Chapter 2 Flashcards
Matter is defined as?
Anything that takes up space and that has mass
The smallest chemical units of matter are?
Atoms
A nucleus is composed of? What is an exception?
Uncharged neutrons and positively charged protons.
The only exception is the nucleus of a normal hydrogen atom, which is composed of only a single proton and no neutrons.
Where can you find electrons in an atom?
Orbiting the nucleus
The number of electrons in an atom typically equals?
The number of protons, so overall atoms are electrically neutral
What is an element?
Matter that is composed of a single type of atom. For example, gold is an element because it consists of only gold atoms. In contrast, the ink in your pen is not an element, because it is composed of many different kinds of atoms
How do elements differ from one another?
In their atomic number, which is the number of protons in their nuclei. For example, the atomic number of hydrogen, carbon, and oxygen are 1, 6, and 8, respectively, because all hydrogen nuclei contain a single proton, all carbon nuclei have six protons, and all oxygen nuclei have 8 protons
What is the atomic mass of an atom?
Sometimes called its atomic weight, it is the sum of the masses of its protons, neutrons, and electrons
Protons and neutrons each have a mass of what?
Electron?
Of approximately 1 atomic mass unit, which is also called a dalton.
An electron is much less massive, with a mass of about 0.00054 dalton.
Why are electrons often ignored in discussions of atomic mass?
Because their contribution to the overall mass is negligible, therefore the sum of the number of protons and neutrons approximates the atomic mass of an atom
There are ___ naturally occurring elements known, however organisms typically utilize only about ___ elements, each of which has its own symbol that is derived from its English or Latin name
93
20
Every atom of an element has the same number of protons, but atoms of a given element can differ in the number of? What is it called?
Neutrons in their nuclei which are called isotopes. For example there are three naturally occurring isotopes of carbon, each having six protons and six electrons
Over ___% of carbon atoms also have six neutrons. Because these atoms have six protons and six neutrons, the atomic mass of this isotope is about ___ daltons, and it is known as carbon-__, symbolized as ____
95%
12 daltons
carbon-12
12^C
Atoms of carbon 13 have how many neutrons?
Atoms of carbon 14 have how many neutrons? Why is carbon 14 unstable?
carbon-13 have7 neutrons per nucleus
Carbon-14 have 8 neutrons per nucleus. Unlike the first two isotopes, the nucleus of 14^C is unstable because of the ratio of its protons and neutrons
What do unstable atomic nuclei release?
Energy and subatomic particles such as neutrons, protons, and electrons in a process called radioactive decay.
Atoms that undergo radioactive decay are called?
Radioactive isotopes
Radioactive decay and radioactive isotopes play important roles in?
Microbiological research, medical diagnosis, the treatment of disease, & the complete destruction of contaminating microbes (sterilization) of medical equipment and chemicals
Although the nuclei of atoms determine their identities, it is what the determines an atoms chemical behavior? Why?
Electrons because the nuclei of different atoms almost never come close enough together to interact. Typically only the electrons of atoms interact. Thus, because all of the isotopes of carbon (for example) have the same number of electrons, all these isotopes behave the same way in chemical reactions, even though their nuclei are different.
An electron shell depicts?
The probable locations of electrons at a given time
Each electron shell can hold how many electrons?
Only a certain maximum number of electrons. For example the first shell can accommodate a maximum of 2 electrons, and the second shell can hold no more than 8 electrons.
Electrons in the outermost shell of atoms are called?
Valence electrons
Outer electron shells are stable when they contain how many electrons (except for the first electron shell, which is stable with only ___ electrons, because that is the maximum number)
8
2
When atoms’ outer shells are not filled with eight electrons, they either?
Have room for more electrons or have “extra” electrons, depending on whether it is easier for them to gain electrons or lose electrons. For example, an oxygen atom with 6 electrons in its outer shell has 2 unfilled spaces, because it requires less energy for the atom to gain two electrons than to lose 6 electrons. A calcium atom by contrast, has two “extra” electrons in its outer (fourth) shell, because it requires less energy to lose these two electrons than to gain 6 new ones. When a calcium atom loses two electrons, its third shell, which is then its outer shell, is full and stable with eight electrons
An atom’s outermost electrons are called valence electrons, & thus the outermost shell of an atom is the?
