MOLEC BIOTECH EXAM 1

Nucleus

located in the cytoplasm of a cell & contains the cell’s DNA

nuclear envelope

A double membrane structure that surrounds the nucleus, separating it from the cytoplasm and regulating the passage of molecules in and out of the nucleus.

what happens in the nucleus

transcription

ribosome assembly location

occurs in the nucleolus, where ribosomal RNA (rRNA) is synthesized and combined with proteins to form ribosome subunits.

transcription location

occurs in the nucleus, where DNA is transcribed into messenger RNA (mRNA) by RNA polymerase.

endoplasmic reticulum

a network of membranes involved in protein and lipid synthesis, often connected to the nuclear envelope.

protein synthesis location

occurs in the ribosomes, where mRNA is translated into amino acid sequences, forming proteins.

translation location

occurs in the cytoplasm, specifically at the ribosomes, where mRNA is translated into proteins.

rough er

the portion of the endoplasmic reticulum studded with ribosomes, primarily responsible for the synthesis of proteins.

smooth er

a part of the endoplasmic reticulum that lacks ribosomes, involved in lipid synthesis and detoxification.

golgi complex

A cellular organelle that modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

golgi location

Located near the rough endoplasmic reticulum, typically in the cytoplasm.

vaculoes

Membrane-bound sacs that store and transport substances

vaculoes location

Typically found throughout the cytoplasm, often near the cell membrane and endoplasmic reticulum.

mitochondria

Organelles that generate ATP through cellular respiration

mitochondrial DNA

small circular DNA molecule responsible for encoding some of the proteins essential for function and energy production.

B-oxidation

A metabolic process that breaks down fatty acids into acetyl-CoA units, which can enter the citric acid cycle for energy production.

krebs cycle

A series of enzymatic reactions in the mitochondria that generate energy through the oxidation of acetyl-CoA, producing NADH and FADH2.

oxidative phosphorilation

A process occurring in the mitochondria where ATP is produced from ADP and inorganic phosphate using energy derived from the electron transport chain and the proton gradient.

chloroplasts

Organelles found in plant cells and some algae that conduct photosynthesis, converting light energy into chemical energy in the form of glucose.

calvin cycle

A set of biochemical reactions that occur in the chloroplasts during photosynthesis, converting carbon dioxide into glucose using ATP and NADPH.

structure of a common phospholipid

hydrophilic head containing a phosphate group and two hydrophobic fatty acid tails.

phospholipid

A type of lipid that forms the structural basis of cell membranes.

choline

The polar part of a phospholipid that interacts with water, consisting of a phosphate group.

primary structure

peptide bonds that link amino acids into a polypeptide chain

secondary structure

hydrogen bonds between C=O and N-H groups to stabilize alpha helix or beta sheets

tertiary structure

interactions between amino chains that result in the 3D shape of the protein, (hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.)

quarternary structure

interactions between separate polypeptides to form a functional protein complex.

(H-bonds, VDW, hydrophobic, ionic)

why DNA and not RNA

DNA is more stable and less prone to hydrolysis compared to RNA, making it a better long-term storage molecule for genetic information.

differences between DNA and RNA

• deoxy vs ribose

• thymine vs uracil

• double vs single strand

• 2’ OH in RNA

uracil vs thymine

structurally identical, except uracil lacks a methyl group at the 5' position.

deamination of C

is the process where cytosine is converted to uracil by the removal of an amino group (amine). This reaction can lead to mutations if not repaired.

Lack of 2’-OH

causes DNA to be more stable than RNA, making RNA more prone to hydrolysis.

RNase selectivity

RNases are selective towards RNA because of the presence of the 2'-OH group, which facilitates substrate recognition and cleavage.

