Lecture Notes Quiz Flashcards
What are all materials in nature made up of?
Elements
Atoms consist of?
Protons, neutrons, and electrons
How are electrons distributed around the nucleus?
Shells (different energy levels)
What is the outermost electron shell of an atom called?
Valence shells
How will you distribute the electrons in an electron shell diagram?
1st shell: 2 electrons
2nd shell: 8 electrons
3rd shell: 8 electrons
What do all atoms want for their valence shells?
Full valence shells
How can atoms fill their valence shells?
Sharing, donating, and gaining electrons
What are the 4 types of chemical bonds?
Non-polar covalent, polar covalent, ionic bonds, and hydrogen bonds
What are chemical bonds influenced by?
Electronegativity (tendency to attract electrons) of atoms
What is electronegativity?
The tendency to attract electrons. The more electronegative an atom is, the more it attracts electrons.
When do non-polar covalent bonds occur? (THINK: electronegativity)
Electrons that are equally shared between two atoms are due to their electronegativities being equal
When do polar covalent bonds occur? (THINK: electronegativity)
Electrons that are unequally shared between two atoms are due to their differences in electronegativities
When do Ionic bonds occur? (THINK: electronegativity)
Electrons that are donated by an atom and gained by the other atom due to their large differences in electronegativities
When do Hydrogen bonds occur?
Partial positive hydrogen (H) of one molecule interacts with a partial negative atom of a different molecule
What are water’s properties?
Polar covalent bonds, partial positive hydrogen/partial negative oxygen, and forms hydrogen bonds with other molecules
What is a solvent?
A property that can dissolve solutes. Ex. Water
What does pH of solution measure?
Its [H+]
What is the ratio of hydrogen and [OH-] in an acidic solution? (THINK: Compare [H+] and [OH-]
[H+] > [OH-]
What is the ratio of hydrogen and [OH-] in a basic solution? (THINK: Compare [H+] and [OH-]
[H+] < [OH-]
What are the 4 major elements that make up the human body?
Carbon, oxygen, hydrogen, and nitrogen
Molecules that contain carbon are called what?
Organic molecules
What are the 4 types of organic molecules?
Proteins, nucleic acids, carbohydrates, and lipids
What is the function of proteins?
Provide structural support and act as catalyst to facilitate chemical reactions
What is the building blocks of proteins?
Polypeptides
What makes up polypeptides?
It is a polymer. It is formed by amino acid monomers that are linked together via peptide bonds
What is the function of nucleic acids?
They encode and transmit genetic information
How are nucleic acids formed?
Formed by nucleotide monomers linked together via phosphodiester bonds
What is the function of carbohydrates?
Provide structural support for many organisms and a source of energy
What are carbohydrates formed by?
Formed by monosaccharide monomers that are linked together via glycosidic bonds
What are the function of lipids?
Make up cell membranes, store energy, and are important in cell communication
What organic molecule is not a polymer?
Lipids
What are the 3 hydrophobic molecules of lipids?
Triglycerides (fats), steroids, and phospholipids
What are triglycerides (fats)?
Fatty acids that are long chains of carbon with a carboxyl group at the end
What are the 2 types of fatty acids?
Saturated fatty acids and unsaturated fatty acids
Describe saturated fatty acids
- single-bonded carbons
- max # hydrogens
- straight structure
- solid at room temperature
Describe unsaturated fatty acids
- double-bonded carbons
- less than max # of hydrogens
- bent structure
- liquid at room temperature
What does amphipathic mean in terms of a phospholipid?
Both a hydrophilic (polar head) and hydrophobic (non-polar tails) part of phospholipid
What are Prokaryotes?
- They are bacteria
- Small (size)
- No nucleus
- No organelles surround the membrane
- Has a cell membrane
What are Eukaryotes?
- Complex and large (size)
- Has a nucleus (chromosomes are inside)
- Organelles surround the membrane
- Has a cell membrane
What does the cell membrane do?
