BIO 1A FINAL- UC BERKELEY

carbohydrates

sugars & polymers of sugars

monossacharides

simple sugars, simplest carb

- molecular form.'s usually have multiples of CH2O

- glucose is most common

- pentose or hexose

- aldose or ketose

-serve as a major fuel for cells andas raw material for building molecules

polyssacharides

carb macromolecules, polymers composed of many building blocks

dissacharides

2 monossacharides linked by dehydration synthesis

used for sugar transport or energy storage

-sucrose, lactose, maltose

dehydration synthesis

FORM OF CONDENSATION REACTION!

occurs when two molecules or compounds are joined to form a larger molecule following the removal of water

combines 2 molecules into a single molecule with the loss of water

REMEMBER:

rhymes with "stay hydrated" --> say hi drated!

aka addison rae (2 names/ 2 molecules)

but she will drop rae (loss of water) in order to become a larger popstar (larger molecule)

lipids

large biological molecules that do not include true polymers

- little or no affinity for water

- hydrophobic bc they consist of mostly hydrocarbons which form nonpolar covalent bonds

ex: fats, phospholipids, steroids

fats

constructed by two types of smaller molecules: glycerol and fatty acids

-major function is energy storage

glycerol

three carbon alcohol w a hydroxyl group atatched to each carbon

fatty acids

consistes of carboxyl group (COOH) attatched to a long carbon skeleton

saturated fatty acid

Solid, no bends, also known as trans fat

REMEMBER: this one is Straight (Saturated/ Straight) aka heterosexual (but theyre tranSgender) but still Straight

unsaturated fatty acid

Liquid, and has a bend (aka a cis-double bond)

REMEMBER: it is gay bc it is bent aka not straight, and they are cis bc they are the same gender they were born as, they're just gay

U in Unsaturated also looks like a bend

also if u turn the u sideways it looks like a c aka cis fat

Phospholipids

two fatty acids and a phosphate group that are attatched to a glycerol

Structure:

- two fatty acid tails (hydrophobic)

- head (hydrophilic)

phospholipids are essential for cells bc they make up cell membranes

Steroids

lipids that are characterized by a carbon skeleton consisting of 4 fused rings

cholesterol

important type of steroid that is a component in animal cell membranes

proteins

have many structures which have wide range of functions

consist of one or more polypeptides

- more than 50% of dry mass of most cells

FUNCTION:

- catalyze biochem reactions

- structural support

- transport

- cell communication

- movement

- defense against foreign substances

polypetides

polymers built from same set of 20 amino acids

make up proteins

amino acids

organic molecules with carboxyl and amino groups

differ in properties due to side chains (R groups)

chirality

whether u can get the mirror image of a molecule and rotate it and be able to superimpose it to the original molecule

4 levels of protein structure

primary, secondary, tertiary, quarternary

2 types of nucleic acids

1.) deoxyribonucleic acid (DNA)

- genes are stores ads DNA

- formed through condensation

2.) ribonucleic acid (RNA)

- formed through condensation

polynucleotide

nucleic acids

- they are polymers called polynucleotides

nucleotides

monomers which make up polynucleotide

- each consists of a nitrogenous base, a pentose sugar (RNA or DNA), and a phosphate group

nucleoside

portion of a nucleotide without the phosphate group

DNA

type of nucleic acid

- has 2 polynucleotides spiraling, forming a double helix

- in the double helix, 2 backbones run in opposite 5'-> 3' directions aka are antiparallel

- one DNA molecule includes many genes

- nitrogenous bases in DNA pair up and for H bonds

- A -> T, G -> C

glycosidic linkage

covalent bond, connects a sugar molecule to another molecule which can be another sugar or something else

cell fractionation

takes cells apart and seperates the major organelles from one another

- can be done w ultracentrifuge

all cells have:

plasma membrane cytosol, chromosomes (carry genes), ribosomes (make proteins)

Prokaryotic cells

organisms: bacteria & archaea

defining features:

- no nucleus

- dna in unbound region called the nucleoid

- no membrane bound organelled

- cytoplasm bound by the plasma membrane

very small (1-10 um)

Eukaryotic cells

organisms: animals, humans, plants, amoebas, paramecia

defining features:

- dna in nucleus that is bound by nuclear envelope

- membrane bound organelles

- cytoplasm in region between the plasma membrane and the nucleus

bigger (10-100um)

nucleus

contains most of the cells genes

nuclear envelope

encloses the nucleus, seperating it from the cytoplasm

ribosomes

protein factories! carry out protein synthesis in two locations! in the cytosol (free ribosomes) or on the outside of the endoplasmic eticulum or the nuclear envelope (bound organelles)

smooth endoplasmic reticulum

lacks ribosomes

-synthesizes lipids

-metabolizes carbs

detoxifies poison

-stores calcium

Rough Endoplasmic Reticulum

ribosomes studding its surface

-ribosomes secrete glycoproteins (proteins covalently bonded to carbs)

