Bio exam 4U

The 4 macromolecules

Carbohydrates, Lipids, proteins, nucleic acid

Carbohydrates

• C:H:O = 1:2:1 → (CH2O)n  where n= the number of carbon atoms

• Monosaccharides = single sugar units. Contain single chain of carbon to which hydroxyl groups are attached 

• triose= 3C | pentose= 5C | Hexose = 6C

• Glucose, oligosaccharide, polysaccharide

Glucose beta vs alpha

Alpha has the right OH at bottom and beta has the right OH at top

Oligosaccharide

• Sugars with a few monosaccharides attached (2-8)

• Bonds form by condensation rxn

Polysaccharide

• Many Many monosaccharides held together by glycosidic linkages (ether linkages)

• Hydrolysis rxn 

• Used for storage or structural support

• 4 kinds: starch, Glycogen, cellulose, chitin

Starch

how glucose is stored (stored in chloroplast and other plastids). Can be branched or unbranched.

Glycogen

when starch is eaten and hydrolyzed turning into glucose subunits the excess glucose is relinked to form ____. more branches. Stored in muscle and liver.

Cellulose

Structure of plant walls. No branch (straight chain) hydrogen bonds form between chains. Every other glucose molecule is inverted. fibre (humans can’t digest beta particles)

Chitin

cellulose is similar. Found in exoskeletons of bugs and mushrooms. Used to make tampons, degradable stitches…

Lipids

• No set C:H:O ratio

• Used for long term energy storage (cell membrane, synthesis of vits and hormones, insulation, cuticle in plants, protection of organs)

• 2x more energy than carbs

• Triglycerides, phospholipids, sterols, waxes

Triglycerides

• most common form of energy storage

• 1 glycerol attached to 3 fatty acids

• esterification rxn —> condensation rxn between hydroxyl group on glycerol and carboxyl group of fatty acids (creates ester linkage)

• 2 types of fatty acids (saturated and unsaturated)

Saturated fatty acid

0 carbon double bonds. Has max # of H atoms. Linear. Found in animal fats. Gets packed in blood vessels

Unsaturated fatty acids

1/ more C double bonds. Less than max # of H. Kinked chains. In plant oil/fish. Resists packing in blood vessels

Phospholipids

• make up cell membrane

• glycerol backbone with 2 fatty acid chains and a phosphate group attached —> phosphate group is polar and fatty acid chains are non polar. 

Sterols

• 4 fused hydrocarbon rings with various functional groups

• Is cholesterol (important in cell membrane high [ ] :. Increases risk of heart attack. Also synthesis of vit D) is sex hormones

Waxed

• Long chain fatty acids attached to alcohols or carbon rings

• Forms waterproof coating on some plants and animals (cutin)

Protein

• most diverse molecules (structures and functions)

• enzymes, hemoglobin, keratin, fibrin, collagen

• Amino acids

• 4 levels of ____ structure

Amino acid

• 20 different ones found in living things

• amino and carboxyl groups are ionized 

• ”amphiprotic” amino group is basic and carboxyl is acidic

• H+ from carboxyl group donated to amino group when dissolved in H2O.

• Can be polar, nonpolar or ionic

• Polypeptide 

4 levels of protein structure

1. Primary structure: covalent (peptide) bonds. Polypeptide chain.

2. Secondary structure: Coils and folds caused by H bonds between H and O atoms near peptide bonds

3. Tertiary structure: supercoiling turns into globular structure. Structure determined by polar/nonpolar R groups, different bonds between opposite chains, proline causes a kink (R bonds to amino), 2 cysteine monomers form a disulfide bridge.

4.  Quaternary structure: only in some proteins. Contains bonding from previous 3 levels. More than 1 chain interacts.

Nucleic acid

• large polymers made of nucleotide monomers 

• each consisting of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base. 

• store hereditary information and determine organism's traits.

• Phosphodiester bond links the phosphate group to the sugar

• Both DNA and RNA have helical structures.

Dna

• Double-stranded

• carries genetic information for replication and protein synthesis

• helical structures

• Adenine, thymine, guanine, cytosine 

RNA

• Single-stranded

• helps read DNA information to assist in protein creation.

• Adenine, uracil, guanine, cytosine 

What are enzymes

• Catalysts that speed up chemical reactions without being consumed in the process during digestion

How do enzymes work

• Substrate binds to enzyme in active site (perfect match) (AB + E)

• Enzyme then changes shape “induce fit” 

• Creates enzyme-substrate complex (ABE)

• Substrate is broken into its products (A+ B)

• Enzyme reused.

