Biology Midterm

Covalent bonds

Atoms share one or more electrons between the 2 of them

Ionic bonds

Oppositely charged atoms transfer an electron to balance out their charge

Polar covalent bonds

One side of the bond is positively charged, while the other side is negatively charged

Nonpolar covalent bonds

both sides of the bond have the same charge

Hydrogen bonds

A weak attraction between the positive and negative parts of 2 molecules

Why are hydrogen bonds important to biomolecules

They are responsible for the formation of larger biomolecules

isomers

two molecules with the same molecular formula but different structures- structure changes function

hydroxyl functional group

A polar side group that forms hydrogen bonds

carboxyl functional group

Polar side group that loses its H and becomes negatively charged

amino functional group

Polar side group that gains its H and becomes positively charged

methyl functional group

HYDROPHOBIC side group, least reactive of the side groups

phosphate functional group

polar side group, usually loses its hydrogens to become negatively charged

cohesion

the binding of like substances (specifically water) to each other, through hydrogen bonds

adhesion

the binding of unlike substances to each other

surface tension

the surface of a liquid can resist external force due to hydrogen bonds formed by water molecules

capillary action

the movement of water AGAINST GRAVITY due to the forces of adhesion, cohesion, and surface tension

basic solution

a solution with a pH higher than 7, turns litmus blue, slippery

acidic solution

a solution with a pH lower than 7, turns litmus red, sour

neutral solution

a solution with a pH of 7, pure

buffer solution

a solution with a specific pH and no other properties to be used for experiments

H+ ion concentration rules

the amount of H+ ions increases 10x as the pH goes down by 1

OH- ion concentration rules

the amount of OH- ions increases 10x as the pH goes up by 1

glycogen

a type of digestible carb, used to store glucose in animals

starch

a type of digestible carb, used to store glucose in plants

cellulose

a type of non digestible carb, used for structure

monosaccharide

one sugar molecule, like glucose, fructose, lactose

polysaccharide

many sugar molecules, like starch, or cellulose

dehydration synthesis

an -OH group removed from one part of a monomer and an -H removed from another monomer to bond them together, creating water

hydrolysis

adding water to macromolecules to break them down into their monomers

Saturated fats

a fatty acid with only single bonds, makes them tightly packed together, solid at room temperature

unsaturated fats

a fatty acid with one or more double bonds, making “kinks” in the structure, liquid at room temperature

phospholipid

a lipid with a polar phosphate head, glycerol backbone, and 2 nonpolar fatty acids

steroid

4 interconnected rings, different from other lipids

amino acid

made with a carboxyl group, amine group, and an R group. R group determines how the polypeptide functions

primary structure of a protein

no shape/function, made up of amino acids connected w peptide bonds

secondary structure of a protein

alpha helix or beta pleated sheets, made with hydrogen and peptide bonds, functions are structural framework and movement

tertiary structure of a protein

bridges form between the R-groups of the amino acids, functions are metabolism, storage, transport, and defense

quaternary structure of a protein

many tertiary polypeptides clumped together to form a larger protein, functions are metabolism, storage, transport, and defense

R group interactions

the R group determines if the polypeptide is hydrophobic, hydrophilic, or ionic

nucleotide structure

made up of a phosphate group, sugar, and a nitrogenous base (adenine=thymine, cytosine(3 bonds)guamine

dna structure

backbone made from sugar and phosphate group, and nitrogenous base “rungs” connected in the middle of the 2 strands

The purpose of internal membranes

Increasing surface area, and compartmentalization (minimizing competing interactions)

cell wall

a rigid and semi-permeable wall that provides a barrier between the internal and external parts of the cell, only in plant cells. Responsible for turgor pressure

cell membrane

a flexible and fluid semi-permeable membrane that surrounds all cells. The larger the SA:V ratio, the more efficient the cell is

ribosomes

made from ribosomal RNA and proteins, used to synthesize protein according to mRNA sequence, support common ancestry, can be found on the ER or free-floating

endoplasmic reticulum

has 2 forms, meant for detox and transport. Smooth ER is used for detox and lipid transport, rough ER compartmentalizes the cell and synthesizes protein

mitochondria

has a double membrane for efficiency, and its own DNA and ribosomes (supports endosymbiotic theory). Converts food into ATP; cell respiration

golgi apparatus

made of flattened membrane sacs. folds and chemically modifies new proteins, then send proteins to lysosomes, vesicles (exocytosis), or other organelles

vacuoles

Plants: large sacs of water that support the cell wall (turgor pressure). Animals: small sacs of water

