Cell and Molecular Bio Ch.2

covalent bonds

bonds between atoms in which electrons are shared

molecule

stable combinations of atoms held together by covalent bonds

compound

molecules with more than one type of atom

polar molecules

asymmetrical distribution of electrical charge

nonpolar molecules

lack asymmetrical electrical charge

what are the two biological molecules with both polar and nonpolar regions

proteins and phospholipids

• how many kilocalories does it take to break a covalent bond

• shared electrons stay closest to the atom with the greatest (blank)

• electronegativity depends on what

• 80-100

• electronegativity

• the number of protons in the nucleus and the distance of the shared electrons from the nucleus

• how do ions form

• anions

• cations

• ions form when strongly electronegative nuclei capture electrons

• have extra electrons

• have lost electrons

free radical

• unstable atoms or molecules with unpaired electrons

• formed during normal metabolism

• may play a role in aging

• highly reactive and damages macromolecules such as DNA

antioxidants

• molecules that defend the body from free radicals

• prevent and repair damage done by free radicals

• donate electrons to free radicals to neutralize them and stop the oxidation process

superoxide dimutase (SOD)

• enzyme that destroys the superoxide radical (O₂⁻)

• protects cells from damage

• extends the life of laboratory animals that overproduce superoxide

two other enzymes that can help destroy free radicals

• catalases and glutathione peroxidases

calorie restriction

• extends lifespan of experimental animals

• results in decreased production of free radicals

• reduced DNA damage

• attractive bonds that are weaker than covalent bonds

• chemical energy needed to break non-covalent bonds

• weak bonds are (blank) then (blank)

1. non-covalent

2. 1-5 kilocalories

3. broken, reformed

types of non-covalent bonds and how they form

1. ionic bonds: attractions between charged atoms that are weakened by water (i.e. NaCl)

2. Hydrogen bonds: form when a hydrogen atom is covalently bonded to an electronegative atom and thus adopts a partial positive charge and attracts to another electronegative atom of another molecule (determine the structure and properties of water)

3. hydrophobic interactions: nonpolar molecules associate and minimize their exposure to polar molecules

4. Van der waals: transient dipole formationin nonpolar molecules

1. hydrogen bond

2. hydrophobic interaction

• (blank) forms four covalent bonds and is essential to life

• (blank) containing molecules produced by living organisms are called (blank)

• carbon

• carbon, biochemicals

hydrocarbons

• contain only carbon and hydrogen

• vary in the number of carbons and number of bonds between carbons

macromolecules

large structural and functional molecules in cells

name the four macromolecules and their monomers

1. Proteins: amino acid monomer

2. Lipids: fatty acid monomer

3. Polysaccharides/Carbohydrates: sugar monomer

4. Nucleic Acids: nucleotide monomer

what are the 7 functional groups (answers to picture not in order)

1. Methyl (CH₃)

2. Hydroxyl (OH)

3. Amino (NH₂)

4. Carboxyl (COOH)

5. Carbonyl (CO)

6. Sulfhydryl (SH)

7. Phosphate (PO₃H₂)

1. Carbohydrates include simple (blank) and (blank)

2. Lipids are a diverse group of (blank) molecules. how are fats made?

3. Proteins are polymers of (blank)

4. nucleic acids are the polymers of (blank) which store and transmit (blank)

1. sugars, sugar polymers

2. nonpolar, fats are made by bonding a glycerol molecule to 3 fatty acid chains via 3 esther linkages

3. amino acids

4. nucleotides, genetic information (DNA and RNA)

1. Carbohydrates function as (blank)

2. What is the general formula for a carbohydrate

3. what is a polysaccharide

4. glycogen

5. starch

1. energy storage

2. CH₂O

3. polymers of sugars joined by glycosidic bonds

4. animal product made by branched glucose polymers

5. plant product made up of both branched and unbranched glucose polymers

• what are fatty acids

• what does it mean if a fatty acid is saturated or unsaturated

1. fatty acids are unbranched hydrocarbons with one carboxyl group (COOH), making them amphipathic

2. a fatty acid is saturated if it does not contain any double bonds between the carbons of the hydrocarbon chain; it is unsaturated if it contains a double bond between the carbons and thus, the max amounts of hydrogen are not able to bond

1. are unsaturated fatty acids solid or liquid at room temp

2. are saturated fatty acids solid or liquid at room temp

1. liquid

2. solid

1. saturated fatty acid

2. unsaturated fatty acid

1. what are the components of an amino acid

2. how are amino acids joined together

3. what are the 3 things an R-group could be

1. an amino group, a carboxyl group (COOH), a phosphate group, and an “R” group, which varies among amino acids