Valence shell
An atom’s valence, defined as its combining capacity, is considered to be positive if? Negative if? Give calcium as an example
Positive if its valence shell has extra electrons to give up
Negative if its valence shell has spaces to fill
Thus a calcium atom, with two electrons in its valence shell, has a valence of +2, whereas an oxygen atom, with 2 spaces to fill in its valence shell, has a valence of -2
Atoms combine with one another by? What is this called?
Either sharing or transferring valence electrons in such a way as to fill their valence shells.
Such interactions between atoms are called chemical bonds
Define molecule and compound. Give two hydrogen atoms bonded together and two hydrogen and an oxygen (water) as an example.
Molecule- Two or more atoms held together by chemical bonds form a molecule.
Compound- A molecule that contains atoms of more than one element is a compound.
Two hydrogen atoms bonded together form a hydrogen molecule, which is NOT a compound because only one element is involved. However, two hydrogen atoms bonded to an oxygen atom form a molecule of water which is a compound
What is a covalent bond? Give two hydrogen as an example and two oxygen.
The sharing of a pair of electrons by two atoms.
Each hydrogen atom consists of a single proton orbited by a single electron. Because the valence shell of each hydrogen atom requires two electrons to be filled, each atom shares its single electron with the other, forming a hydrogen molecule in which both atoms have full shells.
Two oxygen atoms can share electrons but they must share two pairs of electrons for their valence shells to be full. Because two pairs of electrons are involved, oxygen atoms form two covalent bonds, or a double covalent bond with one another.
What is electronegativity?
The attraction of an atom for electrons
The more an atom is electronegative (attraction of an atom for electrons) the greater the?
Pull its nucleus exerts on electrons
Electronegativities tend to increase from left to right in the periodic table. The reason for this is?
Electronegativities of elements decrease from top to bottom in the chart because?
Increase from left to right because elements towards the right of the chart have more protons and thus exert a greater pull on electrons.
Decrease from top to bottom because the distance between the nucleus and the valence shell increases as elements get larger
Atoms with equal or nearly equal electronegativities, such as two hydrogen atoms or a hydrogen and a carbon, share electrons?
Equally or nearly equally
What are “poles”?
Opposed forces. Atoms with similar electronegativites, the shared electrons tend to spend an equal amount of time around each nucleus of the pair, and no pole exist; therefore, the bond between them is a nonpolar covalent bond
An example of structural formula for two shared hydrogen atoms
1) H — H and 2) H:H
1) In the first symbol, the dash represents the chemical bond between the atoms.
2) In the second symbol, the dots represent the electron pair of the covalent bond.
These are known as structural formulas
An example of molecular formula for hydrogen
H2 The subscript 2 indicates the number of hydrogen atoms that are bonded, not the number of shared electrons
A line in the structural formula represents?
A double line in the structural formula represents?
Single line- Covalent bond formed from the sharing of two electrons.
Double line- indicates the sharing of 4 electrons
How are carbon atoms critical to life?
Because a carbon atom has 4 electrons in its valence shell, it has equal tendency to either lose or gain 4 electrons. Either event produces a full outer shell. The result is that carbon atoms tend to share electrons and form four covalent bonds with one another, and with many other types of atoms. Each carbon atom in effect acts as a four-way intersection where different components of a molecule can attach. One result of this feature is that carbon atoms can form very large chains that constitute the “backbone” of many biological important molecules. Carbon chains can be branched or unbranched, and some even close back on themselves to form rings.
What are organic compounds?
Compounds that contain carbon and hydrogen atoms. Among the many biological important organic compounds are proteins and carbohydrates.
What happens if two covalently bound atoms have significantly different electronegativities?
Their electrons will not be shared equally. Instead, the electron pair will spend more time orbiting the nucleus of the atom with greater electronegativity. This type of bond, in which there is unequal sharing of electrons, is a polar covalent bond
Is water a polar or non polar covalent bond?