-distributes transport vesicles (proteins surrounded by membranes

-serves as the membrane factory of the cell

Golgi apparatus

consists of flat membranous sacs called cisternae

-modifies products of the ER

-manufactures cerain macromolecules

-sorts/packages materials into trabspirt vesicles

lysosomes

digestive compartments, fuses w the food vacuole and digests the molecules

- cells can engulf other cells (phagocytosis) which forms food vacuole

- can also use the enzymes to recycle the cell's own organelles (autophagy)

mitrochondria

site of cellular respiration, aka the metabollic process that generates ATP

- contain own dna

- have proteins made by free ribosomes

- have double membrane

- not a part of the endomembrane system

- nearly in all eukaryotic cells

- have smooth outer membrane and an inner membrane which is folden into cristae, inside is the matrix

• Mitochondria are organelles in eukaryotic cells

• They have a smooth outer membrane and an inner membrane folded into cristae

• The inner membrane creates two compartments: intermembrane space and mitochondrial matrix

• Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix

• Cristae present a large surface area for enzymes that synthesize ATP

chloroplasts

found in plants and algae, are the sites of photosynthesis

- contain own dna

- have proteins made by free ribosomes

- have double membrane

- not a part of the endomembrane system

- contain chlorophyll

- found in leaves and other green organs

- part of plastids

preoxisomes

oxidative organelles

cytoskeleton

network of fibers that organize structures and activities in the cell

made of:

- microtubules

- microfilaments (actin filaments)

- intermediate filaments

interacts with motor proteins to produce motility, can help regulate biochemical activites, helps support shape and structure

- cells can travel along monorails which are provided by the cytoskeleton

actin and myosin help produce...

cell motility

actin forms thin filaments

myosin forms thick filaments

...then, myosin walks along actin filaments which causes either muscle contraction or shape/movement/division

myosin moves towards the positive end of the acting filament bc they have polarity

cell wall

only in plant cells and prevents excessive uptake of water, are made of cellulose fibers

intercellular junctions

Structures that connect adjacent cells in tissues, allowing communication, adhesion, or barrier formation between them

ex:

- Plasmodesmata

- Tight junctions

- Desmosomes

- Gap junctions

tight junctions

At tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

desmosomes

(anchoring junctions) fasten cells together into strong sheets

gap junctions

(communicating junctions) provide cytoplasmic channels between adjacent cells

amphipathic molecules

molecules that contain hydrophobic and hydrophilic regions

Membrane proteins

Peripheral proteins: bound to the surface of membrane

Integral proteins: penetrate the hydrophobic core

- if they span the membrane, they are transmembrane proteins

SIX MAJOR FUNCTIONS:

1. transport

2. enzymatic activity

3. signal transductions

4. cell-cell recognition

5. intercellular joining

6. attatchment to cytoskeleton and extracellular matrix

MEMBRANE STRUCTURE:

polar molecules like sugar dont cross membrane easily, hydrophobic molecules dissolve in lipid bilayer and pass through membrane rapidly

selective permeability

The property of a cell membrane that allows some substances to pass through while blocking others

diffusion

tendency for molecules to spread out evenly into the available space

osmosis

the diffusion of water across a selectively permeable membrane

Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration

flow of water through a selectively permeable membrane from a region of low solute concentration to high!

tonicity:

the ability of a solution to cause a cell to gain or lose water

Isotonic solution

Solute concentration is the same as that inside the cell; no net water movement across the plasma membrane

Hypertonic solution:

Solute concentration isgreater than that inside the cell; cell loses water

Hypotonic solution:

Solute concentration is less than that inside the cell; cell gains water

aquaporins

channel proteins which facilitate the passage of water

transport proteins

allow the passage of hydrophillic substances across membrane

ion channels

open/close in response to stimulus (gated channels)

active transport

moves substances against and across concentration gradients

requires energy ususally atp

membrane potential

voltage difference across a membrane (inside of cell is negatively charged

voltage is created by differences in distribution of positive and genative ions

electrochemical gradient

two collective combined forces that drive the diffusion of ions across a membrane. these forces are:

- A chemical force (the ion's concentration gradient)

- An electrical force (the effect of the membrane potential on the ion's movement)

electrogenic pump

a transport protein that generates voltage across a membrane

animals: sodium potassium pump

plants/fungi: proton pump

exocytosis

the cell exports large molecules by packaging them into vesicles that fuse with the membrane and release their contents outside

when transport vesicles migrate to the membrane, fuse with it, and release their contents

endocytosis

the cell takes in large molecules by engulfing them in a vesicle

when the cell takes in macromolecules by forming vesicles from the plasma membrane

metabolism

the totality of an organism's chemical reactions

Metabolism is an emergent property of life that arises from interactions between molecules within the cell

never at equlibrium

metabolic pathway

begins with a specific molecule and ends with a product, each step is catalyzed by a specific enzyme

catabolic pathways

release energy by breaking down complex molecules into simpler compounds

releases free energy in a series of reactions

ex: cellular respiration

REMEMBER:

imagine a cat giving birth to multiple kittens, which means that they are breaking down the bigger and more complex molecule AKA THE CAT into smaller and simpler compounds THE KITTENS

