Biology 1 - Chapter 3.1-4.1

Lipids (p. 56)

- (Fats) Hydrocarbons that are insoluble in water b/c of their many nonpolar covalent bonds held together by weak but additive van der Waals forces - Nonpolar, hydrophobic molecules that include fats, oils, waxes, steroids, and the phospholipids that make up biological membranes.

Condensation Reaction

- A chemical reaction in which two molecules become connected by a covalent bond and a molecule of water is released (AH + BOH → AB + H2O.) - Store energy

Bilayer

- A sheet 2 molecules thick with water excluded from the core

Glycerol

- A three-carbon alcohol with three hydroxyl groups; a component of phospholipids and triglycerides.

β (beta) pleated sheet

- A type of protein secondary structure - Results from hydrogen bonding between polypeptide regions running antiparallel to each other.

Saturated Fatty Acids

- All bonds b/w carbon atoms in hydrogen chain are single bonds - all bonds saturated with hydrogen atoms - Relatively straight chains packed tightly

What happens when an amino group is substituted for an -OH group?

- Amino sugars, like glucosamine and galactosamine (major component of cartilage) are produced

Structural Isomers

- Atoms joined differently together

Phospholipid Bilayer

- Basic structural unit of biological membranes - Sheet of phospholipids two molecules thick in which the phospholipids are lined up with their hydrophobic "tails" packed tightly together and their hydrophilic, phosphate-containing "heads" facing outward

Hydrolysis Reaction

- Breakdown of polymers into their component monomers - Releases energy - Breaks bond by inserting the components of water

Transcription

- Certain DNA sequences can be copied into RNA (p.65) - Depend on the base-pairing properties of nucleic acids

Functional Group

- Characteristic combination of atoms that contributes specific properties (charge or polarity) when attached to larger molecules

Genome

- Complete set of DNA in a living organism (p. 66)

Secondary Structure

- Consists of regular, repeated spatial patterns in different regions of a polypeptide chain - Alpha Helix - Right handed coil resulting from hydrogen bonds. Repetition of coiling stabilizes coil - Beta Sheet - Formed from 2 or more polypeptide chains that re almost completely extended or aligned. Stabilized by H bonds. Forms between separate polypeptide chains or between different regions of a single polypeptide chain that's bent back on itself

Unsaturated Fatty Acids

- Contains one or more double bonds which create kinks in the molecule that prevent it from being packed tightly - Kinks important in determining the fluidity and melting points of lipids

DNA Replication

- DNA can be reproduced exactly by polymerization using an existing strand as a base-pairing template (p. 65) - Depend on the base-pairing properties of nucleic acids - Involves entire DNA molecule (p. 66)

Complementary Base Pairing

- DNA: Thymine and adenine (T-A) & cytosine and guanine (C-G) - RNA: A-U & C-G - Held together by H bonds (which, since they are not as strong as covalent bonds, are relatively easy to break) - Can take place b/w RNA & DNA (p. 65)

Triglycerides

- Fats: solids at room temp. - Oils: liquids at room temp. - Simple lipids - Composed of 3 fatty acids and 1 glycerol

Phospholipids

- Fatty acids bound to glycerol by ester linkages - Any one of several phosphate-containing compounds replaces one of the fatty acids, so it has amphipathic (2 opposing chemical properties) properties - Phosphate portion is hydrophilic; fatty acid portion is hydrophobic - Lipid containing a phosphate group - Important constituent of cellular membranes

Nucleic Acids

- Form from 4 different nucleotides - Specialize in information storage and transmission

Amino Acid

- Has a carboxyl functional group and an amino functional group attached to the same carbon atom (called alpha carbon), and attached to the alpha carbon atom are a hydrogen atom and a side chain (or R group) - Can exist as optical isomers called D-amino acids and L-amino acids - Simultaneously acids and bases - Side chains contain functional groups important in determining the 3D structure and protein function - Proteins are polymers of these

Cis-Trans Isomers

- Have double bond between 2 carbon atoms and then remaining two bonds go to 2 different atoms or groups of atoms - Cis: Different atoms or groups of atoms are on the same side - Trans: If different atoms or groups of atoms are on opposite sides

