Chapters 2&3 Flashcards
Describe the general structure of atoms
Protons and neutrons are in the nucleus
Electrons are in orbit around the nucleus
Define orbital and electron shell
Orbital - the region surrounding the nucleus of an atom and the probability of finding an electron is high
Electron shells are the energy levels; larger atoms have more electron shells than smaller atoms
Relate atomic structure to the periodic table of the elements
The number of protons and electrons determine an atom’s position on the periodic table.
Explain how elements can exist as isotopes
Elements that have a different number of neutrons than protons is considered an isotope
Compare and contrast ionic, covalent, and hydrogen bonds; atomic interactions that lead to the formation of molecules
Ionic bonds - happens when an atom or molecule gains or loses one or more electrons and acquires a net charge
Covalent bonds - chemical bond where two atoms share a pair of electrons
Hydrogen bonds - a weak interaction between a hydrogen atom in a polar molecule and an electronegative atom in another polar molecule
Explain the concept of electronegativity and how this contributes to the formation of polar and nonpolar covalent bonds
Electronegativity is the measure of an atom’s ability to attract electrons in a bond with another atom. Atoms that have fuller valance electron clouds (O,N, F) do not like to share the electrons, so they take them majority of the time and rarely return them. This creates polar and nonpolar bonds.
Nonpolar - strong covalent bond formed between 2 atoms with similar electronegativities and the electrons are shared
Polar - a covalent bond between 2 atoms with different electronegativities. FON
Identify the properties of water that support life
Can provide force or support for the bodies of organisms and plants
can remove toxic waste compounds from animal’s bodies
Distinguish between hydrophilic and hydrophobic substances
hydrophilic - water loving
Hydrophobic - water hating
Relate the concept of electronegativity to hydrophilic and hydrophobic substances
Similar to electronegativity, hydrophilic substances have a strong pull towards water and create strong bonds like nonpolar.
what is matter?
Anything that has mass and takes up space
Element
a pure substance made up of one atom
Atom
smallest functional units of matter that form all chemical substances and ultimately all organisms
Proton, electrons, and neutrons. What are they
proton - positive particle found in nucleus and determines the atomic number that defines each element
Neutrons - neutral particle found in the nucleus
Electrons - negative particle found in orbitals around nucleus
Orbital
Electron Shell
Valence Electron
Electron cloud
Orbital - region surrounding the nucleus where electrons are found
Electron shell - energy level
Valence electron - electrons in the outermost shell
Electron cloud - general term when referring to the location of the electrons
Ion
when an atom or molecule loses or gains one or more of its valence electrons
Isotopes
when the neutron count differs from proton count
Electronegativity
a measure of an atom’s ability to attract electrons in a bond with another atom
Solvent
liquid in which the solute is dissolved
Solute
A substance dissolved in a liquid
Density
mass of a unit volume of a material substance
ice is less dense than water = floats on top
Equilibrium
Basically when the equation is balanced
- A state of a chemical reaction in which the rate of formation of products equals the rate of formation of the reactants
Reactant
A substance that participates in a chemical reaction and becomes changed by that reaction
Product
End result of a chemical reaction
Chemical Reaction
A process in which one or more substances are changed into other substances by the making or breaking of bonds
Covalent bond
A chemical bond where two atoms share a pair of elections, whether fairly or unfairly
Polar molecule
have one or more polar covalent bonds
Van der Waals interaction
Attractive forces between molecules in close proximity to each other, caused by the variations in the distribution of electron density around individual atoms
- results from small differences in electron clouds in nonpolar bonds
- between nonpolar molecules
- very weak but collectively strong
Hydrogen Bond
A weak interaction between a hydrogen atom in a polar molecule and an electronegative atom in another polar molecule
Hydrophobic vs. Hydrophilic
Hydrophobic is water hating
hydrophilic is water loving
Why are valence electrons important?
Valance electrons are the part of the atom actually participating in bonding
Why is water so important? How does it accomplish this?
