Biology 1107 Exam 1 and 2 Review Notes

Supplemental Instruction Exam 6: Exam 1 and Exam 2 Review

Sessions Information

• Days: Tuesday and Thursday
• Times: 6:30-7:30pm
• Room: FSB 202
• Office Hours: Tuesdays 2:00-4:00pm, Rowe 217

Exam Notes

• Exam is in about a week and a half.
• The exam is cumulative. Anything covered in lecture or any learning objective is fair game.
• Prioritize studying what you don't know. Identify and fix content gaps.
• Use the textbook and slides together.
• Don't get too caught up in details not discussed in class.
• The provided slides are not exhaustive.

Intermolecular Forces (IMFs)

• Hydrogen bond: Strongest of the IMFs.
  • Not a "real" bond.
  • Driven by polarity and electronegativity.
  • Electropositive Hydrogen forms a transient interaction with an electronegative N or O (sometimes F).
  • Usually due to functional groups interacting (hydroxyl, carbonyl, carboxyl, etc.).
• Van Der Waals forces: Weak individually, very strong collectively.
  • Brief electron interactions between molecules.
  • Does not require any polarity or electronegativity differences.
  • The more electrons a molecule has, the more Van der Waals forces.
  • The larger the molecule, the more relevant van der Waals forces become.
  • Play a big role in lipids.

Macromolecules

• Know the monomer names, polymer names, structures, and uses of macromolecules.

Types of Lipids

• Neutral lipids: energy storage, Glycerol+3 Fatty acids.
• Phospholipids: make up membranes, covalently bound to a PO_4.
  • AMPHIPATHIC: 2 separate regions, a polar region and nonpolar region.
• Steroids: lipid molecules found in membranes or on their own as signaling molecules.
  • Have a skeletal base structure of 3 6-carbon rings and 1 5-carbon ring.
  • Can have modifications on top of this structure to carry out their various functions.
• Cell membranes have all of these lipids.

Protein General Structure

• Monomer: Amino Acid.
  • Literally has an Amino group and a carboxylic acid group.
  • Has a variable “R” group.
  • The amino group is basic and positively charged, the carboxylic acid group is acidic and negatively charged (AT pH 7.4!!), meaning that the R group determines the properties of the amino acids
  • R group can basically be anything.
  • Amino acids can be anything! All depends on functional groups.
    • Polar
    • Nonpolar
    • Aliphatic (no ring-like structures)
    • Aromatic (ring link structure with double bonds)
    • Acidic
    • Basic

Properties of Amino Acids

• Amino Acids can have basically “any” properties!
  • Polar
  • Nonpolar
  • Aliphatic (no ring-like structures)
  • Aromatic (ring link structure with double bonds)
  • Acidic
  • Basic
• Be able to identify polarity of an amino acid or protein based on R groups.

Protein Polymer

• Monomer: Amino Acid
• Polymer: polypeptide or peptide
• A dehydration synthesis occurs to link the “N terminus” to the “C terminus” of the adjacent amino acid
  • N Terminus: the amino side
  • C terminus: the carboxyl side

Protein Shape

• Form DETERMINES function!!
• All proteins that your body makes are “intended” to have a certain shape so they can perform a function.
• Even slight differences in shape can render a protein useless.
• Ex. Cystic Fibrosis is caused by a mutation to a gene that codes for a channel protein that changes its shape.
• Because R groups are so variable, we can put them in literally infinite combinations
• Proteins are some of the most diverse molecules in your bodies
• Proteins can be membrane channels, identification proteins (like covid spike protein!), receptors, enzymes, and much more
• Cannot encode our genome

