biochem--quiz 1

describe the plasma membrane

• barrier to keep in and out separate

• all organisms have one

describe the cytoplasm

• organelles

• supramolecular structures (ribosomes)

• cytosol: highly concentrated soluble material (proteins, lipids, nucleic acids, carbohydrates)

how do cells differ from one another

by the dimensions (radius and surface:volume)

• different shapes based on their function

what are some of the universals with life on earth

• lipids are cell membranes (all organisms we know about have them)

• DNA replication is semi-conservative

• glucose is a preferred sugar source for energy (glycolysis is an ancient pathway

• ATP as an energy currency

what does aerobic mean

likes oxygen

what does anaerobic mean

does not like oxygen

give an example of chirality making a big difference

• thalidomide helped with morning sickness in one form and the other caused malformations and miscarriages due to downregulation of transcription factors

• our body naturally switches between the two forms

how can biochemistry teach us how organisms are evolving

gene duplication events are a driving force for organisms evolving new abilities

what are the main elements pertienent to biochemistry

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphurous, sulfur)

describe the common chemical bonds in cells and organisms

• H, O, C, N make up 99% of the atoms in the human body

• their ability as the lightest elements to form covalent bonds by electron-pair sharing makes life on Earth possible

name the functional group

methyl

name the functional group

ethyl

name the functional group

phenyl

name the functional group

carbonyl (aldehyde)

name the functional group

ketone

name the functional group

carboxyl

name the functional group

hydroxyl (alcohol)

name the functional group

enol

name the functional group

ether

name the functional group

ester

name the functional group

acetyl

name the functional group

anhydride (two carboxylic acids)

name the functional group

amine (protonated)

name the functional group

amido

name the functional group

imine

name the functional group

guanidinium

name the functional group

imidazole

name the functional group

sulfhydryl

name the functional group

disulfide

name the functional group

thioester

name the functional group

phosphoryl

name the functional group

phosphoanhydride

draw the functional group methyl

draw the functional group ethyl

draw the functional group phenyl

draw the functional group carbonyl (aldehyde)

draw the functional group carbonyl (ketone)

draw the functional group carboxyl

draw the functional group hydroxyl (alcohol)

draw the functional group enol

draw the functional group ether

draw the functional group ester

draw the functional group acetyl

draw the functional group anhydride (two carboxylic acids)

draw the functional group amino (protonated)

draw the functional group amido

draw the functional group imine

draw the functional group guanidinium

draw the functional group imidazole

draw the functional group sulfydryl

draw the functional group disulfide

draw the functional group thioester

draw the functional group phosphoryl

draw the functional group phosphoanhydride

what do the different colors in this molecule represent

• blue: Nitrogen

• red: Oxygen

• black: Carbon

describe macromolecules

• thousands of atoms held by strong covalent bonds

• four types: carbohydrates, lipids, proteins, amino acids

describe catabolism

break down covalent bonds

describe anabolism

build up covalent bonds

what are the four types of noncovalent (“weak”) interactions among biomolecules aqueous solvent

1. hydrogen bonds

2. ionic interactions

3. hydrophobic effect

4. van der Waals interactions

describe ionic bonds

• rare in aqueous solutions

• not nearly as strong as covalent

• either hold molecules together or repulse them

describe hydrogen bonds

• unequal distribution of charge that results when a hydrogen atom (partially positive) is covalently bonded to an electronegative atom, such as oxygen or nitrogen (partially negative)

• further spacing between molecules decreases the space

describe van der waals interactions

• transient attractive interactions when atoms are spaced appropriately

• the molecules have equal amounts of electrons sharing but the electrons have to be somewhere at sometime, making partial positives and partial negatives that cause the attraction

what is the bond strengths of the bonds typically found in living organisms

covalent > ionic > h-bonding > van der waals

describe molecular complementarity

• the language of biochemical interactions

• mediated via noncovalent interactions that permits tight, highly specific binding of biomolecules

• depending on the number and strength of the noncovalent interactions between two molecules and their environment, their binding may be tight or loose and, as a consequence, either long-lasting or transient, respectively

describe proteins

• long polymers of amino acids

• catalytic enzymes, structural, signal receptors, trasnporters

• size =. MW 5000-1,000,000 Daltons

describe nucleic acids

• polymers of nucleotides to make DNA or RNA

• store/transmit genetic information

• size = MW up to 1,00,000,000 Daltons

• monomers act as energy sources—ATP

describe polysaccharides

• polymers of simple sugars

• energy-yeilding fuel stores

• extracellular structural elements

• size = up to 1,000,000 Daltons

describe lipids

• greasy hydrocarbons

• structural components of membranes, energy-rich fuel stores, pigments, intracellular signals

• size = MW 750-1500 daltons

what is one dalton equivalent to

1 g/mole or about one hydrogen atom

what is the concentration of proteins in a typical cell

200-300 g/L

describe the basics of water

• over 70% of weight of most organisms

• chemical reactions occur in aqueous environments

• water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes

• a significant amount of life lives in an aqueous environment

• each molecule can H-bond with up to four other water molecules, but they only last picosecons

