Chapters 2-6

Rutherford's experiment

Rutherford's experiment

Used gold foil to scatter alpha particles and discover the atomic nucleus.

Element

Any substance that can't be broken down by chemical means.

Mass

The amount of substance, the same on Earth or Moon.

Weight

The force gravity exerts on a substance, varies between Earth and Moon.

Cation

An ion with more protons than electrons.

Anion

An ion with more electrons than protons.

Isotopes

Atoms of the same element with different numbers of neutrons. ex: C12, C14

Radioactive isotopes

Unstable isotopes that decay at a constant rate measured as half-life.

Electronegativity

The affinity of an atom for electrons.

What has the highest and lowest affinity for electrons?

Highest O=3.5 Lowest H=2.1

Hydrogen bonding in water

Results from water's polarity, favoring O-acceptors and H-donors.

Cohesion

The sticking of water molecules to each other at the surface.

Adhesion

The sticking of water molecules to other polar molecules. Such as glass

Hydrophobic molecules

Aggregate in water, forming structures like monolayers and micelles.

Acids

Proton donors in a chemical reaction.

What happens to strong acids in water?

They completely disassociate

What happens to weak acids in water?

they partially disassociate

Bases

Proton acceptors in a chemical reaction.

Buffer

A mixture of a weak acid and its salt that resists changes in pH.

How does buffering compromise?

1 pH unit above and 1pH unit below the pKa of the acid

Functional groups

Primary functional groups include hydroxyl, carbonyl, and carboxyl among others.

Structural isomers

Isomers that differ in the structure of the carbon skeleton.

Stereoisomers

Isomers that differ in how groups are attached.

Enantiomers

are chiral and mirror image

Polymers

Large molecules made from monomers like carbohydrates, nucleic acids, and proteins.

Macromolecules (including polymers)

Large molecules made by dehydration and broken by hydrolysis.

Monosaccharides

Simple sugars with 3-9 carbons and have carbonyl and hydroxyl

Oligosaccharides & Polysaccharides

Also called glycans; include multiple monosaccharides.

Linear D-glucose has:

4 stereoisomers

D-Glucose

A monosaccharide that forms cyclic structures. with stereocenters with orientations a and B

Sucrose

Disaccharide formed from aD-glucose and aD-fructose.

Maltose

formed by 2 aD-Glucose

Starch

A polymer of glucose including amylose and amylopectin. has linear amylose and branched amylopectin

Cellulose

A linear polymer of bD-glucose.

Nucleotide

A basic unit of DNA and RNA, consisting of a sugar, nitrogenous base, and phosphate.

DNA and RNA

DNA has deoxy ribose and RNA has ribose. Both have only one phosphate.

Purine

Nucleic bases including adenine and guanine.

Pyrimidines

Nucleic bases including cytosine, thymine, and uracil.

DNA

encodes information for protein synthesis. has a double helix with H-bonding: A:T and G:C

RNA

Uses DNA information to specify amino acid sequences. RNA is a single strand

ATP

The primary energy currency of the cell.

What are electron carriers?

NAD+ and FAD

How many amino acids does DNA need in protein synthesis.

There are 20 amino acids. All amino acids are L

Protein structure

Four levels: primary, secondary, tertiary, and quaternary.

What gives shape to protiens

hydrogen bonding, disulfide bridge, ionic bond & hydrophobic interactions

Motifs

is a folding pattern

Domain

a unit of a protein that has a function such as catalysis

Native state

the function form of a protein

Chaperones

Assist in the proper folding of proteins.

Lipids

material that is insoluble in water such as fats, oils, waxes, terpenes, steroids.

What part of the protein determines its tertiary structure?

The primary structure

Triglycerides

Esters of glycerol with three fatty acids.

Fatty acids

acids with 12-20 carbons

Phospholipids have:

glycerol + 2 fatty acids + phosphate

Unsaturated fatty acids

animal unsaturated fatty acids are cis

Phospholipids

are amphiphilic (surfactants/soap) with polar head and non polar tail

Cell

The basic unit of an organism, arise from pervious cells, most are less than 50 um

Who was the first to observe microspores?

