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Tuesday, December 20, 2016

MCAT · Biology 1 · Chapter 1 · Section 1.7

Chapter 1: Biological Molecules and Enzymes

Section 1.7: Minerals

STUDY

Question 1:
Minerals are the dissolved _____ (organic or inorganic) ions inside and outside the cell. By creating _____ across membranes, they assist in the transport of substances entering and exiting the cell. They can combine and solidify to strengthen a matrix; an example for this is _____ in bone. They can also act as cofactors to assisti enzyme and protein function; an example for this is _____ in heme, the prosthetic (AKA _____) group of _____.
→ Inorganic
    Electrochemical gradients
    Hydroxyapatite
    Iron
    Non-proteinaceous
    Cytochromes

Question 2:
Name 9 levels of organization in an organism, from lowest to highest.
→ Atoms
    Molecule
    Macromolecule
    Organelle
    Cell
    Tissue
    Organ
    Organ system
    Organism

PRACTICE

Question 1:
Minerals are the dissolved _____ (organic or inorganic) ions inside and outside the cell. By creating _____ across membranes, they assist in the transport of substances entering and exiting the cell. They can combine and solidify to strengthen a matrix; an example for this is _____ in bone. They can also act as cofactors to assisti enzyme and protein function; an example for this is _____ in heme, the prosthetic (AKA _____) group of _____.

Question 2:
Name 9 levels of organization in an organism, from lowest to highest.

ANSWER KEY

Question 1:
→ Inorganic
    Electrochemical gradients
    Hydroxyapatite
    Iron
    Non-proteinaceous
    Cytochromes

Question 2:
→ Atoms
    Molecule
    Macromolecule
    Organelle
    Cell
    Tissue
    Organ
    Organ system
    Organism

MCAT · Biology 1 · Chapter 1 · Section 1.6

Chapter 1: Biological Molecules and Enzymes

Section 1.6: Amino Acids and Proteins

STUDY

Question 1:
A single protein is built from a chain of _____ linked together by _____ bonds; thus, proteins are AKA _____.
→ Amino acids
    Peptide
    Polypeptides

Question 2:
Variety of structures and functions of proteins is resulted from variety of _____ of amino acids.
→ Possible combinations

Question 3:
_____ bond creates _____ functional group (which is an amine connected to a carbonyl carbon). It's formed via _____ reaction of 2 amino acids. The reverse reaction is _____ of aforementioned bond.
→ Peptide
    Amide
    Dehydration
    Hydrolysis

Question 4:
Explain how peptide bond has a partial double bond character and describe this character's function.
→ Since nitrogen is most stable with 4 bonds and oxygen attracts electron density, resulting in a
    partial negative charge, electrons delocalize to give peptide bond a partial double bond character.
    This double bond character prevents the bond from rotating freely. It also affects secondary and,
    to some extent, tertiary structure of the polypeptide.

Question 5:
There're _____ (number) common α-amino acids. They're called α-amino acids because _____. In humans, 9 of the amino acids are _____, meaning that they can't be manufactured by the body and, thus, must be ingested directly. Digested proteins reach the cells of human body as _____.
→ 20
    The amine is attached to the carbon in α position to the carbonyl
    Essential
    Single amino acids

Question 6:
Draw a general structure of amino acids and label its groups. 
→ 
(Source: http://study.com/cimages/multimages/16/amino_acid_structure.png)

Question 7:
R groups have different chemical properties, which can be divided into 4 categories: _____, _____, _____, and _____.
→ Acidic (also polar)
    Basic (also polar)
    Polar
    Non-polar

Question 8:
Generally, if R group contains carboxylic acids, then it's _____ (acidic or basic). Whereas if R group contains amines, then it's _____ (acidic or basic).
→ Acidic
    Basic

Question 9:
Acidity or basicity of R groups _____ (does or does not) affect the overall structure of the protein.
→ Does

Question 10:
Categorize 20 common α-amino acids based on their R groups' chemical properties. Provide their corresponding names, 3-letter codes, and 1-letter codes. Don't have to memorize their structures. 
→ 
(Source: http://dnangelica.com/dnangelica/wp-content/gallery/bioquimica-1/Tema01-aminoacids.jpg)
     
     GROUP 1: Non-polar, aliphatic R groups
     Glycine (Gly, G)
     Alanine (Ala, A)
     Proline (Pro, P)
     Valine (Val, V)
     Leucine (Leu, L)
     Isoleucine (Ile, I)
     Methionine (Met, M)

     GROUP 2: Polar, uncharged R groups
     Serine (Ser, S)
     Threonine (Thr, T)
     Cysteine (Cys, C)
     Asparagine (Asn, N)
     Glutamine (Gln, Q)

     GROUP 3: Aromatic R groups
     Phenylalanine (Phe, F)
     Tyrosine (Tyr, Y)
     Tryptophan (Trp, W)

     GROUP 4: Positively charged R groups
     Lysine (Lys, K)
     Arginine (Arg, R)
     Histidine (His, H)

     GROUP 5: Negatively charged R groups
     Aspartate or Aspartic Acid (Asp, D)
     Glutamate or Glutamic Acid (Glu, E)

Question 11:
The structure of a protein is described according to several levels of organization. These 4 structures are _____, _____, _____, and _____.
→ Primary structure
    Secondary structure
    Tertiary structure
    Quaternary structure

Question 12:
The _____ and _____ of amino acids in a polypeptide is called the primary structure. Once this structure is formed, the _____ (single or double) chain(s) can form into distinct shapes known as the secondary structure. This polypeptide can twist into a(n) _____, or lie alongside itself and form a(n) _____ - both of which are reinforced by _____ bonds between _____ of 1 amino acid and the _____ on another amino acid. A single protein usually contains _____ (only one structure or both structures) at various locations along its chain. These areas of secondary structure contribute to the _____, or overall shape, of the protein. The tertiary structure refers to _____ shape formed by _____ and _____ of the peptide chain. The quaternary structure is formed when 2 or more _____ bind together.
→ Number
    Sequence
    Single
    α-helix
    β-pleated sheet 
    Hydrogen
    Carbonyl oxygen 
    Hydrogen
    Both structures
    Conformation
    3 dimensional 
    Curls
    Folds
    Polypeptide chains 

