Gen Bio 1 FInal

Essential and common elements in organisms

C, H, O, and N = 96% of living matter, Ca, P, K, S = 4%

Require H2O

• Atomic structure and properties (subatomic particles, isotopes, etc.)

• Atomic # - number of protons in nucleus

• Mass # - number of protons + neutrons

• Atomic Mass - atom’s total mass

• Molecular mass - sum of all masses of atoms in a molecule

• Isotopes - same protons, dif neutrons

  • Radioactive isotope - decay spontaneously relasing particles + energy; used for fossil dating, tracing metabolic processes, and diagnosing medical disorders

Electron shells, valence, energy states

• Energy - capacity to cause change

• Potential energy - energy that matter has because of its location or structure

• Chem behavior of an atom determined by distributions of electrons in e- shells

• Valence electrons - those in the outermost (valence) shell

• Orbital - 3D space that an electron occupies 90% of the time

Covalent bond

sharing of a pair of valence electrons by two atoms, shared e- count as part of each’s valence shells; strongest bonds in organisms that from cell molecs

• Molecule - consists of 2 or more atoms held by co-bond

Ionic bonds

• an attraction btw and anion and a cation; when an atom strips e- from their bonding partners leading to change in charge

  • Cation - positive charge

  • Anion - negative charge

  • Ionic compounds (or salts) - compounds  formed by ionic compounds

Hydrogen bond

when an H-atom covalently bonded to 1 electronegative atom is also attracted to another electronegative atom (in living cells usually O or N atoms)

Van der Waals interactions

• attractions between molecules that are close together as result of these charges 

  • E- are distributed asymmetrically in molecs/atoms, they can result in “hot spots” of positive or negative charge 

Polar covalent vs. nonpolar covalent

• Nonpolar Covalent bond - atoms share e- equally

• Polar Covalent bond - shared unequally because 1 atom is more electronegative

Electronegativity

atom’s attraction for e- in a co-bond

Water molecule structure

• Water molecs = polar because made of 2 polar co-bonds

  • Polarity and “V” geometry allow for 

    • Multiple h-bonds

    • Liquid H2O h-bonds break/reform = bond “flickering”

Water molecule emergent properties

• Cohesive behavior

• Ability to moderate temp because of high specific heat 

  • absorbs heat from warmer air + releases stored heat to cooler air functions as heat bank, can absorb or release large amount of heat with only a slight change in its own temp

• Expansion upon freezing

  • Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense

    • If ice sank, all water would freeze = no life on earth

• Versatility as solvent

pH

• f a solution is defined by the negative logarithm of H + concentration, written as: pH = –log [H +]

  • internal pH of most living cells must remain close to pH 7

Buffers

• substances that minimize changes in concentrations of H + and OH – in a solution

  • Most buffers consist of an acid-base pair that reversibly combines w H +

  • Blood buffer = carbonic acid H2CO3 (dissociates to bicarb and H+)

Macromolecules

carbs, lipids, proteins, and nucleic acids; large co-bonded molecs

Polymer

arge molecule composed of many similar or identical smaller units called monomers, linked together by covalent bonds. (ex: carbs, proteins, nucleic acids)

Carbs

include sugars + polymers of sugars; forms ring in aq

Carb macromolecules

= polysaccharides

Monosaccharides

• molec formula is multiples of CH2O

  • Major fuel for cells + new material for building molecs

Disaccharide

•  formed when a dehydration reaction joins two monosaccharides

  • Glycosidic linkage - co-bond between 2 monosaccharides to make disaccharide

Glycogen

storage polysaccharide in animals

• Humans + other vertebrates store glycogen in liver + muscle cells

Cellulose

polysaccharide that makes cell wall 

• Glycosidic linkage dif from disaccharide because of two ring forms for glucose, alpha (helical) and beta (straight)

Chitin

polysaccharide, found in exoskeletons and cell walls

Lipids

ne class of large bio molecs that don’t form polymers

• Major function - energy storage (in animals inside fat cells), cushions organs, insulates body

• Hydrophobic

• Most bio important lipids: fats,  phospholipids, and steroids

Lipids : Fats

• made of glycerol + fatty acids

  • Glycerol - 3-C alcohol w hydroxyl group attached to each C

  • Fatty acid - carboxyl group attached to long C skeleton 

  • Separate from H2O because H2O molecs form h-bonds w each other excluding fats

  • Triglyceride (triaglycerol) - 3 fatty acids joined to glycerol by ester linkage

