BIOL 107

from lectures 1-12

taxonomy

a way of classifying life by naming things

homologous structures

structures inherited from a common ancestor

similar in anatomy - may or may not be similar is function

analogous structures

structures arise through convergent evolution

independently develop these traits that are similar in function but not anatomy

fossil records

can help establish ancestry but difficult/impossible to obtain DNA

physical structures

similarities/differences in physical characteristics of organisms but it’s not always reliable

genetic similarities

accurately determines how closely related two organisms are based off the number of sequence differences

Cladograms

show only the pattern of branching (relationships)/branching order

phylograms

a representation of relatedness where the branch lengths are proportional to change

biological taxonomy

(most inclusive) - dear king Phillip came over for ginger snaps - (most specific)

domains of life

archaea, eukarya, bacteria

bacteria

prokaryotic

cell walls contain peptidoglycan

membrane composed of unbranched fatty acid chains attached to glycerol by ester linkages

archaea

prokaryotic

cell walls do not contain peptidoglycan

often live in extreme environments

membrane composed of unusual lipids (ether linkages)

eukarya

eukaryotic

contains membrane bound organelles

has a cytoskeleton

plant walls do not produce peptidoglycan

membrane composed of unbranched fatty acid chains attached to glycerol by ester linkages

elements that make up living organisms

carbon, hydrogen, phosphorous, oxygen, sulfur, nitrogen

the universal solvent

water - able to surround polar and charged molecules to dissolve them

hydrophobic

substances that do not dissolve well in water, water hating

hydrophilic

substances that easily dissolve in water, water loving

macromolecules

large molecules made up by the addition of small monomeric subunits to make polymers

major macromolecules in a cell

proteins, lipids, carbohydrates, nucleic acids

hydrolysis

disassembles polymers into monomers through the addition of water

dehydration reaction

assembles monomers into polymers through removing a hydrogen

monosaccharides

3,5,6 Carbon atoms (typically)

can exist in a ring or chain structure

hydroxyl and carbonyl group are the functional groups

for carbonyl atoms if its in the middle it’s a ketone, if its on the end its a aldehyde

alpha glucose

the hydroxyl group is below the the plane of the ring

beta glucose

the hydroxyl group is above the plane of the ring

disaccharides

2 monosaccharides join together via dehydration reaction and are linked together through a glycosidic linkage

1,4-Glycosidic Linkage

𝛼-1,4-glycosidic linkage (glucose + glucose)

β-1,4-glycosidic linkage (glucose + glucose)

𝛽-1,4-glycosidic linkage (galactose + glucose).

polysaccharides

more than 10 monosaccharides attached together

polysaccharides with storage roles (energy storage)

starch and glycogen

starch

• main sugar storage of plants and some algae made of glucose monomers

types of starch

amylose and amylopectin

amylose

a simple starch that is unbranched and helical and is joined together via 𝛼-1,4-glycosidic linkage

amylopectin

a branched starch that is not as helical due to branching

• monomers joined via 𝛼-1,4-glycosidic linkage

• branches via 𝛼-1,6-glycosidic linkage

glycogen

main sugar storage for animals and is made of glucose monomers

• similar structure to amylopectin but is WAY more branched

polysaccharides with structural roles

cellulose and chitin

cellulose

main component of plant cell walls made of an isomer of glucose monomers (different than starch)

• glucose monomers linked together by 𝛽-1,4-glycosidic linkage

• straight polymer that never branches

• extremely strong because OH groups are free to hydrogen-bond between different polymers lying parallel (microfibrils)

Chitin

main component of arthropod exoskeletons (hard shell)

made of N-acetylglucosamine monomers

Lipid roles

used as structural components, as energy storage ("burning fat"), or even as part of signaling molecules (hormones).

types of lipids

1. Fats and Oils (Triglycerides)

2. Phospholipids

3. Steroids

fats and oils (triglyceride or triacylglycerol)

3 fatty acids + glycerol (each of the three Cs has a hydroxyl group)

dehydration reaction occurs → the three fatty acids are joined to glycerol by an ester linkage creating a fat molecule (triglyceride or triacylglycerol)