Water is a polar covalent bond, there is unequal sharing of electron pairs. Because oxygen is more electronegative than hydrogen, the electrons spend more time near the oxygen nucleus than near the hydrogen nuclei, and thus the oxygen atom acquires a transient (partial) negative charge. The hydrogen nuclei each have a corresponding transient positive charge. The covalent bond between an oxygen atom & a hydrogen atom is called polar because the atoms have opposite partial electrical charges.
Generally, molecules with polar covalent bonds are?
Water soluble, and nonpolar molecules are not.
The most important polar covalent bonds for life are those that involve?
Hydrogen because they allow hydrogen bonding
Both nonpolar and polar covalent bonds form?
Angles between atoms such that the distances between electron orbits are maximized
What is an ion?
An atom or group of atoms that has either a full negative charge or a full positive charge. (One atom loses an electron and one atom gains electrons, no sharing)
What are cations?
Positively charged ions
What are anions?
Negatively charged ions
What is an ionic bond?
Cations and anions attract each other because of their opposite charge. They form crystalline compounds composed of metallic and nonmetallic ions known as salts, such as sodium chloride (NaCl), & potassium chloride (KCl)
How do ionic bonds differ from covalent bonds?
Ions do not share electrons. Instead, the bond is formed from the attraction of opposite electrical charges
How does water molecules interfere with ionic bonds of salts?
The polar bonds of water molecules interfere with the ionic bonds of salts, causing dissociation (also called ionization). This occurs as the partial negative charge on the oxygen atom of water attracts cations, & the partial positive charge on hydrogen atoms attracts anions.
What are electrolytes?
When cations and anions disassociates from one another & become surrounded by water molecules (are hydrated), they are called electrolytes because they can conduct electricity through the solution. Electrolytes are critical for life because they stabilize a variety of compounds, act as electron carriers, & allow electrical gradients to exist within cells.
Electrons are shared between atoms in ________ bonds and transferred from one atom to another in ________ bonds
Shared- covalent
Transferred- ionic
Hydrogen atoms bind to oxygen atoms by means of?
Polar covalent bonds, which results in transient positive charges on the hydrogen atoms. Hydrogen atoms form polar covalent bonds with atoms of other elements as well.
Describe a hydrogen bond
The electrical attraction between a partially charged hydrogen atom and full or partial negative charge on either a different region of the same molecule or another molecule.
Hydrogen bonds can be likened to weak ionic bonds in that they?
Arise from the attraction of positive and negative charges. Although they are a consequence of polar covalent bonds between hydrogen atoms and other, more electronegative atoms, hydrogen bonds themselves are not covalent bonds- They do not involve the sharing of electrons.
Covalent bonds are essential for life because they strongly link atoms together to form molecules. Hydrogen bonds, though weaker than covalent bonds, are also essential. The cumulative effect of numerous hydrogen bonds is to?
Stabilize the three-dimensional shapes of large molecules. For example, the familiar double helix shape of DNA is due in part to the stabilizing effects of thousands of hydrogen bonds holding the molecule together. Exact shape is critical for the functioning of enzymes, antibodies, intercellular chemical messengers, & the recognition of target cells by pathogens.
Because hydrogen bonds are weak, they can be overcome when necessary. For example, the two complementary halves of a DNA molecule are held together primarily by hydrogen bonds, & they can be separated for?
DNA replication and other processes
Scientists define chemical reactions as?
The making or breaking of such chemical bonds
All chemical reactions begins with?
All chemical reactions results in?
Reactants, the atoms, ions, or molecules that exist at the beginning of a reaction.
Results in products, the atoms, ions, or molecules left after the reaction is complete
Biochemistry involves?
The chemical reactions of living things
Reactants and products may have very different physical and chemical characteristics. For example, hydrogen & oxygen are gases and have very different properties of?
Water, which is composed of hydrogen & oxygen atoms.
The numbers and types of atoms never change in a?
Chemical reaction; atoms are neither destroyed nor created, only rearranged.