Lipids: Phospholipid

fatty acids + phosphate group attached to glycerol

• Fatty acid tails = hydrophobic

• Phosphate group = hydrophilic head

Lipids: Steroids

• lipids characterized by a C-skeleton of 4 fused rings

  • Cholesterol - important steroid (animal cell membranes), but high lvls = cardiovascular disease

Saturated fatty acid

most animals fats saturated, hydrocard chains of fatty acids - the tails of the fat molec - don’t have double bonds = flexible + pack tightly together

• Solid at room temp

Unsaturated fatty acid

most plant and fish fats

• Liquid at room temp

• Kinks where the cis-double bonds are located = spread apart molec → can’t solidi

Polypeptides

• polymers built from same set of 20 amino acids

• range in length from a few to more than a thousand monomers

• Each polypeptide has a unique linear sequence of amino acids

Protein

1 or more polypeptides

Amino acids

organic molecules with carboxyl + amino groups 

• Linked by peptide bonds

4 Levels of Protein Structure: Primary structure

sequence of amino acids in a protein, is like the order of letters in a long word; determined by inherited genetic info

• 4 Levels of Protein Structure: Tertiary structure

• determined by interactions between R groups, rather than interactions between backbone constituents

  • interactions between R groups include h-bonds, ionic bonds, hydrophobic interactions,and van der Waals interactions

  • Disulfide bridges - strong co-bonds that reinforce protein’s structure 

  • Reacting functional groups on amino acid R groups

• 4 Levels of Protein Structure: Quaternary structure

• when two or more polypeptide chains form one macromolecule (non-covalent forces as in tertiary)

  • Ex: collagen (3 polypes coiled like rope) and hemoglobin (4 polyps: 2 alpha and 3 beta)

Eukaryotic

DNA in nucleus bounded by double membrane, membrane- bound organelles, larger, cytoplasm in region between plasma membrane + nucleus

Prokaryotic

domains bacteria and archaea, dna in non-membrane bound nucleoid, no membrane bound organelles, smaller, cytoplasm bound by plasma membrane

actin

 globular protein that links into chains, 2 of which twist helically forming microfilaments (actin filaments) in muscle + other cells 

actin monomers

actin subunits made of globular actin

actin microfilaments

• solid rods about 7nm in diameter, built as twisted double chain of actin subunits; they bear tension reducing pulling forces on the cell, form 3D network called cortex inside plasma membrane to support shape 

• Actin - globula

Tubulin

globular proteins that are dimers, a molecule made of 2 components

tubulin monomers

made from a-tubulin and B-tubulin, microtubules grow in length by adding tubulin dimers

 microtubules

hollow rods constructed from globular proteins called tubulins that shape + support cell + serve as tracks organelles w motor proteins can move on

intermediate filaments

8-12nm, larger than microfilaments, smaller than m-tubules; support cell shape + fix organelles in place (form cage around nucleus + form nuclear lamina),  more permanent than other two, only found in some animal cells, made of proteins including keratin

(9+2 doublet)

nine doublets of microtubules arranged in a ring w 2 single microtubules in its center, found in eukaryotic flagella + cilia

basal body (9+0 triplet)

Similar to centriole: microtubule triplets in a 9+0 pattern (no central pair of microtubules)

centrioles

• a pair found w/i centrosome, each composed of nine sets of triplet microtubules arranged in a ring

  • 9+0 triplet 

Diffusion

the tendency for molecules to spread out evenly into the available space

• Substances diffuse down concentration gradient + is passive transport 

osmosis

diffusion of water across selectively permeable membrane, goes from region of lower [solute] to higher [solute] or more free water to less free water

Passive transport

diffusion of substance across bio membrane w no energy used

• Facilitated Diffusion - transport proteins speed the passive movement of molecules across the plasma membrane, solute moves down concentration gradient

Active Transport

moves substances against their concentration gradient using energy

Pumps

move substances into/out of cell against concentration gradient 

Sodium-potassium pump actions/outcomes

• Type of active transport, exchanges Na+ for K+ across plasma membrane of animal cells

  • Works through ATP’s terminal phosphate group is transferred directly to transport protein causing protein to change its shape which translocates solute bound protein across membrane 