Levels of Protein Structure

• Primary Structure: This is the actual sequence of Amino acids that a peptide is made up of, nothing more, nothing less
  • This can ONLY be changed if there is a mutation of DNA or some other extreme circumstance, not by anything environmental like temp. pH, etc
• Secondary Structure: This is caused by hydrogen bonding between the N and C termini of individual AAs in the peptide back bone. Two shapes are possible
  • Alpha helices: made up of many AAs with small R groups that make a tight helix
  • Beta sheets: made up of many AAs with larger R groups that make a flat sheet like structure
  • Because these are mediated by H-bonds, environment DOES matter
• Tertiary Structure: THIS is where R groups start to play!
  • The different properties of R groups cause the protein to assume a shape to make certain groups “happy”.
  • Ex. AAs with Nonpolar R groups are usually buried on the interior of a protein because they are hydrophobic
  • Cysteine: Special AA with a Sulfhydryl (SH) group as its R group
    • Cysteines tend to “find” each other on longer protein strands and form a covalent bond called a disulfide bridge.
    • Polypeptides with many cysteines tend to be very stable due to all this extra covalent bonding that “locks” the shape in
  • R group Acidity, basicity, size, structure, etc all can make an impact here
• Quaternary Structure:
  • This ONLY comes into play when we have multiple “subunits” in our polypeptide protein situation
  • Not all proteins are just a single strand of amino acid
  • Some are made up of multiple polypeptide chains (can be the same or different) for function
  • Quaternary structure is how proteins with multiple subunits interact and shaped
  • This can happen for all the same reasons as tertiary (polarity, size, etc)

Structure of Nucleic Acids

• Prime(‘) notation: used to note the carbon of the ribose sugar ring something is attached to
  • Ex. The 5’ phosphate group is the phosphate group bound to the 5th carbon of the ribose or deoxyribose sugar of a nucleotide
• All nucleotides need to have a 5’ phosphate and a 3’ hydroxyl
  • Dehydration synthesis forms a bond between these groups
  • Resultant bond is a phosphodiester bond
• As a result, polymerized NA’s are asymmetric, and have directionality
  • The end with an exposed 5’ phosphate is called the 5’ end
  • The end with an exposed 3’ hydroxyl is the 3’ end

Central Dogma

• DNA: contains the “master copy” of all of an organisms genetic information
• RNA: used to carry only specific genes to sites of protein synthesis
  • mRNA is transcribed or copied from DNA and carries the specific gene you want to make a protein from.
  • Ex. You eat a lot of high protein food, digestive cells transcribe more mRNA for genes that make enzymes to break down the food
• Proteins: the final desired product of genes. All your genes code for proteins!
• DNA→ messenger RNA (mRNA) →Ribosome (site of protein synthesis)→ protein
• DNA→ Transcription to RNA→ Protein synthesis

DNA Replication

• Overall: A process that takes existing double stranded DNA (dsDNA) and replicates it to form 2 identical copies of dsDNA
• Semiconservative: each resultant copy contains one “parent” strand and one newly replicated strand
• Many Important enzymes

Replication Enzymes

• DNA helicase: breaks apart dsDNA so that bases are no longer H-bonding to each other, causes the replication fork
• DNA polymerase: actually polymerizes a new complementary strand of DNA
  • READS existing parent DNA in the 3’→ 5’ direction
  • SYNTHESIZES an antiparallel daughter strand in the 5’→3’ direction ALWAYS
  • Requires a free 3’ hydroxyl to synthesize dna, hence the predefined direction
• RNA primase: makes a primer made of RNA that DNA polymerase requires to get started
• Topoisomerase: relieves tension that is a result of supercoiling of the DNA around itself, prevents it from breaking apart downstream of the replication form
• Single stranded binding proteins: bind to the newly separated strands of DNA to prevent them from coming back together
• DNA ligase: catalyzes phosphodiester bond formation between fragments of DNA that are part of the same strand

Replication Process

• Starts: DNA helicase starts separating the dsDNA at the origin of replication
• Creates 2 strands: leading strand (the newly synthesized strand being made in the 5’→ 3’ direction) and the lagging strand (the newly synthesized strand being made in the 3’→ 5’ direction)
• Leading strand is replicated continuously by DNA polymerase in 5’→3’direction due to the 3’ free hydroxyl
• Lagging strand is replicated discontinuously in the NET 3’→5’ direction
• DNA polymerase can still only read 3’→5’ and write 5’→3’, so how is the net direction of replication 3’→5’?
• This requires some gymnastics…

Replication of the Lagging Strand

• Instead of DNA polymerase jumping on once and continuously making new DNA, it jumps on and off using many primers
  1. RNA primase lays down a primer away from the replication fork
  2. DNA polymerase synthesizes DNA in the 5’→ 3’ direction AWAY from the fork
  3. DNA polymerase dissociates from the strand
  4. RNA primase makes another primer closer to the fork, DNA polymerase again jumps on, synthesizes away from the fork, and jumps off
  5. Creation of many fragmented pieces of DNA, called Okazaki fragments
  6. DNA ligase ligates or sticks all the fragments together to make one strand
  7. Steps 1-6 continue until full replication of the lagging strand

Replication Questions

• Which strand (leading or lagging) is replicated faster?
• Which strand would suffer more with reduce RNA primase activity?
• Which strand would have more errors?
• What direction (5’ or 3’) is the NET direction of replication in each strand?

