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214 terms

BIOLOGY 1

STUDY
PLAY
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.
Two important classifications of vitamins:
Water-soluble
Fat-soluble
Enzymes
o All enzymes are proteins. (This is not a strictly true statement, but it is true about 99% of the time, RNA is a noteable exception)

Enzymes are designed to work only on a specific substrate or group of closely related substrates.
What is the difference between a catalyst and an enzyme?
All enzymes are catalysts, but not all catalysts are enzymes. Enzymes are proteins. Catalyst can be a metal.
How do enzymes affect:
• Reaction rate?
• Activation energy?
• Equilibrium?
• Keq?
• Yield?
• Percent yield?
How do enzymes affect:
• Reaction rate: like catalysts enzymes speed up the reaction.
• Activation energy: it lowers the activation energy
• Equilibrium: it does not effect equilibrium
• Keq: no effect
• Yield: no effect
• Percent yield: no effect
Substrate
a substrate is the reactant or reactants upon which an enzyme works
Active site
the position on the enzyme to where the substrate binds, usually with numerous noncovalent bonds, is called the active site.
Enzyme-substrate complex
The enzyme bound to the substrate
Two theories of enzyme specificity are?
• The Lock and Key Theory: is an example of enzyme specificity. In this theory, the active site of the enzyme has a specific shape like a lock that only fits a specific substrate, the key.
• Induced Fit: In this model, the shape of both the enzyme and the substrate are altered upon binding.
Coenzymes vs Prosthetic Groups?
Coenzymes: non-protein species NOT permanently attached to the enzyme but required by the enzyme to function

Prosthetic Groups: non-protein species that are permanently attached to the enzyme and are required by the enzyme to function

Cofactors: a general term for any species required by an enzyme to function; coenzymes and prosthetic groups are both examples of cofactors.
Cofactors
a general term for any species required by an enzyme to function; coenzymes and prosthetic groups are both examples of cofactors.
RXN RATE vs. [Substrate] graph
Draw this graph and label the axes
Where is Vmax on a rxn rate vs substrate concentration graph?
Vmax is where if you add anymore substrate it will have no more effect on the reaction. As the relative concentration of substrate increases, the rate of reaction also increases, but to a lesser and lesser degree until a maximum rate has been achieved.
Where is Km on a rxn rate vs substrate concentration graph?
Km is where the substrate concentration has reached ½ of V max.
How do each of the following affect enzymatic reaction rate?
a) pH
b) temperature
c) substrate concentration:
d) enzyme concentration:
o Enzymatic Reaction Rates:
How do each of the following affect reaction rate?
a) pH reaction happens at the desired rate when pH is at an optimal level
b) temperature increases rate up to a certain point (optimal temperature) and then denaturing of enzymes takes place.
c) substrate concentration: increases the reaction rate until you reach Vmax
d) enzyme concentration: increasing the concentration of the enzyme (like with catalysts) has no effect on the reaction rate
pH vs enzymatic reaction rate graph
enzymatic reaction rate vs temperature reaction graph
Enzyme Inhibition:
o Competitive:
o Non-competitive:
o Irreversible:
Enzyme Inhibition:
o Competitive: inhibitor binds at the active site; the effect can be overcome by increasing [substrate]
o Non-competitive: inhibitor binds away from the active site and changes the shape of the enzyme
o Irreversible: inhibitor bonds covalently to the enzyme and permanently disables it.
Positive feedback:
is where the product returns to activate the enzyme; labor contractions
Negative feedback
is where one of the products downstream in a reaction series comes back and inhibits the enzymatic activity in an early reaction; TSH levels
Zymogens
Zymogens (Notice the "-ogen" ending, as seen in pepsinogen, trypsinogen, etc.) zymogens are the inactive form of an enzyme. When you see "-ogen" THINK INACTIVE FORM OF ENZYME.