- Separates the inside of the cell from the surrounding environment
- Maintains homeostasis (constant environment) inside of the cell
- Determines the cell’s shape and size
What does selectively permeable mean?
The cell membrane is “selective” in allowing only some things to move in or out of the cell
What is Passive Transport?
THINK “passively”
- Does NOT require energy
- Materials move WITH the concentration gradient (High to Low)
What is Active Transport?
- Requires energy expenditure
- Materials move AGAINST the concentration gradient (Low to High)
What are some types of Passive Transport?
- Simple diffusion
- Osmosis (diffusion of water)
- Facilitated diffusion
- uses proteins
- channels
- carriers
What is simple diffusion?
Passive movement across a permeable membrane
How is simple diffusion done?
Moves molecules from an area of high concentration to low concentration (with/down the concentration gradient) to achieve equilibrium. It does not require energy.
What is Osmosis?
Diffusion of water across a semi-permeable membrane
How is osmosis done?
Water molecules are moved from an area of high concentration to low concentration
What is osmolarity/tonicity?
The amount of solutes in a solution
What is the ratio of solute :water lead to in an increased solute condition?
Decreased water
What is the ratio of solute:water in a decreased solution condition?
Increased water
What is a isotonic solution?
2 solutions that have EQUAL [solute] and EQUAL [water] concentration
What is a hypertonic solution?
2 solutions of HIGH [solute] and LOW [water]
What is a hypotonic solution?
2 solutions of LOW [solute] and HIGH [water]
What will water always do? [THINK: Osmosis]
Water will always diffuse from high to low concentrations [hypotonic to hypertonic solutions]
How is facilitated diffusion done?
It passively transports (passive transport) material through a channel protein or carrier protein
How is active transport done?
Substances are moved against their concentration gradient (low to high)
- Energy (often ATP) is expended
What are some examples of active transport?
- Proton (H+) pump: moves H+ against their concentration gradient
- Na+/K+ (an antiporter): uses energy from ATP to move 3 Na+ ions OUT of the cell and 2 K+ ions INTO the cell against their concentration gradients
What is primary active transport?
Produces an electrochemical gradient (ion gradient) to drive the movement of other molecules (secondary active transport)
What are some examples of primary active transport?
Proton (H+) pump and Na+/K+ pump
What organisms have a contractile vacuole? What is the function of a contractile vacuole?
Single-celled organisms. A contractile vacuole is an organelle absorbs excess water in the cell and expels it to prevent lysis
What is the function of a vacuole? Is it located in animals or plant cells?
Function: absorbs water and contributes to turgor pressure
Location: plant cells
What is exocytosis and endocytosis?
Processes that occur when vesicles fuse with the cell membrane
What is the nuclear envelope?
A double membrane that surrounds the nucleus
What is the function of nuclear envelope?
This organelle contains pores that allow molecules to move into and out of the nucleus
What does the rough endoplasmic reticulum contain?
Ribsomes
What is the function of the smooth endoplasmic reticulum?
Important in lipid and steroid synthesis
What is the function of the Golgi apparatus?
- Modifies proteins and lipids produced in the ER (ex. adds carbohydrates to them)
- Sorts proteins and lipids as they move to their final destinations
- Synthesizes the cell’s carbohydrates
What is the function of the lysosome?
A specialized vesicle that’s derived from the Golgi apparatus. Degrades damaged or uneeded macromolecules. (internal pH [five] and external pH [7]
What does the theory of endosymbiosis say?
Mitochondria and chloroplasts were once independent prokaryotes (bacteria) that were engulfed by another cell
What is the function of the mitochondria?
Harnesses energy from organic molecules such as sugars and convert it into ATP in plant and animals cells
What is the function of chloroplasts?
Captures the energy of sunlight to fix atmospheric carbon and synthesizes simple sugars in plant cells and photosynthetic organisms
What is DNA main functions?
- Stores genetic information
- Copies itself
What are the purines?