Lipids

- Held together by noncovalent forces

Polypeptide

- Large molecule made up of many amino acids joined by peptide linkages

Carbohydrates

- Link monosaccharides to form polysaccharides - Organic compounds containing carbon, hydrogen, and oxygen in ratio 1:2:1

Polynucleotides

- Longest polymers - AKA Nucleic Acids - Include DNA and most RNA (p. 63)

DNA (deoxyribonucleic acid)

- Macromolecule that encodes hereditary information and passes it from generation to generation (p. 63) - Sugar: Deoxyribose - Bases: Adenine, Cytosine, Guanine, Thymine - Name of Nucleoside: Deoxyadenosine, Deoxycytidine, Deoxyguanosine, Deoxythymidine - Strands: Double - Can be reproduced exactly (p.65) - Twists into a double helix where two polynucleotide strands for a "ladder" with the sugar-phosphate groups forming the sides of the ladder and the bases with their H bonds form the "rungs" on the inside - Carry hereditary information from one generation to the next, gradually accumulating changes in its base sequences over long periods of time (reveal evolutionary relationships)

Polymers

- Made up of covalent bonded monomers - Formed from similar/identical monomers by condensation reactions (loss of water) which form as a result of covalent bonds between monomers - Form only if water molecules are removed and energy added to system

Fatty Acid

- Molecule made up of a long nonpolar hydrocarbon chain and polar carboxyl group - Found in many lipids

Nucleoside

- Molecules consisting of a pentose sugar and a nitrogenous base but no phosphate group (p. 63)

Nucleotide

- Monomers that make up nucleic acids - 3 components: nitrogen-containing base, a pentose sugar, and one to three phosphate groups (p. 63) - Play role as carriers in the synthesis and breakdown of carbs and lipids (p. 67)

Cellulose

- Most abundant organic compound - Polysaccharide of glucose whose monosaccharides are connected by BETA glycosidic linkages which make it more stable - Excellent structural material that can withstand harsh environmental conditions w/o substantial change

Glucose

- Most common monosaccharide - Monomer of starch, glycogen, cellulose

C-N Linkage

- N terminus denotes the "capital letter" marking the beginning of a polypeptide in the amino group of the first amino acid added to the chain - C terminus denotes the "period" of the carboxyl group of the last amino acid added - Not free to rotate fully, which limits the folding of the polypeptide chain

Translation

- Nucleotide sequence in the RNA can be used to specify a sequence of amino acids in a polypeptide chain AFTER TRANSCRIPTION (p. 65)

ATP

- Nucleotide that acts as an energy transducer in many biochemical reactions (p. 66)

cAMP

- Nucleotide that helps the actions of hormones and transmission of info. by the nervous system (p. 67)

GTP

- Nucleotide that serves as an energy source in protein synthesis and helps transfer of info. from environment to cells (p. 67)

Nucleoside Monophosphate

- Nucleotides that make up nucleic acids containing just one phosphate group (p. 63)

Optical Isomers

- Occur when carbon atom has 4 different atoms or groups of atoms attached to it

Amphipathic

- Of a molecule, having both hydrophilic and hydrophobic regions

Nucleic Acids

- Polymers made of nucleotides specialized for the storage, transmission, and use of genetic information - Two types: DNA & RNA (p. 63) - Two forms: pyrimidine (six-membered single-ring structure), purine (fused double-ring structure)

Protein

- Polymers made up of 20 amino acids in different proportions and sequences - Have one or more polypeptide chain - unbranched (linear) polymers of covalently linked amino acids - Products of genes

Macromolecules

- Polymers over 1,000 in weight (nucleic acids, proteins, carbohydrates) - Proteins, polysaccharides, nucleic acids

Starches

- Polysaccharides of glucose with alpha glycosidic linkages that can be distinguished by the amount of branching at Carbons 1 and 6 - Principal energy storage compound of plants - Readily binds water - Easily degraded by actions of chemicals or enzymes

Primary Structure

- Precise sequence of amino acids in a polypeptide chain held together by peptide bonds - Determines final shape - Backbone of polypeptide chain - Last to denature b/c of covalent bonds