Electrogenic pumps

transport protein that generates voltage across a membrane

• Main pump of plants, etc = proton pump which transport protons (H+) our of cell 

Cell cycle (what happens during each stage)

• Mitotic (M) phase - mitosis + cytokinesis

• Interphase - cell growth + chromosome copying before cell division, 90% of cell cycle 

Interphase: G1, S, G2, G0

• G0

• G1

• S

• G2 

G1

“first gap” - metabolic activity and growth

G1 Checkpoint

proteins in the cell determine if cell division is necessary, growth factor present, cell size large enough, enough nutrients; if yes -> proceed, if no -> G0

S 

synthesis” - metabolic activity, growth, + DNA synthesis

S checkpoint

if DNA damage -> stop

G2

“second gap” - metabolic activity + growth + prep for cell division 

G2 checkpoint

checks if DNA was replicated correctly + cell big enough

M

distribution of chromosomes into 2 daughter nuclei + cytokinesis

M checkpoint

are all chromosomes attached to microtubules?

Mitosis 

• Division of genetic material in the nucleus followed by cytokinesis 

• PPMAT- prophase, prometaphase, metaphase, anaphase, telophase 

Prophase

Chromatin condenses into discrete chromosomes, mitotic spindle begins forming, nucleolus disappears, nucleus intact

Prometaphase

Nuclear envelope fragments + spindle microtubules connect to kinetochores of chromosomes 

Metaphase

Spindle complete + chromosomes attached to microtubules at kinetochores, all aligned at metaphase plate

Anaphase

Chromatids of each chromosome have separated + daughter chromosomes are moving to poles

Telophase

daughter nuclei form + cytokinesis begins 

Cytokinesis

Splitting of cells

Meiosis (stages)

Meiosis I and II 

Meiosis I

• Prophase I

• Metaphase I

• Anaphase I

• Telophase I + cytokinesis

Prophase I

• 90% of meiosis: chromosomes begin to condense; in synapsis, homologous chromosomes pair up; crossing over, nonsister chromatids exchange DNA 

  • Crossing over forms tetrad w x-shaped regions called chiasmata where crossing over happened + they hold pair together 

Metaphase I

tetrads line up at metaphase plate, 1 chromosome facing each pole; microtubules from each pole attach to kinetochore of one chromosome of each tetrad

Anaphase I

pairs of homologous chromosomes separate because of cohesin breakdown, sister chromatids remain attached at centromere + move as one unit toward respective poles 

Telophase I + cytokinesis

Telophase I + cytokinesis

Meiosis II

• Prophase II

• Metaphase II

• Anaphase II 

• Telophase II + cytokinesis

Prophase II

spindle forms then chromosomes move towards metaphase plate 

Metaphase II

sister non-identical chromatids at metaphase plate, kinetochores of sister chromatids attach to microtubules from poles

Anaphase II 

chromosomes arrive at poles, nuclei form, chromosomes decondense, cytokinesis , and then 4 genetically distinct haploid daughter cells

Origins of replication

Replication fork

a Y-shaped region where the parental strands of DNA are being unwound.

helicase

enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands

single strand binding proteins

binds to and stabilizes single-stranded DNA until it can be used as a template stopping strands from re-pairing 

Topoisomerase

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

DNA polymerase

• adds nucleotides to the free 3’ end if a growing strand; DNA strands can elongate only in the 5’ to 3’ direction 

  • Most DNA polymerases require a primer and a DNA template strand

DNA polymerase III

adds a DNA nucleotide to the RNA primer + continues adding DNA nucleotides, which are complementary to the parental DNA template strand, to the growing end of the new DNA strand.

DNA polymerase I

replaces the RNA nucleotides of the adjacent primer with DNA nucleotides one at a time

Primase

Enzyme that synthesizes RNA primer chain 

Lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

RNA primer

An initial nucleotide chain that can be used as a pre-existing chain is produced during DNA synthesis; this is actually a short stretch of RNA, not DNA.

Okazaki fragments

 short segment of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.

DNA ligase

Enzyme that joins sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand

Transcription

synthesis of RNA under the direction of DNA

three stages: initiation, elongation, and termination.

Translation

synthesis of a polypeptide, which occurs under the
direction of mRNA

codons read from 5’ to 3’ direction

three stages: initiation, elongation, and termination