Transcription

• Required to actually use what is in our genome!
• Process that transcribes or copies information in one form, DNA, into another form, RNA
• Steps
  • DNA helicase splits DNA with help from SSBPs, topoisomerase
  • RNA polymerase reads the DNA in a 3’→5’ direction and writes new, complimentary RNA in a 5’→3’ direction
    • Same logic as DNA polymerase, needs a free 3’ hydroxyl
  • Only portions of the DNA that contain desired genes are transcribed, not everything!
• RNA remains single stranded, does not usually form double stranded molecules like DNA

Translation

• Translating the code of RNA into actual proteins that the body can use
• Transcribed mRNA leaves the nucleus via nuclear pores and enters the cell cytoplasm
• In the cytoplasm the mRNA interacts with a ribosome
• RNA is read by the ribosome in sets of 3 nucleotides
  • These are called codons
  • Each codon codes for a specific amino acid to be brought to the ribosome and added to the polypeptide chain
• tRNA- transfer RNA
  • Can be charged with a specific amino acid by an enzyme called aminoacyl tRNA synthetase
  • Contains an anticodon, a 3 base pair sequence that is complementary to the codon
  • A tRNA with an specific anticodon will carry only an Amino acid that corresponds to that anticodon
• Ribosome contains 3 “sites”
  • A- Aminoacyl
  • P- Peptidyl
  • E- Exit

Translation: Initiation and Elongation

• Initiation- After association with a ribosome, the ribosome scans the RNA for the start codon
  • AUG (adenine, uracil, guanine), which codes for the amino acid methionine.
  • tRNA amino acylated with methionine enters the ribosome and sits in the P site
  • This starts the overall process of translation

Translation: Elongation

• Elongation- Ribosome continues to move down the mRNA after the start codon
  1. The next codon in the mRNA is in the A site
  2. tRNA charged with an amino acid with an anticodon complimentary to the codon enters the A site
  3. Peptidyl transferase- cuts the bond between the AA/peptide bound to P site tRNA and transfers it on top of the new AA bound to the A site tRNA
  4. Elongation factors and GTP are used to shuffle the now uncharged p- site tRNA into the E site where it can exit.
  5. Elongation factors and GTP used to shuffle A site tRNA with the new peptide into the P site
  6. Ribosome continues to move down the mRNA strand so that a new codon for the next amino acid is present in the A site
  7. Process continues until termination

Translation: Termination

• Eventually, the ribosome reaches the end of the gene transcribed by the mRNA and reaches a stop codon
  • There are 3 stop codons: UAA, UGA, UAG
• After the stop codon is read by the ribosome, GTP and release factors release the newly synthesized polypeptide from the attached tRNA
• Note: Stop codons do NOT code for a specific amino acid, they simply tell the ribosome and other enzymes to let the polypeptide go

Phospholipid Bilayer

• Cell membranes are DOUBLE layered
  • 2 layers of phospholipids
• Phospholipids: amphipathic
  • 2 regions polar and nonpolar
• Membrane interior has fatty acid tails facing each other
  • Hydrophobic, nonpolar
• Membrane exterior has phosphate group heads facing away from each other
  • Hydrophilic, polar

Membrane Composition

• Made predominantly of phospholipids
• Can also contain cholesterol to regulate membrane fluidity
  • Increases fluidity at low temperatures (prevents from freezing)
  • Decreases fluidity at high temperatures (prevents from the membrane disintegrating and letting everything through)
• Contains various proteins
  • Glycoproteins- contain a sugar group, usually involved in immune recognition
  • Transport proteins- channels, pumps, carriers, that let things that normally cannot pass through the membrane in or out
  • Receptor proteins- involved in cell signaling

