Bio Exam #1

Eukaryote

\- has a nucleus

\- animals, plants, fungi

Prokaryote

\- no nucleus

\-

3 domains of life

archaea, bacteria, eukarya

metabolism

chemical process that by which cells convert energy from one form to another, and build and break down molecules

kinetic energy

the energy of motion

potential energy

stored energy that is released by a change in an object’s structure or position

catabolism

the set of chemical reactions that break down molecules and produce ATP to meet the energy needs of the cell

anabolism

the set of chemical reactions that build molecules utilizing an input of energy (ATP)

hydrolysis

a chemical reaction of the interaction of chemicals with water, leading to the decomposition of both the substance and water

phototrophs

energy from sunlight

chemotrophs

energy from chemical compounds

chemoheterotrophs

energy and carbon from organic molecules

\- animals, bacteria etc

gibbs free energy (change in G)

\- amount of energy free to do work

\- overall energy released during reaction

spontaneous reaction

exergonic reaction: more free energy on the reactant side, so energy is released and available to do work

\- neg gibbs free energy

non-spontaneous reaction

endergonic reaction: more energy on the product side, so energy is required to drive the reaction

\- pos gibbs free energy

identify each aspect

A: activation energy for catalyzed reaction

B: activation energy for uncatalyzed reaction

C: gibbs free energy

D:

E:

transition state

a brief period where old bonds are being broken and new ones are being formed

\- very unstable

\- lots of free energy

activation energy (EA)

the energy input needed to reach the transition state

reaction coupling

an energetically favorable reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction to help drive the endergonic reaction

enzyme

a protein that functions as a catalyst to accelerate the rate of chemical reactions

\- stabilizes the transition state

\- less gibbs free energy

inhibitors

decreases the activity of enzymes by binding to the active site (competes with the enzyme), or by binding to another part of the enzyme to which changes its shape

activators

increase the activity of enzymes

allosteric site

a site that allows molecules to either activate or inhibit (or turn off) enzyme activity

different than the active site on an enzyme, where substrates bind.

carbon

\- can form 4 bonds due to 4 valence electrons

\- oriented at the center, so it can freely rotate

heterotrophs

carbon from organic compounds

autotrophs

carbon from inorganic compounds

cellular respiration

in: glucose and oxygen react to create ATP

out: carbon and H2O released

substrate-level phosphorylation

a way of generating ATP in which a phosphate group is transferred to ADP from an organic molecule, which acts as a phosphate donor or substrate.

location: cytoplasm and in the mitochondria

in: ADP

out: ATP, phosphate group

oxidative phosphorylation

a set of metabolic reactions that occurs by passing electrons along an electron transport chain to the final electron acceptor, oxygen, pumping protons across a membrane, and using the proton electrochemical gradient to drive synthesis of ATP

location: inner membrane of the mitochondria

in: FADH2, NADH, ADP

products: ATP, NAD+, FAD, and H2O

chemical reaction of cellular respiration

oxidized: glucose molecules

reduced: oxygen to generate water molecules

stage 1 of cellular respiration

glycolysis

location: cytoplasm

in: 6-carbon molecules

out: 2 3-carbon molecules of pyruvate

stage 2 of cellular respiration

pyruvate oxidation

location: cytoplasm to mitochondrial matrix

in: pyruvate

out: 2acetyl-CoA, NADH, CO2

\
NAD+ oxidizes the pyruvate which releases CO2

CoA attaches to the oxidized pyruvate to create acetyl-CoA

\- the CoA allows the molecule to pass through the membrane.

state 3 of cellular respiration

citric acid cycle

location: mitochondrial matrix

in: 2acetyl-CoA, 6NAD+, 2FAD, 2ADP, H2O

out: 2ATP, 2CoA, 6NADH, 2FADH2, GTP, 4CO2

stage 4 of cellular respiration

oxidative phosphorylation

location: inner membrane space

in: ADP, NADH, FADH2 and O2

out: ATP, NAD+, FAD+ and H2O

\
a cellular process that harnesses the reduction of oxygen to generate high-energy phosphate bonds in the form of ATP

mitochandria

inner membrane space, matrix, membrane, inner membrane

electron transport chain

The electrons flow through the electron transport chain, causing protons to be pumped from the matrix to the intermembrane space. Eventually, the electrons are passed to oxygen, which combines with protons to form water.

proton gradient

The proton gradient has two components: a chemical gradient that results from the difference in concentration and an electrical gradient that results from the difference in charge between the two sides of the membrane

\
intermembrane space - protons

matrix - negatively charged

fermentation

A variety of metabolic pathways that produce ATP from the partial oxidation of organic molecules without oxidative phosphorylation or an electron acceptor, such as oxygen.

fermentation

\- can break down pyruvate in the absence of oxygen

\- extracts energy from fuel molecules without the electron transport chain

\- uses an organic electron acceptor

\- for anaerobic organisms, or when oxygen isn’t delivered fast enough

location: cytoplasm

fermentation pathways

\- ethanol

\- lactic acid

glycogen

the stored form of glucose that's made up of many connected glucose molecules

photosynthesis

energy from sunlight is used to synthesize carbohydrates from CO2

redox in photosynthesis

oxidation: H2O (electron donor) is oxidized and O2 is released

reduction: CO2 is reduced to form carbohydrates

chloroplast

where photosynthesis takes place

thylakoid: disk

grana: stack of thylakoid

storma: surrounding liquid

lumen: inside of the thylakoid

calvin cycle

synthesis of __carbohydrates__ from CO2


1. carboxylation: CO2 is added to a 5-carbon molecule
2. reduction: energy and electrons are added to the compound
3. regeneration: 5-carbon molecule recreated to keep the cycle moving