Question 13:
With _____ (α-helices or β-pleated sheets), connecting segments of the 2 strands can lie in the same or opposite directions. 
→ β-pleated sheets

Question 14:
Amino acids in solution, such as in biological environment, will always carry one or more charges. The position and nature of the charges will depend upon the _____ of the solution.
→ pH

Question 15:
_____ (all or most) proteins have a primary structure and _____ (all or most) have areas of secondary structure. _____ (larger or smaller) proteins can have a tertiary and quaternary structures. 
→ All
    Most
    Larger 

Question 16:
Name 5 forces that contribute to tertiary and quaternary structures. 
 Covalent disulfide bonds between 2 cysteine amino acids on different parts of the chain, creating
    dimer cystine (not a typo, not "dimer cysteine")
    Electrostatic (ionic) interactions, mostly between acidic and basic side chains
    Hydrogen bonds
    Van der Waals forces
    Hydrophobic side chains pushed away from water toward the protein's center (hydrophobic
    bonding)

Question 17:
In addition to the 5 forces that contribute to tertiary structure, there're turns that disrupt both α-helix and β-pleated sheet formation. These turns are induced by the amino acid _____ due to its physical structure: _____.
→ Proline
    R group binds to amine group, causing protein to be more rigid than a typical amino acid and
    creating kink in the protein's structure

Question 18:
Though many different conformations are possible for any 1 protein, it'll generally exist in 1 of a few possible conformations that have the highest _____ and allow the protein to carry out its necessary functions. 
→ Stability

Question 19:
The water surrounding proteins in biological environment helps stabilize these native conformations. Due to the presence of _____ (hydrophobic or hydrophilic) R groups on the protein, surrounding molecules assemble into an organized structure known as a _____ that forces these R groups _____ (toward or away from) the surrounding water and _____ (toward or away from)  the inner area of the protein. This action is highly _____ (favorable or unfavorable) because it _____ (increases or decreases) the size of highly ordered solvation layer, _____ (increasing or decreasing) the entropy of the system. 
→ Hydrophobic
    Solvation layer
    Away from
    Toward
    Favorable
    Decreases
    Increasing

Question 20:
When the native conformation is disrupted, the protein is said to be _____; it has lost most of its _____, _____, and _____ structures. Very often, once the denaturing agent is removed, the protein _____ (will or will no longer) be able to spontaneously refold to its original conformation. This suggests that the _____ plays a key role in the conformation of a protein. 
→ Denatured 
    Secondary
    Tertiary 
    Quaternary
    Will
    Amino acid sequence

Question 21:
The large array of possible functions of proteins is made possible by _____.
→ The large array of possible combinations of amino acids that have different physical properties 

Question 22:
Name 2 types of proteins. Which type is more abundant than the other?
→ Globular (more abundant) and structural 

Question 23:
Name 7 major functions of globular proteins and give an example for each function. 
→ Enzymes: pepsin
    Hormones: insulin
    Membrane pumps and channels: Na+/K+ pump and voltage-gated Na+ channels
    Membrane receptors: nicotinic receptors on a post-synaptic neuron
    Intercellular and intracellular transport and storage: hemoglobin and myoglobin
    Osmotic regulators: albumin
    Immune response: antibodies

Question 24:
Structural proteins maintain and strengthen _____ and _____ structures. _____, a structural protein made from a unique type of _____ (sheet or helix), is the _____ (most or least) abundant protein in the body. Collagen fibers _____ (strengthen or weaken) skin, tendons, ligaments, and bones, among other structures. _____, which make up flagella and cilia, are made from _____, which polymerizes under the right conditions to become a structural protein.
→ Cellular
    Matrix
    Collagen
    Helix
    Most
    Microtubules
    Globular tubulin

Question 25:
Draw a basic cell structure to illustrate the differences between cytosol (AKA cytoplasmic matrix), cytoplasm, and nucleoplasm.

Question 26:
Glycoproteins are proteins with _____ groups attached. Glycoproteins are a component of cellular _____. Proteoglycans are a mixture of proteins and _____, but the latter takes up more than _____%. Proteoglycans are the major component of extracellular _____. Cytochromes are proteins that require a(n) _____ group to function. Cytochromes get their name from the _____ (hint: what does chrome mean?) that they add to the cell. Examples of cytochromes are _____ and the cytochromes of the _____ in mitochondria's inner membrane. Proteins containing non-proteinaceous (= prosthetic) components are called _____ proteins.
→ Carbohydrate
    Plasma membranes
    Carbohydrates
    50
    Matrix
    Prosthetic (= non-proteinaceous) heme
    Color
    Hemoglobin
    Electron transport chain
    Conjugated

Question 27:
Denatured form of protein doesn't contain any of the _____ (α-helices or β-sheets) that the properly folded protein has. Denaturing agents rarely affect the _____ (primary, secondary, tertiary, or quaternary) structure of a protein, which contains the essential information for conformation. Thus, mildly denatured proteins often _____ (can or cannot) spontaneously return to their original conformation. 
→ α-helices
    Primary
    Can

Question 28:
Name 5 denaturing agents and which forces they disrupt.
→ Urea disrupts hydrogen bonds.
    Salt or change in pH disrupts electrostatic bonds.
    Mercaptoethanol disrupts disulfide bonds.
    Organic solvents disrupt hydrophobic forces.
    Heat disrupts all forces.

Question 29:
Cytochrome proteins carry out electron transport via oxidation and reduction of _____ group.
→ Heme

PRACTICE

Question 1:
A single protein is built from a chain of _____ linked together by _____ bonds; thus, proteins are AKA _____.