Water is the solvent for most chemical reactions in all living organisms, inside and outside of cells. Hydrolysis reactions break down large molecules into smaller units. Water provides support, eliminates wastes, dissipates body heat
Are hydrogen bonds typically within or between molecules
between
If Van Der Waals forces are so weak, why are they important? Give a couple examples
They allow nonpolar molecules and atoms to become solids and liquids and are responsible for surface tension, which allows for bugs to walk on water
Grease is hydrophobic. How does soap help to remove grease form your hands?
The soap has both polar and nonpolar ends, so the hydrophobic ends of the soap molecules attract the grease, form a drop around the grease (ball) and then allow the oil ball to roll off the skin
Compare and contrast covalent and ionic bonds
Covalent is when they share electrons, whether fairly or unfairly. Ionic is when the atom/molecule actually loses or gains an electron
Why are some covalent bonds polar and some covalent bonds non-polar?
It depends on if the atoms/molecules are sharing the electrons fairly. If they are, the bonds are nonpolar. However, if one atom is hogging the electrons (has a higher electronegativity), then the bond is polar
A polar covalent bond is created when
a. electrons transferred from one atom to another disrupt the balance between the
two sides of the bond, making the bond very unstable.
b. bonded atoms have an equal pull on the shared electron so that the electron
spends approximately equal amounts of time around each.
c. bonded atoms have unequal pull on the shared electron so that the electron
spends more time around one atom than the other.
d. electrons and protons are shared between atoms, creating a strong bond, which
can only be broken with a large input of energy
c
Carbon and hydrogen have similar electronegativities and combine together to form
hydrocarbon molecules. What type of bonds form between these atoms?
a. hydrogen
b. ionic
c. polar covalent
d. nonpolar covalent
e. electrostatic
c
What type of bonds form from the unequal sharing of electrons?
a. hydrogen
b. ionic
c. polar covalent
d. nonpolar covalent
e. electrostatic
c
The LEAST hydrophilic substance is
a. salt.
b. an ion.
c. oil.
d. an amphipathic molecule.
c
Define an organic molecule.
A carbon-containing molecule, so named because such molecules were first discovered in living organisms
Identify common functional groups of organic compounds
functional group - a group of atoms with a characteristic chemical structure that exhibits particular properties
Amino (-NH2)
Carbonyl Ketone (-CO)
Aldehyde (-CHO)
Carboxyl (-COOH)
Hydroxyl (-OH)
Methyl (-CH3)
Phosphate (-PO4^2-)
Sulfate (-SO4^-)
Sulfhydryl (-SH)
Explain the roles of dehydration and hydrolysis reactions in the formation and breakdown of organic molecules
Hydrolysis reaction - When a polymer is broken down into monomers by water because each monomer is replaced by a molecule of water
Dehydration reaction - a type of condensation reaction where water is lost (a molecule of water is removed when a monomer is added to a growing polymer)
List the four main classes macromolecules of cells
Carbohydrates, lipids, proteins, and nucleic acids
Compare and contrast the structures of carbohydrates, lipids, proteins, and nucleic acids
Carbohydrates - (CnH2On) *n is a whole number
Lipids - primarily composed of carbon and hydrogen, with some oxygen; can have phosphorous (phospholipids, steroids, & waxes); hydrophobic
Proteins - a polypeptide (or more) composed of a linear sequence of amino acids
Nucleic acids - linear sequence of nucleotides (DNA is double-stranded; RNA is single-stranded but may have double-stranded regions)
Describe the different functions of carbohydrates in cells
- supply energy to all cells in the body
- build macromolecules
- Assists in lipid metabolism
Sugars, small carbohydrates, are broken down by enzymes, which releases energy
List the classes of lipid molecules important in living organisms
Triglycerides - made from glycerol and three fatty acids (fatty acids - chain of carbon and hydrogen atoms with a carboxyl group [-COOH])
Phospholipids - similar to triglycerides except the third hydroxyl group of glycerol is linked to a phosphate group rather than a fatty acids
Steroids - four fused rings of carbon atoms form the general structure of all steroids
Waxes - contain one or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain
Discuss the different functions of the classes of lipid molecules in cells
Triglycerides - (fats) are important for storing energy; hydrolysis releases the fatty acids from glycerol which can then provide energy to make ATP
Phospholipids - form the structural components of the cell membrane, regulate membrane permeability, and participate in the absorption of fat from the intestine
Steroids - (cholesterol) responsible for whether an animal exhibits male or female characteristics
Waxes - provide a barrier to water loss
Illustrate the general structure of an amino acid and explained how they are joined together
The alpha carbon is in the middle, amino group (-NH2) is attached on one side, there’s a side chain, and there is a carboxyl group (-COOH) on the other side