rubisco

enzyme that catalyzes the incorporation of CO2 to the 5-carbon molecule

chlorophyll

\- in the photosynthetic membrane system

\- key role in the cell’s ability to capture energy from the sunlight

photosystem

a protein pigment complex that absorbs light energy to drive redox reactions and thereby sets the photosynthetic electron transport chain in motion

accessory pigment

another light-absorbing pigment in the photosynthetic membrane

antenna chlorophyll

energy is transferred between chlorophyll molecules until it is transferred to a specifically configured pair of chlorophyll molecules known as the reaction center

reaction center

specifically configured chlorophyll molecules where light energy is converted

photosystem II

oxidation of water

\- H2O donates an electron

\- releases O2

photosystem I

reduction of NADP+

\- photosystem gives an electron to NADP+ to form NADPH

proton pump

lumen: high proton concentration

stroma: low proton concentration

atp synthase pumps the protons

why are two photosystems needed

it takes a lot of energy to break water apart, so they electron transport chain needs an extra surge of energy to keep the chain moving.

ATP synthase

ADP + phosphate group = ATP

powered by the proton gradient

photorespiration

A process in which rubisco acts as an oxygenase, resulting in release of carbon dioxide and a net loss of energy.

phospholipid

structure: hydrophilic head, and hydrophobic tails

amphipathic

a molecule that has both a hydrophobic and hydrophilic region

phospholipid bilayer

structure formed in aqueous solutions

creates a membrane

hydrophilic head on outside

hydrophobic tails on inside

micelle

structure formed with one tail rather than 2

saturated fatty acid tail

straight tail

no double bonds, so they are tightly packed which limits lipid mobility

unsaturated fatty acid tail

kinks in tail

double bonds which is the reasoning for the kinks in the tail

this enhances lipid mobility

cholesterol

hydrophilic head, hydrophobic body & tail

attaches

helps the phospholipid bilayer maintain its fluidity in different environments

why do lipids not “flip-flop”?

It is energetically unfavorable for the hydrophilic heads to pass through the hydrophobic regions

transporter proteins

membrane proteins that move ions or other molecules across the membrane

anchor proteins

attaches to other proteins and helps maintain cell structure and growth

receptor proteins

a molecule on cell membranes that detects signals outside of the cell

enzymes

catalyze chemical reactions

critical in determining which reactions take place in a cell

integral membrane proteins

permanently attached to the cell membrane, cannot be removed without destroying the bilayer

section inside of the membrane hydrophobic

section outside of the membrane hydrophilic

\

peripheral membrane proteins

temporarily associated with the membrane or integral membrane proteins through weak non fcovalent bonds

transmembrane proteins

these are all integral membrane proteins

span across the whole membrane

fluid mosaic model

proposes that the lipid bilayer is a fluid structure that allows molecules to move laterally within the membrane and is mosaic two types of molecules (proteins and lipids)

homeostasis

the tendency toward a relatively stable __equilibrium__ between __interdependent__ elements, especially as maintained by physiological processes.

selectively permeable

the phospholipid bilayer is selective about what can pass through

permeable:

gases (O2, CO2 etc..)

non polar molecules

small uncharged polar molecules (H2O)

impermeable:

ions

sugars

charged molecules

protein

diffusion

the movement of molecules from higher concentration to lower concentration (energetically favorable)

facilitated diffusion

diffusion through a transmembrane protein into the cell, or out of the cell

simple diffusion

passing directly through the membrane without assistance

active transport

the movement of substances against a concentration gradient requiring an input of energy

primary active transport

uses ATP directly to drive the movement

by a pump

secondary active transport

uses the energy of a chemical gradient to drive the movement

will move with the molecule using active transport into the desired location

two domains of prokaryotic life

bacteria and archaea

plasmid

in bacteria, a circular molecule of DNA carrying a small number of genes.

peptidoglycan

a complex polymer of sugars and amino acids making up the bacteria cell wall

horizontal gene transfer

the transfer of genetic material between organisms that aren’t parent and offspring

conjugation

cells connect through a pilus, DNA passes through a small opening formed between the cells

transformation

DNA released into the environment by dead cells is picked up by a recipient cell

transduction

transferred through a virus

key ideas

1) eukaryotic cells have nuclei and membrane-bound organelles, whereas bacteria and archaea don’t

(2) eukaryotic cells have linear chromosomes, whereas bacterial and archaeal DNA is circular

(3) eukaryotes and prokaryotes have ribosomes of different sizes

(4) membrane lipids, RNA polymerase, \n and ribosomes in Archaea are more like those in eukaryotes than those in bacteria

(5) methanogenesis occurs only in Archaea

(6) nitrogen fixation and chemoautotrophy are found only in prokaryotes

(7) Both Archaea and Eukaryotes have histone proteins.

carbon cycle

Decomposing prokaryotes break down dead organic matter and release carbon dioxide through cellular respiration

aerobic respiration vs anaerobic respiration (process in which carbohydrates are broken down to create energy)

aerobic takes place in the presence of oxygen

anaerobic takes place in the absence of oxygen

respiration vs fermentation (produce energy for the cells to use)

respiration: complete oxidation of glucose into CO2 and H2O

fermentation: partial oxidation of glucose

sulfur & nitrogen cycles

sulfur and nitrogen cycles on Earth \n depend on some of the prokaryote-only anaerobic metabolic pathways

nitrogen fixation

N2 → NH3

nitrification

NH3 (oxidized) → NO2- → NO3

denitrification

NO3 reduction → N2 (released into the environment)

eukaryotic cell

phagocytosis

eukaryotic cells surround food particles and package them in vesicles that bud off from the cell membrane

endocytosis

the cytoskeleton and membrane system also enable eukaryotic cells to engulf molecules or particles, including other cells, in a process called endocytosis

diploid

describes a cell with two complete sets of chromosomes.