Question 2:
Variety of structures and functions of proteins is resulted from variety of _____ of amino acids.

Question 3:
_____ bond creates _____ functional group (which is an amine connected to a carbonyl carbon). It's formed via _____ reaction of 2 amino acids. The reverse reaction is _____ of aforementioned bond.

Question 4:
Explain how peptide bond has a partial double bond character and describe this character's function.

Question 5:
There're _____ (number) common α-amino acids. They're called α-amino acids because _____. In humans, 9 of the amino acids are _____, meaning that they can't be manufactured by the body and, thus, must be ingested directly. Digested proteins reach the cells of human body as _____.

Question 6:
Draw a general structure of amino acids and label its groups. 

Question 7:
R groups have different chemical properties, which can be divided into 4 categories: _____, _____, _____, and _____.

Question 8:
Generally, if R group contains carboxylic acids, then it's _____ (acidic or basic). Whereas if R group contains amines, then it's _____ (acidic or basic).

Question 9:
Acidity or basicity of R groups _____ (does or does not) affect the overall structure of the protein.

Question 10:
Categorize 20 common α-amino acids based on their R groups' chemical properties. Provide their corresponding names, 3-letter codes, and 1-letter codes. Don't have to memorize their structures. 

Question 11:
The structure of a protein is described according to several levels of organization. These 4 structures are _____, _____, _____, and _____.

Question 12:
The _____ and _____ of amino acids in a polypeptide is called the primary structure. Once this structure is formed, the _____ (single or double) chain(s) can form into distinct shapes known as the secondary structure. This polypeptide can twist into a(n) _____, or lie alongside itself and form a(n) _____ - both of which are reinforced by _____ bonds between _____ of 1 amino acid and the _____ on another amino acid. A single protein usually contains _____ (only one structure or both structures) at various locations along its chain. These areas of secondary structure contribute to the _____, or overall shape, of the protein. The tertiary structure refers to _____ shape formed by _____ and _____ of the peptide chain. The quaternary structure is formed when 2 or more _____ bind together.

Question 13:
With _____ (α-helices or β-pleated sheets), connecting segments of the 2 strands can lie in the same or opposite directions. 

Question 14:
Amino acids in solution, such as in biological environment, will always carry one or more charges. The position and nature of the charges will depend upon the _____ of the solution.

Question 15:
_____ (all or most) proteins have a primary structure and _____ (all or most) have areas of secondary structure. _____ (larger or smaller) proteins can have a tertiary and quaternary structures.  

Question 16:
Name 5 forces that contribute to tertiary and quaternary structures. 

Question 17:
In addition to the 5 forces that contribute to tertiary structure, there're turns that disrupt both α-helix and β-pleated sheet formation. These turns are induced by the amino acid _____ due to its physical structure: _____.

Question 18:
Though many different conformations are possible for any 1 protein, it'll generally exist in 1 of a few possible conformations that have the highest _____ and allow the protein to carry out its necessary functions. 

Question 19:
The water surrounding proteins in biological environment helps stabilize these native conformations. Due to the presence of _____ (hydrophobic or hydrophilic) R groups on the protein, surrounding molecules assemble into an organized structure known as a _____ that forces these R groups _____ (toward or away from) the surrounding water and _____ (toward or away from)  the inner area of the protein. This action is highly _____ (favorable or unfavorable) because it _____ (increases or decreases) the size of highly ordered solvation layer, _____ (increasing or decreasing) the entropy of the system. 

Question 20:
When the native conformation is disrupted, the protein is said to be _____; it has lost most of its _____, _____, and _____ structures. Very often, once the denaturing agent is removed, the protein _____ (will or will no longer) be able to spontaneously refold to its original conformation. This suggests that the _____ plays a key role in the conformation of a protein. 

Question 21:
The large array of possible functions of proteins is made possible by _____.

Question 22:
Name 2 types of proteins. Which type is more abundant than the other?

Question 23:
Name 7 major functions of globular proteins and give an example for each function. 

Question 24:
Structural proteins maintain and strengthen _____ and _____ structures. _____, a structural protein made from a unique type of _____ (sheet or helix), is the _____ (most or least) abundant protein in the body. Collagen fibers _____ (strengthen or weaken) skin, tendons, ligaments, and bones, among other structures. _____, which make up flagella and cilia, are made from _____, which polymerizes under the right conditions to become a structural protein.

Question 25:
Draw a basic cell structure to illustrate the differences between cytosol (AKA cytoplasmic matrix), cytoplasm, and nucleoplasm.

Question 26:
Glycoproteins are proteins with _____ groups attached. Glycoproteins are a component of cellular _____. Proteoglycans are a mixture of proteins and _____, but the latter takes up more than _____%. Proteoglycans are the major component of extracellular _____. Cytochromes are proteins that require a(n) _____ group to function. Cytochromes get their name from the _____ (hint: what does chrome mean?) that they add to the cell. Examples of cytochromes are _____ and the cytochromes of the _____ in mitochondria's inner membrane. Proteins containing non-proteinaceous (= prosthetic) components are called _____ proteins.

Question 27:
Denatured form of protein doesn't contain any of the _____ (α-helices or β-sheets) that the properly folded protein has. Denaturing agents rarely affect the _____ (primary, secondary, tertiary, or quaternary) structure of a protein, which contains the essential information for conformation. Thus, mildly denatured proteins often _____ (can or cannot) spontaneously return to their original conformation. 

Question 28:
Name 5 denaturing agents and which forces they disrupt.

Question 29:
Cytochrome proteins carry out electron transport via oxidation and reduction of _____ group.

