BY 30 – Fall 2001
4.1.
Amino Acids and Peptide Bonds
a. The basic building blocks of proteins are ____________________________, of which there are _______________________ common types.
b. All amino acids have a central carbon atom that forms 4 covalent bonds with a(n) __________________________, _______________________________, ____________________________, and ______________________________.
c. Of the four groups bound to carbon, it is the ___________________________ group which differs between different amino acids, and confers chemical properties to that amino acid. For example, the simplest amino acid is glycine which has a _____________________ R group. By contrast many amino acids have polar R groups which can be either _________________________ or __________________________.
d. In general, amino acids with acidic R groups carry a ____________________ charge while those with basic R groups carry a _________________________ charge.
e. Two amino acids are joined together by a _____________________ bond to form a ___________________________. If we were to add one more amino acid, the result would be a ________________________________.
f. Peptide bonds form between the carbon of the _______________________ group and the ___________________________ of the amino group. This process is considered to be a ______________________________ reaction.
4.2.
Structural Levels of Proteins
a. In general there are four different levels of structural organization of proteins called ____________________________, ____________________________, ____________________________, and ______________________________.
b. The primary structure of a protein refers to the _________________________ sequence.
c. When a polypeptide chain undergoes repeated clockwise spiral, this is an example of _______________________________ structure that is specifically referred to as a(n) __________________________ helix. Another example is when two or more polypeptide chains form an undulating ribbon-like structure, referred to as a __________________________. In both examples, these structures are stabilized by ___________________ bonds.
d. The three dimensional shape of a polypeptide chain is referred to as its _____________________________ structure which results from interactions between ________________________________ and between R groups and _________________________________.
e. Within the tertiary structure of a protein, amino acids with _______________ R groups tend to be found in the middle of the protein, while those with ________________________ R groups tend to be found on the surface.
f. Cysteine is an amino acid that has a ___________________ atom in its R group. As a result, two cysteines can interact to form _________________________ linkages which stabilize tertiary structure.
g. _________________________ structure refers to the arrangement of more than one polypeptide chain. In these structures, the chains tend to be stabilized by _________________________ bonds and ____________________ linkages.
4.3.
Types of Proteins and their Functions:
a. The biological function of a protein is largely determined by its _______________________________ allowing us to distinguish between two general types of proteins called _________________________________ and _________________________________________.
b. The class of proteins that include those which are extended, strand-like proteins is called ____________________________ proteins, also known as ___________________________ proteins based on their mechanical strength. These proteins are usually ___________________________ in water.
c. Examples of fibrous proteins include _____________________________, the most abundant protein in the body; _______________________ the structural protein in skin; and ______________________ and ____________________ which are found in muscle.
d. The class of proteins which are usually spherical with tertiary, and often quaternary structure is called ____________________________ proteins, also known as _____________________________ proteins based on their role in biological processes. These proteins are usually _______________________ in water.
e. Examples of globular proteins include _______________________________ which take part in the immune response; _____________________________ which are signaling molecules that travel in blood; and __________________ which is found in red blood cells and binds O2.
f. _____________________________ are a class of globular proteins that act as catalysts by reducing the __________________________ energy of chemical reactions thereby ___________________________ reaction rates.
g. Often enzymes require the presence of a non-protein part called a ______________________________, which may be an ion or in some cases some organic molecule called a ___________________________________. In these cases, the protein part of the enzyme is referred to as the _______________________________ while the combination of protein and cofactor is called the ______________________________________.
h. The ____________________________ of an enzyme refers to the fact that an enzyme usually catalyzes only a single reaction. The basis of specificity is the _________________________, which is a portion of the molecule which binds to the reactants, in this case called ____________________________.
i. The active site of an enzyme is dependent on the tertiary structure of the protein and so can be disrupted through changes in _____________________ and/or _________________________. When the protein unfolds as a result, the protein is said to be ______________________________. Also enzyme activity is highest at a pH known as the _____________________________.
j. Enzyme activity can be affected by cellular __________________________. In some cases, enzymes are first released in __________________________ form, and later activated – an example being the _______________________ enzymes of the pancreas that are only activated once they reach the ___________________________________.
k. Most enzyme names end in _________________________, and are grouped according to chemical reaction. For example, ________________________ catalyze reactions that add O2; ______________________________ catalyze reactions that remove H; __________________________ catalyze hydrolysis reactions; ________________________________ catalyze reactions that add phosphate; and _______________________ catalyze reactions that split ATP.
4.4.
Nucleotides and Nucleic Acids
a. The basic structural unit of nucleic acids is the ________________________.
b. Each nucleotide consists of three parts which are a _____________________, a __________________________ and a _____________________________.
c. The nitrogen containing bases of nucleotides come in two classes called ______________________________________, which contain 2 rings; and the ______________________________________, which contain only 1 ring.
d. Purines consist of _____________________ and ______________________.
e. Pyrimidines consist of ______________________, ____________________, and ____________________________. Of these three, _________________ is present only in DNA and _______________________ only in RNA.
f. Each DNA molecule consists of _____________________________ chains of nucleotides coiled into a spiral known as the __________________________. The backbone of each chain consists of repeating _______________________ and ____________________________. The __________________________ is directed inward where it interacts with the base of the other strand via ______________________________ bonds.
g. Base pair bonding is specific, forming what is known as ______________________________ base pairs. In this case, adenine always pairs with _____________________________ and guanosine with __________________________________.
h. Each DNA molecule consists of segments called _______________________, which direct the synthesis of a particular protein.
i. DNA has the ability to create an exact copy of itself during cell division in a process called _____________________________________.
j. RNA differs from DNA in that is has __________________________ strand; has ______________________ as its sugar instead of ___________________; and ___________________________ as a base instead of thymine. There are _________________________ major types of RNA.
k. ATP is the abbreviation for _______________________________________, which is an adenine-containing _______________________ nucleotide which has ____________________ additional phosphate groups added.
l. When ATP is broken down in a hydrolysis reaction, the products formed are ___________________________ + _____________________________ + _________________________________.
m. ATP temporarily stores energy which when released can be transferred to such cellular activities as ________________________________________, ___________________________, and ______________________________.
n. When the RNA nucleotide contains guanosine instead of adenine and three phosphate groups, the molecule is called _____________________________.