lysosomes

contains hydrolytic enzymes to break down old organelles, used for digestion, responsible for apoptosis

chloroplast

Supports endosymbiotic theory, and converts sunlight, water, and CO2 to sugar; photosynthesis, only in plants

nucleus

supports endosymbiotic theory, found only in eukaryotes, controls cell functions and contains DNA

nucleolus

an organelle within the nucleus that produces ribosomes and RNA

cytoskeleton

a dynamic structure that maintains shape and allows for movement

qualities of an animal cell

eukaryotic, no cell wall, no chloroplasts, small vacuoles, centrioles (used for reproduction)

qualities of a plant cell

eukaryotic, cell wall, chloroplasts, large vacuole (turgor pressure), no centrioles

qualities of a prokaryotic cell

all bacterial cells, single celled, has a cell membrane and wall, has ribosomes, cytoplasm, and flagella, and dna is free-floating

qualities of a eukaryotic cell

every cell that is not bacteria, has a nucleus and other membrane bound organelles, and the organelles have structure

diffusion

molecules going from high to low concentrations

osmosis

WATER going from high to low concentrations through aquaporins

isotonic

equal concentrations of solute and solvent, 0 net movement

hypertonic

greater concentrations of solute in the solution than in the cell (water moves out of the cell and shrivels)

hypotonic

greater concentrations of solute in the cell than in the solution (water moves into the cell and lyses)

concentration gradient

 the difference in concentration of molecules in 2 given areas. The greater the difference in concentration, the faster the rate of diffusion

water potential equation

Water potential = pressure potential + solute potential (Ψ=Ψp+Ψs )

solute potential equation

\-(1)(molar concentration)(constant)(temp in kelvins)

pressure potential

in animal cell or open container- 0

how does water travel (in terms of water potential)

High Ψ to low Ψ

how does water travel (in terms of osmotic pressure)

Low osmotic pressure to high osmotic pressure

phospholipid bilayer

a fluid mosaic model with embedded proteins (channels, carriers, pumps)

role of embedded proteins

used for active transport and facilitated diffusion

facilitated diffusion

similar to simple diffusion where molecules move from high to low concentrations, but with the help of carrier proteins

active transport

the use of energy and embedded proteins to transport proteins (typically against the gradient): pumps, endocytosis, exocytosis

passive transport

no energy is used, molecules travel from high concentrations to low: facilitated diffusion, osmosis, diffusion

endocytosis

Intake of material (food) using the cell membrane, Cell membrane surrounds material and encloses it – forming a vesicle/vacuole

exocytosis

Removal of material (waste) from a cell. Golgi Apparatus “packages” the material into a vesicle and sends it to the cell membrane. The vesicle fuses with the membrane,material is deposited outside the cell

kelvin

temperature in celcius + 273 = degrees in kelvin

Factors that affect enzyme activity

pH, temperature, enzyme concentration, substrate concentration

catalyst

a substance that speeds up a reaction but does not change (enzyme)

substrate

a substance that the catalyst acts on

active site

the specific part of an enzyme that combines with the substrate

reactants

the substances that go into the reaction

products

the substance that come out of the reaction

endergonic reactions

a reaction that requires energy, A+B→ AB, greater energy in products, anabolic, increasing complexity, etc

exergonic reactions

a reaction that releases energy, AB→A+B, greater energy in reactants, catabolic, decreasing complexity, etc

Activation energy

The energy required for a chemical reaction to start and continue on its own

how does an enzyme affect activation energy

Enzymes lower the activation energy needed for reactions

2nd law of thermodynamics

more energy is put into an exchange than what leaves, b/c some energy leaves as heat; every reaction contributes to the disorder of the universe

denaturation

when an enzyme is in unsubstantial conditions and the hydrogen bonds weaken, returning the protein to its primary state

4 stages of cell respiration

glycolysis, link reaction, krebs cycle, ETC/chemiosmosis

glycolysis yield

2 ATP, 2 NADH, 2 pyruvate

does glycolysis require O2?

no

where does glycolysis happen

in the cytosol

glycolysis inputs

2 ATP, 2 NAD+, glucose

where does the link reaction occur

inner mitochondria

what is the purpose of link reaction

to recycle all carbons and create more “energy on hold” (NADH) for ETC

what happens in link reaction

the pyruvate is turned into acetyl CoA due to the addition of coenzyme A

what is the yield of krebs cycle in 2 cycles

4 CO2, 6 NADH, 2 FADH2, 2 ATP

where does krebs cycle occur

in the mitochondrial matrix

how many cycles of krebs happen

2