ANSWER KEY

Question 1:
→ Amino acids
    Peptide
    Polypeptides

Question 2:
→ Possible combinations

Question 3:
→ Peptide
    Amide
    Dehydration
    Hydrolysis

Question 4:
→ Since nitrogen is most stable with 4 bonds and oxygen attracts electron density, resulting in a
    partial negative charge, electrons delocalize to give peptide bond a partial double bond character.
    This double bond character prevents the bond from rotating freely. It also affects secondary and,
    to some extent, tertiary structure of the polypeptide.

Question 5:
→ 20
    The amine is attached to the carbon in α position to the carbonyl
    Essential
    Single amino acids

Question 6:
(Source: http://study.com/cimages/multimages/16/amino_acid_structure.png)

Question 7:
→ Acidic (also polar)
    Basic (also polar)
    Polar
    Non-polar

Question 8:
→ Acidic
    Basic

Question 9:
→ Does

Question 10:
(Source: http://dnangelica.com/dnangelica/wp-content/gallery/bioquimica-1/Tema01-aminoacids.jpg)
     
     GROUP 1: Non-polar, aliphatic R groups
     Glycine (Gly, G)
     Alanine (Ala, A)
     Proline (Pro, P)
     Valine (Val, V)
     Leucine (Leu, L)
     Isoleucine (Ile, I)
     Methionine (Met, M)

     GROUP 2: Polar, uncharged R groups
     Serine (Ser, S)
     Threonine (Thr, T)
     Cysteine (Cys, C)
     Asparagine (Asn, N)
     Glutamine (Gln, Q)

     GROUP 3: Aromatic R groups
     Phenylalanine (Phe, F)
     Tyrosine (Tyr, Y)
     Tryptophan (Trp, W)

     GROUP 4: Positively charged R groups
     Lysine (Lys, K)
     Arginine (Arg, R)
     Histidine (His, H)

     GROUP 5: Negatively charged R groups
     Aspartate or Aspartic Acid (Asp, D)
     Glutamate or Glutamic Acid (Glu, E)

Question 11:
→ Primary structure
     Secondary structure
     Tertiary structure
     Quaternary structure

Question 12:
→ Number
     Sequence
     Single
     α-helix
     β-pleated sheet 
     Hydrogen
     Carbonyl oxygen 
     Hydrogen
     Both structures
     Conformation
     3 dimensional 
     Curls
     Folds
     Polypeptide chains 

Question 13:
→ β-pleated sheets

Question 14:
→ pH

Question 15:
→ All
     Most
     Larger 

Question 16:
→ Covalent disulfide bonds between 2 cysteine amino acids on different parts of the chain, creating
    dimer cystine (not a typo, not "dimer cysteine")
    Electrostatic (ionic) interactions, mostly between acidic and basic side chains
    Hydrogen bonds
    Van der Waals forces
    Hydrophobic side chains pushed away from water toward the protein's center (hydrophobic
    bonding)

Question 17:
→ Proline
    R group binds to amine group, causing protein to be more rigid than a typical amino acid and
    creating kink in the protein's structure.

Question 18:
→ Stability

Question 19:
→ Hydrophobic
    Solvation layer
    Away from
    Toward
    Favorable
    Decreases
    Increasing

Question 20:
→ Denatured 
    Secondary
    Tertiary 
    Quaternary
    Will
    Amino acid sequence

Question 21:
→ The large array of possible combinations of amino acids that have different physical properties 

Question 22:
→ Globular (more abundant) and structural 

Question 23:
→ Enzymes: pepsin
    Hormones: insulin
    Membrane pumps and channels: Na+/K+ pump and voltage-gated Na+ channels
    Membrane receptors: nicotinic receptors on a post-synaptic neuron
    Intercellular and intracellular transport and storage: hemoglobin and myoglobin
    Osmotic regulators: albumin
    Immune response: antibodies

Question 24:
→ Cellular
    Matrix
    Collagen
    Helix
    Most
    Microtubules
    Globular tubulin

Question 25:

Question 26:
→ Carbohydrate
    Plasma membranes
    Carbohydrates
    50
    Matrix
    Prosthetic (= non-proteinaceous) heme
    Color
    Hemoglobin
    Electron transport chain
    Conjugated

Question 27: 
→ α-helices
    Primary
    Can

Question 28:
→ Urea disrupts hydrogen bonds.
    Salt or change in pH disrupts electrostatic bonds.
    Mercaptoethanol disrupts disulfide bonds.
    Organic solvents disrupt hydrophobic forces.
    Heat disrupts all forces.

Question 29
→ Heme

Thursday, December 15, 2016

MCAT · Biology 1 · Chapter 1 · Section 1.5

Chapter 1: Biological Molecules and Enzymes

Section 1.5: Nucleotides

STUDY

Question 1:
Nucleotides involve in the cell's use of _____ and comprising the building blocks of every organism's _____. They're composed of 3 components: _____, _____, and _____.
→ Energy
     Genetic material
     A 5-carbon (pentose) sugar
     A nitrogenous base
     A phosphate group
**Review**
(Source: http://image.slidesharecdn.com/organicchemistry-131105135539-phpapp02/95/organic-chemistry-7-638.jpg?cb=1383659789)

Question 2:
In DNA, the highly stable _____, along with the _____, are able to link together to form a stable and organized backbone.
→ Sugars
     Phosphate groups

Question 3:
Both sugars and phosphate groups are _____ (polar or non-polar) and, thus, can face _____ (outward or inward) into the watery solvent of the cell.
→ Polar
     Outward

Question 4:
Nitrogenous bases can form _____ (weak, moderate, or strong) _____ bonds with each other that stabilize the _____-stranded (single or double) structure of DNA but can also be separated to allow the replication of genetic material.
→ Weak
     Hydrogen
     Double

Question 5:
Nucleoside = _____ sugar + _____ base + _____ (number) phosphate groups
Nucleotide = _____ sugar + _____ base + _____ (number) phosphate groups
→ Pentose
     Nitrogenous
     0
     Pentose
     Nitrogenous
     1 or more

