bio final fr

what macromolecule is responsible for storing energy

carbohydrates

what linkage is responsible for branches

1-6 linkage

what linkage is responsible for chains

1:4 linkage

what is special about cellulose

-responsible for giving plant cells walls

-1:4 linkage since every oxygen is pointing in the opposite direction (connected through glycosidic bond)

-made of polysaccharides

-stack on top of each other due to hydrogen bonds → H bonds also give a sheet like structure

what is amylose?

-not a ring structure

-is a polysaccharide

-molecule with 1:4 linkage and no branching

how do polysaccharides break down

Hydrolysis → h2O comes in and breaks a molecule

what is activation energy

energy needed to start a process and release energy because molecules are already stable

→ more bonds mean more stability

what are enzymes?

proteins that help lower the activation energy

→ if activation energy is lower then reaction is more likely to happen

why are carbohydrates important?

all living things use carbohydrates to store energy

how do monosaccarhides bond?

undergo dehydration synthesis, and a covalent bond forms known as glycosidic bond

polysaccharide

-used to store energy for later use in cellular structure

-chain of multiple sugars

how is a function of a polysaccharide determined?

-look at individual monosaccharides

-look at how they are linked together

types of glycosidic bonds and what they are used for

-branches: 1’6 glycosidic bond

-chains: 1’4 glycosidic bond

starch

-energy storage in plants

-energy sent to roots and is stored for later usage

glycogen

-energy stored in animals

cellulose

-polysaccahride that is composed of several glucose molecules linked together

-form a linear chain

-hydrogen bonds allows cellulose to stack on top of each other and gives it a sheet like structure

-provides structural support to plant cells

how do polysaccharides break down?

hydrolysis: process where water is added and molecules break

what is an enzyme?

protein which helps to lower the activation energy within reactions

what does lower activation energy mean?

if activation energy is lower it means that a reaction is more likely to occur

what is the process of cellular respiration

converts energy from food storage molecules (ex: glucose) into usable energy in the form of ATP

Inputs of glycolysis

glucose (C6H12O6), 2NAD+, 2ADP, 2 Pi

Outputs of glycolysis

2 pyruvate, 2NADH, 2 ATP

Investment phase glycolysis

1) OH group on glucose is replaced by phosphate group from 1 ATP, converting ATP→ADP making glucose 6 phosphate

2) glucose 6 phosphate creates an isomer of itself called fructose 6 phosphate

3) fructose 6 phosphate has another phosphate group added, another ATP is used turning ATP→ADP and creates fructose 1-6 biphosphate

4) fructose 1-6 biphosphate splits into DHAP and G3P (creates 2 3C mlcls)

5) DHAP is converted into G3P → at this point everything needs to be doubled during payoff phase

pay-off phase glycolysis

6) G3P is oxidized and the electrons convert NAD+ to NADH (which will later move to ETC), energy allows for P from outside enviorment to attach and create 1-3 biphosphoglycerate

7) phosphate group from biphosphoglycerate is given to ADP to produce ATP which results in 3 phosphoglycerate

8) 3 phosphoglycerate creates an isomer 2 phosphoglycerare

9) 2 phosphoglycerate has a water removed (dehydration reaction) resulting in PEP

10) PEP has another phosphate removed and donated to ADP creating ATP and pyruvate which will be available for pyruvate oxidation

when does fermentation occur?

fermentation occurs when there is no oxygen or mitochondria (also known as anerobic respiration)

what are the two types of fermintation

lactic acid and alchol fermination, occurs within cytoplasm

lactic acid fermination

occurs within animals (humans, muscel cells, and bacteria)

-glucose → pyruvate → lactate

-within glycolysis 2ADP turns into 2ATP and 2 NAD+ turns into NADH

-pyruvate is reduced, when something is reduced something needs to be oxidized which turns NADH to NAD+ which goes back into glycolysis to create the 2 ATP net

ethanol/alchol fermination

alc forms at the end and you can find yeast/alc

-glucose → pyruvate → aceytalhyde → ethanol (beer). CO2 leaves also called decarboxylation (why bread rises)

-within glycolysis 2 ADP turn into 2 ATP and 2NAD+ is oxidized to create NADH, when the pyruvate turns into aceytalhyde it is reduced to ethanol and when something is reduced something else is oxidized which makes NADH turn into NAD+ in order to repeat glycolysis and make the 2 ATP net

where does glycolysis happen?

cytoplasm

where is the location for cellular respiration processes in eukaryotic cells?