Three general categories of biochemical reactions (reactions that occur in organisms)
1) Synthesis
2) Decomposition
3) Exchange reactions
Synthesis reactions involve?
The formation of larger, more complex molecules. Synthesis reactions can be expressed symbolically as: Reactant + Reactant —-> Product(s)
The arrow indicates the direction of the reaction & the formation of new chemical bonds
What is dehydration synthesis?
Two smaller molecules are joined together by a covalent bond, and a water molecule is also formed.
The word dehydration in this reaction refers to the fact that one of the products is a water molecule formed when a hydrogen ion from one reactant combines with a hydroxyl ion from another reactant.
Synthesis reactions require energy to?
Break bonds in the reactants & to form new bonds to make products.
What are endothermic reactions?
Reactions that require energy because they trap energy within new molecular bonds.
What is anabolism?
Taken together, all of the synthesis reactions in an organism
What are decomposition reactions?
The reverse of synthesis reactions in that they break bonds within larger molecules to form smaller atoms, ions, and molecules. These reactions release energy and are therefore exothermic
Decomposition reactions can be represented by the following formula
Reactant —–> Product + Product
Reactions that release energy
Exothermic
Synthesis and decomposition reactions are often reversible in?
Living things
Hydrolysis is what type of reaction?
A common type of decomposition reaction in biochemistry. It is the reverse of dehydration synthesis. In these reactions a covalent bond in a large molecule is broken, & the ionic components of water are added to the products
What is catabolism?
All of the decomposition reactions in an organism
What are exchange reactions (also called transfer reactions)?
Have features similar to both synthesis and decomposition reactions. They involve breaking and forming covalent bonds, & they involve both endothermic & exothermic steps. Atoms are moved from one molecule to another. These reactions can be represented as either:
A + BC —> AB + C OR AB + CD ——> AD + BC
What is metabolism?
The sum of all of the chemical reactions in an organism, including catabolic, anabolic, and exchange reactions.
Living things depend on organic compounds, those that contain carbon and hydrogen atoms. They also require a variety of inorganic chemicals, which typically lack carbon. Such inorganic substances include?
Water, oxygen molecules, metal ions, & many acids, bases, and salts.
The most abundant substance in organism, constituting 50-99% of their mass
Water
Most of the special characteristics that make water vital result from the fact that a water molecule has?
Two polar covalent bonds, which allow hydrogen bonding between water molecules & their neighbors
Water molecules are cohesive which means?
They tend to stick to one another through hydrogen bonding. This property generates many special characteristics of water, including surface tension, which allows water to form a thin layer on the surface of cells. This aqueous layer is necessary for the transport of dissolved materials into and out of a cell.
Water is an excellent solvent that is?
It dissolves salts and other electrically charged molecules because it is attracted to both positive & negative charges
Water remains a liquid across a wider range of temps. than other molecules of its size. This is critical because?
Living things require water in liquid form
Water can absorb significant amounts of heat energy without itself changing temp. Further, when heated water molecules eventually evaporate, they take?
Much of this absorbed energy with them. These properties moderate temperature fluctuations that would otherwise damage organisms
Water molecules participate in many chemical reactions within cells, both as?
Reactants in hydrolysis and as products of dehydration synthesis
What is an acid?
A substance that dissociates into one or more hydrogen ions and one or more anions. Can be inorganic molecules, such as amino acids & nucleic acids. Familiar organic acids are found in lemon juice, black coffee, and tea.
What is a base?
A molecule that binds with hydrogen when dissolved in water. Some bases dissociate into cations and hydroxyl ions, which then combine with hydrogen ions to form water molecules. Other bases, such as household ammonia directly accept hydrogen ions & become compound ions such as ammonium
Metabolism requires a relatively constant balance of acids and bases because?
Hydrogen ions & hydroxyl ions are involved in many chemical reactions. Many complex molecules such as proteins lose their functional shapes when acidity changes
The concentration of hydrogen ions in a solution is expressed using a?
Logarithmic pH scale
The term pH comes from?