Membrane Structure

• The nonpolar region is a lot bigger than the polar region, it is harder to get through, so…
  • Small, Nonpolar molecules can sneak past the smaller hydrophobic heads and ALSO survive the nonpolar membrane interior for free entrance/exit
  • Polar molecules and ions can survive the polar heads BUT are repelled by the very nonpolar membrane interior, and cannot pass through without protein help
• In effect, the membrane acts as a FILTER, letting only certain things in without help
  • Semipermeable

Types of Passive Transport

• Passive Transport- requires no external source of energy for transport. Uses solely energy found in a molecule’s electrochemical gradient to push itself
• Simple Diffusion
  • DOWN an electrochemical gradient
  • Goes through lipid bilayer ALONE
  • NO protein help
• Facilitated Diffusion
  • DOWN an electrochemical gradient
  • Requires a transport protein to give it a path through the membrane
  • REQUIRES a transport protein

Types of Active Transport

• Primary active- Involves use of an energy carrying molecule ATP, GTP, etc to active give a protein energy to PUMP a molecule or ion AGAINST its concentration gradient
• Secondary active- Uses an EXISTING concentration gradient. Allows one thing to go in its gradient direction to provide energy to push another molecule against its concentration gradient
  • Kind of like wind opening a door, and something else sneaking in behind

Types of Secondary Active Transporters

• Symporter
• Antiporter

Gibbs Free Energy

• DeltaG- A calculated value that takes into account entropy, enthalpy, and temperature
  • Entropy- the level of disorder in a system (can be expressed as a value)
  • Enthalpy- the heat released or used by a reaction
• Overall: Gibbs can be used to assess the favorability of a reaction to occur
  • Negative Gibbs (-DeltaG)= Spontaneous reaction
    • Reaction occurs without external energy input
  • Positive Gibbs (+DeltaG)= Non-spontaneous reaction
    • Reaction REQUIRES external energy input

Catabolic vs Anabolic

• Multiple Reactions can be coupled or put together
• A nonspontaneous reaction can be coupled with a spontaneous reaction to make the net pathway spontaneous
  • This is why ATP hydrolysis is used so often, it is VERY spontaneous
• Catabolic- breaking down
  • Involves the overall release of energy
  • Spontaneous, negative delta G
• Anabolic- Building up
  • Involves an addition of energy to get the reaction going
  • Nonspontaneous, positive delta G

ATP

• A nucleotide!
• Adenosine Triphosphate
  • The bond between the 2nd beta phosphate and the 3rd gamma phosphate is very high energy
• Cellular “energy currency”
• Can be COUPLED
  • Used in a variety of reactions to make non-spontaneous spontaneous
  • Primary active transport!

Enzymes

• Speed up biological reactions
• Decrease the activation energy
  • Activation energy is the initial input of energy to get any reaction started
• DO NOT AFFECT GIBBS FREE ENERGY!!!
• Reusable, unchanged after the reaction
  • Catalysts!
• Heat can also speed up reactions
• Structure=Function
  • An enzyme that no longer is in its correct shape can no longer perform its function
  • An enzyme exposed to conditions that change its shape is said to be denatured

Enzyme Kinetics

• The more substrate the higher the rate of reaction UNTIL all of the enzyme is used
  • There is only so much enzyme and so many active sites, once all of them are full, we have reached maximum reaction speed AKA reaction velocity
• Km- the Michaelis constant, the substrate concentration at which we have reached HALF of the maximum velocity
• Vmax- the maximum rate of reaction we can achieve with a given amount of enzyme

Inhibition

• Inhibitors- slow reaction rate
  • Competitive- Bind at the active site to prevent substrate binding
    • Increase Km, no affect Vmax
  • Non competitive- Bind at the allosteric site to either prevent substrate binding OR any reaction with a bound substrate
    • No effect on Km, decreased Vmax

Enzyme Denaturation

• Again: If enzyme structure is altered, enzyme function will also be altered
• Anything that changes a protein structure has a potential to either decrease or eliminate enzymatic activity!
  • pH
  • Temperature
  • Specific denaturing agents like urea or beta mercaptoethanol
  • Mutation in gene