-glycolysis: cytoplasm

-pyruvate oxidation: mitochondrial matrix

-citric acid cycle: mitochondrial matrix

-electron transport chain: inner mitochondrial membrane

chemiosmosis and ATP synthase: H+ pumped into intermembrane space

Cellular Respiration in Prokaryotic Cells

Glycolysis

Cytoplasm

Pyruvate Oxidation

Cytoplasm

Citric Acid Cycle (Krebs)

Cytoplasm

Electron Transport Chain (ETC)

Plasma Membrane

Chemiosmosis / ATP Synthase

Plasma Membrane, with H⁺ pumped to periplasmic space (between membrane & cell wall)

Citric Acid Cycle

-occurs within the mitochondrial membrane of eukaryotes (prokaryotes: cytoplasm)

1) aceytal coA 2C combines with oxoacetate 4C to create the 6C mlcl citrate

2) citrate creates isomer isocitrate

3) isocitrate is made into alpha ketoglutarate which is a 5C mlcl where NAD+ is reduced to NADH

4) alpha ketogluterate is converted into succinyl coA 4C mlcl and reduced NAD+ to NADH and also releases CO2

5) substrate level phosphorylation occurs and ADP turns into ATP which turns succinyl coA to succinate

6) succinate turns into fumerate (both are 4C mlcls) where FAD is reduced to FADH2

7) isomer is made of fumerate by adding water and creates malate (4C mlcl)

8) NAD+ is converted to NADH and regenarates oxaloacetate → whole cycle starts again

what is the point of the citric acid cycle

to get electrons in order to put through the ETC to make more ATP

inputs of citric acid cycle

aceytal coA, 3NAD+, 1FAD, 1ADP, 1Pi, 1 oxoacetate

outputs of citric acid cycle

3 NADH, 1 FADH2, 1 ATP, 2 CO2, 1 oxoaceltate

what is pyruvate oxidation and why is it useful?

converts pyruvate to aceytal co A so it can enter the citric acid cycle

inputs for pyruvate oxidation

pyruvate, coA, NAD+

outputs for pyruvate oxidation

CO2, NADH and acetyl co A

what happens during pyruvate oxidation

3C molecule pyruvate is created after glycolysis and aceytal COA is created (2C mlcl) where 1 carbon is removed (making aceytal coA a 2C mlcl), NAD+ is reduced to NADH

Electron transport chain

-occurs within inner mitochondrial membrane of eukaryotic cells and plasma membrane of prokaryotes

-NADH passes through complex 1 and FADH2 passes through complex 2

-electrons move which causes energy to be released and the energy is used to pump H+ ions from the mitochondrial matrix into the intermembrane space which creates a proton gradient

-high H+ concentration outside and low inside

-at end of chain (complex 4) electrons combine with o2 and 2H to create water → OXYGEN IS LAST e- ACCEPTOR (no o2=chain stops=cell dies)

-chemosomosis occurs and H+ flows back into the matrix through ATP synthase which creates more ATP

inputs of ETC

NADH, FADH2, O2, H+

outputs of ETC

28 ATP, H20, NAD+, FAD

inputs of photosynthesis

6H20, 6CO2, light

outputs of glycolysis

glucose, 6O2

anatomy of chloroplast

-have their own ribosomes and DNA

-3 membranes: outer, inner, and thylakoid

-thylakoid: contains stacks of membrane bound structures which have integral membrane proteins which are responsible for conducting photosynthesis → responsible for ETC and ATP synthase → light reactions happen here

-lumen within thylakoi is where H+ builds up

-stroma: fluid that fills internal space of chloroplasts → calvin cycle happens here

