AP bio Midterms

Stanley Millers experiment

demonstrated the abiotic synthesis of organic compounds

Carbon atoms

4 valence electrons, 4 covalent bonds

Carbon skeletons

the chain of carbon atoms in an organic molecule
- vary in length
- may be branched/unbranched
- may have double bonds
- may be arranged in rings (each corner represents a carbon and its attached hydrogens)

hydrocarbon

Compounds composed of only carbon and hydrogen

isomers

Two different molecules that have the same chemical formula
- ex/ ibuprofen: s is effective, r is not

structural isomers

differ in the covalent arrangements of their atoms

cis-trans isomers

carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

cis isomer

two groups are on the same side of the double bond

trans isomer

two groups are on opposite sides of the double bond

Enantiomers

differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images (hands)

Ibuprofen

reduces inflammation and pain
s ibuprofen - effective enantiomer
r ibuprofen - ineffective enantiomer

Albuterol

asthma medication
r albuterol - effective isomer
s auterol - ineffective isomer

Functional groups

a specific configuration of atoms that are commonly attached to carbon skeletons of organic molecules and are involved in chemical reactions

hydroxyl group

\[-OH]
- alcohol (ex. ethanol)
- polar due to electronegative oxygen
- forms hydrogen bonds with water to help dissolve compounds like sugars

carbonyl group

\[C\=O]
- polar
- keytone and aldehyde

keytone

carbonyl group within carbon skeleton

aldehyde

Carbonyl group at the end of a carbon skeleton

carboxyl group

\[O\=C-OH]
- acts as an acid because the covalent bond between oxygen and hydrogen is so polar
- carboxylic acid

amino group

\[H-N-H]
- acts as a base; can pick up H+ ions from the surrounding solution
- amine
- glycine + H+ ⇌ inonized -NH2

sulfhydryl group

\[—SH]
- two -SH groups can interact and for a "cross-link" that stabilizes proteins
- thiol
- Hair treatment

phosphate group

\[-OPO₃⁻²]
- Contributes a negative charge
- negative charge of 1 when in a chain of phosphates
- negative charge of 2 when on the end
- gives molecule the ability to react with water, releasing energy
- organic phosphate
- ATP

methyl group

\[-CH₃]
- affects the expression of genes when on DNA or when on proteins bonded to DNA
- affects structure/function of sex hormones
- methylated compound

Adenosine Triphosphate (ATP)

stores the potential to react with water

ATP energy reaction

ATP + water→ ADP + inorganic phosphate + energy

Large molecules of life

carbs, lipids, proteins, nucleic acids

macromolecules

carbs, proteins, nucleic acids

enzymes

specialized macromolecules that speed up chemical reactions; a catalyst for the reaction, does not get consumed by the reaction

hydrolysis reaction

add water to break down a polymer
polymer → monomer

dehydration synthesis

remove water to form a polymer
monomer → polymer

Monosaccharaides

- monomer for a carb
- 1:2:1 ratio
- glucose, fructose, galactose

trioses

\[C₃H₂0₃]; glyceraldehyde (aldehyde) and dihydroxyacetone (keytose)

pentoses

\[C₅H₁₀0₅]; ribose (aldehyde) and ribulose (keytone)

hexoses

\[C₆H₁₂0₆]; glucose & galactose (aldehyde) and fructose (keytose)

energy sources for organisms

glycosidic linkages

- bond between carbohydrate molecules through an intervening oxygen atom
- forms disaccharide

maltose

disaccharide: glucose + glucose (1-4 linkage)

sucrose

disaccharide: glucose + fructose (1-2 linkage)*

Disaccharide

A double sugar, consisting of two monosaccharides joined by glycosidic linkages
- must be broken down for an organism to get the nutrients

lactose

disaccharide: glucose + galactose (1-2 linkage)

polysaccharides

polymers of monosaccharides linked together by dehydration reactions; storage and structure

glycogen

- polymer of glucose that animals store
- like amylopectin but more branched
- liver/muscle cells
- short term storage

starch

A storage polysaccharide in plants consisting entirely of glucose
- 1-4 linkages
- amylose is unbranched (simplest form)
- amylopectin is more complex (1-6 linkages)
- animals get starch from plants
- alpha glucose monomer

cellulose

a structural polysaccharide of plant cell walls, consisting of glucose monomers joined by beta glycosidic linkages

Glucose (alpha vs beta)

\[C₆H₁₂0₆]

chitin

A structural polysaccharide found in many fungal cell walls and in the exoskeletons of arthropods.

lipids

fats, phospholipids, steroids

triglyceride (triacylglycerol)

a lipid consisting of 3 fatty acids linked to one glycerol

glycerol

A three-carbon alcohol to which fatty acids are covalently bonded to make fats and oils.

fatty acid

a carboxylic acid consisting of a hydrocarbon chain and a terminal carboxyl group, especially any of those occurring as esters in fats and oils
- vary in length and in location of double bonds

satturated fatty acid

a fatty acid with all single bonds in the hydrocarbon tail, maximizing the number of hydrogen atoms attached to the carbon skeleton (butter, animal fat)

unsaturated fatty acid

a fatty acid that has 1+ double bonds between carbons in the hydrocarbon tail, reduces the number of hydrogen atoms attached to the hydrocarbon skeleton (olive oil, plant fat)

trans fatty acids

fatty acids with hydrogens on opposite sides of the double bond, made artificially by hydrogenating vegetable oils

