Biochemistry Flashcards
Inorganic and Organic Compounds
Inorganic does not contain carbon, including salts and HCl.
Organic are made by living systems and contain carbon. Include carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates
Composed of the elements carbon, hydrogen, and oxygen in a 1:2:1 ratio, respectively. They’re used as storage forms of energy or as structural molecules.
Monosaccharide
Singular sugar subunits. Like glucose and fructose.
Disaccharide
Compsoed of two monosacchatide subunits joined by dehydration synthesis, which involves loss of a water molecule. Examples include maltose and sucrose.
Polysaccharide
Polymers or chains of repeating monosaccharide subunits. Glycogen and starch are examples of polysaccharides. Cellulose is a polysaccharide that serves a structural role in plants. These polysaccharides are insoluble in water.
Formed by removing water (dehydration). By adding water, large polymers can be broken down into smaller subunits in a process called hydrolysis.
Lipids
Also compsoed of C, H, and O, but their H:O ratio is much greater than 2:1 because they have much more H than O. A triglyceride is a type of lipid that consists of 3 fatty acid molecules bonded to a single glycerol backbone. Fatty acids have long carbon chains that give them their hydrophobic (fatty character) and carboxylic acid groups that make them acidic. Three dehydration reactions are needed to form one fat molecule. Lipids don’t form polymers.
Chief means of food storage in animals. They release more energy per gram weight than any other class of biological compounds. They also provide insulation and protection against injury because they’re a major component of fatty (adipose) tissue.
Phospholipids
Lipid derivative. Contain glycerol, two fatty acids, a phosphate group, and nitrogen-containing alcohol; e.g., lecithin (a major constituent of cell membranes) and cephalin (found in brain, nerves, and neural tissue).
Waxes
Lipid derivative. Esters of fatty acids and monohydroxylic alcohols. They’re found as protective coverings on skin, fur, leaves of higher plants, and on the exoskeleton of many insects.
Steroids
Lipid derivative. Have 3 fused cyclohexane rings and one fused cyclopentane ring. They include cholesterol, the sex hormones testosterone and estrogen, and corticosteroids.
Carotenoids
Lipid derivative. Fatty, acid-like carbon chains containing conjugated double bonds and carrying six-membered carbon rings at each end. These compounds are the pigments that produce red, yellow, orange, and brown colors in plants and animals. Two subgroups are the carotenes and the xanthophylls.
Porphyrins
Lipid derivative. Also called tetrapyrroles. Contain four joined pyrrole rings. They’re often complexed with a metal. For example, the polyphyrin heme complexes with Fe in hemoglobin. Chlorophyll is complexed with Mg.
Proteins
Compsoed primarily of C, H, O, and N but may also contain P and S. They are polymers of amino acids.
Amino acids are joined by peptide bonds through dehydration reactions. Chains of such bonds produce a polymer called a polypeptide, or simply peptide. This is another term for protein. The sequence or amino acids in a protein is referred to as the primary structure. Proteins can also coil or fold to form alpha-helices and beta-pleated sheets. These are considered part of the protein’s secondary structure.
Protein: Primary Structure
Sequence of amino acids.
Protein: Secondary Structure
Based on hydrogen bonding between adjacent amino acids and results in beta-pleated sheets of alpha helices.
Protein: Tertiary Structure
3D structure that’s based on R-group interactions between adjacent amino acids. Results in globular or fibrous proteins. The hydrophobic amino acids are crowded in the center with hydrophilic amino acids at the outer edge and periphery.
Protein: Quaternary Structure
The interaction and joining of two or more independent polypeptide chains.
Simple Proteins
Composed entirely of amino acids.
Albumins and Globulins
Primarily globular in nature. Functional proteins that act as carriers or enzymes.
Scleroproteins
Fibrous in nature and act as structural proteins. Collagen is a fraction.
Lipoproteins
Proteins bound to lipids.
Glycoproteins
Proteins bound to carbohydrates.
Chromoproteins
Proteins bound to pigmented molecules.
Metalloproteins
Proteins complexed around a metal ion.
Nucleoproteins
Proteins containing histone or protamine (nuclear protein) bound to nucleic acids.
Hormones
Proteins that function as chemical messengers secreted into the circulation. Insulin and ACTH are protein hormones.
Enzymes
Biological catalysts that act by increasing the rate of chemical reactions important for biological functions.
Structural Proteins
Contribute to the physical support of a cell or tissue. They may be extracellular or intracellular.
Transport Proteins
Carriers of important materials. For example, hemoglovin carries oxygen in circulation, and the cytochromes carry electrons during cellular respiration.
Antibodies
These bind to foreign particles (antigens), including disease-causing organisms, that have entered the body.
Mutable
DNA is mutable and can be altered under certain conditions, altering the corresponding characteristics int he organism. Changes form basis of evolution.
Purines and Pyrimidines
The two types of bases. Purines are adenine and guanine. Pyrimidines are cytosine and thymine.
DNA Structure
Basic unit is the nucleotide, which is composed of deoxyribose bonded to both a phosphate group and a nitrogenous base.
Double stranded helix with sugar phosphate chains on the outside of the helix and the bases on the inside. T always forms two hydrogen bonds with A, and G always forms three hydrogen bonds with C. This base-pairing forms “rungs” on the interior of the double helix that link the two polynucleotide chains together. This is known as the Watson-Crick DNA Model.