Zymogens are transformed into enzymes. This would be an on/off effect and wouldn't match a continuum of up- or down- regulation.
zymogens are only made once and then turned into their enzymes. If an enzyme is disabled due to phosphorylation or something similar, we would call that "irreversible inhibition" of an enzyme, not reformation of a zymogen. zymogens are not a way of disabling an already active enzyme.
Phosphorylation/De-phosphorylation
Phosphorylation adds a phosphate group to a molecule (kinase), dephosphorylation removes a phosphate group from a molecule (Phosphatase)
Allosteric Regulation
regulation away from the active site; feedback inhibitors do this, they bind to the enzyme and cause a conformational change.
Explain the significance of : "-ase", "-tase," "kinase," and "Phosphatase
"-ase" means enzyme
Kinase phosphorylates
"-tase" removes something
Phosphatase dephosphorylates
Metabolism
"the sum of all chemical reactions in the body."
Respiration
although we often associate this with breathing, its definition in this context is "the breakdown of macromolecules into smaller species to harvest energy."
Clarify the difference between aerobic and anaerobic respiration. Which one do humans use?
• Aerobic respiration is a form of cellular respiration that requires oxygen
• Anaerobic respiration is a form of cellular respiration that occurs when oxygen is absent of scarce. Does not require oxygen.
• Humans who are aerobes, carry out anaerobic respiration when muscles perform strenuous exercise resulting in oxygen debt.
• Humans use aerobic oxygen regularly when oxygen is not in short supply.
What is the difference between an obligate aerobe and a facultative aerobe?
• Obligate aerobe requires oxygen for aerobic respiration; one that cannot live without oxygen
• Facultative aerobe one that can live in the presence of oxygen, but does not require it.
What is the difference between an obligate anaerobe and a facultative anaerobe?
• Obligate Anaerobe an organism, such as bacterium, that can live only in the absence of oxygen
• Facultative Anaerobe an organism which is capable of producing energy through aerobic respiration and then switching back to anaerobic respiration depending on the amounts of oxygen and fermentable material in the environment.
Glycolysis
The metabolic pathway that converts glucose into pyruvate
C6H12O6 + 2 NAD+ + 2 ADP + 2 P ---> 2 pyruvic acid, (CH3(C=O)COOH + 2 ATP + 2 NADH + 2 H+
draw a simplified glycolysis chart and note the changes in the carbon skeleton
The species that enter and exit glycolysis?
If 1 glucose enters; 2 ATP 2 NADH
The number of pyruvate produced per glucose?
1 glucose = 2 pyruvate
How many ADP and NAD+ are required for glycolysis if 1 glucose enters?
2 ADP 2 NAD+ Requierd
The difference between Substrate Level Phosphorylation and Oxidative Phosphorylation:
• Substrate Level Phosphorylation: synthesis of high energy phosphate bonds through reaction of inorganic phosphate with an activated (usually) organic substrate; phosphate group comes from a substrate
• Oxidative Phosphorylation: a metabolic pathway that generates ATP from ADP through Phosphorylation that derives the energy from the oxidation of nutrients
Substrate Level Phosphorylation and Oxidative Phosphorylation:
Which process occurs during glycolysis?
Both substrate level phosphorylation and oxidative phosphorylation occur during glycolysis.
what is gluconeogenesis
gluconeogenesis is the reversal of glycolysis
Fermentation:
Recycles NADH back to NAD+ to be used in glycolysis
o Sole route for many bacteria; used by animals only during oxygen debt (i.e., during strenuous exercise)
In ethanol fermentation (happens in bacteria), ____ is produced and is the final electron acceptor.

In lactic acid fermentation (happens in animals), ____ is produced and is the final electron acceptor
ethanol; lactic acid
Fermentation is important because??
Fermentation is important because it regenerates NAD+ so glycolysis can continue.
Kreb Cycle: Draw a chart and notice the changes in the carbon skeleton
primary purpose: create ATP
The species that enter and exit the Kreb's Cycle
• 2 C enter from pyruvate transferred by Acetyl CoA; 1 GTP, 1 FADH2 3NADH, 1ATP
The number of cycles of the Kreb Cycle per glucose:
1 glucose = 2 citric acid cycles (because 2 pyruvates result from glycolysis);