2. peptide bonds which bond amino acids into a polypeptide chain to make proteins

3. polar charged, polar uncharged and nonpolar

what are the polar charged amino acids (His Glue Lysis the ArG ASaP)

1. Histidine

2. Glutamic Acid

3. Lysine

4. Arginine

5. Aspartic Acid

properties of polar charged r groups

• act as strong acids or bases and can form ionic bonds

• form ionic bonds due to charges

• histidine is usually only partially charged at pH 7 and can gain or lose a proton in physiologic pH ranges

polar uncharged r-groups (SAGTT)

1. serine

2. asparagine

3. glutamine

4. threonine

5. tyrosine

properties of polar uncharged r-groups

• make weak acids or bases

• not fully charged at pH 7

• can form H bonds due to partial positive or negative charge

nonpolar r-groups

1. Alanine

2. Valine

3. Leucine

4. Isoleucine

5. Phenylalanine

6. Tryptophan

7. Methinonine

properties of nonpolar side chains

• hydrophobic

• pack tightly into protein core

• cannot interact with water or form electrostatic bonds

what are the special properties associated with glycine, cysteine and proline

1. glycine has a side chain that only contains a hydrogen atom and can fit in both hydrophilic and hydrophobic environments

2. cysteine has a side chain with a sulfhydryl group, which forms disulfide bonds

3. proline has a hydrophobic side chain that creates kinks in polypeptide chains and disrupts secondary structure

Proteins

1. primary structure

2. secondary structure

3. tertiary structure

4. quaternary structure

1. sequence of amino acids in the polymer

2. alpha helixes or beta pleated sheets formed by bonds between adjacent amino acids (hydrogen bonds form between the carboxyl group of one amino acid and the amino group of another)

3. Confirmation of the entire polymer stabilized by non-covalent bonds (disulfide bonds, ionic bonds, van der Waals, hydrophobic interactions) creates fibrous or globular proteins

4. proteins composed of subunits

• protein domains

• dynamic changes within proteins

• form when a protein is composed of one or two distinct regions (each domain is a functional region)

• Conformational changes are non-random movements triggered by the binding of a specific molecule

multiprotein complex

different proteins become physically associated to form a multiprotein complex

explain how a change at the DNA level leads to effects at the organismal level with sickle cell disease

• a change in the DNA sequence leads to the sickle cell mutation

• at the protein level, the mutation changes the shape of the hemoglobin molecule, allowing it to clump together

• at the cellular level, red blood cells carrying the mutant hemoglobin are deprived of oxygen and become sickle shaped, which hinders blood flow

• leads to pain and fatigue at the organismal level

NOTE: carriers of the sickle cell allele are resistant to malaria because the parasites are killed in sickled blood cells

Alzheimer’s disease (AD)

• involves misfolded proteins that accumulate in the brains of affected individuals

• amyloid precursor protein (APP), which is a membrane-bound protein in brain neurons, is cleaved by two secretase enzymes

• in individuals predisposed to AD, this cleavage results in Aβ42, a protein that misfolds and associates into amyloid plaques

Creutzfeld-Jakob Disease (CJD)

• results from misfolded protein in the brain

• Healthy brains contain the normal protein PrPc

• CJD brains have PrPsc which is misfolded

• causes kuru and mad cow disease

Gleevec

• drug used for treatment of rare cancers that used computer simulations of protein binding sites that allowed to test drug effectiveness

• proteome

• proteomics

• entire inventory of an organism’s proteins

• uses advanced technologies to perform large-scale studies on diverse proteins

1. proteins are separated using

2. proteins are identified using

1. gel electrophoresis

2. mass spectometry and high speed computers

• nucleic acids are polymers of (blank) that store and transmit (blank)

• two types of genetic information

• how are nucleotides connected

1. nucelotides, genetic information

2. DNA (all organisms and some viruses), RNA (viruses)

3. 3’-5’ phosphodiester bonds between the phosphate group of one nucleotide and the number 3 carbon of the next

• 3 components of a nucleotide

• purine nitrogenous bases

• pyrimidine nitrogenous bases

• phosphate group, 5-carbon sugar, nitrogenous base

• Adenine, guanine

• cytosine, thymine, uracil

1. RNA is usually (blank) and DNA is usually (blank)

2. RNA may have (blank) activity, such molecules are called (blank)

1. single stranded, double stranded

2. catalytic, ribozymes

Note: RNA may fold on itself to make complex 3D structures as in ribosomes