- Adenine
- Guanine
What are the pyrimidines?
- Thymine
- Cytosine
What is base stacking?
Nitrogenous bases are non-polar (hydrophobic) and
What do complimentary base pairing ensure?
Complimentary base pairing ensures the fidelity (preciseness) of DNA replication
Where does transcription and translation occur in prokaryotes?
In the cytoplasm
What is DNA read from in transcription (THINK: primes)?
From 3’ to five’
How is RNA produced in transcription (THINK: primes)?
From five’ to 3’
What is and the function of a promoter?
The region on the DNA at the start of the gene. They indicate the start of a gene.
What are prokaryotes initiation proteins for transcription?
- Sigma factor
- RNA polymerase
- Bind to promotor sequence of the gene
What are eukaryote initiation proteins in transcription?
- General transcription factors (GTFs) bind to promoter
- Transcriptional activator proteins (TAPs) bind to an “upstream” region on the DNA called an enhancer
- Mediator complex proteins brings GTFs, TAPs, and RNA polymerase together on the promoter
When does initiation end?
Initiation ends with the formation of transcription bubble
What are the steps of transcription?
- Initiation
- Elongation
- Termination
What enzyme is responsible for elongation
RNA polymerase
What occurs during Elongation?
Addition of RNA nucleotides to the growing RNA strand
What are the RNA transcripts that are in BOTH prokaryotes and eukaryotes?
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
What does ribosomal RNA (rRNA) do?
Combines with proteins to make ribosomes
What does transfer RNA (tRNA) do?
Carries amino acids during translation (protein synthesis)
What are the RNA transcripts that are only in eukaryotes?
- Small nuclear RNA
- microRNA (miRNA) and small-interfering RNA (siRNA)
What is the function of the small nuclear RNA?
Used to “process” mRNA
What is the function of microRNA (miRNA) and small-interfering RNA (siRNA)?
- Stops translation of mRNA intro protein
- Control for when the cell has enough of that protein
Where is RNA processed in?
RNA is processed in eukaryotes. RNA processing does NOT occur in prokaryotes.
What is said about the RNA world hypothesis?
Many scientists believe the first nucleic acids were RNA molecules
- Variety of different types of RNA
- RNA is involved in many cellular processes, including all the steps of the central dogma
- Some ribosomal RNA have enzymatic properties
What is the role of the R group of an amino acid?
It’s role affects the structure (shape) and function of amino acids
What is denaturation?
Denaturation of proteins causes them to lose its function
What can protect cells from denaturation?
Protein chaperones
What is the role of tRNA?
Carry amino acids to the ribosome during translation
What is metabolism? (TRY: describe in your own words)
The set of biochemical reactions that transforms biomolecules and transfers energy
What are the requirements of a cell?
- A membrane that separates the internal and external environment
- A way to encode/transmit information
- Energy to do work of the cell
What is the 1st Law of Thermodynamics?
Energy cannot be created or destroyed; it can only be transformed
What is the 2nd Law of Thermodynamics?
Some energy is not available to do work because the amount of disorder (entropy) increases
What is chemical energy in a form of?
Potential energy. It is held in the chemical bonds between pairs of atoms in a molecule.
DESCRIBE Endergonic reactions.
- Products > reactants
- +(triangle)G
- Requires energy input
- Nonspontaneous
- Anabolism (THINK: build)
DESCRIBE Exergonic reactions.
- Products < Reactants
- (triangle) G
- Energy is released
- Spontaneous
- Catabolism (THINK: break down)
What are the characteristics of enzymes?
- Reduce the activation energy (EA) of chemical reactions
- Bind to specific substrates and catalyze their conversion to products
- Their activity can be regulated
REMEMBER: enzymes are catabolic
Why do enzymes lower/reduce activation energy?
Enzymes lower/reduce activation energy to catalyze (speed up) the rate of chemical reaction
What does an enzyme’s activity require?