Distinguish the four levels of protein structure
Primary - sequence of amino acids
Secondary - Alpha helices (spiral/helix) and beta sheets (ribbon), the shapes of random coiled regions are specific and important for the protein’s structure
Tertiary - 3D structure of the over protein (polypeptide)
Quaternary - when two or more polypeptides associate to form a protein complex; ONLY PROTEIN COMPLEXES HAVE LEVEL 4 STRUCTURE
Describe the three components of a nucleotide
A phosphate group
A pentose (five-carbon) sugar (either ribose or deoxyribose)
A single or double ring of carbon and nitrogen atoms known as a base
Distinguish between a polypeptide and a protein
A polypeptide is a structural unit made of a linear sequence of amino acids
A protein is a functional unit composed of one or more polypeptides that have folded and twisted into a precise three-dimensional shape
Discuss the four levels of protein structure
Primary - sequence of amino acids; determines the identity and characteristics of the protein
Secondary - Alpha helices (spiral/helix) and beta sheets (ribbon), the shapes of random coiled regions are specific and important for the protein’s structure; affects the protein shape
Tertiary - 3D structure of the over protein (polypeptide); allows amino acids to interact with each other that are not close in primary structure
Quaternary - when two or more polypeptides associate to form a protein complex; ONLY PROTEIN COMPLEXES HAVE LEVEL 4 STRUCTURE
Describe the three components of a nucleotide
A phosphate group
A pentose (five-carbon) sugar (either ribose or deoxyribose)
A single or double ring of carbon and nitrogen atoms known as a base
Distinguish between the structure of DNA and RNA
DNA is a double helix and has Adenine + Thymine and Cytosine + Guanine
RNA is single stranded and has Adenine + Uracil and Guanine + Uracil
Identify the role of hydrogen bonding in nucleic acids
Hydrogen bonds are responsible for specific base-pair formation in the DNA double helix (A+G and C+T)
Carbon
is life’s fundamental building block and is essential to all life on this wretched Earth :)
Covalent bonds relating to carbon
Carbon can form four covalent bonds with other atoms including with other carbon atoms
Organic molecules
A carbon-containing molecule
Functional groups
a group of atoms with a characteristic chemical structure that exhibits particular properties. Each functional group shows the same properties in all molecules in which it occurs
Macromolecules
Many molecules bonded together to form a polymer. Carbohydrates, proteins, and nucleic acids (DNA and RNA) are important macromolecules found in living organisms
Dehydration reaction
Forming a polymer with two smaller molecules that are combined by a condensation reaction; a molecule of water is removed when the monomers are added to the growing polymer
Hydrolysis reaction
polymer is broken down into monomers = molecule of water is added back each time a monomer is released
Monomer vs Polymer
Monomer - An organic molecule that can be used to form a larger molecule (polymer) consisting of many repeating units of the monomer.
Polymer - A large molecule formed by linking many smaller molecules called monomers.
Carbohydrate
simple carbohydrates are broken down to make ATP and larger carbohydrates store energy or may play a structural role
Monosaccharide vs Polysaccharide
mono - a simple sugar, such as pentose or hexose
poly - long carbohydrate polymer formed of many monosaccharides linked together
Glycosidic bond
A covalent bond formed between two sugar molecules via dehydration reaction
Disaccharide
A carbohydrate composed of two monosaccharides
Fats
aka triglycerides
formed when glycerol bonds to three fatty acids
Saturated vs unsaturated
Saturated fatty acid - all the carbons are linked by single covalent bonds
Unsaturated - A fatty acid that contains one or more C=C double bonds
Triglyceride
A molecule composed of three fatty acids linked by ester bonds to a molecule of glycerol
Phospholipid
A type of lipid that’s similar in structure to a triglyceride, but with the third hydroxyl group of glycerol linked to a phosphate group instead of a fatty acid; a key component of biological membranes
Amphipathic
molecules that contain a hydrophobic (water-hater) region and a hydrophilic (water-lover) region
Steroid
A lipid containing four interconnected rings of carbon atoms; functions as a hormone in animals in plants
Cholesterol
found in the blood and cellular membranes of animals
aids in the production of sex hormones, such as testosterone and estrogen
Protein
a functional unit composed of one or more polypeptides
- play a key role in cell structure and carry out a diverse array of cellular functions (proteins are involved with gene expression and regulation, cell-signaling proteins, metabolic enzymes
Amino Acid
Any of the monomers that are linked to form a protein. Amino acids have a common structure in which a carbon atom, called the α-carbon, is linked to an amino group (─NH2) and a carboxyl group (─COOH), as well as to a hydrogen atom and a side chain that distinguishes the particular amino acid.