Potential hydrogen, which is the negative of the logarithm of the concentration of hydrogen ions
Acidity increases as pH values do what?
Decrease, and that each decrease by a whole number in pH indicates a 10-fold increase in acidity
Water is neutral because it dissociates into?
One hydrogen cation and one hydroxyl anion in the formula
H2O —> H+ + OH-
Alkaline (basic) substances have pH values greater than 7.0. They reduce the number of free hydrogen ions by?
Combining with them.
Define buffers
Substances, such as proteins, that prevent drastic changes in internal pH.
Organisms can tolerate only a certain, narrow pH range. Fluctuations outside an organism’s preferred range inhibits its?
Metabolism and may even be fatal
Photosynthetic bacteria known as cyanobacteria grow well in what type of pH environment?
Basic solutions
Acid loving prokaryotes
Acidophiles, requires acid conditions
Microorganisms can change the pH of their environment by?
Utilizing acids and bases & by producing acidic or basic wastes
A compound that dissociates in water into cations and anions other than H+ and OH-
Salts
Cations and anions of salts are electrolytes. A cell uses electrolytes to create?
Electrical differences between its inside and outside, to transfer electrons from one location to another, and as important components of many enzymes
Certain organisms also use salts such as calcium carbonate to provide?
Structure and support for their cells
Inorganic molecules play important roles in an organism’s metabolism; however, water excluded, they compose only about ___% of its mass
1.5%
Organic molecules contain _____ and ______ atoms, and each ______ atom can form four _______ bonds with other atoms
carbon and hydrogen
each carbon
covalent
Carbon atoms that are linked together in branched chains, unbranched chains, and rings provide the basic framework of? What are bound to these carbon frameworks and what do they form?
Organic molecules.
Atoms of other elements are bound to these carbon frameworks to form an unlimited number of compounds
Atoms often appear in certain common arrangements called?
Functional groups
There are a great variety of organic compounds, but certain basic types are used by all organisms. These molecules-known as macromolecules because they are very large, are?
Lipids, carbohydrates, proteins, and nucleic acids
Lipids are a diverse group of organic macromolecules not composed of regular subunits. They have one common trait- they are hydrophobic; insoluble in water. They have little or no affinity for water because they are composed almost entirely of?
Carbon and hydrogen atoms linked by non polar covalent bonds. Because these bonds are non polar, they have no attraction to the polar bonds of water molecules
There are four major groups of lipids in cells
Fats, phospholipids, waxes, and steroids
Organisms make fats via?
Dehydration synthesis reactions that form esters between three chainlike fatty acids and an alcohol named glycerol
Fats are called triglycerides because they contain?
3 fatty acid molecules linked to a molecule of glycerol
An important difference among fatty acids is the presence and location of double bonds between the carbon atoms. When the carbon atoms are linked solely by single bonds, every carbon atom, with the exception of the terminal ones, is covalently liked to two hydrogen atoms. Such a fatty acids is?
Saturated with hydrogen
Fatty acids that contain at least one double bond between adjacent carbon atoms, and therefore contain at least one carbon atom bound to only a single hydrogen atom
Unsaturated fatty acids
If several double bonds exist in even one fatty acid of a molecule of fat, then it is?
Polyunsaturated fat
What are saturated and unsaturated fats at room temp.?
Saturated fats- Usually solid at room temp. because their fatty acids can be packed closely together.
Unsaturated fats- Liquid at room temp. because they are bent at every double bond, and so cannot be packed tightly
Fats contain an abundance of energy stored in their?
Carbon-carbon covalent bonds.
A major role of fats in organisms is?
To store energy. Fats can be catabolized to provide energy for movement, synthesis, and transport.
Phospholipids are similar to fats, but they contain how many fatty acid chains compared to fats? Why are they called phospholipids?
Phospholipids contain only two fatty acid chains instead of three.
In phospholipids, the third carbon atom of glycerol is linked to a phosphate (PO4) functional group instead of to a fatty acid.
The fatty acid “tail” portion of a phospholipid molecule is?
The phospholipid “head” is?
As a result of this what happens when phospholipids are placed in a watery environment?
