bio final

macromolecules

polymers made of long chains linked by covalent bonds between monomers

dehydration reaction

forms polymers by removing water molecules during the bonding of monomers.

hydrolysis

The process that breaks down polymers into monomers by adding water molecules.

what are the monomers of carbs

monosaccharides + disaccarides

how to identify carbs

a lot of hydroxyl groups, straight chain of carbons, carbonyl on C-1

cellulose

used for plant structure and cell walls, 1-4 𝛃, not branched

starches

plant energy storage, 1-4 𝛂 & 1-6 𝛂, branched

glycogen

animal energy storage, liver and muscles, 1-4 𝛂 & 1-6 𝛂, the most branched

lipids - fats

1 gylcerol + 3 fatty acid tails = 1 triglyceride (ester linkage), completely hydrophobic

unsaturated fats

contains double bonds that cause bending, liquid at room temperature

saturated fats

no double bonds, solid at room temperature

lipids- phospholipids and steroids(cholesterol)

cholesterol maintains membrane fluidity, amphipathic, two fatty acid tails

structure of an amino acid

amino group, carboxyl group, R group

monomers of proteins

amino acids

peptide bond

formed between two amino acids backbones through dehydration reactions

directionality of peptide synthesis

N-terminus (amino end) to C-terminus (carboxyl end)

primary protein structure

linear polypeptide chain of amino acids

secondary protein structure

𝛂 helices and 𝛃 pleated sheets, stabilized by hydrogen bonding between C and N in the backbones.

tertiary protein structure

3D shape of protein, stabilized by interactions between R groups, hydrogen bonding, van der waals, disulfide bonding.

quaternary protein structure

two or more polypeptide chains into one functional protein (stabilized by the same types of interactions as tertiary structure

purines

A and G

pyrimidines

C and T

how many hydrogens between A and T vs G and C

AT= 2 h bonds

GC= 3 h bonds

monomers of nucleic acids

nucleotides

origin of replication

DNA sequence where DNA replication begins, us where the replication bubble opens.

replication forks

at either end of the replication bubble, where DNA is being unwound for replication

topoisomerase

rejoins parent DNA ahead of the replication fork to relieve strain from unwinding

helicase

unwinds and separates DNA for replication

single strand binding proteins

stablize unwound DNA strands to prevent rejoining

DNA polymerase 1

Removes RNA primers and replaces them with DNA

DNA polymerase 2

DNA repair

DNA polymerase 3

Synthesizes most of the new DNA strand on the leading and lagging strands

primase

makes RNA primers

RNA polymerases

catalyze RNA polynucleotide synthesis in the 5’ to 3’

direction, do not need primers

what does initiation of transcription include

the promotor (TATA) signals where to transcribe and what direction to go in

then transcription factors regulate gene expression by binding to the promotor which enables RNA polymerase 2 to bind to the promotor.

when polymerase 2 binds to promotor it creates transcription initation complex.

start codons

AUG

stop codons

TAA/TAG/TGA

describe elongation

RNA polymerase unwinds base pairs and adds nucleotides to the 3’ end of mRNA, RNA polymerase doesnt proofread

describe termination

RNA Polymerase II reaches and transcribes polyadenylation (5’-AAUAAA-3’)

Termination proteins bind this termination signal and cleave the pre-mRNA transcript 10-35

bases downstream.

5’ modified guanine cap and 3’ poly A tail

1. Facilitate export of mature mRNA from nucleus

2. Protect against degradation by hydrolytic enzymes

3. Facilitate ribosome attachment in cytoplasm

splicing

The process of removing intervening introns and splicing together expressed exons, spliceosomes catalyze splicing

three main components of translation

1. Mature mRNA template

2. tRNAs with attached amino acids

3. Ribosome (small & large subunits)

tRNA

contains anticodon attachment complementary to mRNA attachment

aminoacyl-tRNA synthetases

catalyze the covalent binding of an amino acid to its respective tRNA creating a charged tRNA ready to deliver their amino acid to a growing polypeptide chain on a ribosome.

small ribsomes subunits in translation

Forms peptide bonds and contains the A, P, and E sites for tRNA binding.