RNA intra strand double helix

is a structure formed when a single strand of RNA folds back on itself, creating complementary base pairing that results in a double helix formation packed into a protein-like strucutre

simple diffusion

is the process by which molecules move from an area of higher concentration to an area of lower concentration without the need for energy or transport proteins, allowing substances like gases and small nonpolar molecules to pass through cell membranes.

ionophones

are membrane-permeable compounds that facilitate the transport of ions across lipid bilayers, typically enhancing the permeability of membranes to ions like sodium, potassium, and calcium.

facilitated diffussion

passive transport of molecules across a cell membrane via specific transmembrane integral proteins, allowing substances that cannot directly diffuse through the membrane to enter or exit the cell.

types of facilitated diffussion

include carrier-mediated diffusion and channel-mediated diffusion, both allowing specific molecules to cross membranes more efficiently.

diffussion through carriers

involves specific proteins that bind to molecules and change shape to transport them across the membrane.

types of carriers

uniporters, symporters, and antiporters, each serving different transport functions.

uniporters

transport proteins that move a single type of molecule across the membrane.

symporters

transporters that move two different molecules in the same direction across the membrane.

antiporters

transport proteins that move two different molecules in opposite directions across the membrane.

osmosis

the diffusion of water across a selectively permeable membrane following a solute concentration gradient

potassium ion channel

a type of membrane protein that selectively allows the passage of potassium ions (K+) across the cell membrane, playing a key role in maintaining cell potential and regulating cellular functions.

why the potassium ion channel selectively allows K ions to pass

due to its specific pore structure and charge distribution that facilitates K+ transport while excluding other ions, such as Na+.

why potassium ion channel doesnt let Na+ pass

100x more permeable to K than Na

potassium ion selectivity filter

a component of potassium ion channels that ensures only K+ ions pass through, based on size and charge interactions.

energy selectivity of potassium ion channel

G of hydration for Na (-72) is higher than that for K (-55)

there is a larger cost to dehydrate Na compared to K. The energy cost is offset by K interacting with carbonyl agents and leaving the water molec behind

energy from transport

comes from ion gradient and the electrochemical gradient created across membranes.

Na & glucose symporter

binding of either enhances binding of the other

Na+ bind to empty sites and glucose binds due to cooperativity and they are released in that same way due to low concentration

Na/glucose symporter second classification

indirectly relies on ATP-generated energy but does not directly use ATP, it can be classified as secondary active transport

Na+/K+ pump

is a primary active transport mechanism that pumps sodium ions out of the cell and potassium ions into the cell, utilizing ATP hydrolysis to move them against their concentration gradient.

Na+/K+ pump in intestine cells

pumps 3 Na+ out & 2 K+ ions in for every ATP use

indirect;y helps intestinal cells by maintaining the Na+ gradient needed for the Na+/glucose symporter

P-type ATPase

relies on transfer of a phosphate group from ATP to an amino acid residue and its subsequent removal for transport

description of oxidative phosphorilation

• cells use energy from the electrons carried by NADH and FADH2 to produce ATP; this takes place in the inner mitochondrial membrane.

• they donate their high energy electrons to the electron transport chain in the inner mitochondrial membrane and the energy released inthe form of electrons move through the chain, creating a proton gradient (used to pump H+ gradient from the matrix into the intermembrane space)

• The H+ gradient then provides energy for ATP synthase to produce ATP from ADP and inorganic phosphate (Pi)

• H+ moves back across the membrane and O2 accepts electrons at the end of the e- transport chain and forming water.

NADH & FADH2 in oxy phospho

generated during glycolysis in cytosol and pyruvate oxidation and the citric acid cycle taking place in the mitochondrial matrix.

nucleosome

147 bp long basic units of DNA wrapped around a group of 8 histone proteins

core histones

H2A, H2B, H3, H4

two of each come together to form the octamer core that the DNA wraps around

linker histones

H1 (variant is H5)

sit outside the core to bond spacer DNA and stabilize higher order chromatin structures

lagging strand

The DNA strand that is synthesized discontinuously in short fragments, known as Okazaki fragments, during DNA replication.

it is produced in the opposite direction of the replication fork.

leading strand

The DNA strand that is synthesized continuously in the same direction as the replication fork during DNA replication (5’ → 3’)

this is because the DNA polymerase only adds nucleotides in the 5’→3’ direction

DNA ligase

enzyme that joins Okazaki fragments together on the lagging strand during DNA replication, facilitating the formation of a continuous DNA strand.

telomerase

An enzyme that adds repetitive nucleotide sequences to the ends of chromosomes, called telomeres, to protect them from degradation during DNA replication.

RNA primer

Short RNA sequence that provides a starting point for DNA synthesis during replication. It is synthesized by primase and is necessary for DNA polymerase to begin adding nucleotides.