R group
represents the side chain that is bonded with the alpha carbon
Peptide bond
The covalent bond between a carboxyl and amino group that links amino acids in a polypeptide
Peptide vs. Polypeptide
A molecule consisting of a linear sequence of amino acids; the term denotes structure
Subunit
A protein subunit is an individual polypeptide within a functional protein; most functional proteins are composed of two or more polypeptides
Primary progressive level
Primary - sequence of amino acids; determines the identity and characteristics of the protein
Secondary - Alpha helices (spiral/helix) and beta sheets (ribbon), the shapes of random coiled regions are specific and important for the protein’s structure; affects the protein shape
Tertiary - 3D structure of the over protein (polypeptide); allows amino acids to interact with each other that are not close in primary structure
Quaternary - when two or more polypeptides associate to form a protein complex; ONLY PROTEIN COMPLEXES HAVE LEVEL 4 STRUCTURE
Secondary
Secondary - Alpha helices (spiral/helix) and beta sheets (ribbon), the shapes of random coiled regions are specific and important for the protein’s structure; affects the protein shape
Tertiary
Tertiary - 3D structure of the over protein (polypeptide); allows amino acids to interact with each other that are not close in primary structure
Quaternary
Quaternary - when two or more polypeptides associate to form a protein complex; ONLY PROTEIN COMPLEXES HAVE LEVEL 4 STRUCTURE
Alpha Helix
The polypeptide backbone forms a repeating helical structure that is stabilized by hydrogen bonds along the length of the backbone. The hydrogen bonds occur at regular intervals along the polypeptide backbone and cause the backbone to twist into a helix
Beta sheet
the regions of the polypeptide backbone lie parallel to each other; hydrogen bonds between a hydrogen linked to a nitrogen atom and a double-bonded oxygen form between these adjacent, parallel regions. The polypeptide backbone adopts a repeating zigzag, PLEATED, shape
Disulfide bond
aka disulfide bridge
covalent chemical bond formed between two sulfhydryl groups on cysteine side chains in a protein; important in the tertiary structure of proteins
Domain
- A defined region of a protein with a distinct structure and function. 2. One of the three major categories of life: Bacteria, Archaea, and Eukarya.
DNA vs RNA
They both are nucleic acids
DNA: There are two strands of nucleotides coiled around each other to form a double helix, held together by hydrogen bonds according to the Adenine + Thymine and Guanine + Cytosine rule
RNA: There is one strand of nucleotides; the sugar in each nucleotide is ribose; abides by the Adenine + Uracil and Guanine + Cytosine rule
Nucleotide
An organic molecule having three components: one or more phosphate groups, a five-carbon sugar (either deoxyribose or ribose), and a single or double ring of carbon and nitrogen atoms known as a base
Phosphodiester Bond vs. hydrogen bond
Phosphodiester: The glue that holds DNA and RNA together, linking sugar and phosphate groups of nucleotides; bonds the phosphates that makes up the backbones of DNA and RNA
Hydrogen: bonds the bases (ATGC) of DNA together
Nitrogenous base
One of the bases of a nucleotide
Ribose vs Deoxyribose
Deoxyribose: a five-carbon sugar found in DNA
Ribose: a five-carbon sugar found in RNA
Phosphate group
a component of a nucleotide
Double helix
two strands coiled around each other in DNA
Complementary
The nucleotide bases at each position in the sequences [DNA and RNA] will be complementary (A+T or U and C+G)
Anti-parallel
two strands of DNA have opposite orientations; one strand of DNA runs from 5’ to 3’ and the other strand runs from 3’ to 5’ which allows for the base pairs to align and form hydrogen bonds
Hydrogen bond
The bases of DNA are bonded by hydrogen bonds (A+T and G+C)
Adenine, Guanine, Cytosine, Thymine, Uracil. Which ones go together?