APE during translation

• A site (Aminoacyl): The incoming charged tRNA carrying the next amino acid binds here.

• P site (Peptidyl): Holds the tRNA with the growing polypeptide chain.

• E site (Exit): The empty tRNA leaves the ribosome from this site.

• Remember: The initiator tRNA starts in the P site, not the A site.

what happens in initiation of translation

• The small ribosomal subunit binds to the mRNA.

• The initiator tRNA carrying methionine (Met) binds to the start codon (AUG) in the P site.

• The large ribosomal subunit joins to form the complete ribosome.

• Translation is now ready to enter the elongation phase, where amino acids are added to the growing protein.

elongation

• A charged tRNA enters the A site carrying the next amino acid.

• The large ribosomal subunit forms a peptide bond between the amino acids.

• The ribosome moves one codon along the mRNA (translocation).

• The growing polypeptide shifts to the P site, and the empty tRNA moves to the E site and exits.

• This cycle repeats until a stop codon is reached.

termination

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

• A release factor binds to the stop codon (instead of a tRNA).

• The completed polypeptide is released from the ribosome.

• The ribosomal subunits, mRNA, and release factor separate, ending translation.

Localization Sequence

short amino acid sequence that directs a protein to its correct location in the cell.

Post-Translational Modifications

• Post-translational modifications are changes made to a protein after translation to make it functional.

• They can include:

  • Proteolysis: Cutting the protein to activate it.

  • Glycosylation: Adding sugars to help with stability, signaling, or targeting.

  • Phosphorylation: Adding phosphate groups to regulate protein activity.

energy coupling

using energy released during exergonic reactions to power endergonic reactions

two phases of glycolysis and net output

Energy Investment Phase (5 steps)

2 ATP used to split glucose (6C) into 2 sugars (3C)

Energy Payoff Phase (5 steps)

4 ATP & 2 NADH made from oxidizing 2 sugars (3C) to 2 pyruvates (3C)

2 NET ATP

pyruvate oxidation

pyruvate is oxidized to acetyl- CoA to make NADH and CO2

what does acetyl CoA do to keep citric cycle continuous

Adds oxaloacetate to form citrate.

where is H+ pumped for ETC

H+ is pumped from the mitochondrial matrix to the intermembrane space using energy released from redox reactions

chemiosmosis

The high potential energy of the electrochemical gradient(H+) establishes the proton motive force which drives ATP synthesis via ATP synthase, harnessing the energy stored in a H+ gradient across a membrane to drive cellular work

what makes up oxidative phosphorylation

ETC + chemiomosis

what metabolic adaptions happen during hibernation

uncoupling proteins along the inner mitochondrial membrane are activated which allow H+ to flow down their concentration gradient and generate heat without generating ATP

feedback inhibitions

High concentrations of Adenosine monophosphate (AMP) stimulates PFK, while high concentrations of ATP inhibits PFK

3 bacteria shapes

Cocci (round)

Bacilli (rod)

Spiral (helical)

flagella

rotor-like protein complexes that can be powered by the proton motive force generated from the ETC pumping H+ out of the cell. Positive chemotaxis toward nutrients or negative chemotaxis away from toxins

pili

short, hollow, tread-like structures used for adherence to surfaces and other bacteria

Importins

ecognize nuclear

localization signals (NLS)

Exportins

recognize nuclear

export signals (NES)

Necessary

must be present for x to occur, but may not be enough to cause it alone

Sufficient

it alone is enough to cause x, but may not be only way

Cis face of golgi

receives proteins and lipids from the ER

trans face of golgi

ships chemically modified glycoproteins, glycolipids and phospholipids to cell surface

Lysosomes

acidic, membrane-bound vesicles that break-down and recycle cellular materials via hydrolases, which are synthesized in the ER, then transported to the Golgi, where they are tagged for lysosomes by adding mannose-6-phosphate (M6P)

Endosymbiotic Theory

mitochondria & chloroplasts evolved from aerobic & photosynthetic bacteria, respectively, engulfed by ancestral eukaryote.