Phosopholipids

found in cell membranes, glycerol + 2 fatty acids + phosphate group, nonpolar, hydrophilic head

Cholesterol

steroid for animal cell membranes, sex cell precursor, synthesized in the liver and obtained from diet

steroids

lipids characterized by a carbon skeleton consisting of four fused rings

enzymatic proteins

accelerate chemical reactions

defensive proteins

antibodies of the immune system

storage proteins

store amino acids (casein)

transport proteins

transport of substances (hemoglobin)

hormonal proteins

coordinate organism's activities (insulin)

receptor proteins

response of cell to chemical stimuli

contractile proteins

movement

structural proteins

support (keratin)

amino acid

compound with an amino group on one end and a carboxyl group on the other end
- monomer of polypeptide
- asymetric carbon at center

polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds
- carboxyl group is adjacent to amino group

primary structure protein

sequence of amino acids

secondary structure of protein

alpha helix and beta pleated sheet

teritary structure

The complex 3-dimensional structure of a single peptide chain; held in place by disulfide bonds between cysteines
- hydrophobic interactions: proteins with hydrophobic side chains end up in a cluster in the center
- disulfide bridges: covalent bonds between sulfhydryl groups

Quaternary structure of protein

association of 2+ polypeptides
- ex/ collagen and hemoglobin
- consist of subunits

denatured protein

a protein whose structure has been changed by physical or chemical agents

central dogma of biology

genome → transcriptome → proteome

gene expression

process by which a gene produces its product and the product carries out its function

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

Pyrimidines

6-membered ring: cytosine, thymine, uracil (CUT)

purine

6-membered ring bonded to 5-membered ring: adenine and guanine

phosphodiester linkage

forms sugar-phosphate backbone by linking the sugars of 2 nucleotides

polynucleotides

A polymer consisting of many nucleotide monomers in a chain; nucleotides can be those of DNA or RNA
- antiparallel 5' → 3'
- one end has a phosphate attached to a 5' carbon
- one end has a hydroxyl attached to a 3' carbon d

transformation

process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria

frederick griffin

experimented with bacteria on mice and discovered there was a "transforming principle" that was passed down from parent to offspring and determined that one of the four biological molecules contained heredity instructions

Phage T2 reproductive cycle

1952: Alfred Hershey and Martha Chase found that DNA was the genetic material in phage 2 (not protein)
- labeled cells proteins with radioactive sulfur and DNA with radioactive phosphorus
- agitation frees outside phage parts from cells
- centrifuged cells form pellet
- measured radioactivity found in liquid
- DNA \= genetic material

Chargaff's Rule

A\=T and G\=C

Rosalind Franklin and Maurice Wilkins

Used x-ray crystallography to study DNA structure, discovered sugar-phosphate backbones

watson and crick

Developed the double helix model of DNA (double helix, width/spacing of nitrogenous bases) using Franklin's photo

antiparallel

The opposite arrangement of the sugar-phosphate backbones in a DNA double helix

Bacterophage

A virus that infects bacteria (study structure)

virus

An infectious particle incapable of replicating outside of a cell, consisting of an RNA or DNA genome surrounded by a protein coat (capsid) and, for some viruses, a membranous envelope.

capsid

Outer protein coat of a virus

DNA replication

the process of making a copy of DNA; happens in S phase

DNA replication steps

1) Helicase- unwinds the parental double helix

2) DNA topoisomerase - upstream of helices alleviating torsional strain

3) Single-strand binding proteins (SSBP) stabilize unwound DNA, aided by DNA gyrase.

4) Primase synthesizes a short RNA primer for DNA polymerase to bind to in the 5' to 3' direction to start replication on each strand.

5) DNA polymerase synthesizes the leading strand in 5' to 3' direction while the lagging strand is made discontinuously by primase making short pieces and then DNA polymerase extending these to make Okazaki fragments.

6) DNA ligase joins the Okazaki fragments together

origin of replication

multiple origins because it happens in sections
- where DNA strands are separated, opening up in a replication bubble
- replication proceeds in both directions from each origin until the entire molecule is copied

Prokaryotic DNA replication

starts in a single spot and goes around in 2 directions until the entire chromosome is copied

Eukaryotic DNA replication

begins at many different spots on the DNA molecule and proceeds in 2 directions until the entire chromosome is copied

helicase

An enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands.

single stranded binding proteins

bind to and stabilize single-stranded DNA

Toposiomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

RNA primer (primase)

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

DNA polymerse III

synthesizes new DNA only in the 5' to 3' direction
- joins with dehydration
- dATP for energy

Enzymes in DNA replication

Helicase, binding proteins, primase, DNA polymerase, ligase

leading strand

synthesized continuously (replication fork follows helicase)

lagging stand

The template that the strand is coping runs in the 5-3' direction. Needs okazaki fragments and DNA ligase to make this strand

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.