Oxidative phosphorylation

inputs: ADP, Pi, H+

outputs: ATP

4 steps of transcription

1) initiation

2) elongation

3) termination

4) RNA processing (transcriptional modifications)

initiation in transcription

Goal: start transcription at the correct location

1. TF bind to promoter region which contains the TATA box

2. RNA polymerase II binds to transcription factors and then binds to the starting site of the tempelate strand of DNA

3. The DNA unwinds and creates a bubble and only 3’5 tempelate strand is used

Elongation step of transcription

Goal: build RNA by adding nucleotides

1. RNA polymerase reads the RNA strand in the 5’ 3’ direction

2. New strand of RNA detaches from DNA and the RNA polymerase continues to move down the gene

Termination step of transcription

Goal: Stop transcription when the gene ends

1. RNA polymerase will hit a termination sequence which releases the RNA→ signal is (AAUAAA)

2. this newly made RNA turns into mRNA (

RNA Processing (Post-Transcriptional Modifications)

• 5’ cap is added which protects the RNA and helps prepare for the ribosome to bind later

• The 3’ poly A tail is added which helps stabilize the RNA and allows it to help leave the nucleus

• Splicing occurs due to a ribosome where introns are cut out and exons are added

This process leads to mature MRNA which prepares it to leave the nucleus and go to the cytoplasm to undergo transcription

Steps for translation

1. initiation

2. elongation

3. termination

inititation in ribosome

Goal: get ribosomes to correction region of mRNA to begin the process

1. small ribosomal subunit binds to the 5’ cap of mrna

2. finds the start codon

3. TRNA that has methionene comes in and binds to AUG via the anticodon UAC

4. large ribosomal subunit also joins and full ribosome is assembled and tRNA is in the P site

Elongation

Goal: link amino acids to growing polypeptide chain

During translation elongation, a tRNA carrying an amino acid enters the A site of the ribosome, matching its anticodon with the next codon on the mRNA. The ribosome forms a peptide bond between the new amino acid and the growing chain held in the P site, using its peptidyl transferase activity. Then, the ribosome shifts forward, moving the tRNA from the P site to the E site (where it exits), and the A-site tRNA (now holding the chain) moves to the P site. The A site becomes empty for the next tRNA, and this cycle repeats to build the protein.

Termination

Goal: Stop translation & release the finished protein

Steps:

1. A stop codon (UAA, UAG, or UGA) enters the A site

2. No tRNA binds to stop codons — instead, a release factor binds

3. The ribosome breaks apart:

   • Polypeptide is released

   • mRNA and tRNAs are released

   • Ribosome subunits detach

elements of a gene

1. Enhancer (optional)

   • Regulatory sequence that increases transcription (can be far away)

2. Silencer (optional)

   • Regulatory sequence that represses transcription

3. Promoter

   • Binding site for transcription factors and RNA polymerase

   • Often includes a TATA box

4. Transcription Start Site (+1)

   • First nucleotide transcribed into RNA

5. 5′ Untranslated Region (5′ UTR)

   • Transcribed but not translated

   • Helps regulate translation initiation

6. Start Codon (AUG)

   • First codon translated → codes for methionine

7. Coding Sequence (CDS)

   • Includes exons (coding) and introns (non-coding)

   • Gets transcribed and spliced → used to make protein

8. Stop Codon (UAA, UAG, UGA)

   • Signals end of translation

9. 3′ Untranslated Region (3′ UTR)

   • After stop codon

   • Regulates mRNA stability, transport, and translation

10. Polyadenylation Signal (AAUAAA)

    • Signals for cleavage of mRNA and addition of poly-A tail

purines and prymides

purine (2 ring): CT

prymide (1 ring): AG

centromeres

is a DNA region that links sister chromatids and helps them attach to spindle fibers → middle of chromatids

telomeres

repetitive sequence at the end of sequence and protects chromosome from degrading

histone

compacts DNA and is made out of 8 polypeptides in the quatrenary structure and a double strand of DNA is wrapped around it 1.6times per protein which shrinks the size by 40k

calvin cycle

3 phases of calvin cycle

need 2 turns → purpose to make glucose

1) carbon fixation

-CO2 is attached to 5C molecule RuBP → reaction is catalyzed by rubisco

-this 6C molecule splits into 2 3PGA (so 2, 3 carbon molecules)