Nonpolar and thus hydrophobic- fear of water.
Head- Polar is thus hydrophilic- water loving.
When placed in a watery environment they will always self assemble into forms that keep the fatty acid tails away from water. They form a spherical phospholipid bilayer. The tails congregate in the water-free interior of bilayers. The polar heads orient toward the water because they are hydrophilic.
Phospholipid bilayers make up the?
Cytoplasmic membranes of all cells, as well as the internal membrane of plant, fungal, and animal cells
Carbohydrates, proteins, and nucleic acid macromolecules are composed of?
Simpler subunits known as monomers, which are basic building blocks. The monomers of these macromolecules are joined together to form chains of monomers called polymers.
What are carbohydrates?
Organic molecules composed solely of atoms of carbon, hydrogen, and oxygen. Most carbohydrate compounds contain an equal number of oxygen and carbon atoms, and twice as many hydrogen atoms as carbon atoms
How do carbohydrates play important roles in organisms?
Large carbohydrates such as starch and glycogen are used for the long-term storage of chemical energy, and a smaller carbohydrate molecule- glucose_ serves as a ready energy source in most cells.
Carbohydrates also form part of the backbones of?
DNA & RNA, and other carbohydrates are converted routinely into amino acids.
Polymers of carbohydrates form?
The cell walls of most fungi, plants, and algae, and prokaryotes and are involved in intercellular interactions between animal cells
What are the simplest carbohydrates?
Monosaccharides which are simple sugars
Sugar component of DNA
Deoxyribose which is a pentose meaning they are sugars with 5 carbon atoms
The general names for the classes of monosaccharides are formed from?
A prefix indicating the number of carbon atoms and from the suffix -ose. For example pentoses are sugars with five carbon atoms, and hexoses are sugars with six carbon atoms.
Pentoses and hexoses are particularly important in?
Cellular metabolism
Monosaccharides may exist as linear molecules, but because of energy dynamics they usually take what kind of forms?
Cyclic (ring) forms. In some cases, more than one cyclic structure may exist. For example, glucose can assume an alpha configuration or a beta configuration, these configurations play important roles in the formation of different polymers.
What is a disaccharide?
It is when two monosaccharide molecules are linked together via dehydration synthesis. For example, the linkage of two hexoses, glucose and fructose, forms sucrose (table sugar) and a molecule of water
What is maltose (malt sugar) and lactose (milk sugar)
They are disaccharides
Disaccharides can be broken down via?
Hydrolysis into their constituent monosaccharides
What are polysaccharides?
They are polymers composed of tens, hundreds, or thousands of monosaccharides that have been covalently linked in dehydration synthesis reactions.
Polysaccharides can be diverse because they can differ according to their?
Monosaccharide monomer configurations (either alpha or beta) and their shapes (either branched or unbranched)
Cellulose, the main constituent of the cell walls of plants and some green algae, is a?
Long unbranched molecule that contains only beta-monomers of glucose linked between carbons 1 and 4 of alternating monomers; such bonds are termed beta 1,4 bonds
The cell walls of bacteria are composed of?
Peptidoglycan, which is made of polysaccharides and amino acids
Polysaccharides may be linked to lipids to form?
Glycolipids, which can form cell markers such as those involved in the ABO blood typing system in humans
The most complex organic compounds are?
Proteins, which are composed mostly of carbon, hydrogen, oxygen, nitrogen, and sulfur.
Proteins perform many functions in cells, including;
1) Structure
2) Enzymatic catalysis
3) Regulation
4) Transportation
5) Defense and offense
Proteins are structural components in cell walls, in membranes, and within cells themselves. Proteins are also the primary structural material of?
Hair, nails, the outer cells of skin, muscle, and flagella and cilia (the last two act to move microorganisms through their environment).
Enzymatic catalysts. Catalysts are chemicals that enhance the speed or likelihood of a chemical reaction. Protein catalysts in cells are called?
Enzymes
Protein regulation. Some proteins regulate cell function by stimulating or hindering either the action of other proteins or the expression of genes. Hormones are examples of?