Fatty Acids

composed of a hydrophilic head (carboxyl/polar) and a hydrophobic tail (hydrocarbon tail/non-polar)

saturated fatty acids

only single bonds between carbons

• all Cs are bonded to H

• commonly made in animals and solid at room temperature

unsaturated fatty acids

one or more double bonds between carbons

• common in plant/fish fats

• Cis or trans configuration around the double bond. (If cis bending occurs, and the tails have a “kink” (not straight).)

phospholipids

amphipathic nature because of hydrophilic phosphate head and hydrophobic tail

• lipid bilayer

• lyposome (lipid-bilayer sphere)

• micelle

Steroids

Their structure is composed of four fused carbon rings. → makes them rigid and planar

Types of steroids

Cholesterol, testosterone, cortisol

Cholesterol

• provides strength and flexibility in animal cell membranes.

• Prevents extremes in membrane fluidity, acting as a buffer (low temp→maintains fluidity. high temps→stabilizes by restraining phospholipids)

• Is amphipathic, allowing it to interact with both the exterior of the membrane and the interior

amino acid

basic monomer that makes up proteins

joined together by peptide bonds which are formed from a dehydration reaction - The peptide bond forms between the carboxyl group of one amino acid (C terminus) and the amino group of the other amino acid (N terminus)

hydrophobic R group

all hydrocarbons (non-polar)

hydrophilic R group

polar

charged R groups (hydrophilic)

negatively charged → acidic

positively charged → basic

Primary Structure

the linear sequence of amino acids with an amino acid end (N-terminus) which is the start and a carboxyl end (C-terminus) which is the end in a polypeptide chain. - covalent bonds

Secondary Structure

hydrogen bonding between backbone atoms, (the O of the carbonyl and the H of the amino group) → formation of alpha-helices or beta-sheets depending on how the amino acids line up

Tertiary Structure

interactions between R groups that gives the protein its distinctive shape (e.g. R groups can interact and form hydrogen bonds, disulphide bridges, Van der Waals interactions, and ionic bonds).

Quaternary Structure

interactions between two or more fully folded proteins. (aggregation of two or more polypeptide subunits)

• - non-covalent bonds

denaturation

loss of a protein’s native structure (due to factors like change in Ph, salt concentration, temperature, chemicals, etc)

functions of proteins

Enzymes - catalyze (increase the speed of) reactions.

Transportation (shuttle things around/in/out of the cell)

Support (maintaining cell structure.)

Communication between different parts of the cell or the entire body.

Movement ( of things in the cell or movement of the cell itself)

Defense

what determines protein shape

the sequence of amino acids and the chemical interactions between their side groups, resulting in secondary, tertiary or quaternary structures.or they may require assistance from other proteins called chaperones.

nucleic acids

made up of monomers called nucleotides

contains coded information that cells can transmit to future generations and the messages determine protein production

the two types are RNA and DNA

nucleotides

contain a phosphate head, a sugar, and a nitrogenous base

head attatches at the 5’C, base attaches at the 1’ C, 3’C contains an OH

monomers added together through dehydration to form nucleic acid polymers

DNA

the sugar is deoxyribose (has a H at 2’ C)

RNA

the sugar is ribose (has an OH at 2’C)

types of nitrogenous bases

pyrimidines (single 6 sided rings; C,T,U) and purines (6- and 5-sided rings fused together; A and G)

carbohydrates

fuel and burning material

composition of membranes

lipids and proteins

peripheral proteins

attached to the surface of the membrane, typically hydrophilic

integral proteins

embedded IN the bilayer, has hydrophilic and hydrophobic parts

glycoproteins

membrane component that have a sugar attached. Important function in cell recognition

glycolipids

a membrane component that has a sugar attached

cholesterol

inserts in the bilayer and influences membrane permeability/fluidity

diffusion

passive transport

small hydrophobic molecules

osmosis

type of diffusion (movement of water molecules)

facilitated diffusion

passive transport

uses protein carriers and channels

protein carrier

molecule binds to the protein and the protein changes shape

protein channel

only one type of molecule can pass through

gated - cellular conditions determine whether to open or close

active transport

goes against the concentration gradient (requires energy)

uses only carrier proteins

potassium sodium pump starting materials

3 Na+ (in), 2 K+ (out), ATP

potassium sodium pump ending materials

3 Na+ (out), 2 K+ (in), ADP +Pi

membrane potential

unequal distribution of anions/cations across the plasmid membrane