Anabolic pathways

consume energy to build complex molecules from simpler ones

ex: protein from amino acids

REMEMBER: the criminal ana who stole money from celebrities. she took smaller simpler fortunes AKA SMALLER SIMPLER MOLECULES to make one big fortune for herself A BIG COMPLEX MOLECULE

energy

is the capacity to cause change

kinetic energy

energy associated w motion

thermal energy

kinetic energy associated w random movement of atoms or molecules

potential energy

is energy that matter posseses because of its location or structure

chemical energy

PE available for release in a chemical reaction

law of conservation of energy/ the first law of thermodynamics

Energy cannot be created or destroyed, only transferred or transformed

closed system

such as that approximated by liquid in a thermos, is isolated from its surroundings

Reactions in a closed system eventually reachequilibrium and then do no work

open system

energy and matter can be transferred between the system and its surroundings

organisms are open system

the second law of thermodynamics

During every energy transfer or transformation, some energy is unusable, and is often lost as heat

Every energy transfer or transformation increases the entropy (disorder) of the universe

free energy

energy that is available to do work when temperature and pressure are uniform, as in a living cell

The free-energy change of areaction tells whether or not thereaction occurs spontaneously

spontaneous reaction

A reaction that will proceed without any outside energy DOESNT need energy input

so, For a process to occur without energy input, it must increase the entropy of the universe (ΔS is positive) or its total energy must decrease (ΔH is negative)

During a spontaneous change, free energy decreases and the stability of a system increases

nonspontaneous reaction

a reaction that does need input from outside and delta G is positive

exergonic reactions

• Exergonic reactions release energy to the system.

• ΔG < 0

• Exergonic reactions proceed spontaneously

Endergonic reactions

• Endergonic reactions absorb energy from the system.

• ΔG > 0

• Endergonic reactions are not spontaneous

enzymes

catalysts of chemical reactions

Enzymes do not alter the reaction equilibrium, but they alter the forward and reverse reaction rates.Enzymes remain unchanged after the reaction

typically ends in -ase

ENZYME ACTIVITY CAN BE AFFECTED BY:

- temperature

- pH levels

- chemicals that specifically influence the enzyme

• Each enzyme has an optimal temperature at which it can function

• Each enzyme has an optimal pH at which it can function

--> can be regulated by structural changes

Regulation of enzyme activity helps control metabolism

- A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

active site

active site of an enzyme is usually a cleft pocket where chemistry takes place

substrate

A molecule that binds in the active site and is acted upon by the enzyme

Enzymes bind better to transition states than to substrates

a cell does three kinds of work

chemical, transport, mechanical

ATP (adenine triphosphate) energy

acts as the immediate source of energy that powers most energy coupling to perform cellular work

is composed of ribose (a sugar),adenine (a nitrogenous base),and three phosphate groups

ATP hydrolysis

A chemical reaction where ATP (adenosine triphosphate) is broken down into ADP (adenosine diphosphate) and a phosphate group, releasing energy.

ATP is converted to ADP & phosphate energized myosin heads (removal of phosphate) need energy

The term "hydrolysis" literally means "breaking with water."

In ATP hydrolysis, a water molecule (H₂O) breaks the bond between the second and third phosphate groups of ATP.

free energy of activation, or activation energy (EA)

The initial energy needed to start a chemicalreaction

The active site can lower an EA barrier by- Orienting substrates correctly- Straining substrate bonds- Providing a favorable microenvironment- Covalently bonding to the substrate

Michaelis-Menten kinetics

• Vo is the initial velocity of the reaction

• Vmax is the maximum velocity

• [S] is the substrate concentration

• Km is Michaelis-Menten constant: the substrate concentration at which the reaction velocity is half of the maximum velocity

cofactors

nonprotein enzyme helpers

may be inorganic or organic

tightly bound cofactors are called prosthetic croups

organic cofactor is a COENZYME

- coenzymes include vitamins

-coenzymes are loosely bound cofactors

feedback inhibition

Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

this is when the end product of a metabolic pathway shuts down the pathway

competitive inhibitors

bind to the active site of an enzyme, competing with the substrate

noncompetitive inhibitors

bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

allosteric regulation

• Allosteric regulation may either inhibit or stimulate an enzyme's activity

• Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein's function at another site

ex: hemoglobin

--> mostly quaternary structure

cooperativity

- is a form of allosteric regulation that can amplify enzyme activity

• Cooperativity is considered allosteric regulation because binding by a substrate to one active site affects catalysis at another active site

Fermentation

a partial degradation of sugars that occurs without O2

Fermentation and anaerobic respiration enable cells to produce ATP without using oxygen

-> In the absence of O2 , glycolysis couples with fermentation or anaerobic respiration to produceATP

Fermentation uses substrate-level phosphorylationinstead of an electron transport chain to generate ATP

• Fermentation consists of glycolysis plus reactions that regenerate NAD+ , the oxidizing agent of glycolysis• Two common types are alcohol fermentationand lactic acid fermentation

Obligate anaerobes

carry out fermentation or anaerobic respiration and cannot survive in the presence of O2

facultative anaerobes

can survive using either fermentation or cellular respiration

In a facultative anaerobe, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes

Aerobic respiration

consumes organic molecules and O2 (uses oxygen) and yields ATP