Regulatory proteins
Protein transportation. Certain proteins act as channels and “pumps” that move substances where/
Into or out of cells
Protein defense and offense. Antibodies and complement are examples of proteins that defend your body against?
Microorganisms, and some bacteria produce proteins called bacteriocins that kill other bacteria.
A proteins function is dependent on its?
Shape, which is determined by the molecular structures of its constituent parts.
Proteins are polymers composed of monomers called?
Amino acids
Amino acids contain?
A basic amino group, a hydrogen atom, and an acidic carboxyl group.
All amino acids attach to the same carbon atom, which is known as the?
Alpha carbon. A fourth bond attaches the alpha carbon to a side group that varies among different amino acids. The side group may be a single hydrogen atom, various chains, or various complex ring structures. Hundreds of amino acids are possible, but most organisms use only 21 amino acids in synthesizing proteins.
The different size groups of amino acids affects?
The way amino acids interact with one another within a given protein, as well as how a protein interacts with other molecules.
A change in an amino acid’s side group may seriously interfere with?
A protein’s normal function
What is the charge of amino acids?
Because amino acids contain both an acidic carboxyl group and a basic amino group, they have both positive and negative charges and are easily soluble in water.
Scientists refer to covalent bonds between amino acids by a special name called?
Peptide bonds
A molecule composed of two amino acids linked together by a single peptide bond is called a?
Dipeptide
Longer chains of amino acids are called?
Polypeptides
Proteins are unbranched polypeptides composed of?
Hundreds to thousands of amino acids linked together in specific patterns as determined by genes
The structure of a protein molecule is directly related to?
Its function; therefore, understanding protein structure is critical to understanding certain specific chemical reactions, the action of antibiotics, and specific defense against pathogens
Every protein has at least three levels of structure, and some proteins have four levels. What are the levels?
1) Primary structure
2) Secondary structure
3) Tertiary structure
4) Quaternary structure
What is the primary structure of a protein?
Its sequence of amino acids. Cells use many different types of amino acids in proteins, though not every protein contains all types. The primary structures of proteins vary widely in length and amino acid sequence
The replacement of the amino acid valine by alanine in position 136 of the primary structure of a particular sheep brain protein, called cellular prion protein, may result in a disease called scrapie. The altered protein spreads into?
Cows, causing mad cow disease, and from cows into humans, causing variant Creutzfeldt Jakob disease
Ionic bonds, hydrogen bonds, and hydrophilic characteristics cause many polypeptide chains to fold into either?
Coils called alpha helices, or accordion-like structures called beta pleated sheets
Proteins are typically composed of?
Both alpha helices and beta pleated sheets linked by short sequences of amino acids that do not show secondary structure.
Describe the tertiary structure of proteins
Polypeptides further fold into complex three-dimensional shapes that are not repetitive like alpha helices and beta pleated sheets, but are uniquely designed to accomplish the function of the protein.
Describe the quaternary structure of proteins
Some proteins are composed of two or more polypeptide chains linked together by disulfide bridges or other bonds. The overall shape of such a protein may be globular or fibrous (threadlike)
What are glycoproteins?
Proteins covalently bound with carbohydrates
What are lipoproteins?
Proteins bonded with lipids
What are metalloproteins?
Contain metallic ions
What are nucleoproteins?
Proteins bonded with nucleic acids
Because protein shape determines protein function, anything that severely interrupts shape also disrupts function. As we have seen, amino acid substitution can alter shape and function. Additionally, physical and chemical factors such as heat, changes in pH, and salt concentration can interfere with hydrogen and ionic bonding, with in turn disrupts the three-dimensional structure of proteins. This process is called?
Denaturation
Denaturation of of proteins can be?
Temporary (if the denaturation protein is able to return to its original shape again) or permanent
What are vital as the genetic material of cells and viruses?
The nucleic acids deoxyribonucleic acid (DNA) & ribonucleic acid (RNA)
RNA acting as an enzyme binds?
Amino acids together to form polypeptides
DNA & RNA are both?
