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A certain genetic engineering experiment requires a lab worker to inject a segment of DNA into the nucleus of a living cell. To access the nuclear lumen, the microscopic needle must pierce a minimum of how many layers of lipid membrane?

A) 2
B) 3
C) 4
D) 6

The nucleus is surrounded by a DUAL bi- layer lipid membrane. The outer of those two membranes is continuous with the ER. To enter the nuclear lumen, the needle must pass thru the cell membrane (2), plus the outer nuclear membrane (2), plus the inner nuclear membrane (2), for a total of six single layers of lipids. Answer D is thus correct.

A karyotype is somewhat like a photographic list of all of the chromosomes found in a cell. If homologous pairs are present, they appear next to one another on the exposed film. all of the chromosomes for the entire cell are presented on the same slide, making differences in the relative length, size and orientation of the chromosomes readily apparent. If a karyotype were produced for a cell that had just undergone Telophase I of Meiosis, the entire karyotype slide should contain:

A) 23 pairs of homologous chromosomes, all of similar size
B) 46 chromosomes, increasing in size from 1 to 23
C) 92 chromosomes, decreasing in size from 1 to 92
D) 23 chromosomes, decreasing in size

D
Meiosis I takes a cell with 23 pairs of homologous chromosomes, or 46 total chromosomes, and creates two cells each with 23 non-paired, non-homologous chromosomes. You should also know that chromosomes generally decrease i size, with chromosome One being by far the largest. Thus answer D is the best answer.

If a student has four amino acids, Glycine, Phenylalanine, Glutamine, and Aspartamine, how many unique proteins can he form without using any amino acid more than once in any protein?

A) 8
B) 16
C) 24
D) 256

Solution: the safest way to approach this question is to write out all of the chains you can create starting with one of the four amino acids. This is the more conceptual approach. For example, starting with Gly you could form: Gly-Phe-Glu-Asp, Gly-Phe-Asp-Glu, Gly-Glu-Phe-Asp, Gly-Glu-Asp-Phe, Gly-Asp-Glu-Phe, and Gly-Asp-Phe-Glu. That is six unique chains by starting with Gly. This could be done once for each of the four amino acids, so there are 6 times 4, or 24 possible proteins. Answer C is thus correct. using n! (n factorial) will also work in this case, only because each item can only be used once. the n represents the number of items and the math becomes: 4x3x2x1=24. Be careful, however, using the factorial method. We have seen many students who rely on this method use it when each item could be used more than once--in which case it gives an incorrect answer. Had thsi question allowed you to use each item multiple times (proteins such as Gly-Gly-Gly-Gly, and Phe-Phe-Phe-Phe would have been possible), you could obtain the answer using x^y where x is the number of slots, and y is the number of values possible for each slots. This only works, however , if any slot can use any of the available values (i.e., license plates). It is also pertinent to this question to remember that proteins are not reversible. In other words, A-B-C is not the same as C-B-A because in the first case A is the N-terminus and in the second case A is the C-terminus. This would also be true of combinations of nucleotides, where one side would be 5' and the other 3'

To find the possible total of combinations for something where you can only use an option once, what method should you use?

use the factorial method. n=number of items. 4 items would be 4x3x2x1= 24

To calculate the possible total of combinations for something where you can use an option as many times as you want use:

x^y where x is the number of slots, and y is the number of values possible for each slot. so for examples if you have 4 amino acids that means it would be 4⁴=256

Based on their interaction in the Electron Transport Chain, it can be said of Complex III and Cytochrome C that:
A) Complex III has a hgiher oxidation potential than Cytochrome C because Complex III gets reduced.
B) Complex III has a higher reduction potential than Cytochrome C because Complex III gets reduced.
C) Cytochrome C has a higher reduction potential than Complex III because Cytochrome C gets reduced.
D) Cytochrome C has a higher oxidation potential than Complex III because Cytochrome C gets reduced.

This is a classic MCAT-style question. The answer choices look complex, but properly and calmly analyzed it is not that difficult. First, you should know that Complex III passes an electron to Cytochrome C, meaning Complex III is oxidized and Cytochrome C is reduced. this makes A and B impossible. Answer D is incorrect because if Cytochrome C had a higher oxidation potential than Complex III it would tend to give up an electron to Complex III rather than accept it.