2) reduction

-each 3PGA is phosphorylated to become 1,3 phosphoglycerate

-1,3 phosphoglycerate is reduced by NADPH to become 2 G3P (a 3 carbon sugar)

-the two G3P can combine later to make glucose

3) Regeneration of RuBP

-most of the G3P is not used to make sugar directly

-ATP is used to turn some of the G3P back into RuBP for the cycle to continue

input of calvin cycle

1 G3P, 9 ADP, 6 NADP+, Pi

output of calvin cycle

for one glucose molecules → need 2 cycles

6 CO2, 18 ATP, 12 NADPH, 2 net G3P

what are biofilms?

-a community of microorganisms attatched to a surface and grow on top of each other

-occur when surface is moist and there is nutrients available

-dye helps produce images of biofilms

-important for medicine because they can form on catheters and other medical devices

what happens to the middle portion of biofilms?

-middle portion has low access to oxygen bc cells stack on top of each other

-bacteria in the middle hibernate if biofilm has access to oxygen it will come out of hibernation

what are basic features of a lipid

hydrophobic or amphillic small molecules

types of lipids

-cholesterol (a type of steroid)

-a free fatty acid

-a triglyceride

-a phospholipid

properties of steroids

-all living things produce steroids

-all steroids have 4C-H rings that are attatched to each other

-are ampiphillic (C-H makes it nonpolar and OH makes it polar)

correlation between steroids and hormones

-steroids can be hormones, but not all hormones are steroids

examples: testosterone, proestrogene, cortisol, aldosterone

hormones

-a signaling molecule

-produced in a tissue and has an effect on another tissue

-are part of the endocrine system

-lead to changes in physiology and behavior

functions of steroids → cholesterol membranes

-regulate membrane fluidity in animals

-all mammals have cholesterol in their membranes

-30% of most membranes are made of cholestrol

-neurons have a lot of cholestrol because they need more fluidity

functions of steroids- bile acids

-bile acids are made of cholestrol have COOH

-they are responsible for the digestion of lipids

-made by digestive system and helps break down fats

phospholipid

-have polar head

-have fatty acids

-most phospholipids have a saturated and unsaturated tail (2 total so 1 of each)

-responsible for making the membrane

• H2O is outside and inside of the cell and the membrane separates the in and out

• also makes mitochondria, endomembrane, and chloroplast membranes

fluidity of membrane

-membranes can exist at lots of different temperatures → need right amount of fluid

-the amount of saturated and unsaturated fatty acids determines how fluid the membrane is

-unsaturated → leads to fluidity in the membrane

-saturated → leads to viscous or frigid membrane

what does cholesterol do for membranes?

-fills gaps between phospholipids

-they help the membrane stay at the perfect fluidity

-the ring portion of cholesterol is stiff

-bottom portion of the cholesterol fluid

correlation between temperature and membrane fluidity

as temp increases which leads to more fluidit\y

how are phospholipids selectively permeable

-nonpolar molecules CAN move through → diffuse through membrane (ex:o2)

-small polar molecules can move across the membrane really slowly (ex: H2O can move through the membrane but slowly which is why it requires an aquaporin)

-large polar molecules cannot move through the membrane unless there is a membrane protein that can facilitate this movement (ex: glucose)

what are 2 roles that membrane plays in functioning cells?

-separate internal environment from outside

-internal membrane can be compartmentalized → through membrane bound organelles

what are the two components of the endoplasmic reticulum

Rough and Smoothe

-rough → makes proteins for the membrane, other organelles, or is exported from the cell

(ex: cells make hormones → is later exported through the bloodstream)

-smoothe: makes lipids but has different functions based on cell type

rough ER making proteins

-protein creation starts in the cytoplasm where mRNA leaves the nucleus into cytoplasm

-mRNA combines with small ribosome subunit of amino acylated tRNA and the large subunit also comes in

-the 1st 16-30 amino acids encode for a signal sequence → this sequence is recognized by a signal protein and it attatches to the sequence and says that protein should be created in the ER