Unbranched macromolecular polymers that differ primarily in the structures of their monomers
Each monomer of nucleic acids is a nucleotide and consists of three parts
1) Phosphate
2) A pentose sugar, either deoxyribose or ribose
3) One of five cyclic (ring-shaped) nitrogenous bases: adenine (A), guanine (G), cytosine (C), thymine (T), or uracil (U)
Adenine and guanine are double-ringed molecules of a class called? Whereas cytosine, thymine, and uracil have single rings and are?
A & G are Purines
C, T, & U are pyrimidines
DNA contains?
RNA contains?
DNA- A, G, C, and T bases
RNA- A, G, C, and U bases
What sugars are in DNA?
DNA nucleotides contain deoxyribose, and RNA nucleotides contain ribose
What are nucleosides
Nucleotides lacking phosphate, that is, a nucleoside is one of the nitrogenous bases attached only to a sugar
Each nucleotide or nucleoside is also named for the base it contains. Thus a nucleotide made with ribose, uracil, and phosphate is a? Likewise, a nucleoside composed of adenine and deoxyribose is an?
- uracil RNA nucleotide, which is also called a uracil ribonucleotide
- adenine DNA nucleoside (or adenine deoxyribonucleoside)
Nucleic acids, like polysaccharides and proteins, are?
Polymers. They are composed of nucleotides linked by covalent bonds between the phosphate of one nucleotide and the sugar of the next.
Polymerization results in a linear spine composed of?
Alternating sugars and phosphates, with bases extending from it rather like the teeth of a comb
The two ends of a chain of nucleotides are different. Describe them.
At one end, called the 5’ end (five end prime), carbon 5’ of the sugar is attached to a phosphate group. At the other end (3’ end), carbon 3’ of the sugar is not attached to a phosphate group.
The atoms of the bases in nucleotides are arranged in such a manner that what readily forms?
The hydrogen bonds readily form between specific bases of two adjacent nucleic acid chains. Three hydrogen bonds form between an adjacent pair composed of cytosine (C) and guanine (G), whereas two hydrogen bonds form between an adjacent pair composed of adenine (A) and thymine (T) in DNA, or between an adjacent pair composed of adenine (A) and uracil (U) in RNA. Hydrogen bonds do not readily form between other combinations of nucleotide bases; for example, adenine does not readily pair with cytosine, guanine, or other adenine nucleotide
In cells & most viruses that use DNA as a genome, DNA molecules are double stranded. The two strands of DNA are?
Complementary to one another; that is, the specificity of nucleotide base pairing ensures that opposite strands are composed of complementary nucleotides. For instance, if one strand has the sequence AATGCT, then its complement has TTACGA
The two strands of nucleotides are also antiparallel meaning
They run in opposite directions. One strand runs from the 3’ end to the 5’ end, whereas its complement runs in the opposite direction, from its 5’end to its 3’end.
Although hydrogen bonds are relatively weak bonds, thousands of them exist at normal temps., forming a what in nucleotides?
Stable double-stranded DNA molecule, which looks much like a ladder: the two deoxyribose-phosphate chains are the side rails, and base pairs form the rungs. Hydrogen bonding also twists the phosphate-deoxyribose backbones into a helix. Thus, typical DNA is a double helix. Parvoviruses use single-stranded DNA, which is an exception to this rule.
DNA is the?
Genetic material of all organisms and of many viruses; it carries instructions for the synthesis of RNA molecules and proteins. By controlling the synthesis of enzymes and regulatory proteins, DNA controls the synthesis of all other molecules in an organism.
Genetic instructions are carried in the sequence of?
Nucleotides that make up the nucleic acid. Even though only four kinds of bases are found in DNA (A, T, G, and C), they can be sequenced in distinctive patterns that create genetic diversity and code for an infinite number of proteins
Cells replicate their DNA molecules and pass copies to?
Their descendants, ensuring that each has the instructions necessary for life.
Ribonucleic acids play several roles in the synthesis of?
Proteins, including catalyzing the synthesis of proteins. RNA molecules also function as structural components of ribosomes and in place of DNA as the genome of RNA viruses.
