exam one

cell membrane

A phospholipid bilayer with transport and receptor proteins that invaginates and surrounds different parts of the cytoplasm to create (spaces?) for organelles

Cell wall

The larger “skin” that surrounds a cell and provides structural support and protection from physical damage and pathogens

cytoskeleton

Long spindle like protein fibers that act as intracellular vesicle transport, anchors cells/organelles, makes up cilia and flagella, and supports and maintains cell shape

Mitochondria

Site of chemical reactions of cellular respiration that supply most of the cellular energy (ATP production) (uses 2 membranes, inner and outer); acquired by endosymbiosis

Chloroplasts

site of photosynthesis in plants (light into chem energy) which helps pigments and enzymes which use that light to make sugars (has 3 plasma membranes, outer, inner, thylakoid); acquired by endosymbiosis

vacuoles

a single membrane organelle that can store ions, toxic compounds, and pigments that helps with digestion and recycling as well as providing structure for plants through turgor pressure

nucleus

a organelle surrounded by two plasma membranes, contains the nucleolus (where RNA is made) and is the holding site for genetic information (DNA) in the cell/transmission of said info as well as provides some structural support

ribosomes

makes proteins using info copied from DNA either free floating in cytoplasm in prokaryotes and or attached to the RER in eukaryotes

rough endoplasmic reticulum (RER)

network of branching sacs with ribosomes attached to the plasma membrane; associated that synthesis proteins and process them through folding and quality control

smooth endoplasmic reticulum

does not have ribosomes on its surface; synthesizes and modifies lipids (cholesterol) as well as stores Ca2+

golgi apparatus

a single membrane organelle with distinct cisternae that process carbs, lipids, and proteins; cis receives vesicles from ER and trans sends vesicles of proteins to where they function

vesicles

motor proteins guided by cytoskeletal filaments to help move molecules between other organelles (proteins & lipids back and forth between ER, golgi, and cell membrane) and take proteins to the extracellular matrix

peroxisome

enzymes that oxidize/detoxify lipids (fatty acids) and alcohols

lysosomes

breaks down worn out organelles, bacteria, hydrolyzes biopolymers and has a low pH (the low pH is meant to protect/make sure proteins don’t destroy the cell from the inside out)

extracellular matrix

a web of proteins that provide structure outside of an animal cell

common features of all cells on planet earth

cell membrane, cytoplasm, genome of DNA (whether circular and free floating in prokaryotes or linear and inside the nucleus in eukaryotes), ribosomes, and cytoskeleton

endomembrane system

the lipid and protein synthesis and distribution factory in eukaryotes; consists of the nucelus, endoplasmic reticulum, golgi apparatus, and vesicles

hydrogen bonding; covalent bonding

________ happens BETWEEN molecules while _________ happens WITHIN molecules

five properties of water

high specific heat, universal solvent, “sticky” (adhesion and cohesion), surface tension, denser as a liquid

adhesion

the attraction between unlike molecules

cohesion

attraction between like molecules

proteins characteristics

polymer of amino acids, can have polar and nonpolar monomers, vary in size/shape/function, covalent bonds provide structure while hydrogen bonds hold 3D shape

carbohydrate

polymer of simple sugars, is branched when alpha glycosidic bonds connect monomers and is linear when beta glycosidic bonds connect monomers, provide structure to plant cells and nucleotides; act as cell identity markers

nucleic acids

have distinct 5’ => 3’ ends dependent on carbon not bonded to another monomer (5’ has free phosphate group while 3’ has free hydroxyl group), polymer of nucleotides, monomers have important functions seperate from polymer formation

cholesterol

acts as a stabilizing agent making lipid bilayers more stable at high temps and more fluid at lower temps; without it, the bilayer is too rigid in low temps and too fluid in high ones

saturated fatty acids (lipids)

have straighter tails that are more stable at higher temps because there is more surface area for molecules to bond and VDWs to form; because of this, more energy is required to break forces/bonds in order to see any change in stability or form (think like butter); single bonds only

unsaturated fatty acids (lipids)

have short, kinked tails that allow for more fluidity in the bilayer because the kinks stifle the ability to make bonds and for VDW interactions (think olive oil); single and double bonds that be arranged in trans or cis variations

difference between simple and facilitated diffusion

facilitated diffusion requires the presence of a protein tunnel; non-polar is simple and polar is facilitated

active transport

moves substances against their concentration gradient, requiring a form of energy (ATP)

prokaryote

unicellular organism without a nucleus and membrane-bound organelles, with DNA free floating in the cytoplasm

eukaryote

multicellular or unicellular organism with a nucleus and membrane-bound organelles, containing DNA organized within chromosomes

primary level of protein structure

order of amino acids in polypeptide from n to c terminus which is crucial for its folding and function/flexibility

secondary level of protein structure

first 3D folding step that hydro bonds between amino and carboxyl groups resulting in either alpha helicies or beta pleated sheets