Differences between catabolic and anabolic reactions (& Specific examples)

Catabolic: 

• breaks apart large macromolecules

• Hydrolysis reaction. (cell respiration, digestion)

Anabolic:

• creates large molecules from small subunits

• Condensation reactions. (photosynthesis, protein synthesis)

Kerbs cycle equation

2 acetyl-CoA + 2ADP + 2Pi + 6 NAD+ + 2 FAD → 2CoA + 2 ATP + 6 NADH + 6H+ + 2 FADH2 + 4CO2

Kerbs cycle

• Aerobic

• Net +2 atp

• 8 enzymes for 8 different reactions

• Turns twice for every glucose molecule oxidised

Pyruvate oxidase

• After glycolysis

• In mitochondria matrix

• Aerobic

• Net 0 ATP

• Pyruvate transported from cytosol to mitochondria

• 2 Pyruvate (3C) becomes 2 Acetyl-CoA (2C)

Pyruvate oxidase equation

2 pyruvate + 2 NAD+ +2CoA → 2 acetyl-CoA + 2 NADH + 2 H+ + 2 CO2

Calvin cycle

• Light independent reactions

• Occurs in stroma of chloroplasts

• Uses ATP and NADPH from the light reactions to create carbohydrates from atmospheric carbon.

• A cycle that begins and ends with ribulose bisphosphate (RuBP)

• Occurs in 3 phases

Calvin cycle equation

3 RuBP + 3 CO2 + 9 ATP + 6 NADPH + 5 H2O → 9ADP + 8 Pi + 6 NADP + G3P + 3 RuBP

Oxidative phosphorylation

• Electron transport chain and chemiosmosis (mitochondria)

• Forming ATP through the transfer of electrons

• a more efficient, oxygen-dependent process that generates most of the ATP in a cell.

Substrate level phosphorylation

• Glycolysis (cytoplasm)  and krebs cycle (mitochondria)

• Adding a phosphate group to ADP to form ATP

• is a quicker, oxygen-independent process that generates ATP in specific steps of metabolism

Glycolysis

• Occurs in cytoplasm

• anaerobic

• Purpose is to break glucose (6C) into 2 pyruvate (3C) 

• Net 2 atp

Glycolysis equation

Glucose + 2 ADP + 2 Pi + 2 NAD+ → 2 pyruvate + 2 ATP + 2 (NADH+H)

Electron transport chain

• NADH and FADH2 transfer their electrons to a series of compounds 

• In inner mitochondrial membrane

• Each compound is reduced by gaining 2 electrons from the one before it and oxidised by giving the 2 electrons to the compound after it.

• For every O2 that we breathe, 4 electrons are pulled through the ETC and 2 water molecules are produced

• At final acceptor, O joins with 2 protons (H2) and forms water

• 3 ATP are formed from NADH and 2 ATP are formed from FADH2

• Aerobic

Alternate pathways for other macromolecules

• Other Sugars, fats, and proteins can enter CR at different points

• Proteins can enter with a Pyruvate or acetyl-CoA or enter into the CAC

• Fats can enter glycolysis as G3P or, after beta oxidation, as an acetyl-CoA

Protein catabolism

• When we use proteins for energy by digesting them into individual amino acids

• Steps include:

1. Amino group is removed first (called deamination)

2. Amino group is converted to ammonia (NH3)

3. Other chemical reactions occur and the components are fit into the glycolysis or Krebs Cycle stages.

4. Where the components enter is based on the amino acid that is being broken down (because they all have different R-groups)

Lipid catabolism

• When the triglycerides are digested into glycerol and fatty acids, and then used for energy

• Steps include: 

  1. Glycerol is converted into glucose (gluconeogenesis) or converted into G3P and fed right into glycolysis.

  2. Fatty acids go into the matrix of the mitochondria and they go through a process called 𝜷-oxidation

  3. 𝜷-oxidation is when a number of enzymes keep removing 2-carbon acetyl groups from the fatty acids starting at the carboxyl end. Acetyl groups then combine with CoA and enter into the Krebs Cycle

Role of oxygen in CR

• Not involved in glycolysis

• Needed in the rest due to them being aerobic processes

• Primarily involved in the electron transport chain as the final electron acceptor.

• Without oxygen, the electron transport chain can't function, and ATP production would cease, making oxygen vital for efficient energy production.