Answer C is correct.

Where can DNA in the cell be found?

nucleus and mitochondria

what kind of membrane surrounds the nucleus?

the nucleus is surrounded by a dual bi-layer membrane continuous with the ER; it contains nuclear pores.

nucleolus

site of rRNA transcription and ribosome assembly (found inside the nucleus)

Rough ER

covered with ribosomes; all proteins not bound for the cytosol are made here

Smooth ER

lipid synthesis/modification (but NOT lipid metabolism; many students get this confused.

Golgi Apparatus

the cellular "post-office"; organize, package, modify, excrete, etc.

Know the structure of a mitochondrion and be able to draw and label one.

Mitochondria have their own DNA and variations to the nuclear genetic code. What line are mitochondrial genes passed down through?

the maternal line ONLY.

Theory suggest that mitochondria evolved from?

Theory suggests that mitochondria evolved from aerobic prokaryotes in symbiosis with a eukaryotic cell.

How do the pH values of the matrix and the intermembrane space in the mitochondria compare?

The intermembrane tends to have a low pH compared to the matrix because of the proton gradient which results when protons are pumped into the intermembrane space from the matrix during electron transport.

The mitochrondrial matrix has a pH of about 7.8

An MCAT favorite is to suggest a disease or condition that interrupts the gradient across the inner mitochondrial membrane. Predict as many consequences as you can think of for the insertion of hydrogen channels within either of the two mitochondrial membranes.

Myopathy, diabetes, diseases with the stomach pH.

Centrioles/ Centrosome

The centrosome is an amorphous area of proteins and nucleating fibers within which the centrioles are located.

Centrosomes are composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein

It organizes microtubules, flagella and cilia; it also plays a key role in cell division.

Lysosomes
function?
pH?

pH of 5, digest cell parts, fuse with phagocytotic vesicles, participate in cell death (apoptosis), etc.; lysosomes form by budding off from the Golgi.

Peroxisomes

self-replicate, detoxify chemicals, participate in lipid metabolism.

Microtubules vs. Microfilaments

Microtubules: play roles in cells structure; provide a platform for intracellular transport, forming the mitotic spindle, etc.

Microfilaments: thinnest filaments of the cytoskeleton; found in the cytoplasm in eukaryotic cells. Roles in structure and motility.

Tubulin:

protein that makes up microtubules

Cytoskeleton

internal framework of a cell composed of protein filaments and microtubules in the cytoplasm.

Has a role in controlling the shape, intracellular organization, and movement of a cell.

Spindle Apparatus

a network of filaments that collectively form a mitotic spindle (mitosis) and a meiotic spindle (meiosis). Chiefly involved with segregating chromosomes in nuclear division.

Actin

(thin filaments): filamentous protein involved in muscle contraction; main constituent in thin filaments

Myosin

(thick filaments): motor proteins that have a role in muscle contraction; responsible for actin base motility.

Is myosin a microfilament?

No, but myosin interacts with microfilaments to produce muscle contraction and movement. It is a motor protein

Flagella vs. Cilia

Flagella: Long, whip-like protrusion that drives a cell through a fluid medium by its beating. Eukaryotic flagella are longer versions of cilia.
• Function more for moving a cell

Cilia: Hair-like extension on the surface of a cell with a core bundle of microtubules and capable of performing repeated beating movements. Cilia in large numbers, drive the movement of fluid over epithelial sheets, as in the lungs.
• More for sweeping fluid, etc. along

In humans, cilia are found exclusively in the__________.

• Respiratory System (lungs)
• Nervous System (ependymal cells)
• Reproductive System (fallopian tubes)

Microtubules are found in
A) Respiratory System (lungs)
B) Nervous System (ependymal cells)
C) Reproductive System (fallopian tubes)
D) All of the above

D
Microtubules are found in all the places listed (because cilia contain them), in the flagella of sperm, and in all cells as part of the spindle apparatus.

What problems would a disease that prevented microtubule production cause?

