutral pH?

A) It exhibits a large decrease in free energy when it undergoes hydrolytic reactions

B) The phosphate ion released from ATP hydrolysis is very reactive

C) It causes cellular processes to proceed at faster rates

D) Adenine is the best energy storage molecule of all the nitrogenous bases.

A) bc it directly addresses the energetics of ATP hydrolysis

--------------------------

B) can be eliminated (CBE) because it describes the reactivity of the released phosphate and not the structure of ATP

C) CBE bc describes the rate of cellular processes and not the energy of ATP

D) CBE bc the structure of adenine is not related to why ATP is a good energy storage molecule

* Freestanding Practice Question*

Which of the following best describes the secondary structure of a protein?

A) Various folded polypeptide chains joining together to form a larger unit

B) The amino acid sequence of the chain

C) The polypeptide chain folding upon itself due to hydrophobic/ hydrophilic interactions

D) Peptide bonds hydrogen-bonding to one another to create a sheet-like structure

D) bc initial folding of the polypeptide chain into alpha helices or beta pleated sheets

------------------------

A) CBE bc it describes quaternary protein formation

B) CBE bc it describes primary protein structure

C) CBE bc it describes tertiary protein structure

* Freestanding Practice Question*

Phenylketonuria (PKU) is an autosomal recessive disorder that results from a deficiency of the enzyme phenylalanine hydroxylase. This enzyme normally converts phenylalanine into tyrosine. PKU results in intellectual disability, growth retardation, fair skin, eczema and a distinct musty body odor. Which of the following is most likely true?

A) Treatment should include a decrease in tyrosine in the diet

B) The musty body oder is likely caused by a disorder in aromatic amino acid metabolism

C) Patients with PKU should increase the amount of phenylalanine in their diet

D) PKU can be acquired by consuming too much aspartame (an artificial sweetener that contains high levels of phenylalanine)

B) it is true that phenylalanine and its derivatives are aromatic amino acids and that the high levels of these compounds lead to the distinct musty body odor

Process of Elimination (POE) is best for this question

--------------------------

A) CBE bc patients with PKU should increase tyrosine in their diet, not decrease

C) CBE bc patients with PKU should decrease phenylalanine in their diet, not increase

D) CBE bc PKU is an autosomal recessive disorder that can not be ACQUIRED by consuming too much phenylalanine

* Freestanding Practice Question*

A genetic regulator is found to contain a lysine residue that is important for its binding to DNA. If a mutation were to occur such that a different amino acid replaces the lysine at that location, which of the following resulting amino acids would likely be the least harmful to its ability to bind DNA?

A) Glycine

B) Glutamate

C) Aspartate

D) Arginine

D) because it is basic

-----------------------

Basic: Histidine, arginine, and lysine

Acidic: Glutamate and aspartate

Neutral: Glycine

B & C) CBE bc they are acidic and will cause the most harm to its ability to bind DNA

A) CBE bc it is a neutral amino acid

* Freestanding Practice Question*

Increasing the amount of cholesterol in a plasma membrane would lead to an increase in:

A) membrane permeability

B) Atherosclerotic plaques

C) Membrane fluidity at low temperatures but a decrease in membrane fluidity at high temperatures

D) Membrane fluidity at high and low temperatures

C) because cholesterol at low temperatures increases fluidity and cholesterol at high temperatures decreases fluidity

ring structure at low temperatures prevents packing and increases fluidity

OH group on cholesterol prevents phospholipid dispersion at high temperatures and decreases fluidity

--------------------------

A) CBE bc cholesterol fills the "holes" between the fatty acid tails and decreases membrane permeability, not increase

B) Atherosclerotic plaques relates to high levels of blood cholesterol, not membrane cholesterol

D) CBE bc temperature affects fluidity in the presence of cholesterol

* Freestanding Practice Question*

A human space explorer crash-lands on a planet where the native inhabitants are entirely unable to digest glycogen, but are able to digest cellulose. Consequently, they make their clothing out of glycogen-based material. The starving space explorer eats one of the native inhabitants' shirts and the natives are amazed. Based on this information, which of the following is/are true?