Adenine + Thymine [Sub. Uracil] and Guanine + Cytosine
What are the four major macromolecule groups?
Carbohydrates, proteins, lipids, and nucleic acids
What bonds create the polymers for polysaccharides?
Glycosidic bonds
What bonds create the polymers of amino acids?
Peptide bonds
What is the role of water in making or breaking of polymers?
Hydrolysis: Polymers are broken down into monomers b/e water molecules replace the monomers that are released
Dehydration: two molecules combine to form a polymer through condensation reaction/dehydration; a water molecule is removed when a monomer is added to the growing polymer
What are the major parts of an amino acid?
there’s an alpha carbon in the middle, a side chain (R), carboxyl group, and amino group, and a hydrogen atom
How are amino acids similar? How are they different?
Amino acids all have the same groups connected to the alpha carbon (carboxyl, amino, and a hydrogen atom). The thing that’s changing is the side chain (R)
How are DNA and RNA similar? How are they different?
DNA and RNA both are made of nucleotides. They both have a phosphate backbone and four nitrogenous bases. However, DNA is double stranded (RNA is single stranded), RNA codes for amino acids and acts as a messenger and DNA stores genetic material, DNA molecules are self-replicating while RNA molecules are synthesized by transcription, they have different bases (RNA has uracil instead of thymine)
Discuss the major functions of proteins.
Make mRNA from a DNA template and synthesize polypeptides from mRNA and regulate genes
Initiate movement [motor proteins]
Increase rates of chemical reactions [metabolic enzymes]
Enables cells to communicate with each other and the environment [cell-signaling proteins]
Support and strengthen structures [structural proteins]
What do proteins, polysaccharides and nucleic acids have in common?
They are all macromolecules
Polysaccharide is a carbohydrate
List and briefly describe the levels of protein structure.
Primary - sequence of amino acids
Secondary - Alpha helices (spiral/helix) and beta sheets (ribbon), the shapes of random coiled regions are specific and important for the protein’s structure
Tertiary - 3D structure of the over protein (polypeptide)
Quaternary - when two or more polypeptides associate to form a protein complex; ONLY PROTEIN COMPLEXES HAVE LEVEL 4 STRUCTURE
What level of protein structure involves alpha helices and beta sheets?
Secondary structure - determines the protein’s structure
What are some of the types of chemical bonds that influence a protein’s structure?
hydrogen and ionic
Discuss the functions of carbohydrates.
broken down to make ATP, store energy, provide structure
The plasma membrane is made up of a phospholipid bilayer, with
the _________blank of the phospholipids_________blank.
a. hydrophobic tails; sticking out toward the interior and exterior of the cell
b. hydrophilic heads; facing in toward one another
c. hydrophilic heads; sticking out toward the interior and exterior of the cell
d. hydrophobic and hydrophilic sides; facing in toward one another
c
A dehydration reaction
a. results in the splitting of a water molecule.
b. breaks down complex molecules to simple ones.
c. is used to form polymers.
d. forms glucose monomers from glycogen.
e. form glycerol and fatty acids from triglycerides.
c
The portion of an amino acid that makes the amino acid unique among the 20
different amino acids is
a. carboxyl.
b. amino.
c. hydrocarbon.
d. the side chain or R-group.
e. peptide bonding
d
Which of the following biological molecules contain peptide bonds?
a. Proteins
b. Carbohydrates
c. Lipids
d. Nucleic Acids
a
The 2 strands of DNA are covalently bonded together. These bonds are called
phosphodiester bonds.
a. This is true
b. This is false
a
the bonds between the actual bases are hydrogen bonds
C-H is a nonpolar group.
a. This is true
b. This is false
a