Question 6:
Nucleotides are _____ (monomers or polymers), whereas nucleic acids are _____ (monomers or polymers). _____ (nucleotides or nucleic acids) form polymers to create _____ (nucleotides or nucleic acids).
→ Monomers
     Polymers
     Nucleotides
     Nucleic acids

Question 7:
Nucleotides form polymers to create nucleic acids, _____ and _____, which allow for expression of genetic traits by specifying the production of _____ (carbohydrates, proteins, or lipids).
→ DNA (DeoxyriboNucleic Acid)
     RNA (RiboNucleic Acid)
     Proteins

Question 8:
In nucleic acids, nucleotides are joined together into long strands by _____ bonds between phosphate group of 1 nucleotide and 3rd carbon of pentose sugar of the other nucleotide, forming a _____ backbone.
→ Phosphodiester
     Sugar-phosphate

Question 9:
Nucleotides are written in the _____ (5' to 3' or 3' to 5') direction, so that the top strand runs _____ (5' to 3' or 3' to 5') and the bottom strand runs _____ (5' to 3' or 3' to 5').
→ 5' to 3'
     5' to 3'
     3' to 5'

Question 10:
Name 4 nitrogenous bases and their abbreviation in DNA. Identify which 2 are purines and which 2 are pyrimidines. Identify complementary strands  and how many H-bonds are formed between them, with " = " means 2 H-bonds and "  " means 3 H-bonds.
→ Adenine (A) = Thymine (T)
     Guanine (G)  Cytosine (C)
**Mnemonic**
Pyrimidine: cytosine and thymine
 
Question 11:
Purine is a _____-ringed (number) structure, whereas pyrimidine is a _____-ringed (number) structure.
→ 2
     1

Question 12:
DNA usually exists in double-stranded structure described by the _____ model, named after 2 scientists who are credited with 1st theorizing DNA structure.
→ Watson-Crick
**Self-notes**
Special thanks to Rosalind Franklin, an unsung hero

(Source: https://askabiologist.asu.edu/sites/default/files/resources/articles/crystal_clear/Rosalind_Franklin_Plate_1_DNA_B_form_1000.jpg)

Question 13:
In double-stranded structure, AKA the B form, the 2 strands run side-by-side in opposite _____ (5' to 3' or 3' to 5') direction (thus, anti-parallel) bound together by _____ bonds between nitrogenous bases. This bonding is often referred to as _____. The length of DNA strands is measured in _____.
→ 3' to 5'
     Hydrogen
     Base-pairing
     Base-pair (bp)

Question 14:
2 strands that match up in the correct order with each other are called _____ strands. When they bind together, they curl into a _____ which contains 2 distinct grooves called the _____ and the _____. Each groove spirals _____ (once or twice) around the structure for every _____ (number) base-pairs. This DNA structure is _____ (stable or unstable) in the cellular environment and allows for replication of genetic material.
→ Complementary
     Double helix
     Major groove
     Minor groove
     Once
     10
     Stable
(Source: http://www.biologynoteshelp.com/wp-content/uploads/2016/06/MAJOR-AND-MINOR-GROOVES-210x300.jpg)

(Source: https://classconnection.s3.amazonaws.com/251/flashcards/704251/png/grooves1316409303998.png)

Question 15:
DNA (which stands for _____) is a polymer of _____, each of which is composed of 3 parts: _____, _____, and _____. Purines are _____ and _____, whereas pyrimidines are _____ and _____.
→ DeoxyriboNucleic Acid
     Nucleotides
     Phosphate group
     5-carbon (pentose) sugar

Question 16:
_____, a nitrogenous base in RNA that is complementary to Adenine, is a _____ (purine or pyrimidine).
→ Uracil
     Pyrimidine

Question 17:
2 _____ (phosphodiester bonds or H-bonds) hold Adenine and Thymine together, whereas 3 _____ (phosphodiester bonds or H-bonds) hold Guanine and Cytosine together. This means that more energy is required to separate _____ (Adenine = Thymine bond or Guanine  Cytosine bond).
→ H-bonds
     H-bonds
     Guanine  Cytosine bond

Question 18:
RNA (which stands for _____) is identical to DNA (which stands for _____) in structure except that:
1. Carbon #_____ on pentose sugar is not _____, meaning that it has a _____ group attached;
2. RNA is almost always _____-stranded (single or double); and
3. RNA contains the pyrimidine _____ instead of _____, both of which are complementary to _____.
→ RiboNucleic Acid
     DeoxyriboNucleic Acid
     2
     Deoxygenated
     Hydroxyl
     Single
     Uracil (U)
     Thymine (T)
     Adenine (A)

Question 19:
Unlike DNA, RNA _____ (can or cannot) move through the nuclear pores and _____ (is or is not) confined to the nucleus.
→ Can
     Is not

Question 20:
3 important types of RNA are _____ (which stands for _____), _____ (which stands for _____), and _____ (which stands for _____).
→ mRNA
     Messenger RNA
     rRNA
     Ribosomal RNA
     tRNA
     Transfer RNA

Question 21:
A common cause of mutations in DNA is the similarity in structure between uracil and thymine. Draw their structures and circle what differentiates one from the other.
→ 
(Source: http://4.bp.blogspot.com/-V-XfixJp-RQ/ThG2OiuYBOI/AAAAAAAAAI8/EoIt1cRJ1n0/s1600/uracil-thymine.png)

Question 22:
Draw the structures of Adenine, Thymine, Guanine, and Cytosine. Demonstrate which ones pair together and how they pair.
→ 
(Source: https://biochemistry3rst.files.wordpress.com/2014/04/hydrogen-bonds.gif)

Question 23:
In addition to forming genetic material, nucleotides also serve other purposes in the cell. Name 4 other important nucleotides and briefly describe their purposes.
→ ATP (= Adenosine TriPhosphate): main source of readily available energy for the cell
     cAMP (= cyclic AMP): important component in many second messenger systems
     NADH and FADH2: co-enzymes involved in Krebs cycle

PRACTICE

Question 1:
Nucleotides involve in the cell's use of _____ and comprising the building blocks of every organism's _____. They're composed of 3 components: _____, _____, and _____.