Role of water in CR

• involved in a few reactions in glycolysis, where it helps hydrolyze (break down) molecules or is produced in small amounts

• Water is produced in pyruvate oxidation when pyruvate is decarboxylated (losing a carbon atom in the form of CO₂) and converted into acetyl-CoA

• Water is both consumed and produced during the citric acid cycle. It is used to hydrate certain intermediates (like fumarate to malate), and water is also produced in the later stages of the cycle.

• Water is produced at the very end of the electron transport chain. When oxygen acts as the final electron acceptor, it combines with electrons and protons (H⁺) to form water (H₂O). This is a crucial part of the process as it prevents the electron transport chain from backing up and allows for continued ATP production

Role of light in photosynthesis

• crucial in the light-dependent reactions that occur in the thylakoid membranes of the chloroplasts.

• Excites electrons: Light energy (photons) is absorbed by chlorophyll in the chloroplasts. This energy excites electrons in the chlorophyll molecules, boosting them to a higher energy state.

• ATP and NADPH production: The excited electrons are passed along the electron transport chain, where their energy is used to generate ATP through phosphorylation (specifically, ATP synthase) and reduce NADP+ to NADPH. These two molecules (ATP and NADPH) are then used in the Calvin cycle (the light-independent reactions) to produce glucose.

Role of water in photosynthesis

• Electron donor: Water molecules are split into oxygen, protons (H⁺), and electrons by the enzyme complex called photosystem II. The electrons released from water replace those that were excited and lost by chlorophyll in photosystem II.

• Oxygen production: As a result of photolysis, oxygen is produced and released as a byproduct. 

• Protons for the proton gradient: The protons (H⁺) released from water help establish a proton gradient across the thylakoid membrane, which is essential for the production of ATP through chemiosmosis.

Photosystem I

• P700 → its absorption wavelength is 700 nm

Photosystem II

• P680 → wavelength absorbed is 680 nm

Structure of chloroplast

• have an inner and outer membrane

• Fluid filled interior, contains Stroma (protein-rich semiliquid)

• Membrane bound sacs called Thylakoids stack to form grana

• Adjacent grana are connected by lamellae

• Thylakoid membranes enclose an interior space, thylakoid lumen

Aerobic respiration

• Mitochondria (inner membrane and matrix)

• Glycolysis, Pyruvate Decarboxylation, Citric Acid Cycle, ETC

• 36 ATP per glucose

• CO₂ and H₂O byproducts

• High energy efficiency

Anaerobic respiration

• Cytoplasm

• Glycolysis, Fermentation

• 2 ATP per glucose

• Lactic acid byproducts

• Low energy efficiency

DNA vs RNA

DNA: 

• Contains deoxyribose sugar

• Double stranded

• A-T and C-G

• Found in nucleus

RNA: 

• Contains ribose sugar

• Single stranded

• A-U and G-C

• Found in both nucleus and cytoplasm

Mitosis

the division of a nucleus into 2 daughter nuclei with identical chromosomes

Cytokinesis

following mitosis, when the 2 daughter cells cytoplasm fully splits apart creating 2 cells

Steps of DNA replication

1. Unwinding and separation of the parent strand

2. DNA synthesis 

3. Dealing with errors

Step 1 (replication)

– Unwinding and separation of the parent strand

the sites where separation is initiated:

• Replication origins

What is a replication fork?

• Structure of 2 unwound DNA strands

• More than one may exist on a DNA molecule in eukaryotes

3 enzymes that work together to unwind and stabilise the double helix

Helicase, Gyrase, and Single stranded binding proteins (SSBs)

Helicase (replication)

Breaks hydrogen bonds that connect the nitrogenous bases which allows the double helix to unwind + separate.

Gyrase (replication)

relieves the tension produced by unwinding of DNA

Single stranded binding proteins (SSBs) (Replication)

Work to keep separated strands of DNA apart

Step 2 (replication)

DNA synthesis

• DNA polymerase III uses nucleoside triphosphates and adds them in the 5’-3’ direction to form new strand 

• leading strand of replication starts with RNA polymerase

• RNA  primer sequences of 10-16 bases bond to The 3’-5’ strand with the purpose of initiating DNA replication

Leading strand

• grows towards the replication fork as the DNA unwinds. It starts with RNA primase adding a short RNA primer to initiate replication.

• DNA polymerase III then adds DNA nucleotides to the primer in the 5' to 3' direction, and no additional primers are needed.

• This process occurs quickly.