Robert Hooke in 1665

Microscope Types

Light (resolves 200nm) and electron microscopes (resolve 0.2 nm)

Light microscopes

have 2 magnifying lenses (compound) and are limited to lights’ wavelengths

Electron Microscopes

beam of electrons can be transmission (through the sample) or scanning (on the surface)

Basic structure of all cells (4)

nucleoid or nucleus, cytoplasm, plasma membrane and ribosomes

Archaea domain walls

have sugar/protein

Bacteria Domain walls

have peptidoglycans

Prokaryotes

Simple organisms with no membrane-bound nucleus, DNA and have cell wall in 2 domains

What do some prokaryotes have for chemical reaction?

Organelles and infoldings in plasma membrane

What does bacteria have for metabolic process?

microcompartments with semipermeable protein shell

What does prokaryotes have and what gives the cell shape?

Prokaryotes have actin and tubulin structures, but cell shape is given by cell wall.

What rotates using proton gradient?

pili and flagella, similar to ATP synthase

What do cell wall of archaea have that gives them thermal protection?

saturated hydrocarbons attached to glycerol

Similarities of animal and plant cells:

plasma membrane, most of the same organelles + cytoskeleton

Plant cells have in addition:

cell wall, chloroplasts, vacuoles and glyoxysome for fat to sugar conversion

Eukaryotes nucleus has:

has nucleolus for RNA synthesis and 2-phospholipid bilayer membrane with pores

What does nuclear pores allow for?

allow the passage of ions and small molecules, control passage of large RNA complexes

Endoplasmic reticulum (ER)

The largest internal membrane, divides the lumen from cytoplasm

RER

has ribosomes that make proteins for export that can be tagged to form glycoproteins

SER

a network of tubules and sacs with enzymes to make sugars, steroids and lipids

What does SER assemble?

membrane lipids, stores Ca ions and modifies foreign substances for detoxification

Golgi

sorts and modifies proteins/ lipids received in cis face from RER/ SER and send those on trans face

Lysosomes (organelles from Golgi)

have enzymes for degradation of many internal substances

Peroxisomes (organelles bud of ER)

oxidize fatty acids and get their name by hydrogen peroxide

What do vacuoles plants serve as via water channels?

storage for food or toxins, maintain osmotic pressure

Osmotic pressure

is the force required to stop flow from dilute to concentrated side on a membrane

What does isotonic solution have in semipermeable membrane?

an equal concentration on both sides

Mitochondria

are semiautonomous and have inner-membrane enzymes for oxidative phosphorylation

Chloroplasts of plants

plants have two membranes and make sugars using CO2 as the source of carbon

Cell Cytoskeleton

has 3 types of proteins: actin, microtubules and intermediate filaments

How does centrioles occur?

in pairs in animal cells and most protist, but not in plants or fungi. They have tubulin

Eukaryotes flagella and cilia have…

have 9 microtubule pairs surrounding 2 microtubules used for movement

Eucaryotic cell walls

have cellulose in plants and protists, and chitin or N-acetyl glucosamine in fungi

What do animals have instead of a cell wall?

collagen, elastin and proteoglycan in the extracellular matrix (ECM)

Cell surface has:

glycolipids and MHC protein: markers (blood types), cell recognition (immune system)

Cell connections

Includes adhesive, tight, and communicating junctions.

Plasmodesmata in plants

are gaps in cell walls that connect ERs of two cells by a central tube

Cellular membrane have

lipids, integral proteins, interior protein network & cell surface markers

membrane lipids

lipids are glycerophospholipids, sphingolipids and sterols such as cholesterol

Saturated and Unsaturated fatty acids

saturated fatty acids are present in warm temperatures, unsaturated FA are present in cold

membrane transport can be:

passive, facilitated and active which requires energy from ATP

Passive transport

Movement of molecules from high to low concentration without energy.

Facilitated diffusion

solute move through channel and carrier proteins from high to low concentration