Chaperone

- Protein that guards other proteins by counteracting molecular interactions that threaten their 3D structure

Tertiary Structure

- Result of polypeptide chain bent at specific sites and then folded back and forth - Structure determined by the interactions b/w the amino acid side chains and b/w R groups and environment - Macromolecule's 3D shape, including a buried interior and surface exposed to environment

Phosphodiester Linkage

- Resulting bond when a phosphate sugar in the last nucleotide of the existing chain and the phosphate on the new nucleotide undergo a condensation reaction - The bond forms in b/w the 5'-carbon atom of the sugar on the new nucleotide and the 3'-carbon on the last sugar of the existing chain (p. 63)

Quaternary Structure

- Results from way sin which subunits (two or more polypeptide chains) bind together and interact - The specific three-dimensional arrangement of protein subunits.

Isomers

- Same numbers and kinds of atoms but with atoms/bonds arranged differently

Genes

- Sequences of DNA that are transcribed into RNA (p. 66)

Oligosaccharides

- Several monosaccharides bound by glycosidic linkages at various sites - Have additional functional groups - Often covalently bonded to proteins and lipids on outer cell surface

Oligonucleotides

- Short - Include RNA molecules that function as "primers" to begin the duplication of DNA; RNA molecules that regulate the expression of genes; and synthetic DNA molecules used for amplifying and analyzing other, longer nucleotide sequences (p. 63)

Glycosidic Linkages

- Single link between two monosaccharides forms a disaccharide - Covalently bonded together monosaccharides that form disaccharides, oligosaccharides, and polysaccharides by condensation reactions form glycosidic linkages - Bond monosaccharides

Polysaccharides

- Store energy and provide structural materials - Capable of branched molecules - Composed of many monosaccharides - Ex: Cellulose and starch

Peptide Linkage

- The bond between amino acids in a protein; formed between a carboxyl group and amino group (—CO—NH—) with the loss of water molecules.

Disulfide Bridge

- The covalent bond between two sulfur atoms (-S—S-) linking two molecules or remote parts of the same molecule.

Gene Expression

- The overall process of transcription and translation (p. 65)

Ester Linkage

- The resulting covalent bond formed from the synthesis of triglyceride which involves three condensation (dehydration) reactions in which the carboxyl group of a fatty acid bonds with a hydroxyl group of glycerol - Lipids formed this way

RNA (rinonucleic acid)

- Through RNA intermediates, the information encoded in DNA is used to specify the amino acid sequences of proteins and control the expression synthesis of other RNAs (p. 63) - Sugar: Ribose - Bases: Adenine, Cytosine, Guanine, Uracil - Name of Nucleoside: Adenosine, Cytidine, Guanosine, Uridine - Strands: Single - Portions can fold back and pair with one another (p.64)

How do triglycerides in plants and animals differ?

- Triglycerides of animal fats are long-chain/saturated fatty acids tightly packed and usually solid at room temp. and have high melting points - Triglycerides of plants (ex. corn oil) have short/unsaturated fatty acids and pack together poorly, have low melting points, and are liquids at room temp

Glycogen

- Water-insoluble, highly branched polymer of glucose - Energy storage polysaccharide for animals & fungi (stores glucose in liver and muscles)

Denatured

- When a protein is slowly heated and moderately heated, the heat energy will disrupt only the weak interactions, causing the secondary and terriary structure to break down

Starch Grains

- When water is removed, Hydrogen bonds form b/w unbranched polysaccharide chains, which aggregate - Ex: storage tissues of plant seeds

The primary structure of proteins is the _______. The primary structure contains the information necessary for the formation of secondary structure, including the _______ and the _______. Secondary structure of proteins is stabilized by the formation of _______ bonds. A. β pleated sheet; α helix; amino acid sequence; hydrogen B. amino acid sequence; α helix; β pleated sheet; hydrogen C. amino acid sequence; α helix; β pleated sheet; peptide D. amino acid sequence; β pleated sheet; α helix; disulfide E. α helix; amino acid sequence; β pleated sheet; hydrophobic

B. Sec 3.2

Nucleotides are composed of A. one or more amino acids. B. one or more phosphates, a sugar, and a base. C. fatty acids and a base. D. a base and at least one phosphate. E. nucleic acids.