- Substrates
- Cofactor
What can affect enzyme activity from occurring or not working efficiently?
- pH
- Temperature
- Competitive and noncompetitive inhibitors
- Allosteric inhibitors and activators
What is and the function of a competitive inhibitor?
An inhibitor that “competes” with the substrate to stay attached to the active site and reduces the rate of the reaction.
(NOTE: no other inhibitor can force/bump it out of the active site)
What is and the function of a noncompetitive inhibitor?
An inhibitor that binds to a site other than the active site and can change the shape of an enzyme, which reduces the rate of reaction
What are allosteric enzymes?
Enzymes that are regulated by internal molecules that bind at sites other than their active sites and can be regulated by inhibitors or activators
How do allosteric inhibitors play a role in negative feedback loops?
These inhibitors (end products of a pathway) prevent/inhibit the first step of a reaction and aids in helping the cell conserve energy
(NOTE: this is why negative feedback looks go “up and down”, they are not constant)
What is needed in Substrate-level phosphorylation to make ATP?
An enzyme and a substrate (THINK: get it? “SUBSTRATE-level”… okay…
What is needed in Oxidative phosphorylation to make ATP?
The electron transport chain (ETC) and oxygen
What are the steps/stages of cellular respiration?
Stage 1: glycolysis (cytoplasm)
Stage 2: pyruvate oxidation (mitochondria)
Stage 3: citric acid cycle (mitochondria)
Stage 4: oxidative phosphorylation (mitochondria)
What does oxidation mean in terms of cellular respiration?
Loss of electrons (and hydrogens)
What does reduction mean in terms of cellular respiration?
Gain of electrons (and hydrogens)
What type of process is Glycolysis?
Anaerobic process (no oxygen required)
How phases does Glycolysis have? What are those phases?
Phase 1: energy input (preparatory phase)
Stage 2: splitting glucose
Stage 3: energy payoff
What are the net INPUTS of Glycolysis?
- Glucose
- ADP + Pi
- NAD+
What are the net OUTPUTS of Glycolysis?
- Pyruvate
- ATP
- NADH (electron carrier)
What processes occur in the mitochondrial matrix (THINK: cellular respiration)?
- Pyruvate oxidation (stage 2)
- Citric acid cycle (stage 3)
- Oxidative phosphorylation (stage 4)
Where in the mitochondria are the electron carrier proteins of ETC and ATP synthase located?
The inner membrane
Where in the mitochondria has a high concentration of H+ ions
The intermembrane space
What are the net INPUTS of Pyruvate Oxidation?
- Pyruvate
- NAD+
- Coenzyme A
What are the net OUTPUTS of Pyruvate Oxidation?
- Acetyl-CoA
- CO2
- NADH (electron carrier)
What are the net INPUTS of the Citric Acid Cycle?
- Acetyl-CoA
- NAD+
- FAD
- ADP + Pi
What are the net OUTPUTS of the Citric Acid Cycle?
- CoA (coenzyme A)
- CO2
- NADH (electron carrier)
- FADH2 (electron carrier)
- ATP
What type of energy is the H+ ions in the intermembrane space? (THINK: forces and motion)
Potential energy: the high concentration of H+ ions in the intermembrane space is potential energy
What is combined with H+ ions in the matrix of the mitchondrion to make H2O?
Oxygen and electrons combined with H+ makes H2O
What are the net INPUTS of the Electron Transport Chain?
- NADH (electron carrier)
- FADH2 (electron carrier)
- ADP + Pi
- O2
What are the net OUTPUTS of the Electron Transport Chain?
- NAD+
- FAD
- ATP
- H2O
What is the terminal (last) acceptor of the electrons in the Electron Transport Chain?
H2O
In the absence of oxygen in Cellular Respiration, what occurs?
Fermentation occurs and produces NAD+ so that glycolysis can continue.
INPUTS: pyruvate and NADH
OUTPuTS: NAD+ - reused in glycolysis