Cystic fibrosis, infertility

Eukaryotic vs. Prokaryotic Flagella

Eukaryotic = whipping motion; microtubules made of tubulin

Prokaryotic = spinning/rotating motion; simple helices made of flagellin

Cellular Junctions

o Tight Junctions: water-proof barriers
o Gap Junctions: tunnels allowing exchange
o Desmosomes: strongest of the cellular junctions; they weld cells together, protecting against stress, but are NOT water tight barriers.

Provide examples of where each cellular junction is utilized in the human body

• Tight Junctions: Internal epithelial, acts as a barrier that prevents movement of material between cells. Holds cells together.
• Gap Junctions: directly connects the cytoplasm of two cells. Allow heart cells to communicate. Important in heart muscle, Neurons, retina
• Desmosomes: Found in simple and stratified squamous epithelium; also found in muscle tissue where they bind muscles cells to one another.

Phospholipids

class of lipids that are a major component of all cell membranes as they can form lipid bilayers.

Structure consists of hydrophobic tails and a hydrophilic head.

Usually found with cholesterol molecules which are found in-between the spaces of the phospholipid.
o Phospholipid synthesis occurs in the ER

phospholipids only have a phosphoester bond, NOT a phosphodiester bond (as found in DNA).

Integral proteins

A protein molecule or protein assembly permanently attached in biological membrane. Its hydrophobic component interacts with phospholipids

Transport proteins

protein that serves the function of moving other materials within an organism.

o Ex membrane transport protein transports materials across a cell membrane

Cholesterol

fatlike steroid alcohol. Found in animal fats and oils. Has a hydrophobic head and tail.

Required to build and maintain membranes; modulates fluidity over the range of physiological temperatures; through interaction with phospholipid fatty-acid chains, cholesterol increases membrane packing, which reduces membrane fluidity

Cholesterol does NOT have any role in ion transport.

Membrane receptors

specialized integral membrane proteins that take part in communication between the cell and the outside world. Signaling molecules attach to the receptor, triggering changes in the function of the cell (cell transduction)

Fluid mosaic model

a model that describes the structural features of biological membranes.
o According to the model, the plasma membrane is a lipid bilayer (interspersed with proteins). It is so because of its phospholipid component that can fold in itself creating a double layer - or bilayer - when placed in a polar surrounding, like water. This structural feature of the membrane is essential to its functions, such as cellular transport and cell recognition

Exocytosis

Process by which most molecules are secreted from a eukaryotic cell. These molecules are packaged in membrane-bounded vesicles that fuse with the plasma membrane releasing their contents to the outside.

hormones exported from the cell leave via exocytosis

Endocytosis

Uptake of material into a cell by an invagination of the plasma membrane.

Phagocytosis

The process by which particulate material is engulfed ("eaten") by a cell.

Pinocytosis

Type of endocytosis in which soluble materials are taken up from the environment and incorporated into vesicles for digestion (cell drinking).
o small particles are brought into the cell, forming an invagination, and then suspended within small vesicles (pinocytotic vesicles) that subsequently fuse with lysosomes to hydrolyze, or to break down, the particles. This process requires a lot of energy in the form of ATP.

"pinocytosis" is random and does not require a receptor.

Diffusion

passive movement of molecules or particles along a concentration gradient (High-> low concentration); does not require energy

Facilitated Diffusion

Transport of substances from an area of high concentration to low concentration with the help of a carrier molecule. Does not require energy.

Active Transport:

type of transport where molecules move against the concentration gradient (low -> high). Requires energy.

Secondary Active Transport

a form of active transport across a biological membrane in which a transporter protein couples the movement of an ion (typically Na+ or H+) down its electrochemical gradient to the uphill movement of another molecule or ion against a concentration/electrochemical gradient.
• Ex symports and antiports

Epithelial Tissue

line the cavities and surfaces of structures throughout the body, and also form many glands.

Functions: secretion, selective absorption, protection, transcellular transport, and detection of sensation.

Nervous Tissue

makes up the central nervous system, and the peripheral nervous system; main component of the nervous system- the brain, spinal cord, and nerves.

Muscle Tissue

tissue that makes up muscles; skeletal muscle, smooth muscle, cardiac muscle

What type of tissue is blood?

connective

What type of tissue is dermis?

Irregular connective tissues

What type are adipocytes?