B. Sec 4.1

Where would the leucine side chain most likely be found in a protein dissolved in water? A. In the interior of the protein in contact with nonpolar side chains B. Either on the interior or exterior of the protein C. On the exterior of the protein D. In the interior of the protein in contact with water E. In the interior of the protein in contact with polar side chains

A. Sec 3.2

Fatty acids are A. carboxylic acids with long hydrocarbon tails. B. generally present in water-soluble proteins. C. saturated hydrocarbons. D. linked to glycerol in fats by phosphodiester bonds. E. large polymers of monosaccharides.

A. Sec 3.4

Replication is the synthesis of _______, while transcription is the synthesis of _______. A. an exact copy of DNA; an RNA copy of DNA B. an exact copy of RNA; an exact copy of DNA C. proteins; an RNA copy of DNA D. an exact copy of DNA; proteins E. an RNA copy of DNA; an exact copy of DNA

A. Sec 4.1

Which of the following amino acids would, when incorporated into a polypeptide chain (not at the N or C terminus), make the charge of the polypeptide more positive? A. Alanine B. Cysteine C. Arginine D. Serine E. Aspartate

C. Sec 3.2

The "building blocks" of polysaccharides are _______ and the blocks are covalently linked together by _______ bonds. A. disaccharides; glycosidic B. amino acids; peptide C. monosaccharides; glycosidic D. glycerol and fatty acids; ester E. phospholipids; ester

C. Sec 3.3

Olive oil melts at a lower temperature than beef fat because A. oils are made by plants whereas fats are made by animals. B. fats contain more unsaturated fatty acids than oils do. C. fats contain more saturated fatty acids than oils do. D. olive trees occur in warmer climates than beef cattle do. E. oils contain glycerol whereas fats do not.

C. Sec 3.4

Oils and fats A. form membranes. B. all contain the same fatty acids. C. have peptide bonds. D. are triglycerides. E. are good for humans in large amounts.

D. Sec 3.4

Which of the following correctly describes a difference between DNA and RNA? A. DNA is single-stranded, whereas RNA is double-stranded. B. DNA contains four nucleotides, whereas RNA contains three. C. DNA occurs in the nucleus, whereas RNA only occurs outside the nucleus. D. DNA is replicated, whereas RNA is translated. E. DNA contains a ribose, whereas RNA contains a deoxyribose sugar.

D. Sec. 4.1

Which of the following statements about to protein structure is false? A. Some proteins contain more than one polypeptide chain. B. α helix and β pleated sheets are common secondary structures in proteins. C. Chaperones may assist in folding proteins. D. Proper folding is essential to the function of a protein. E. Most of the interactions that stabilize folded proteins are covalent.

E. Sec 3.2

The main function of cellulose is A. as a storage compound for energy in plant cells. B. as a component of biological membranes. C. as a storage compound for energy in animal cells. D. to provide mechanical strength to insect cell walls. E. to provide mechanical strength to plant cell walls.

E. Sec 3.3

Cholesterol is soluble in chloroform, a nonpolar organic solvent, but it is not soluble in water. Based on this information, what class of biological macromolecules does cholesterol belong to? A. Carbohydrates B. Proteins C. Oligosaccharides D. Enzymes E. Lipids

E. Sec 3.4

There are a number of functional groups in biological molecules. Which of the following about their presence in different classes of molecules is most accurate? A. Hydroxyl groups are only present in carbohydrates. B. Aldehyde groups are common in proteins. C. Sulfhydryl groups are important features of fats. D. Carboxyl groups are found in small molecules but not in macromolecules. E. Amino groups may be found in modified carbohydrates and in proteins.

E. Sec 3.4

Which of the following biological molecules is/are linked by covalent bonds formed by the removal of water from the reactants (condensation reaction)? A. Oils B. Waxes C. Proteins D. Starch E. All of the above

E. Sec 3.4