-ribosomes travel as proteins are made where there is a docking protein and SRP receptor

• SRP finds the signal on a growing protein, pauses translation, and brings the ribosome to a docking protein (SRP receptor) on the ER, where protein synthesis continues into the ER

Inside the rough ER

-SRP binds to docking protein (also known as the receptor) in order to continue translation

-the signal sequence of 16-30 amino acid chain is cutt off and now its only responsibility is to move to the ER and are later reused

-now polypeptide without sequence is released from ribosome once it reaches the stop codon and is released into the rough ER → ribosomes can separate and make more protein again

proteins being transported out of the ER

-chaperone proteins help other proteins fold correctly → once folded correctly they attach to cargo receptors and leave the ER

-cargo receptors → put proteins into vesicle and then…

-COP2 proteins coat the vesicles and make sure they move from the ER to golgi

elements of the smoothe ER

-there are no docking proteins present

-they make lipids and depending on the cell types they can have other functions

what is transitional ER

located between the smooth and rough ER and makes proteins that are attached to lipids

smoothe ER in muscle cells

-called sacroendoplasmic reticulum → helps regulate the amount of calcium is made and contains calsequestin protein

-calsequentin protein → a calcium storage protein. can bind 50 Ca ions and controls the number of ions

-need the right amount of calcium so muscle cells can function

components of the golgi

-as a vesicle is removed from the ER they move to the cis golgi to the trans golgi

-products get processed and the compartments help for things to be a bit more organized

-enzymes are located in the compartments and there are specific enzymes for each compartment

-cis proteins recieves proteins from ER and modifies them and then moves them to trans

-in trans part of golgi the proteins get processed and packaged in order to leave

-then go to vesicles

components of secretory vesicles and lysosomes

-vesicles sort out products at the golgi

-lysosome: membrane bound organelle that degrades used cell parts so that they can be used again

-in some cases proteins can be pulled of lysosomes or are exerted to other organelles

movement between compartments depends on which proteins…

-integral membrane proteins: made in rough ER (also proteins that are trafficked, hormones)

-proteins are removed from the ER and merge into a thin vesicle then transported to the golgi

-VSNARE and TSNARE also help

VSNARE and TSNARE

v-SNAREs on vesicles bind to t-SNAREs on target membranes to ensure that vesicles fuse with the correct location, enabling precise delivery of proteins and molecules

clathirin

Clathrin is a protein that coats and shapes vesicles, especially during endocytosis and transport from the Golgi, ensuring that cargo is delivered to the right place

how do you figure out what the 3’ and 5’ ends of a DNA molecule are

The 5′ end of DNA has a phosphate group, and the 3′ end has a hydroxyl group, and DNA strands are always read and synthesized in the 5′ to 3′ direction

proteins involved in replication

Hot Sticky Titties Drip Creamy Like Peanut Taffy

helicase

ss binding protein

topoisomerase

DNA polymerase

DNA Clamp

Ligase

Primase

Telomerase

nuclease → During DNA replication, nucleases remove RNA primers, trim DNA flaps, and cut out errors — basically cleaning up so the DNA strand is accurate and continuous

helicase

breaks hydrogen bonds between the strands and results in a single strand of DNA

SS binding protein (single stranded)

stablize single stranded DNA so they stay seperated

Topoisomerase

-2nd structure interactions leads to double helix shape

-topoisomerase relaxes the super coiling and helps relieve the pressure from unwinding the helix

DNA polymerase

comes after the 1st 3 proteins and catalyzes the addition of nucleotides in a growing strand of DNA

DNA Clamp

prevents (new) elongating strand from separating from the template (og) strand

ligase

when we end up with chunks of DNA they need to get attatched with each other so the ligase catalyzes bonds between fragments of DNA and forms one covalent bond between the fragments → connect okazaki framents thru phosphodiester bond

primase

-makes beginning strand for DNA polymerase to start

-makes “primer” so DNA polymerase can elongate off it

Telomerase

extends the telomeres (repetitive DNA sequences found at the end of linear chromosomes and protect the end of chromosomes)

germ line cells

are reproductive cells→ go through mitosis