2 C are taken from pyruvate and transferred by Acetyl CoA to the 4 C oxaloacetic acid to begin the cycle.
How many CO2 are lost in the kreb cycle and where they are produced?
During the cycle two carbons are lost as CO2, and oxaloacetic acid is reproduced to begin the cycle all over again.
The number of ATP, GTP, NADH and FADH2 produced in the Kreb Cycle?
• 1 GTP, 3 NADH, 1 FADH2, 1 ATP
The difference between Substrate Level Phosphorylation and Oxidative Phosphorylation in the Kreb Cycle!
Substrate Level Phosphorylation: The process of ATP production in the Kreb Cycle;
Electron Transport Chain:
o Diagram and describe the flow of electrons form the first molecule that delivers the electron to the chain, through the entire chain, and onto the final electron acceptor
The electron transport chain is a series of protein complexes embedded in the mitochondrial membrane. Electrons captured from donor molecules (NADH) are transferred through these complexes. Coupled with this transfer is the pumping of hydrogen ions. This pumping generates the gradient used by the ATP synthase complex to synthesize ATP.
At the start of the electron transport chain two electrons are passed from NADH into the NADH Dehydrogenase Complex, coupled with this transfer is the pumping of 1 hydrogen ion for each electron. Next the 2 electrons are transferred to ubiquinone. Ubiquione is a mobile transfer molecule and moves the two electrons to the cytochrome b-c1 complex. Each electron is then passed from this complex to cytochrome C which transfers one electron at a time to the Cytochrome oxidase complex. The next step requires 4 electrons. These 4 electrons interact with intermolecular oxygen molecules and 8 hydrgoen ions. 2 water molecules are formed. These steps produce a gradient which is used by ATP synthase to create ATP from ADP and inorganic phosphate (Pi).
o Describe the process of proton pumping and how ATP is produced at the ATP Synthase complex
ATP synthase complex utilizes the energy from a proton concentration gradient to make ATP from ADP and Pi. One hydrogen ion from the intermembrane enters the ATP synthase complex and a second leaves it into the matrix space. The upper part of the ATP synthase complex rotates as a hydrogen enters. One 3 protons have entered the matrix space, there is enough energy to synthesize one ATP.
In the electron transport chain:
o Each NADH = _ATP; Each FADH2 = _ATP
o Each NADH = 3ATP; Each FADH2 = 2ATP
(Note: some books use 2.5 ATP and 1.5 ATP, respectively. Don't be confused or surprised if this shows up on the MCAT)
Explain why FADH2 produces fewer ATP in the electron transport chain?
FADH2 produces less ATP since it passes its electrons to the electron transport chain at a lower energy level than NADH does. NADH contributes its electrons near the start of the chain while FADH2 gives its electrons later on.
Using the NADH and FADH2 equivalents (Each NADH = 3ATP; Each FADH2 = 2ATP) , demonstrate for the complete oxidation of one glucose molecule where each high-energy molecule is created and how they add up to 36 ATP per glucose. (HINT: Two common errors are 1) not considering the "net" ATP from glycolysis and 2) ignoring the ATP required for the transport of NADH into the mitochondria)
Lipid Metabolism
Occurs in the mitochondria; and to a limited degree in the Peroxisomes
Extra long chain fatty acids cannot be metabolized by the mitochondria. They are sent to the Peroxisomes and "chopped up" into smaller pieces. They then return and go thru the same B-oxidation pathway as other smaller fatty acids.
o Remember: lipids are metabolized in the mitochondria, but synthesized/modified at the smooth ER.
Be generally familiar with B-oxidation
Carbons are removed two at a time to form Acetyl-CoA groups that can be fed into the Krebs Cycle.

Uneven carbon chains will result in a 3 carbon residue that is funneled into a separate reaction pathway.

From each 2-carbon cycle we get: 1 FADH2 (2ATP), 1 NADH (3ATP) and 1 Acetyl-CoA (12 ATP)
How many cycles of B-oxidation will be required to completely oxidize a 14-carbon fatty acid?
7
How many cycles will be required to oxidize a 17-carbon fatty acid?
7; if you have an odd number of carbons the cycle leaves 3 carbons alone.
The final step of the ETC involves the transfer of an electron from Complex IV to oxygen, forming which of the following?
The answer is H2O