Lagging strand

• synthesized in short segments called Okazaki fragments, growing in the 5’ to 3’ direction away from the replication fork. This process is slower because DNA polymerase must work in the opposite direction (3’ to 5’ parent strand). RNA primase adds primers, and DNA polymerase III builds short DNA fragments. DNA polymerase I removes the RNA primers and replaces them with DNA. DNA ligase then joins the Okazaki fragments into one continuous strand.

• Is a series of RNA primers and short DNA fragments called okazaki

• DNA poly I Removes RNA primers once they have been used and replaces them with appropriate DNA sequence 

• DNA ligase Joins okazaki fragments into one strand by the creation of phosphodiester bonds

Triple bond nitrogenous base pair

C-G

Double bond nitrogenous base pair

A-T

Step 3 (replication)

dealing with errors:

• DNA polymerase III can back up, and replace incorrect bases if base pairs are mismatched during replication

• If error still exists in replicated DNA even after DNA polymerase does its job, DNA polymerase I and II act as a repair complex (made of protein and enzymes). I will proofread and II will remove incorrect bases.

• This step is necessary to avoid the loss, change of function, or even cancer.
  
  

Sum up DNA replication

• ensures that a cell can divide and pass on its genetic information by making an exact copy of the DNA.

• Copying DNA to ensure the next generation has a full set of genetic material.

• Identical DNA molecules (two copies of DNA)

• In Nucleus (eukaryotes) or cytoplasm (prokaryotes)

• DNA as the template for replication

• Enzymes: DNA polymerase, helicase, ligase

• Steps: unwinding and separation, synthesis, dealing with errors

Restriction enzymes

• discovered in 1970 by Hamilton Smith

• AKA "molecular scissors," cut DNA at a specific recognition site, typically 4-8 base pairs long and palindromic (the same in both directions). They bind to the recognition site and break the phosphodiester bonds through hydrolysis. These enzymes can create "sticky ends" (overhangs) or "blunt ends" (straight cuts) in the DNA.

• Obtained from bacteria. Bacteria use them as an immune system. The enzymes break down viral DNA that are trying to invade the bacteria

DNA ligase

• used to join cut strands of DNA. Complementary sticky ends are attracted to each other and reanneal through hydrogen bonds, but these bonds are weak.

• To restore the DNA backbone, it catalyzes the formation of phosphodiester bonds via a condensation reaction.

• T4 ligase is specifically used to join blunt ends.

Plasmids

• Sequences of DNA that are small, circular that can exit and enter bacterial cells

• Lack protein coat

• Usually 1000 – 200 000 bp long

• Proteins that are the result of genes carried by _____:

1. antibiotic resistance

2. resistance to toxic metals

3. Breaking down herbicides

4. Breaking down industrial chemicals

Gel electrophoresis

• separates DNA fragments by size. 

• DNA, being negatively charged, moves through a gel towards the positive end when an electric current is applied. Smaller fragments move faster.

• The gel is stained with ethidium bromide to visualize the DNA, and the desired fragment can be cut out and purified.

Polymerase chain reaction (PCR)

• Polymerase chain reaction (PCR) amplifies a DNA sequence through repeated cycles of strand separation and replication.

• Each cycle takes minutes, and after 20 cycles, over a million copies can be made.

• Introduced by Kary Mullis in 1987

• PCR is useful in forensic science, criminal investigations, medical diagnoses (e.g., HIV viral DNA), and genetic research.

PCR process

1. Heat DNA to 94-96°C to break hydrogen bonds, creating two single strands.

2. Cool to 50-65°C so DNA primers (forward and reverse) can bind to the template strands.

3. Add Taq polymerase, which extends the primers by adding nucleotides to the template strands.

4. The first cycle produces a mixture of DNA strands of variable lengths.

5. The cycle repeats, producing DNA strands of constant length.

6. By the third cycle, the target DNA sequence increases exponentially.

7. the DNA is separated and purified using gel electrophoresis to analyze its sequence.

Chargaffs rule

• Found that bases came in different ratios

• and that Adenine always was equal to thymine and guanine and cytosine was always equal. 

• 1940s

Negative feedback

• process where a mechanism is activated to restore conditions to their original state (thermostat analogy)

• most common homeostasis 

• TSH targeting thyroid due to hypothyroidism

Positive feedback

• process where a small effect is amplified. 

• less common

• ex. (birth process levels of oxytocin, platelets clotting blood to stop bleeding)

Osmoregulation

• The action of actively regulating osmotic pressure of bodily fluids

• Ex: When you are dehydrated, the kidneys reabsorb more water into the bloodstream, producing concentrated urine. When you're well-hydrated, more water is excreted through urine.