Connective tissue

Tissue Organization

Organ Systems>Organs>Tissues>Cells

Intracellular Communication:
o Endocrine System?

slow, general, long-lasting

Intracellular Communication:
o Nervous System?

fast, specific, short-lived

Intracellular Communication:
o Paracrine System?

local mediator hormones only

What is the main purpose of Chromosomes?

o The major purpose of chromosomes is to efficiently package the very, very long DNA strands so they can easily be stored between divisions and moved during division.

Histones

highly alkaline proteins that package and order DNA into structural units called nucleosomes.

Nucleosomes

the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wrapped around in sequence 4 histone protein cores

Chromatin

combination of DNA and proteins; (unpackaged DNA)

Diploid

two sets of chromosomes; 2n=46

Haploid

one set of chromosomes; n = 23

Homologous

Homologous chromosomes carry the same genes, pair during meiosis I, and separate in the formation of gametes. We have 23 pairs of homologs

Where is DNA found in the cell?

Nucleus and mitochondria

Draw the cell cycle pie chart: Include G1, G2, G0, S and M phases.

Why is G0 significant?

G0 is the resting phase of the cell cycle. It is a period in the cycle in which cells exist as inactive. It is also a checkpoint in the G1 phase.

Which cells are frozen in G0?

Nerve, muscle, and heart muscle cells

For human beings, how many chromosomes are there?
Before Replication:
After Replication:
During interphase:
Before S-phase:
After S-phase:
In a diploid cell:
In a haploid cell:

Before Replication: 2n=46
After Replication: 2n=46
During interphase: 23
Before S-phase: 23
After S-phase: 46
In a diploid cell: 2n=46
In a haploid cell: n=23

Describe how the mass of DNA differs for each for each scenario:
Before Replication:
After Replication:
During interphase:
Before S-phase:
After S-phase:
In a diploid cell:
In a haploid cell:

So before and after replication DNA has about the same weight. Comparing Before and After S-phase, the weight of DNA is doubled, because in this phase DNA is replicated. In S phase chromosomes replicate and form 2 sister chromatids.

Prophase

Chromosomes coil, nuclear membrane breaks down, and spindle fibers form

Metaphase

Chromosomes line up on the midline and spindle fibers attach to the centromeres

Anaphase:

Centromeres divide, spindle fibers shorten, and sister chromatids separate and move to opposite poles of the cell

Telophase

Cell elongates, nuclear membrane reforms, chromosomes uncoil, and spindle fibers disappear

Cytokinesis

cells separate-division of the cytoplasm, cleave furrow forms at cell equator, constriction tightens by contraction filaments; and you now have 2 daughter cells

Spindle Apparatus

sub cellular structure that segregates chromosomes between daughter cell during cell division.

Centriole:

involved with organization of the mitotic spindle and in cytokinesis

Microtubules

made up of tubulin, grow out from centrioles and attach to cetromeres of chromosomes in metaphase. Allow for chromosomes to split etc.

Be able to identify each phase by the events occurring, by a picture, or by the number/types of chromosomes.

Mitosis yields?

two (2) genetically identical, diploid, daughter cells.

Gamete

a mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote.

Zygote

a diploid cell resulting from the fusion of two haploid gametes; a fertilized ovum

Know the stages of meiosis and what happens in each stage. Which stages are similar to mitosis and which stages are different?
What are the key differences between mitosis and meiosis?

Prophase I/II, Metaphase I/II, Anaphase I,II and Telophase I//II.
Meiosis II is similar to mitosis
Meiosis results in 4 gentically distinct haploid daughter cells.

Draw and describe a picture of Meiosis I

...

Draw and describe a picture of Meiosis II

...

Prophase I

o Chromosomes condense and Nuclear Membrane breaks down
o What unique event happens in Prophase I that does not happen in mitosis?

What unique event happens in Prophase I that does not happen in mitosis?