Question 2:
In DNA, the highly stable _____, along with the _____, are able to link together to form a stable and organized backbone.

Question 3:
Both sugars and phosphate groups are _____ (polar or non-polar) and, thus, can face _____ (outward or inward) into the watery solvent of the cell.

Question 4:
Nitrogenous bases can form _____ (weak, moderate, or strong) _____ bonds with each other that stabilize the _____-stranded (single or double) structure of DNA but can also be separated to allow the replication of genetic material.

Question 5:
Nucleoside = _____ sugar + _____ base + _____ (number) phosphate groups
Nucleotide = _____ sugar + _____ base + _____ (number) phosphate groups

Question 6:
Nucleotides are _____ (monomers or polymers), whereas nucleic acids are _____ (monomers or polymers). _____ (nucleotides or nucleic acids) form polymers to create _____ (nucleotides or nucleic acids).

Question 7:
Nucleotides form polymers to create nucleic acids, _____ and _____, which allow for expression of genetic traits by specifying the production of _____ (carbohydrates, proteins, or lipids).

Question 8:
In nucleic acids, nucleotides are joined together into long strands by _____ bonds between phosphate group of 1 nucleotide and 3rd carbon of pentose sugar of the other nucleotide, forming a _____ backbone.

Question 9:
Nucleotides are written in the _____ (5' to 3' or 3' to 5') direction, so that the top strand runs _____ (5' to 3' or 3' to 5') and the bottom strand runs _____ (5' to 3' or 3' to 5').

Question 10:
Name 4 nitrogenous bases and their abbreviation in DNA. Identify which 2 are purines and which 2 are pyrimidines. Identify complementary strands  and how many H-bonds are formed between them, with " = " means 2 H-bonds and "  " means 3 H-bonds.

Question 11:
Purine is a _____-ringed (number) structure, whereas pyrimidine is a _____-ringed (number) structure.

Question 12:
DNA usually exists in double-stranded structure described by the _____ model, named after 2 scientists who are credited with 1st theorizing DNA structure.

Question 13:
In double-stranded structure, AKA the B form, the 2 strands run side-by-side in opposite _____ (5' to 3' or 3' to 5') direction (thus, anti-parallel) bound together by _____ bonds between nitrogenous bases. This bonding is often referred to as _____. The length of DNA strands is measured in _____.

Question 14:
2 strands that match up in the correct order with each other are called _____ strands. When they bind together, they curl into a _____ which contains 2 distinct grooves called the _____ and the _____. Each groove spirals _____ (once or twice) around the structure for every _____ (number) base-pairs. This DNA structure is _____ (stable or unstable) in the cellular environment and allows for replication of genetic material.

Question 15:
DNA (which stands for _____) is a polymer of _____, each of which is composed of 3 parts: _____, _____, and _____. Purines are _____ and _____, whereas pyrimidines are _____ and _____.

Question 16:
_____, a nitrogenous base in RNA that is complementary to Adenine, is a _____ (purine or pyrimidine).

Question 17:
2 _____ (phosphodiester bonds or H-bonds) hold Adenine and Thymine together, whereas 3 _____ (phosphodiester bonds or H-bonds) hold Guanine and Cytosine together. This means that more energy is required to separate _____ (Adenine = Thymine bond or Guanine  Cytosine bond).

Question 18:
RNA (which stands for _____) is identical to DNA (which stands for _____) in structure except that:
1. Carbon number _____ on pentose sugar is not _____, meaning that it has a _____ group attached;
2. RNA is almost always _____-stranded (single or double); and
3. RNA contains the pyrimidine _____ instead of _____, both of which are complementary to _____.

Question 19:
Unlike DNA, RNA _____ (can or cannot) move through the nuclear pores and _____ (is or is not) confined to the nucleus.

Question 20:
3 important types of RNA are _____ (which stands for _____), _____ (which stands for _____), and _____ (which stands for _____).

Question 21:
A common cause of mutations in DNA is the similarity in structure between uracil and thymine. Draw their structures and circle what differentiates one from the other.

Question 22:
Draw the structures of Adenine, Thymine, Guanine, and Cytosine. Demonstrate which ones pair together and how they pair.

Question 23:
In addition to forming genetic material, nucleotides also serve other purposes in the cell. Name 4 other important nucleotides and briefly describe their purposes.

ANSWER KEY

Question 1:
→ Energy
     Genetic material
     A 5-carbon (pentose) sugar
     A nitrogenous base
     A phosphate group
**Review**
(Source: http://image.slidesharecdn.com/organicchemistry-131105135539-phpapp02/95/organic-chemistry-7-638.jpg?cb=1383659789)

Question 2:
→ Sugars
     Phosphate groups

Question 3:
→ Polar
     Outward

Question 4:
→ Weak
     Hydrogen
     Double

Question 5:
→ Pentose
     Nitrogenous
     0
     Pentose
     Nitrogenous
     1 or more

Question 6:
→ Monomers
     Polymers
     Nucleotides
     Nucleic acids

Question 7:
→ DNA (DeoxyriboNucleic Acid)
     RNA (RiboNucleic Acid)
     Proteins

Question 8:
→ Phosphodiester
     Sugar-phosphate

Question 9:
→ 5' to 3'
     5' to 3'
     3' to 5'

Question 10:
→ Adenine (A) = Thymine (T)
     Guanine (G)  Cytosine (C)
**Mnemonic**
Pyrimidine: cytosine and thymine

Question 11:
→ 2
     1
Question 12:
→ Watson-Crick

Question 13:
→ 3' to 5'
     Hydrogen
     Base-pairing
     Base-pair (bp)