Important Note:
Oxygen is the final electron acceptor in the ETC. However, this often leads students to incorrectly assume that oxygen is formed as a product of the chain, with the final electron going onto an O2 molecule. Rather, H2O is the product of the ETC and it is the oxygen within the water molecule that accepts the electron.
Protein Metabolism:
Amino acids are broken down into acetyl-CoA and fed into the Kreb's cycle. Note that we have now seen that Acetyl-CoA can be fed into the Krebs cycle from carbohydrates, fats, or proteins.
What are the possible explanations for nitrogen in the urine?
Nitrogen would be in the urine if the body was using protein as an energy source.
Remember that healthy people burn carbohydrates first, then fats, then proteins.
Order of Metabolism:
Healthy individuals burn carbohydrates first, then fats, then proteins.
How many calories are in one gram of:
Fat:
Protein:
Carbohydrate:
How many calories are in one gram of:
Fat: 1g = 9 calories
Protein: 1g = 4 cal
Carbohydrate: 1g = 4 cal
Which of the following does NOT contribute to the tertiary level of protein folding?
A) Proline turns
B) Covalent bonds
C) Alpha helices
D) Intermolecular repulsions
C; All of the following contribute to tertiary protein folding: hydrogen bonding, hydrophobic interactions, ionic interactions, proline turns, Van der Walls forces and disulfide bonds. This is a good test to see if you are just memorizing. You may be tempted to mark covalent bonds or intermolecular forces because they aren't specifically on the "list" most people memorize. However, disulfide bonds are an example of covalent bonds and hydrophobic interactions are an example of intermolecular repulsions. C, alpha helices, is responsible for secondary structure.
What is the primary reason for nitrogen being in the urine?
Because excess proteins are in the urine, perhaps because they are being broken down somewhere in the body. If you have nitrogen in your urine you are likely
1) Diabetic (because you cannot get sugar into your cells and thus the body must break down proteins for energy
2) starving to death (you cannot get enough food, so you must break down your body's own proteins
3) are experiencing severe damage to organs, cell lysis, etc.
4) are on Atkins diet, eating more protein than your body can process.
Many rodent poisons and pesticides achieve their action by disrupting aerobic respiration. which of the following actions would negatively affect aerobic respiration and decrease ATP production?

I. Opening new protein channels for H+ ions thru the outer mitochondrial membrane.
II. Opening new protein channels for H ions thru the inner mitochondrial membrane
III. Blocking the reaction of NAD+ with Complex I of the electron transport chain.
IV. Blocking the interaction of FADH2 with Complex II of the electron transport chain.

a) I & II only
b) II, III, & IV only
c) II & IV only
d) I,II, & IV
D
Statement I would decrease ATP production, although you may be tempted to say it has no effect because H+ ions do not normally pass thru this membrane. However, what would happen if they suddenly were able to? They would go down their concentration gradient, which would be from the intermembrane space, out thru the outer membrane and into the cytosol. This would compete with their flow thru the ATP synthase on the inner mitochondrial membrane and reduce ATP production. Statement II would also decrease ATP production by providing an alternate route back into the matrix. Statement III cannot be a correct answer because it doesn't occur. NADH reacts with complex one, not NAD+, so preventing a reaction of NAD+ would have no effect. Statement IV would decrease ATP production because FADH2 reacting with Complex II is a source of electrons for the system. Fewer electrons means fewer protons pumped and fewer ATP produced. D is thus the correct answer.
Substance A is necessary to form Substance B. Substance B phosphorylates Substance C. Substance C releases energy as it is transformed into Substance D. Substance D is phosphoantigenitase, a molecule necessary for proper immune function.

Substance C is most likely a polymer of which of the following subunits?

A) amino acids
B) carbohydrate monomers
C) fatty acids
D) Cannot be determined from the information given.
A
Since C is a precursor to D, and we know D is an enzyme, and we also know that all enzymes are proteins, then C must also be a protein; thus A is the correct answer.
Substance A is necessary to form Substance B. Substance B phosphorylates Substance C. Substance C releases energy as it is transformed into Substance D. Substance D is phosphoantigenitase, a molecule necessary for proper immune function.

It can be inferred that which of the aforementioned substances most likely requires ATP to accomplish its described role?

A) Substance B only
B) Substance A only
C) Substance B and C
D) Substances B and D
32) D; Answer choice A is possibly correct because we are told that substance B phosphorylates substance C. In human metabolism, substances are almost always phosphorylated using ATP or a similar high-energy phosphate molecule. ATP transfers one of its phosphates to substance B, creating substance C, which would be an example of SUBSTRATE-LEVEL PHOSPHORYLATION. Substance C releases energy as it forms substance D, indicating it probably loses its phosphate to reform ATP; thus it creates ATP and does not require it as asked for in the question. Substance D is an enzyme, and because of the "-tase" ending, we know it requires ATP for its action. Thus D is the best answer.
ER between the smooth and rough sections
The ER, between the smooth and rough sections, is responsible for detoxifying chemicals, producing lipids, synthesizing extracellular proteins, modifying translated proteins, and various other kinds of functions. The key here is that lipids are MADE at the smooth ER, but are metabolized in the mitochondrial matrix. Thus B is a false statement and is the correct answer.