Homologs pair
Recombination (cross over) occurs

Metaphase I

Chromosome pairs line up on the midline (another unique event (in mitosis individual chromosomes lined up)

Anaphase I

o Centromeres DO NOT DIVIDE (compare to mitosis where they do)
o Chromosome pairs move to opposite poles (homologs separate)

Telophase I

o Cell elongates, nuclear membrane reforms and chromosomes uncoil

After cytokinesis I

o Two haploid cells are produced

Prophase II

o Chromosomes coil, spindle forms, nuclear membrane breaks down

o Each chromosome is composed of two sister chromatids attached at the centromere

Metaphase II

o Chromosomes line up on the midline and attach to spindle fibers

Anaphase II

o Centromeres divide and sister chromatids move to opposite poles

Telophase II

o Cell elongates, nuclear membrane reforms and chromosomes uncoil

After Cytokinesis II how many unique haploid cells are produced?

o 4 unique haploid daughter cells

What is nondisjunction and when can it occur?

Nondisjunction is the failure of chromosome pairs to separate in meiosis 1 and 2 specifically in anaphase.

What would be the ramifications of nondisjunction?

Trisomy in which the daughter cells have one extra chromosome, or monosomy in which the defected daughter cells with the defect have one missing chromosome.

When does crossing-over occur and why is it important? (Very frequent MCAT topic!)

Crossing -over occurs in Prophase I of Meiosis, and it is important because it creates more genetic variation and more independent selection between alleles. If there was no crossing-over, all genes would be inherited together.

Meiosis Yields?

four (4) genetically distinct, haploid, daughter cells!!

What % of a cell's mass is due to water?

About 70%

How does water bond?

Water forms hydrogen bonds due to the polarity that results from the covalent bond between H and O.

Water forms hydrogen bonds due to the polarity that results from the covalent bond between H and O.
Why is this significant?

Hydrogen bonds are the strongest bonds. They allows the molecule to be very stable. It is responsible for the high boiling point in water. Water's high boiling point is important because this allows our bodies to maintain our core temperature (homeostasis).

Explain the difference between hydrophobic and hydrophilic

Hydrophobic is water fearing; Hydrophilic is water loving.

Four Major Roles of Water in the Human Body

1) Solvent for all major reactions (solute is dissolved in the solvent)
2) Reactant for hydrolysis reactions (nearly all catabolic RXNs in the body)
3) Product of nearly all synthesis reactions (e.g. dehydration synthesis)
4) Maintenance of Homeostasis (due to its high specific heat; many reactions release heat that would cause other solvents to boil; water allows the body to absorb considerable heat from exothermic reactions without significant rise in temperature).

DEFINE A LIPID AS?

Any biomolecule soluble in non-polar solvents and insoluble in polar solvents.

What lipids should you be familiar with?
and which one is NOT amphipathic?

fatty acids, carbohydrates, triacylglycerols, cholesterol, phospholipids, steroids, glycolipids

triacylglycerol is NOT amphipathic

Fatty Acid

a carboxylic acid with a long aliphatic tail, which is either saturated or unsaturated.

Triacylglycerol

an ester derived from three glycerol and three fatty acids

Saturated vs. Unsaturated Fats
o Explain what they are and Which one is better for you and why?

A Saturated compound is a chemical compound that has a chain of carbon atoms linked together by single bonds and has hydrogen atoms filling all the other bonding orbitals of the carbon atoms.

An Unsaturated compound is a chemical compound that contains carbon-carbon double bonds or triple bonds.

• Unsaturated fats are better for you because they have been shown to lower blood LDL cholesterol levels and lessen your risk of cardiac disease.
• Because unsaturated fats have a kink in their tails created by double bonds, they are less likely to clump together. Saturated fats have only single bonds in their tails which makes it easier for them to clump together and clog arteries.

Phospholipids:

Made up of two fatty acids and a glycerol (for the hydrophobic tails), and a phosphate (for the hydrophilic head)

All steroids are _____ ringed structures.

All steroids are four ringed structures.

Glycolipids

lipids with a carbohydrate attached. Their role is to provide energy, and they also serve as markers for cell recognition.

What does amphipathic mean?

Part hydrophilic and hydrophobic

Draw the basic amino acid

What amino acids are non polar?

(9) NON-POLAR:
Pro, Gly, Ala, Val, Leu, Ile, Met, Trp, Phe,


Alanine, cysteine, Glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, valine

Which amino acids are polar?

(11) POLAR:
Arg, Asn, Asp, Cys, Gln, Glu, His, Lys, Ser, Thr, Tyr

Arginine, Asparagine, Aspartic Acid, glutamic acid, glutamine, histidine, lysine, serine, threonine, tyrosine

Which amino acids are acidic?