Question 14:
→ Complementary
     Double helix
     Major groove
     Minor groove
     Once
     10
     Stable
(Source: http://www.biologynoteshelp.com/wp-content/uploads/2016/06/MAJOR-AND-MINOR-GROOVES-210x300.jpg)

(Source: https://classconnection.s3.amazonaws.com/251/flashcards/704251/png/grooves1316409303998.png)

Question 15:
→ DeoxyriboNucleic Acid
     Nucleotides
     Phosphate group
     5-carbon (pentose) sugar

Question 16:
→ Uracil
     Pyrimidine

Question 17:
→ H-bonds
     H-bonds
     Guanine  Cytosine bond

Question 18:
→ RiboNucleic Acid
     DeoxyriboNucleic Acid
     2
     Deoxygenated
     Hydroxyl
     Single
     Uracil (U)
     Thymine (T)
     Adenine (A)

Question 19:
→ Can
     Is not

Question 20:
→ mRNA
     Messenger RNA
     rRNA
     Ribosomal RNA
     tRNA
     Transfer RNA

Question 21:
→ 
(Source: http://4.bp.blogspot.com/-V-XfixJp-RQ/ThG2OiuYBOI/AAAAAAAAAI8/EoIt1cRJ1n0/s1600/uracil-thymine.png)

Question 22:
→ 
(Source: https://biochemistry3rst.files.wordpress.com/2014/04/hydrogen-bonds.gif)

Question 23:
→ ATP (= Adenosine TriPhosphate): main source of readily available energy for the cell
     cAMP (= cyclic AMP): important component in many second messenger systems
     NADH and FADH2: co-enzymes involved in Krebs cycle

Tuesday, December 13, 2016

MCAT · Biology 1 · Chapter 1 · Section 1.4

Chapter 1: Biological Molecules and Enzymes

Section 1.4: Carbohydrates

STUDY

Question 1:
Name 2 primary biological importances of carbohydrates.
→ Energy storage
     Provision of easily accessible energy to the body

Question 2:
Similar to _____, carbohydrates are able to store a large amount of energy due to high concentration of _____ bonds in themselves.
→ Lipids
     C-H

Question 3:
Carbohydrates store _____ (more or less) energy per gram than lipids because carbohydrates have _____ (higher or lower) concentration of _____ bonds. _____ are also present along the carbon chain.
→ Less
     Lower
     C-H
     Alcohols

Question 4:
The consistent structure of carbohydrates allows them to be easily stacked together in the cell, which contributes to their usefulness for _____.
→ Energy storage

Question 5:
_____ reaction allows carbohydrates to join together and form long chains of _____ for energy storage, whereas _____ reaction allows the release of single sugar molecules called _____ that tissues can use for energy.
→ Dehydration
     Polysaccharides
     Reverse hydrolysis
     Monosaccharides

Question 6:
Carbohydrates can be thought of as Carbon and _____ in a fixed 1:1 ratio. For each Carbon atom, there exists 1 _____ atom and 2 _____ atoms. The formula for any carbohydrates is: _____.
→ Water
     Oxygen
     Hydrogens
     Cn(H2O)n

Question 7:
Name 2 examples for 6-carbon carbohydrates, one of which should be the most commonly occurring 6-carbohydrate. The terminology for a 6-carbon carbohydrate is _____.
→ Fructose
     Glucose (the most commonly occurring 6-carbon carbohydrate) 
     Hexose

Question 8:
Almost all digested carbohydrates reaching body cells have been converted to _____ by the liver or intestinal cells.
→ Glucose

Question 9:
The cell can _____ (oxidize or reduce) glucose to convert its _____ energy to a more readily usable form, _____. If the cell already has a sufficient amount of this readily usable form, glucose is _____ (polymerized or depolymerized) to the polysaccharide form, _____, or converted to fat.
→ Oxidize
     Chemical
     ATP (= Adenosine TriPhosphate)
     Polymerized
     Glycogen

Question 10:
Glycogen is a _____ (branched or unbranched) glucose _____ (polymer or monomer) with _____ (alpha or beta) linkages. Glycogen is found in all animal cells, but especially abundant in _____ and _____ cells.
→ Branched
     Polymer
     Alpha
     Muscle
     Liver

Question 11:
_____ (organ) regulates the blood glucose level, so its cells are 1 of the few cell types capable of reforming glucose from glycogen and releasing it back into the bloodstream when needed. Only certain epithelial cells in the digestive track and the proximal tubule of the _____ (organ) are capable of absorbing glucose against a concentration gradient. This is done via a secondary active transport mechanism down the concentration gradient of _____. All other cells absorb glucose via _____.
→ Liver
     Kidney
     Sodium
     Facilitated diffusion (a process of spontaneous passive transport of molecules or ions across
     membrane via specific transmembrane proteins)

Question 12:
_____, when present, increases the rate of facilitated diffusion for glucose and other monosaccharides. When absent, only _____ and _____ cells are capable of absorbing sufficient amounts of glucose via facilitated transport system.
→ Insulin
     Neural
     Hepatic

Question 13:
Just like animals, plants join glucose molecules to form polysaccharides. However, while animals use _____ for long-term storage, plants use _____ instead.
→ Glycogen
     Starch

Question 14:
Name 2 forms of starch and briefly describe their components.
→ Amylose: branched or unbranched, has the same alpha linkages as glycogen
     Amylopectin: resemble glycogen but has a different branching structure
(Source: http://image.slidesharecdn.com/lecture14carbohydratescompletetobetaught-140904231611-phpapp01/95/lecture-14-carbohydrates-complete-to-be-taught-17-638.jpg?cb=1409872606)

Question 15:
Glycogen and starch are composed of _____ linkages, whereas cellulose is composed of _____ linkages. Glycogen and starch serve as _____ in animals and plants, respectively; whereas cellulose serves as _____ in plants.

