Cell Molec Full

Amphiphilic helix

Has one hydrophilic side and one hydrophobic side

NxxNxxxNxxNxxxN…

Pattern of non-polar side chains for an amphiphilic helix

Subunits

Polypeptide chains that come together to form a protein

ATP (also NADH and acetyl CoA)

Principal energy carrier moleculesin cells, used in various biochemical reactions.

Enzymes

Proteins that catalyze chemical reactions by lowering the activation energy

Allosteric

A molecule binding to a protein can change the conformation of the protein, allowing/preventing work being done

Positive regulation

A molecule binding to a protein INCREASES the rate of activity

Negative Regulation

A molecule binding to a protein DECREASES the activity or function of the protein.

Different binding sites for molecule and activity

How many binding sites in an allosteric protein?

Kinase

Adds phosphate to a protein

Phosphatase

Removes phosphate from a protein

IDRs

Lack a fixed structure, most common locations for protein phosphorylation, produce elastic structures

SH2 Domains

Only bind phosphorylated tyrosine residues, part of many proteins

Genes

Segments of DNA that encode protein of functional RNAs

Euchromatin

Less condensed, generally associated with gene activity

Heterochromatin

Highly condensed, often transcriptionally inactive

Histone Code Hypothesis

Specific patterns of histone modification act as signals recognized by other proteins

Topologically Associating Domains

Regions where DNA sequences interact more frequently with each other than with regions outside

Semiconservative DNA replication

After replication, each daughter DNA double helix is composed of one old strand and one new strand

Leading strand

DNA strand that is synthesized forward from the origin of replication

Lagging strand

DNA strand the catches up by forming Okazaki fragments

Helicase

Unwinds DNA for replication

DNA polymerase

Synthesizes new strands of DNA during replication

Primase

Adds DNA primers during replication

Nucleases

Remove RNA rimers during DNA replication

Repair DNA polymerace

Replaces RNA primers with DNA during DNA replication

Ligase

Seals gaps between fragments during DNA replication

Toperisomerase

Relieves torsional stress that occurs during DNA replication

Telemorase

Extends telomeres by adding repetitive DNA sequences to chromosome ends

Base excision repair

A DNA repair mechanism that removes damaged or modified single bases from the DNA molecule, initiating a process to replace them with the correct bases.

Nucleotide excision repair

A DNA repair pathway that removes bulky, helix-distorting lesions like thymine dimers or chemical adducts from the DNA.

Mismatch repair

A DNA repair system that recognizes and corrects mismatched base pairs that arise during DNA replication or recombination.

Nonhomologous end joining

A DNA repair mechanism for double-strand breaks that involves direct joining of the broken ends without using a homologous template, often leading to insertions or deletions.

Homologous end joining

A DNA repair mechanism for double-strand breaks that uses a homologous DNA template to accurately repair the break, ensuring the original sequence is restored.

Template strand

Nonsense strand

Coding strand

Sense strand, nontemplate strand

5’ to 3’

Direction of transciption

Elongation factors

Factors that decrease the likelihood of RNA polymerase dissociating before reading the end of a gene

RNA capping

The first modification of eukaryotic pre-mRNAs destined to be translated

7-methylguanine cap

Modification on 5’ end that helps ribosomes identify mRNAs to be translated

Alternative splicing

Modification of RNA transcriptions (pre-mRNAs) that produced distinct mRNAs (and therefore variant proteins)

snRNA

Small nucleolar RNAs that are the RNA within snRNPs

snRNPS

Small nuclear ribonucleoproteins that, combined with other proteins, constitute a spliceosome

SRs, CBCs, hnRNPS

Proteins that coordinate alternative splicing

SRs

Ser and Arg rich proteins, splicing enhancers

CBC

Cap Binding Complex

hnRNP

Heterogenous ribonucleic acid proteins

Translation

tRNAs charged with their appropriate amino acid use their anticodon to pair with an mRNA codon

Cell differentiation

Creating specialized cells from the same genome using differential gene expression

Transcription factors

Proteins that recognize and bind to specific short cis-regulatory sequences in DNA

Recuring structural motifs in DNA used by TFs

Helix-turn-helix proteins

Homeodomain proteins

Leucine zipper proteins

Beta-sheet DNA recognition proteins

Zinc finger proteins

Activators

TFs that bind to an enhancer site and help recruit RNA pol

Repressors

TFs that bind to an operator site and interfere with RNA pol binding

Cis-acting sites

Sites where transcription factors land

Trans-acting elements

Elements that bind to cis-acting sites to impact transcription

Operator site

Binding site for bacterial TFs

“Committee Approach”