Nephron

• the 1 million functional units found in a kidney

•  they play a central role in osmoregulation and excretion

• Comprised of specialized blood vessels and tubes that wrap around each other, filtering wastes from blood and producing urine

Thermorégulation In endotherms

• regulation of internal temperature by negative feedback mechanisms.

• maintain constant internal temperature despite changes in the external environment.

• a decrease in external temp leads to an increase in cellular respiration

Thyroxine (T4 and T3)

Released from: thyroid gland

Lipid based therefore enters the cell easily and then loses an iodine atom, converting to t3. T3 binds to nuclear receptors and alters gene expression (can interact with growth hormone to affect development or increase sensitivity of body cells to epinephrine and norephine

Calcitonin

Release site: thyroid

Target site: bone cells

Released when Ca levels in blood rise above normal.  Inhibits release of Ca from bones.

Parathyroid

Release site: Thyroid

Target: bone cells

Released when Ca levels fall. Stimulates bone cells to release Ca. 

Stimulates kidney enzymes to convert Vitamin D into Calcitriol

→ increasing calcium absorption from food

Aldosterone

Release site: adrenal cortex

Target: kidney tubules

Involved in osmoregulation and control of blood pressure

Cortisol

Release site: adrenal cortex

Target: muscle, liver, and adipose cells

Regulates blood glucose levels and promotes breakdown of fats + proteins

Epinephrine

Release site: adrenal medulla

Preps body for stress and physical activity. Heart rate increases. Glycogen and fats breakdown→ releasing glucose and fatty acids to use as fuel. Slows digestive system.

Norepinephrine

Release site: adrenal medulla

Similar effects as epinephrine on heart rate, BP, and blood flow

Melatonin

Release site: pineal gland

Target: Brain, anterior pituitary gland, reproductive organs, and immune system

Regulates light-dark cycle, when light reaches eyes signals that inhibit melatonin are sent to stay awake

Insulin

Release site: pancreas

Target: muscle, liver…

Causes cells to become permeable to glucose. Coverts glucose to glycogen (storage version of glucose)

Glucagon

Release site: pancreas

Causes increase in blood sugar level, released when glucose is low and converts glycogen to glucose.

Estrogen

Release site: ovaries

Target: female reproductive system

Stimulates maturation of sex organs and development of secondary sex characteristics

Progesterone

Release site: ovaries

Target: uterus

Prepares and maintains uterus for fertilization, growth and development, inhibits GrNH

GnRH

Release site: hypothalamus

Target: pituitary gland

Stimulates release of LH and FSH

FSH

Release site: pituitary gland

Target: reproduction system

Stimulates oocytes to begin meiosis, stimulates estrogen, progesterone and secretion of molecules required for spermatogenesis.

LH

Release site: pituitary gland

Target: reproductive system

Stimulate estrogen, sends enzymes to release egg, stimulates testosterone,

Inhibin

Release site: Sertoli cells in men And ovaries in women

Target: reproductive system

Inhibits FSH

Testosterone

Release site: testes

Target: male reproductive system

Secretes inhibin when high, stimulates puberty and development of secondary sex characteristics

Pathway of urea as it enters the renal artery and leaves through the ureterPathway of urea as it enters the renal artery and leaves through the ureter

• Enters renal artery

• To glomerulus which is connected to bowman's capsule

• The Bowman's capsule leads to a thin tubule called the proximal tubule .

• Urine goes from the proximal tubule around the loop of Henle (U shaped structure) , which descends into the medulla of the kidney.

• Urine then moves through the distal tubule and then into the collecting ducts , which collect urine from many nephrons and lead into the renal pelvis of the kidney.

•  Urine exits through the ureter to the bladder

Diabetes mellitus

insufficient insulin secretion causes blood sugar to rise. Excess sugar remains in nephron. Leads to frequent urination.

Diabetes insipidus

insufficient secretion of ADH leads to frequent urination and urine is often clear and the patient is always thirsty.

Bright’s disease

aka nephritis is inflammation of kidneys, inadequate filtration at the glomerulus leading to the presence of protein in urine.

Kidney stones

buildup of mineral solutes that can combine with Ca to produce crystals that accumulate and form stones. Can be acidic or alkaline.

Hypocalcemia

can result if parathyroids are removed or destroyed.

Sympathetic nervous system

• preps body for stress

• associated with nerves of the chest and abdomen