(Source: https://biochemistry3rst.files.wordpress.com/2014/02/219_three_important_polysaccharides-01.jpg)

→ Alpha
     Beta
     Energy storage
     Structural material

Question 16:
Humans _____ (do or do not) have enzymes to digest the alpha linkages of starch. Humans _____ (do or do not) have enzymes to digest the alpha linkages of glycogen. Humans _____ (do or do not) have enzymes to digest the beta linkages of cellulose. If do not, give an example of how such linkages can be digested and which animals have this mechanism.
→ Do
     Do
     Do not: cows and certain insects have bacteria in their digestive system that release enzyme to
     digest beta linkages in cellulose

Question 17:
For glucose polymers, animals eat alpha linkage, but only _____ break beta linkages. The stability of beta linkages of cellulose makes it a tough, stable molecule that can be used to build plant's _____.
→ Bacteria
     Cell walls

PRACTICE

Question 1:
Name 2 primary biological importances of carbohydrates.

Question 2:
Similar to _____, carbohydrates are able to store a large amount of energy due to high concentration of _____ bonds in themselves.

Question 3:
Carbohydrates store _____ (more or less) energy per gram than lipids because carbohydrates have _____ (higher or lower) concentration of _____ bonds. _____ are also present along the carbon chain.

Question 4:
The consistent structure of carbohydrates allows them to be easily stacked together in the cell, which contributes to their usefulness for _____.

Question 5:
_____ reaction allows carbohydrates to join together and form long chains of _____ for energy storage, whereas _____ reaction allows the release of single sugar molecules called _____ that tissues can use for energy.

Question 6:
Carbohydrates can be thought of as Carbon and _____ in a fixed 1:1 ratio. For each Carbon atom, there exists 1 _____ atom and 2 _____ atoms. The formula for any carbohydrates is: _____.

Question 7:
Name 2 examples for 6-carbon carbohydrates, one of which should be the most commonly occurring 6-carbohydrate. The terminology for a 6-carbon carbohydrate is _____.

Question 8:
Almost all digested carbohydrates reaching body cells have been converted to _____ by the liver or intestinal cells.

Question 9:
The cell can _____ (oxidize or reduce) glucose to convert its _____ energy to a more readily usable form, _____. If the cell already has a sufficient amount of this readily usable form, glucose is _____ (polymerized or depolymerized) to the polysaccharide form, _____, or converted to fat.

Question 10:
Glycogen is a _____ (branched or unbranched) glucose _____ (polymer or monomer) with _____ (alpha or beta) linkages. Glycogen is found in all animal cells, but especially abundant in _____ and _____ cells.

Question 11:
_____ (organ) regulates the blood glucose level, so its cells are 1 of the few cell types capable of reforming glucose from glycogen and releasing it back into the bloodstream when needed. Only certain epithelial cells in the digestive track and the proximal tubule of the _____ (organ) are capable of absorbing glucose against a concentration gradient. This is done via a secondary active transport mechanism down the concentration gradient of _____. All other cells absorb glucose via _____.

Question 12:
_____, when present, increases the rate of facilitated diffusion for glucose and other monosaccharides. When absent, only _____ and _____ cells are capable of absorbing sufficient amounts of glucose via facilitated transport system.

Question 13:
Just like animals, plants join glucose molecules to form polysaccharides. However, while animals use _____ for long-term storage, plants use _____ instead.

Question 14:
Name 2 forms of starch and briefly describe their components.

Question 15:
Glycogen and starch are composed of _____ linkages, whereas cellulose is composed of _____ linkages. Glycogen and starch serve as _____ in animals and plants, respectively; whereas cellulose serves as _____ in plants.

(Source: https://biochemistry3rst.files.wordpress.com/2014/02/219_three_important_polysaccharides-01.jpg)

Question 16:
Humans _____ (do or do not) have enzymes to digest the alpha linkages of starch. Humans _____ (do or do not) have enzymes to digest the alpha linkages of glycogen. Humans _____ (do or do not) have enzymes to digest the beta linkages of cellulose. If do not, give an example of how such linkages can be digested and which animals have this mechanism.

Question 17:
For glucose polymers, animals eat alpha linkage, but only _____ break beta linkages. The stability of beta linkages of cellulose makes it a tough, stable molecule that can be used to build plant's _____.

ANSWER KEY

Question 1:
→ Energy storage
     Provision of easily accessible energy to the body

Question 2:
→ Lipids
     C-H

Question 3:
→ Less
     Lower
     C-H
     Alcohols

Question 4:
→ Energy storage

Question 5:
→ Dehydration
     Polysaccharides
     Reverse hydrolysis
     Monosaccharides

Question 6:
→ Water
     Oxygen
     Hydrogens
     Cn(H2O)n

Question 7:
→ Fructose
     Glucose (the most commonly occurring 6-carbon carbohydrate) 
     Hexose

Question 8:
→ Glucose

Question 9:
→ Oxidize
     Chemical
     ATP (= Adenosine TriPhosphate)
     Polymerized
     Glycogen

Question 10:
→ Branched
     Polymer
     Alpha
     Muscle
     Liver

Question 11:
→ Liver
     Kidney
     Sodium
     Facilitated diffusion (a process of spontaneous passive transport of molecules or ions across
     membrane via specific transmembrane proteins)

Question 12:
→ Insulin
     Neural
     Hepatic

Question 13:
→ Glycogen
     Starch

Question 14:
→ Amylose: branched or unbranched, has the same alpha linkages as glycogen
     Amylopectin: resemble glycogen but has a different branching structure
(Source: http://image.slidesharecdn.com/lecture14carbohydratescompletetobetaught-140904231611-phpapp01/95/lecture-14-carbohydrates-complete-to-be-taught-17-638.jpg?cb=1409872606)

Question 15:
→ Alpha
     Beta
     Energy storage
     Structural material

Question 16:
→ Do
     Do
     Do not: cows and certain insects have bacteria in their digestive system that release enzyme to
     digest beta linkages in cellulose

Question 17:
→ Bacteria
     Cell walls