Glu, Asp

Which amino acids are basic?

Arg, Lys, His

Which amino acids are likely to have a (+) charge at cellular pH?

Arg, Lys, His (basic unstable plus charge)

Which amino acids are likely to have a (-) charge at cellular pH?

Glu, Asp (acidic stable better able to handle a negative charge)

Essential vs Nonessential amino acids

o An essential amino acid is an amino acid that can NOT be synthesized by the body.
o Non-essential amino acid: can be synthesized by the body.

Draw a peptide bond

R-C(=O)NH-R

Name two unique characteristics of peptide bonds

No rotation occurs about the peptide bond due to its double bond character. This is because of the lone pair on the nitrogen that can donate into the N-C bond and then to the C=O bond.

A peptide bond is shorter and stronger than a regular bond

Primary

refers to amino acid linear sequence of the polypeptide chain. Amino acids are held together by covalent or peptide bonds.

Secondary:
Describe the two kinds of secondary protein structure

• Alpha helices
• Beta sheets

Tertiary

Alpha helices and beta sheets are folded into a compact globule.

Name the six things that are responsible for 3˚ structure? (Hint: H-bonding)

1) covalent disulfide bonds between two cysteine amino acids on different parts of the chain
2) electrostatic (ionic) interactions mostly between acidic and basic side chains
3) hydrogen bonds
4) van der Waals forces
5) hydrophobic side chains pushed away from water (toward center of protein)
6) proline

Quaternary

3D structure of a multi-subunit protein, made up of compact globular subunits

What determines protein folding structure?

Amino acid sequence

Protein denaturing (unfolding) agents?

Acid
Heat
Urea-break up non-covalent bonds
Mercaptoethanol

What steps need to be taken to re-nature (re-fold) a protein?

• Remove the denaturing agent
• Identify a refolding buffer
• Make sure the conditions are right.

what is the empirical formula for carbohydrates?

o Empirical Formula: (CH2O)n

A basic carbohydrate

Draw the ring structure for glucose

Draw the ring structure for fructose

Draw the chain structure for glucose

Draw the chain structure for fructose

Draw the alpha & beta anomers of glucose

Which carbohydrates are ketones?

Fructose

Which carbohydrates are aldehydes?

Glucose

Polysaccarides:

Glycogen: branched, alpha-linked glucose polymer, used for storage in animals.
Starch: branched, alpha-linked glucose polymer, used for storage in plants
Cellulose: beta-linked glucose polymer, used for storage in plants, indigestible to animals;
Animals = alpha; Bacteria = beta

Draw an example of a nucleotide.

Know the three components of a nucleotide and the bonds, elements, and connectivity involved.

Sugar, phosphate, base.
Base 1', phosphate 4'

What other biomolecules, besides DNA/RNA are nucleotides?

ADP and ATP, cAMP
Cyclic AMP, ADP, GTP GMP GDP NADH FADH2 and the DNA and RNA subunits are all examples. UTP may look unfamiliar, but it is the equivalent of ATP with a Uracil base instead of an Adenine base.

Vitamins & Minerals:

We get vitamins from plants and animals
We get minerals from the earth

Name some key vitamins.

Vitamin A (Retinol) Cod liver oil
Vitamin B1 (Thiamine) Rice bran
Vitamin C (Ascorbic acid) Citrus, most fresh foods
Vitamin D (Calciferol) Cod liver oil
Vitamin B2 (Riboflavin) Meat, eggs
Vitamin E (Tocopherol) Wheat germ oil, unrefined vegetable oils
Vitamin B12 (Cobalamins) liver, eggs, animal products
Vitamin K1 (Phylloquinone) Leafy green vegetables
Vitamin B5 (Pantothenic acid) Meat, whole grains,
in many foods
Vitamin B7 (Biotin) Meat, dairy products, eggs
Vitamin B6 (Pyridoxine) Meat, dairy products
Vitamin B3 (Niacin) Meat, eggs, grains
Vitamin B9 (Folic acid) Leafy green vegetable

What roles do vitamins usually play?

Vitamins are essential for the normal growth and development.

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