Most eukaryotic genes are controlled by combinations of regulators

Histone alterations

Nucleosome sliding

Nucleosome-free DNA

Histone variants

Destabilized chromatin

Transcription inhibiting mechanisms

Competitive DNA binding

Masking the activation surface

Direct interaction with general TFs

Recruitment of chromatin remodeling complexes

Recruitment of histone deacetylases

Recruitment of histone methyl transferase

Post-transcriptional regulation methods

Splicing

Polyadenylation

Phosphorylation of eiF2

miRNAs

sNRAs

Non-coding sRNAs (CRISPR)

Phospholipid bilayers

Form the fundamental structure of all cell membranes

Cholesterol

Compound that stabilizes membranes and regulates membrane fluidity

Lipid anchors

Control the membrane localization of some signaling proteins

They typically span a lipid bilayer

What do the following have in common?

Alpha helices

Beta sheets

Beta barrels

20-25

How many amino acids to span a lipid bilayer?

Detergents

Compounds that solubilize membranes by disrupting membrane structures

Passive transport

Channel-mediated transport and transporter mediated transport are both examples of what?

Transporters

Proteins that more specific molecules across membranes

Types of transport

Simple diffusion

Channel-mediated

Transporter-mediated

Active transport

Uniport transport

Transports one molecule across a membrane

Symport

Transports 2 molecules across a membrane at the same time

Antiport

Transports 2 molecules across a membrane at the same time, in opposite directions

Secondary active transport

Transporters use the electrochemical gradient created by other transporters or ions to move molecules

ATP-driven pumps

Pumps that hydrolyze ATP to ADP and phosphate, using the energy released to pump substrates across a membrane

P-type pumps

Pump K+, Na+, and Ca+ ions out of the cell

Maintain ion gradients in cells

V-type proton pumps

Pump H+ out

Pump H+ into the lysosome to acidify it

Uses ATP

F-type proton pump

Pump H+ in

AKA ATP synthases

Generate ATP by moving H+

ABC transporters

ATP Binding Cassettes

Use ATP hydrolysis to transport molecules across membranes

Work against the concentration gradient

Primary active transporters

Voltage-gated ion channels

Open and close in response to membrane potential

Ligand-gated ion channels

Selectivity is determined by structure

Mechanically-gated ion channels

Open and close in response to physical stimuli

Molecular condensates

Clusters of proteins etc. that clump together without a membrane

Endoplasmic Reticulum (ER)

A network of interconnected tubes and sacs continuous with the outer nuclear membrane

Site of protein and lipid synthesis

Stores Ca+2

Endomembrane System (EMS)

The ER, Golgi apparatus, and lysosomes

Free ribosomes

Ribosomes that translate cytosolic protein

Ribosomes at the ER

Ribosomes that translate proteins destined for the Endomembrane system, plasma membrane, or secretion

Signal Recognition Protein (SRP)

A chaperone that helps guide actively-translating ribosomes to the surface of the ER

Sec61

SRP docks ribosome polypeptides to this complex on the Er

Co-translational translocation

Proteins are translated directly into their final location by embedded ribosomes

Post-translational translocation

Proteins are translated and then taken to their final destination.

Bip

An ATP-dependent chaperone that works with Sec62/63 to pull the protein through using energy from ATP hydrolysis

Tail-anchored proteins

Always have the N-terminus facing the cytosol

Anchored by their C-terminus

GPI-anchored proteins

Always located on the non-cytosolic side of the membrane

Anchored at the C-terminus

Medicated by transamidase enzymes

Glycolation

The addition of a preformed N-linked oligosaccharide to Asn residues

Unfolded Protein Response (UPR)

Triggered by sensed misfolded proteins in the ER

Changes gene expression

Causes more BipP to be delivered to the ER

Phospholipids

Synthesized on the ER’s cytosolic leaflet

Can be flipped across the bilayer by a translocation enzyme

Mitochondrial proteins

Translated from nuclear genes in the cytosol

Imported post-translationally via a set of protein complexes in the mitochondrial IM and OM

Nuclear Pore Complexes (NPCs)

Allow proteins and RNAs to move between the cytosol and nucleus

Peroxisomal proteins

Generally imported directly from the cytosol post-translationally as folded proteins via specific signal sequences

Cis-golgi

Facing the rough ER