DNA polymerase

Enzyme that synthesizes new DNA strands by adding nucleotides complementary to the template strand during DNA replication.

replication fork

The structure that forms during DNA replication when the double helix unwinds and separates, creating two single strands that serve as templates for synthesizing new DNA strands.

helicase

Enzyme responsible for unwinding the double-stranded DNA helix during replication, allowing the replication fork to form.

transcription in prokaryotes vs eukaryotes

• both use RNA polymerase and have initiation, elongation, and termination modes

genes pro vs euk

pro: organized in operons

euk: transcribed individually

transcription location pro vs euk

pro: spontaneously in the cytoplasm at ~ 50 nt/sec

euk: in the nucleus at ~20 nt/sec

RNA polymerase

An enzyme that synthesizes RNA from a DNA template during transcription, essential for both prokaryotic and eukaryotic gene expression.

RNA polymeras pro vs euk

por: uses only one

euk: different one for rRNA, mRNA, and tRNA

initiation pro vs euk

pro: sigma factor needed to bind

euk: many transcription factors must assemble at the promoter

end pro vs euk

pro: mRNA has triphosphate on 5’ end

euk: 5’ 7-methyl guanosine cap and poly-A tail required

splicing pro vs euk:

pro: no introns present

euk: undergoes splicing of introns joining exons

regulatory proteins pro vs euk:

pro: act close to promoter

euk: act both close and far from promoter

promoter pro vs euk

pro: unse Pribnow box

euk: TATA box

termination pro vs euk

pro: Rho-dependent or independent

euk: prescense of poly-A tail or sequence

translation pro vs euk

both processes occur on ribosomes

follow initiation, elongation, termination

tRNA initiator pro vs euk

Pro: fMet-tRNA initiator binds small subunit

Euk: Met-tRNA initiator binds the small subunit

initiation factors pro vs euk

Pro: IF-1, IF-2, IF-3 assist in ribosome binding

Euk: eIFs (1,1A,2,2B,3,4A,4B,4E,4F,4G,4H,5,5B) help recruit the small ribosomal subunit.

starting translation pro vs euk

pro: ribosome finds AUG with RBS and initiates

euk: first AUG in mRNA sets the reading frame

elongation factor pro vs euk

pro: EF-Tu delivers new AA-tRNA; Translocase/GTP EF-G moves ribosome to 3’ end

euk: eEF-1 delivers AA-tRNA; eEF-2/GTP moves the ribosome one codon

termination pro vs euk

pro: release factor binds to ribosome

eRF1 release factor eRF3 (GTPase) release polypeptide

ribosome binding site pro vs euk

pro: Shine-Dalgarno sequence to recognizr AUG/start

euk: Kozak sequence is initiation site (not RBS)

translation location pro vs euk

pro: occurs in ribosome in cytoplasm

euk: endoplastim reticulum

endocytosis

Process by which cells internalize substances from their environment, encapsulating them in vesicles.

types of endocytosis

• phagocytosis: cell engulfs large particles or other cells

• pinocytosis: cell takes in extracellular fluid & dissolved substances

• receptor-mediated: specific molecules bind to receptors in cell surface

exocytosis

Process by which cells export materials via vesicles releasing their contents outside the cell.

types of exocytosis

• constitutive: continuous release of materials

• regulated: release of materials in response to specific signals

protein translocation

The process by which proteins are moved from the cytoplasm to the endoplasmic reticulum, mitochondria, or other organelles, often involving signal sequences and transport mechanisms.

protein translocation in bacteria

The process by which proteins are moved across the bacterial cell membrane from cytosol to periplasm, often using different mechanisms such as the Sec pathway or Tat pathway, to facilitate their proper localization and function.

co-translational translocation

an unfolded protein is sent to the membrane while its still being synthesized

post-translational translocation

the protein is done being synthesized in the cytoplasm and then transported across the membrane

sec pathway

• universally present

• essential for survival

• transport proteins in an unfolded form

• co-translational

tat pathway

• only in bacteria & chloroplasts

• not essential for survival

• transport proteins in a fully folded & assembled form

• post translational

1st step in importing large molecs from nuclear complex

cargo proteins containing nuclear localization signal are bound by importins and transported into the nucleus

2nd step in importing large molecs from nuclear complex

Ran-GDP also diffuses into nucleus via NPC