Biochemistry: Proteins, Nucleic Acids, and Enzymes (Lecture Notes)

Flashcards cover protein types, conjugation, nucleic acids (DNA/RNA), RNA types, nucleotides/nucleosides, Chargaff's rules, Watson-Crick model, and basic enzyme biology (discovery, apo/holoforms, cofactors, substrates, and enzyme types).

What are acidic proteins?

Proteins that are acidic in nature; most blood proteins are acidic and have low isoelectric points at physiological pH.

How are proteins classified based on composition?

Into three categories: simple proteins, conjugated proteins, and derived proteins.

What is a simple protein?

A protein that on hydrolysis yields only amino acids; soluble in water; examples include albumins, globulins, and histones.

What is a conjugated protein?

A simple protein united with a non-protein substance; the non-protein part is called a prosthetic group.

What is a prosthetic group?

The non-protein component tightly bound to a conjugated protein and essential for its function (e.g., heme in hemoglobin).

Give an example of a conjugated protein and its prosthetic group.

Hemoglobin; prosthetic group is heme (iron-containing pigment).

What are nucleoproteins?

Proteins associated with nucleic acids; histones bound to DNA are examples of nucleoprotein components.

What are glycoproteins?

Conjugated proteins containing carbohydrate moieties attached to the protein.

What are mucoproteins?

Conjugated proteins in which carbohydrate is the non-protein part; examples include mucin of saliva and heparin of blood.

What are lipoproteins?

Lipid-protein complexes; conjugated proteins with lipid components found in brain, plasma membranes, and milk.

What are derived proteins?

Proteins not found in nature as such; derived from native proteins by hydrolysis (e.g., metaproteins, peptones).

Who discovered nucleic acids and when?

Friederich Miescher in 1869.

What are the two main types of nucleic acids?

DNA and RNA.

Where is DNA found and what is its role?

Found in chloroplasts and mitochondria; it is the hereditary material in most organisms.

What three components form a nucleotide?

A five-carbon sugar (deoxyribose in DNA), a phosphate group, and a nitrogenous base.

Which bases are pyrimidines?

Cytosine, thymine, and uracil.

Which bases are purines?

Adenine and guanine.

What did Chargaff observe about base composition in DNA?

Purines and pyrimidines occur in equal amounts; A pairs with T and G with C; the A+T to G+C ratio varies among species but is constant within a species.

Describe the DNA structure proposed by Watson and Crick.

Two antiparallel, helical strands form a double helix with a sugar–phosphate backbone; bases pair via hydrogen bonds (A–T two bonds, G–C three bonds); base-pair distance 3.4 Å; diameter ~20 Å.

What is a nucleoside?

A sugar bound to a nitrogenous base; does not contain a phosphate group.

What is a nucleotide?

A nucleoside with one or more phosphate groups attached; in DNA, the sugar is deoxyribose.

What is the key difference between DNA and RNA in sugar and bases?

DNA uses deoxyribose and thymine; RNA uses ribose and uracil.

What are the ends of a nucleic acid chain called and what characterizes them?

5' end has a phosphate attached to C-5, 3' end has a free hydroxyl on C-3; in RNA and DNA, chains are directional (5' to 3').

What are the three main types of cellular RNA and their roles?

mRNA (messenger RNA) carries genetic information for amino acid sequence; tRNA (transfer RNA) brings amino acids and contains the anticodon; rRNA (ribosomal RNA) forms part of the ribosome.

What is mRNA and what is its role?

Messenger RNA that carries information to form a complete polypeptide; about 3% of total cellular RNA; synthesis begins at the 5' end of DNA and ends at the 3' end.

What is a codon, anticodon, and cistron in the context of mRNA and tRNA?

Codon is a three-nucleotide sequence on mRNA; anticodon is a complementary three-nucleotide sequence on tRNA; a cistron refers to the functional unit of mRNA encoding one polypeptide.

What is tRNA and its structure?

Transfer RNA, about 70–80 nucleotides; has a cloverleaf structure with an anticodon loop and an amino acid acceptor stem at the 3' end.

What is rRNA and its role?

Ribosomal RNA; constitutes 50–60% of the ribosome and 80–90% of cellular RNA; synthesized in the nucleus.

What is an enzyme and why are they important?

A biocatalyst that speeds up biochemical reactions under physiological conditions; without enzymes, reactions would occur too slowly or not at all.

Who coined the term enzyme and what did he discover?

Edward Buchner; discovered that living cells are not strictly necessary for fermentation (yeast extract can catalyze it), coining the term enzyme.

What is an apoenzyme compared to a holoenzyme?

Apoenzyme is the protein part of an enzyme; holoenzyme is the active enzyme with its non-protein cofactor.

What is a substrate in enzymology?

The substance upon which an enzyme acts.

What are cofactors?

Non-protein components required for enzyme activity; include metal ions (e.g., Mg2+, Fe, Mn) and organic molecules (e.g., NAD+, FAD).

What is a prosthetic group in enzymes?

A tightly bound non-protein component that is part of a conjugated enzyme.

What is a conjugated enzyme?

An enzyme consisting of a protein plus a non-protein prosthetic group.

What is the difference between endo- and exo- enzymes?

Endo- enzymes act inside the cell where they are synthesized; exo- enzymes act outside the cell after secretion.

What is renin and its use?

Renin is an enzyme used to coagulate milk protein casein in cheese production; it is obtained from the stomach of calves.

What are the major and minor grooves of DNA?

Structural features of the DNA double helix that provide binding sites for proteins; major groove is wider, minor groove narrower, influencing protein-DNA interactions.