• water hydrogen bonds with polar solutes

• solutes hydrogen bond with solutes

describe water in relationship to the hydration of ions

• increase the entropy of the system (thermodynamically favorable) by breaking apart the extremely organized salt crystal

• ions can’t bond as the water in in the way

describe water and amphipathic molecules

• contain regions that are polar (charged, hydrophilic) and regions that are nonpolar (hydrophobic)

• water molecules position themselves in a specific cage-like manner called clathrate where multiple layers are organized decreasing entropy

describe the hydrophobic effect of water

• the association or folding of nonpolar molecules in aqueous solution is one of the main factors behind:

  • formation of lipid micelles

  • protein folding

  • protein-protein association

  • binding of steroid hormones to their receptors

• nonpolar association does not arise due to direct, attractive forces between molecules

describe clusters of lipid molecules

• only lipid portions at the edge of the cluster force the ordering of water

• fewer water molecules are ordered, and entropy is increased

describe micelles

all hydrophobic groups are sequested from the water; ordered shell of water molecules is minimized, and entropy is further increased

describe water helping substrates and ligands binding

• binding of substrates, or ligands, “frees some water into bulk surrounding (increases entropy)

• helps push formation of enzyme-substrate (ligand-receptor) complexes

describe how water is ionizable

• when a water molecule dissociates, one of its polar H—O bonds breaks and the products are a proton (H+, H3O+) and a hydroxide ion (OH-)

• dissociation of water is a rapid, reversible process

  • most water molecules remain un-ionized (the equilibrium is strongly to the left)

  • approx. 2/1,000,000,000 are ionized which matters because its at a high concentration

  • at about 55M, this ionization can be significant and affect biomolecule structure and function by altering the pH

  • although very weak, ionization is important in maintaining and regulating the body’s acid-base homeostasis

describe pH values and biological fluids

• all aqueous solutions contain specific concentrations of positively charged hydrogen ions (H+) and negatively charged ions (OH-) and therefore all have pH

• because these ions are the dissociation products of water, they are constituents of all living systems, and they are liberated by many reactions that take place between organic molecules within cells

• the relative amount of ions can be measured and used for a pH scale

what are causes of acidosis (blood pH <7.35) in the body

• severe diabetes

• starvation

• obstructive lung disease

• binge drinking

• hypoventilation (due to narcotics, sedatives, anesthesia)

what are causes of alkalosis (blood pH > 7.45) in the body

• prolonged vomiting

• ingestion of excessive amounts of alkaline drugs

• hyperventilation (due to infection, drugs, hormones)

describe the effects of pH on the blood

• the pH affects the structures and function of biomolecules—blood pH is commonly used in medical diagnoses

• the pH range for blood that is compatible with human life is 6.8-7.8 with 7.35-7.45 being considered normal

• if blood pH drops below 7.35, the central nervous system (CNS) becomes depressed, resulting in coma and eventually death

• if blood pH rises above 7.45, the CNS is overexcited and muscles go into a state of spasm, leading to convulsions and respiratory arrest

• microbes live over much broader pH ranges, and some at extremes

what are the different pH equations

what happens when the concentration of hydrogen is greater than the concentration of OH

the blood is acidic

what happens when the concentration of hydrogen is smaller than the concentration of OH

the blood is basic

describe biological buffers that control the pH

• an optimal acid-base balance is maintained in body fluids and cells despite large fluxes of metabolites

• a buffer system protects the body from fluctuations in pH by “soaking up” excess H+ or OH-

• abundant buffering systems in cells:

  • dihydrogen-phosphate buffering system (intracellular pH)

  • carbonic acid buffering system (blood)

  • proteins

describe the dissociation of strong acids

the dissociation is complete so the concentration of H+ is the same as the concentration of acid

describe the dissociation of weak acids

• the dissociation is incomplete

• extent of dissociation is determined by the acid dissociation constant Ka

what does a larger value for Ka mean

the stronger the acid

what does the lower the pKa mean

the larger the Ka and the stronger the acid

how are buffers able to work

• resist the changes in pH because an equilibrium between the buffer’s components is established

• at equilibrium, [conjugate acid] and [conjugate base] are large and therefore able to neutralize small amounts of other acids and bases when they are added to the solution

what does a strong acid react with when mixed with a buffer

reacts with the weak base in the buffer to form a weak acid, which produces few H+ ions in solution and therefore only a little change in pH

what does a strong base react with when mixed with a buffer

reacts with the weak acid to form water

what is special when pH=pKa

• there is a 50:50 mixture of acid and anion forms of the compounds

• when the buffering capacity of acid/anion system is greatest

• buffering capacity is lost when the pH differs from pKa by more than one pH unit

what does the titration curve of acetic acid look like

why do some molecules have multiple pKas

different functional gropus can add to the buffering zones

what is the Henderson-Hasselbalch Equation

describe why enzymes have an optimum pH for activity

maintenance of a specific and constant pH, (typically near 7.0) is needed by cells and organisms—small changes in pH can have a large impact on rate of cellular processes

what are the main rolls of proteins

catalysis, transport, structure, motion

describe proteins for catalysis

• enolase (in the glycolytic pathway)

• DNA polymerase (in DNA replication)