DNA Replication
It unwinds and separates into two single strands. Each strand acts as a template for complementary base-pairing in the synthesis of two new daughter helices. Each new daughter helix contains an intact strand from the parent helix and a newly synthesized strand; thus, DNA replication is semiconservative.
The daughter DNA helices are identical in composition to each other and to the parent DNA. One daughter strand is the leading strand, and the other is the lagging strand.
Leading strand is continuously synthesized by DNA polymeras in the 5’ –> 3’ direction. The lagging strand is synthesized discontinuously int he 5’ –> 3’ direction (since DNA polymerase only synthesizes in that direction) as a series of short segments known as Okazaki fragments; however, overall growth of the lagging strand occurs in the 3’ –> 5’ direction.
The Genetic Code
The language of DNA consists of four letters: A, T, C, and G. The language of proteins consists of 20 words: 20 amino acids. The DNA language must be translated using mRNA intermediate in such a way as to produce the 20 words in the amino acid language; hence, the triplet code. The base sequence of mRNA is translated as a series of triplets, otherwise known as codons. A sequence of three consecutive base codes for a particular amino acid; e.g., the codon GGC specifies glycine, and the codon GUG specifies valine. The genetic code is universal for almost all organisms.
Given that 64 codons are possible based on triplet code, and only 20 amino acids needed to be coded, the code must contain synonyms. Most amino acids have more than one codon specifying them. This property is referred to as the degeneracy or redundancy of the genetic code.
Messenger RNA
mRNA carries the complement of a DNA sequence and transports it from the nucleus to the ribosomes, where protein synthesis occurs. mRNA is assembled from ribonucleotides that are complementary to the “sense” strand of the DNA. The mRNA has the inverted complementary or negative code of the original master on DNA. FOr example, because the DNA code for the amino acid valine is AAC, the mRNA is the complementary UUG. mRNA is monocistronic; i.e., one mRNA strand codes for one polypeptide.
Transfer RNA
tRNA is found in cytoplasm that aids in the translation of mRNA’s nucleotide code into a sequence of amino acids. tRNA brings amino acids to the ribosomes during protein synthesis. There’s at least 1 type of tRNA for each amino acid.
Ribosomal RNA
rRNA is structural component of ribosomes and is the most abundant of all RNA types. Synthesized in nucleolus.
Transcription
Process whereby info coded in the base sequence of DNA is transcribed into a strand of mRNA that leaves the nucleus through nuclear pores. The remaining events of protein synthesis occur in the cytoplasm.
Translation
Process whereby mRNA codons are translated into a sequence of amino acids. Translation occurs in the cytoplasm and involves tRNA, ribosomes, mRNA, amino acids, enzymes, and other proteins.
Protein Synthesis: tRNA
tRNA brings amino acids to the ribosomes in the correct sequence for polypeptide synthesis; tRNA “recognizes” both the amino acid and the mRNA codon. This dual function is reflected in its 3D structure: one end contains a three-nucleotide sequence, the anticodon, which is complementary to one of the mRNA codons; the other end is the site of amino acid attachment. Each amino acid has its own aminoacyl-tRNA synthetase, which has an active site that binds to both the amino acid and its corresponding tRNA, catalyzing their attachment to form an aminoacyl-tRNA complex.
Protein Synthesis: Ribosomes
Ribosomes are composed of two subunits (consisting of proteins and rRNA), one large and one small, that bind together only during protein synthesis. Ribosomes have 3 binding sites: one for mRNA and two for tRNA–the P site (peptidyl-tRNA binding site) and the A site (aminoacyl-tRNA complex binding site). The P site binds to the tRNA attached to the growing polypeptide chain, whereas the A site binds to the incoming aminoacyl-tRNA complex. The third site, the E site, binds the existing tRNA.
Polypeptide Synthesis
Can be divided into 3 stages: initiation, elongation, and termination. Synthesis begins when the ribosome binds to the mRNA near its 5’ end. The ribosome scans the mRNA until it binds to a start codon. The initiator aminoacyl-tRNA complex, methionine-tRNA (with the anticodon 3’-UAC-5’), base pairs with the start codon.
In elongation, hydrogen bonds form between the mRNA codon in the A site and its complementary anticodon on the incoming aminoacyl-tRNA complex. A peptide bond is formed between the amino acid attached to the tRNA in the A site and the amino acid attached to the tRNA in the P site. After peptide bond formation, a ribosome carries uncharged tRNA int he P site and peptidyl-tRNA in the A site. The cycle is completed by translocation, in which the ribosome advances three nucleotides along the mRNA in the 5’ to 3’ direction. In a concurrent action, the uncharged tRNA from the P site is expelled, and the peptidyl-tRNA from the A site moves into the P site. The ribosome then has an empty A site ready for entry of the aminoacyl-tRNA corresponding to the next codon.
Polypeptide synthesis terminates when one of three special mRNA termination codons (UAA, UAG, or UGA) arrives in the A site. These codons signal the ribosome to terminate translation; they do not code for amino acids. Frequently, numerous ribosomes simultaneously translate a single mRNA molecule, forming a structure known as a polyribosome.
After the release of the protein from the ribosome, the protein immediately assumes the chatacteristic 3D native conformation. This conformation is determined by the primary sequence of amino acids. Additional secondary and tertiary structural folding occurs based on the primary sequence. Furthermore, the polypeptide chains can form intramolecular and intermolecular cross-bridges with disulfide bonds. The result is a 3D functional protein or complex of multiple proteins.