Steps of Cell Communication

1. Receptor activation
   • Something (generally a chemical) binds to a receptor
   • Triggered by a LIGAND or First messenger
2. Transduction of the signal
   • Receptor cannot do much on its own (mostly…)
   • Transduction can be thought of as converting a signal into another form
   • TRANSDUCING a message from somewhere else into a specific intracellular response
3. Cellular Response
   • The transduced signal eventually gets so big and far into the cell, so it can actually change something
   • Can have something to do with genetics, NOT ALWAYS
   • Changes gene transcription
4. Termination
   • The signal needs to stop eventually
   • Conservation of resources and homeostasis
   • Some receptors can stop a signal on their own, some have other enzymes that break down signaling molecules

G-Protein Coupled Receptors

• A “G protein” is a protein capable of binding a GTP/GDP molecule
  • Generally found anchored to cell membrane interior
• Structure- G protein COUPLED Receptor
  • Generally activate a target protein
  • A receptor with 7 transmembrane regions
  • G Protein- contains 3 subunits (heterotrimeric)
    • Alpha- primary focus, contains GTP binding site, able to dissociate from other subunits
    • Beta
    • Gamma

GPCR + Adenylyl Cyclase

1. Ligand binds to receptor, causes conformational change in receptor protein AND G alpha
2. G alpha has increased affinity for GTP, SWAPS out bound GDP for GTP and becomes activated
   • INACTIVE G Protein- G alpha bound to GDP (generally resting state)
   • ACTIVATED G protein- G alpha bound to GTP
3. G alpha dissociates from G beta/ gamma and activates an effector enzyme
   • Effector enzyme USUALLY not always Adenylyl Cyclase
4. Adenylyl cyclase turns ATP into cyclic AMP (cAMP)
5. cAMP activates a PK (generally PKA), and the cascade continues. PK eventually phosphorylates a target protein
6. After some time we TERMINATE!
   • The GPCR could automatically hydrolyze its bound GTP to GDP
   • Ligand dissociates from the receptor
   • Inhibitors of effector enzymes like kinases, Adenylyl cyclase, etc.

GPCR- Phospholipase C

1. Receptor activation the same!
2. Activated G alpha activates effector enzyme phospholipase C
3. Phospholipase C cleaves a membrane lipid PIP2 into two products
   • DAG- Diacylglycerol
   • IP3- Inositol Triphosphate
4. IP3 travels to the endoplasmic reticulum which is FULL of Ca^{2+}, and releases it
   • Ca^{2+} is one of the most important, if not THE most important signaling molecule within our body so this matters a LOT
5. DAG triggers activation of some kinases
6. Phosphorylation of Ca^{2+}/Phosphate depended kinases
7. Cellular response!

Receptor Tyrosine Kinases

• Generally, cause changes in gene expression
• Structure
  • Transmembrane proteins with extracellular and intracellular regions
  • Ligand binds extracellularly
  • Dimerize (2 subunits come together) upon ligand binding

RTK Pathway

1. Ligand Binds to a RTK subunit
2. Subunits come together and dimerize due to increased affinity for one another after protein conformation changed CAUSED by ligand binding
3. RTK auto phosphorylates- each one has kinase activity and phosphorylates the other subunit so that both proteins have a bunch phosphate groups on them
4. Other intracellular signaling molecules can bind to the phosphate groups and continue the cascade

Metabolism Overview

• An overall spontaneous, catabolic process that breaks things down to “make” energy
  • Individual reactions within metabolic pathways CAN be nonspontaneous
    • Ex. Phosphorylation of ATP is nonspontaneous
  • The energy released by spontaneous processes is enough to balance the energy needs of spontaneous reactions, making the net pathway spontaneous!
  • Remember reaction coupling?

Redox Reactions

• Redox reactions= Reduction-oxidation reactions
  • Reactions in which chemicals and molecules gain or lose electrons
• OIL RIG
  • Oxidation is losing (electrons)
  • Reduction is gaining (electrons)
• In biological systems, reduction is usually accompanied by addition of a hydrogen
  • Ex. NAD^+ is reduced to NADH by the addition of 2 electrons
• In cellular respiration/metabolism
  • Starting reactants (sugars and fats) contain MANT electrons
  • Metabolism is a series of NET catabolic reactions to release or transfer energy carrying electrons to other substrates or locations to convert their kinetic energy into chemical potential energy in the form of ATP and activated electron carriers