tertiary level of protein structure

2nd 3D step of protein folding where “r” groups (side chains) come in; forming either hydrophobic/vdw interactions for non-polar, disulfide for polar, or ionic for electrically charged acidic or basic

quatenary structure

tertiary bonds together and results in final functional form of a multi-subunit protein complex

prions

misfolded proteins that cause disease (madcow)

denaturation

the unfolding of proteins due to heat, low pH, salt, or specific solvents

general protein functions

regulation of DNA & RNA, work in biochemical reactions as enzymes, transportation, coordinating response to hormones, antibodies, second source of energy

difference between RNA and DNA

depends on OH presence (ribose versus deoxyribose)

hydrogen bonding

happens between base pairs (purines & pyrimidines) to hold the 3D shape of RNA and DNA

chemical evolution

inorganic molecules=>complex molecules=>RNA replicators & lipid structures=>life

RNA world hypothesis

suggests RNA holds information for making copies of itself, can catalyze biochemical reactions as ribozymes, and was likely the molecular replicator responsible for kick-starting life on Earth

phospholipid bubbles

helps cause reactions between molecules to make them more complex and be able to hoard resources to have easier access to them

cell theory

all things are made of one or more cells, cells are the basic units of structure and function in living things, new cells are reproduced from pre-existing ones

plant and animal cell differences

plants have cell walls surrounding plasma membranes, chloroplasts, and a large central vacuole

differential centrifugation

separates cell organelles by density through centripetal and centrifugal force (nuclei being largest, then chloroplasts and mitochondria, then ribosomes and lysosomes)

nuclear pore complex

a gate that can allow proteins and hormones through, determining what regions of DNA are used and further, what and how much of these proteins are made

nuclear localizing signal (NLS)

sends a signal (using specific amino acids series) to the nucleus for entry

nucleus exit signal (NES)

sends a signal (using a different series of amino acids) to the nucleus for exit

we can determine function of proteins by…

looking at the series of amino acids in the primary structure

nuclear shuttle proteins

proteins that fold to bind to the NLS sequence forming the quartenary structure and carrying the protein through the nuclear pore complex

adding an NLS is…

sufficient and necessary to get a protein into the nucleus

protein making journey

starts in the cytoplasm, moving on to dock on the RER, then the ribosome making protein is fed through a channel and into the lumen of the RER where it goes to get folded

the series of amino acids in the primary structure of a protein

infers whether it goes through the endomembrane system or gets made in the cytosol

endomembrane protein life sequence

1) protein enters ER while being synthesized by ribosome

2) protein exits ER after folding, now inside vesicle and travels to the cis face of the golgi apparatus

3) protein is walked by motor proteins on cytoskeleton to golgi apparatus to be further modified

4) protein exits trans face of the golgi apparatus in vesicle and moves to plasma membrane

5) protein is secreted through cell membrane reaching its final destination in the cell or to extracellular space

protein sorting and vesicle transport

1) proteins carry tags in endomembrane that serve as “zipcodes” for different destinations

2) proteins are sorted in the trans golgi cisternae, binding to different receptors

3) transport vesicles bud off the trans face of the golgi apparatus

4) transport vesicles attach and fuse at the different destinations using cytosolic/membrane proteins to deliver their contents correctly

integral membrane proteins in the plasma membrane of the golgi…

bind to localizing sequences

alpha helices and beta pleated sheets…

secondary structures formed from hydrogen bonds between amino and carboxyl groups to fold

endocytosis

bringing molecules into cytoplasm/cell using a membrane as a vesicle (happens with complex carbohydrates and large proteins by engulfing them in the plasma membrane and putting them in a vacuole)

exocytosis

sending molecules out of the cell to extracellular space

phagocytosis

engulfs large particles or entire cells and bringing it into the cell (endosymbiosis!!)

pinocytosis

small dissolved substances or fluids brought into the cell

receptor mediated endocytosis

molecules brought in from extracellular space by binding receptor proteins in the cell membrane; then brought to the lysosome to fuze and reduce pH to build whatever we want, alternatively happening through phagocytosis

microtubules, actin filaments, intermediate filaments

the three different filaments that make up the cytoskeleton that facilitate cell movement and maintain cell structure

impacts the 3D shape of a protein

what the protein binds to, hydrogen bonds between the amino acids of the secondary and tertiary structures of the protein, the pH of the cytoplasm, and the hydrogen bonds formed with water molecules in the cytoplasm

what establishes the polarity of nucleic acid molecules

whether or not the 5’ or 3’ carbon of the sugar is linked to another molecule

the carbon atom

has several unique properties for building molecules and was an important element in early chemical evolution that resulted in biomolecules, and despite note being very common on earth, it makes up 18% of the human body

glycogen and nucleic acids

are polymers synthesized by condensation linking individual monomers that when synthesized have water molecules as waste

hydrogen bonds are found…

between base pairs of complementary strands of DNA and in the second and tertiary structures of proteins