I. The explorer can digest alpha-glycosidic linkages

II. The native inhabitants can digest alpha-glycosidic linkages

III. The native inhabitants can digest starch.

A) I only

B) I and III only

C) II and III only

D) I, II, and III

A) because glycogen (and starch) are alpha-glycosidic linkages

which nitrogenous bases are the purines? the pyramidines?

purines: A and G

pyramidines: C, U, T (you CUT the Py)

nucleoside vs nucleotide

A nucleoside consists of a nitrogenous base (purine or pyrimidine) and a five-carbon sugar (ribose or deoxyribose), while a nucleotide contains a nitrogenous base, a five-carbon sugar, and one or more phosphate groups

nucleotides in the DNA chain are covalently linked by what? where does this bond form?

phosphodiester bonds

-form btw the 3’ hydroxy group of one deoxyribose and the 5’ phosphate group of the next deoxyribose

in what orientation are DNA strands bonded?

antiparallel

what are the nitrogenous base pairs? what type of bond do they have?

A binds to T and G binds to C

-hydrogen bonds

-notice the pairs are always a purine and pyramidine

how many hydrogen bonds hold each pair of nitrogenous bases?

A/T have 2 H bonds

G/C have 3 H bonds

annealing/hybridization of DNA strands

the binding of complementary strands of DNA into a double-stranded structure

genome

the sum total of an organism’s genetic info

chromosome

a structure of protein and DNA

what are prokaryotic genes composed of?

a single circular chromosome

DNA gyrase

used in prokaryotes to twist the circular chromosome to make it more compact, called a supercoil

how is eukaryotic DNA packaged?

the DNA strand is wrapped around globular proteins called histone (called nucleosomes)

chromatin

fully packaged DNA composed of closely stacked nucleosomes

heterochromatin

dense areas of chromatin, rich in repeats

euchromatin

less dense areas of chromatin, higher transcription rates bc it is not as dense as heterochromatin

centromere

structure near the middle of eukaryotic chromosomes to which the fibers of the mitotic spindles attach during cell division

kinetochores

multiprotein complexes that act as anchor attachment sites for spindle fibers

which type of chromatin (hetero or eu) are centromeres composes of?

heterochromatin

telomeres

the ends of linear chromosomes; function to prevent chromosome deterioration and prevent fusion with neighboring chromosomes

intergenic regions

p72

regions composed of non-conding DNA. tandem repeats and transposons are major components

single nucleotide polymorphisms

a single nucleotide change every 1,000 base pairs. occur most frequently in noncoding regions

tandem repeats

short sequences of nucleotides repeated one right after the other

transcription

DNA → RNA

translation

RNA → protein

codon

3 nucleotides that code for a particular AA

what replaces thymine in RNA?

uracil

what are the 3 stop codons (also called nonsense codons)?

UAA, UAG, UGA

what does semiconservative mean in terms of DNA replication?

after replication, one strand of the new double helix is parental and one strand is newly synthesized daughter DNA

what enzyme unwinds DNA for replication?

helicase

where does helicase begin unwinding DNA?

the origin of replication (ORI)

topoisomerase

cut one or both of the DNA strands and unwrap the helix, releasing the excess tension created by the helicases

single-strand binding proteins (SSBPs)

protect DNA that has been unpackaged in prep for replication and help keep the strands separated

what enzyme creates the RNA primer and why is a primer necessary?

-primase

-necessary bc DNA polymerase cannot start a new DNA chain from scratch

DNA polymerase

catalyzes the elongation of the daughter strand using the parental template, and elongates the primer by adding dNTPs to its 3’ end

in what direction does polymerization occur?

5’ to 3’, so the polymer is always added to the 3’ end

replication fork

the region where the helix continues to unwind

leading strand

elongate continuously into the widening replication fork

what is the lagging strand and what is it composed of?

the strand that must wait until the replication fork widens before beginning to polymerize (polymerizes in a discontinuous fashion); composed of Okazaki fragments

what enzyme joins Okazaki fragments?

DNA ligase

how many types of polymerase do prokaryotes have?

5 (I-V)

DNA pol III

responsible for the super-fast, super-accurate elongation of the leading strand

-5’ to 3’ polymerase activity and 3’ to 5’ exonuclease activity (when enzyme moves backwards to cut off the nucleotide it just added in the case that it was incorrect). this ability to correct mistakes is called proofreading function

DNA pol I

adds nucleotides at the RNA primer

poor processivity, so DNA pol III takes over after about 400 bps downstream from the ORI

capable of exonuclease activity

removes the RNA primer and replaced it with DNA

important for excision repair

Hayflick limit

the number of times a normal human cell can replicate before the telomere length stops cell division (it gets shorter with each replication)