Aerobic Cell Respiration in Eukaryotes

1. Glycolysis- the oxidation of glucose into pyruvate
2. Pyruvate oxidation- the oxidation of pyruvate into Acetyl CoA
3. Krebs Cycle/Citric Acid Cycle- Series of redox reactions that oxidize Acetyl CoA into CO_2, transferring electrons to NADH and FADH2
4. Oxidative phosphorylation- Transfer of electrons from NADH and FADH2 through protein complexes, releasing energy that later allows for the phosphorylation of TONS of ADP into ATP

Glycolysis

• First step of both anaerobic and aerobic respiration
• Occurs in the cytoplasm of the cell
• One molecule of Glucose is OXIDIZED to 2 molecules of pyruvate
  • In the process, electrons will flow to REDUCE some activated electron carriers!
    • NAD^+ + 2e- + H^+ → NADH
  • Some chemical energy from glucose is used to convert ADP into ATP
  • Net Energy Carriers: 2 ATP are MADE, 2 NADH are made
    • Both of these have loads of potential energy stored in chemical bonds for future reactions!
• 2 Pyruvates are also made. These are 3 carbons long, they have less chemical energy stored in their bonds, but still have some energy to be harvested from them!
• Something to note: we use 2 ATP to make the reaction favorable in the initial “investment phase” and make 4 ATP in the generation phase. Hence NET ATP made is 2.

Pyruvate Oxidation

• Occurs in the mitochondrial matrix!
  • Pyruvate needs to exit the cytoplasm and enter the mitochondria
• Pyruvate- 3 carbon product of glycolysis
  • The –ate suffix usually means a molecule is in its ionized form meaning… IT NEEDS PROTEIN HELP TO GET THROUGH!
  • Pyruvate is ACTIVELY transported into the matrix via a mitochondrial membrane protein called Pyruvate translocase
• Process: 3C Pyruvate is OXIDIZED to 2C Acetyl-Coenzyme A aka Acetyl CoA
  • The electrons lost by the pyruvate REDUCE a molecule of FAD^+ to FADH_2
  • FADH2 is weird- it cannot travel, its stuck in place, so FADH2 transfers the electrons finally to another molecule of NAD^+, reducing it to NADH
  • NET: 1 Pyruvate + NAD^+→1 Acetyl CoA + NADH

Krebs/Citric Acid Cycle

• Happens in the mitochondrial matrix
  • Pyruvate oxidation happens here, no additional transportation
• BIG Process with many steps- DO NOT LEARN ALL OF THEM
• What you need to know:
  • Acetyl CoA is the starting point.
  • Acetyl Coa is further oxidized through a series of many reactions
  • Makes a BUNCH of activated electron carriers- this is the primary goal of the CAC
    • Many FADH_2s and NADHs made
  • Makes a little bit of ATP, one ATP made per one Acetyl CoA molecule
    • This is still substrate level, oxidative phosphorylation is coming up!
• Net Reaction: 1 Acetyl CoA → 3 NADH + 1FADH + 1 ATP

Oxidative Phosphorylation

• This is where we cash in all of our NADH and FADH to make tons of ATP during oxidative phosphorylation
• The NADHs travel to the inner mitochondrial membrane (FADH is already there)
  • The inner mitochondrial membrane has a bunch of integral membrane proteins that are capable of pumping Hydrogen into the intermembrane mitochondrial space. THIS USES THE ENERGY FROM THE NADH/FADH
• Electron Transport chain- a series of 4 intermembrane protein complexes that pump H^+ ions AKA protons into the intermembrane space FROM the matrix
  • These are in sequence: Complex 1, 2, 3 4

ATP Synthase

• The vast majority of ATP is made like this
• You do not need to worry about the beta, gamma subunits and intricacies of ATP synthase
• You DO need to know that ATP synthase harnesses the energy of the proton gradient
  • It allows passage of H^+ down a gradient to provide energy to phosphorylate ADP to make tons of ATP

Lactic Acid Fermentation

• Used by humans
• Glucose →2 Pyruvate → 2 Lactate
• Lactate is the “deprotonated” or ionized form of lactic acid
  • Build up causes muscle pain
• We switch to lactic acid fermentation when our muscles run out of energy stores and need to rapidly make energy

Ethanol Fermentation

• Does not occur in humans
• Pyruvate → Acetaldehyde→reduced to Ethanol