1. Double-membrane

2. Size (~bacteria)

3. Own DNA/genes (~bacteria)

4. Own ribosomes (~bacteria) that are affected by some antibiotics

5. Reproduce via binary fission (~bacteria)

Proteoglycans

help cushion cells

collagen

a strong, structural protein that provides tensile strength by resisting stretching

Fibronectin

large glycoprotein that helps integrins anchor cells to the ECM

Intermediate filaments

1. Resist stretching and physical stress

2. Maintain cell shape

3. Anchor organelles

4. Form nuclear lamina

Microtubules

hollow tubes made of alpha & beta tubulin dimers that function in cell shape movements and chromosome movements during cell divisions

dynamic instability

reorganize the cell by switching between growth and shortening. Growth occurs when more stable GTP-bound tubulin is added and shortening occurs when less stable GDP-bound tubulin is lost.

what are microtubules organized by

centrosomes, organized in cells by Microtubule Organizing Centers.

controsomes

found close to the nucleus and consist of a pair of centrioles and pericentriolar

matrix

Centrioles are barrel-shaped structures made of 9 × 3 microtubules

Pericentriolar matrix contains γ-tubulin complexes which function as templates for microtubule growth

what falls under motility of microtubules

cilia and flagella as well as motor proteins (kinesin(+) and dyenin(-))

microfilaments

made of actin proteins that are powered by ATP hydrolysis to polymerize at the (+) end and depolymerize at the (-) end via treadmilling

1. Maintain cell shape

2. Adhesion

3. Movement

4. Muscle contraction

5. Cytokinesis

muscle contractions

ATP hydrolysis powers muscle contraction, where the heads of myosin motor proteins pull actin

filaments together

how are sister chromatids held together

attached at the centromere and held together by cohesin proteins

what triggers cell checkpoints in interphase

Active cyclin-CDK complexes phosphorylate proteins that trigger progression through cell cycle checkpoints. CDK only activates wit cyclin present

Mitosis Prophase

1.Duplicated chromatin condenses into duplicated chromosomes held together by cohesin

2. Mitotic spindle begins to form as centrosomes begin to move apart

mitosis prometaphase

1. Nuclear envelope disintegrates

2. Kinetochore microtubules extend from each centrosome and attach to kinetochore proteins at each centromere

mitosis metaphase

Chromosomes align at metaphase plate

mitosis anaphase

1. Cohesin degrades via separase

2. Kinetochore microtubules shorten to move sister chromatids toward opposite poles

3. Polar microtubules extend to elongate cell

mitosis telophase

1. Nuclear envelopes form around two identical daughter nuclei

2. Chromosomes decondense

3. Spindle microtubules depolymerize

cytokinesis

1. In animal cells, a contractile ring of microfilaments pinches and separates daughter cells at the cleavage furrow

2. In plant cells, golgi- derived vesicles form a cell plate between two daughter cells

somatic cells

all body cells

gametes

eggs and sperm

what is the starting material o meiosis 1

a pair of homologous chromosomes in diploid parents cell

whats created after interphase

diploid cell with duplicated chromosomes (4 sisters chromatids)

overall, what does meiosis create

Overall, meiosis makes 4 haploid cells (gametes) from 1 diploid cell.

prophase 1

tetrad forms and the homolgous chromosomes attach to each other. then they cross over and become unique.

meiosis metaphase 1

homologous pairs orient randomly (random assortment) and line up on metaphase plate

nondisjunction

mistake when separating chromosomes in either Meiosis I or Meiosis II.

trisomy

in meiosis 1 and meiosis 2, 3 chromosomes in each cell instead of appropriate amt

monosomy

meiosis 1, 1 copy of each chromosome in each cell instead of appropriate amount