BIOL 3000 - Exam 3 - Gene Expression

Proteins

Large biological molecules (macromolecules) consisting of one or more polypeptide chains that perform a wide variety of functions in living organisms. There are 20 unique versions of these.

List the 3 things that the functional diversity and versatility of a protein derives from

1. chemical diversity of the amino acid side chains

2. flexibility of polypeptide chains

3. large number of ways in which polypeptide chains interact with different amino acids and fold

This identifies and differentiates amino acids from each other.

Side chain

All amino acids have this group.

Carboxylic group

The backbone of a polypeptide is made from:

alpha carbon linked to an amino group and carboxyl group.

the R groups are not part of the backbone

A peptide bond is a COVALENT bond between the _______ _______ and _________ ________ of two adjacent amino acid residues

carboxyl carbon, amide nitrogen

Everytime a peptide bond is formed, ______ is released

water

The peptide bond is in the ______ _____ of the amino acids coming together.

peptide plane

peptide plane

Plane formed by carboxyl carbon, the carboxyl oxygen and the amide nitrogen. Oxygen will always be sticking out and they will all have the same bonding and distance from each other.

True or false: any bond to the alpha carbon has 360 degree rotation

True

What bond is between the amino acid backbone?

Amide bond

___ bond in some excreted or exterior surface proteins between the side chains of cysteine

Disulfide

What is the alpha carbon bound to?

R-group

Why is the peptide plane said to be coplanar?

It can turn in any direction and not change the functionality of the polypeptide chain.

_____ groups can turn the amino acid groups any direction it wants (unless it hits something)

R-groups

Non-polar (hydrophobic) amino acids

These types of amino acids tend to repel water by facing inward and pack closely in together

Polar (hydrophilic) amino acids

These types of amino acids tend to form hydrogen bonds with one another, to the peptide backbone, to other molecules and to water

Charged amino acids

These amino acids tend to reside on the outside of a globular protein and interact with other side chains or macromolecules to give structure

Positive charged amino acid

Lysine, arginine, and histidine

Negative charged amino acid

Aspartic acid and glutamic acid

List the 2 types of chemical interactions that stabilize proteins

1. covalent bonds

2. electrostatic bonds

covalent bonds

Bond created by the sharing of electron pairs creating a very stable reaction. They are stronger (and harder to break) than electrostatic bonds bc they are sharing electrons across.

They make up the amino bonds of the amino acid backbone and disulfide bonds are between the side chains.

electrostatic bonds

Bond from interaction of amino acids based on their charge. Proteins are flexible because of these interactions! They are weaker (and easier to break) than covalent bonds bc they are not sharing electrons across.

Make up the hydrogen bonds and Van der Walls interactions in amino acids.

True or false: the backbone is the same for all amino acids

True

What are the three parts of an amino acid?

Amino group, side chain, and carboxylic group

What type of reaction forms a peptide bond?

Hydrolysis reaction

A peptide bond is a ___ bond between the ___ carbon and ___ nitrogen of two adjacent amino acid residues

Covalent; carboxyl; amide

The functional diversity and versatility of a protein derives from?

CHemical diversity, flexibility of the polypeptide, and interaction diversity (combination lead to higher order protein structure)

List the 4 different levels of protein structure

1. primary

2. secondary

3. tertiary

4. quaternary

For most proteins, what is the final functional form?

Tertiary

How many polypeptide chains are in a tertiary structure?

One

How many polypeptide chains are in a quaternary structure?

Two or more

primary structure

Linear sequence of amino acids; held together by covalent bonds

What are the two ends of the primary structure called?

Amino terminus/NH2 (N-terminus) and Carboxyl terminus/COOH (C-terminus)

secondary structure

highly regular local substructures of protein. LOCALIZED 3D shape.

List 3 types of secondary structures. Which is the simplest one we have? Which is the most common?

1. Beta turn - simplest

2. Beta sheets

3. Alpha helix - most common

Beta turn

Simplest secondary structure. Usually only involves 3 or 4 residues. Will almost always find a glycine residue here, bc it has a small R-group and allows a 180º turn.

This helps reverse the direction of the polypeptide chain and makes compact folding of the chain possible

Beta sheets

Secondary structure. Two or more strands widely separated in a 1º sequence and running side-by-side. Hydrogen bonds run between strands

Beta sheets going in a circle.

Porin

Alpha helix

Most common secondary structure. Highly regular local substructures of a protein. Has a twisted ribbon shape.

Tertiary structure

Made from folding the secondary structural elements into a compact and nearly solid object stabilized by chemical bonding interactions

True or false: All proteins have tertiary structure?

True

Tertiary structure bond interactions are mostly?

electrostatic

How are tertiary structures maintained?

Covalent bonds and elctrostatic interactions

Quaternary structure

3D structure of multi-subunit proteins and how they stick together.

True or false: all proteins have quaternary structure?

False

Which structure is maintained by the sum of covalent and electrostatic interactions?

Tertiary

List 3 types of post-translational modifications that improve protein stability of secondary structures when they are vulnerable outside the cell

1. disulfide bridge

2. metal binding

3. binding of effector molecules

Disulfide bridge

Protein stability method where covalent bonds form between sistine residues to provide tighter structure to the protein. They make the protein bond last as long as possible outside of the cell; reversible and not commonly found in intracellular proteins due to the reducing nature of the cytoplasmic but common in secreted proteins

The disulfide bridge is highly sensitive to the environment and (reversibe/irreversible?)

reversible

Disulfide bridge is not commonly found in ________ proteins due to the receding nature of the cytoplasm.

intracellular proteins

disulfide bridge IS common in?

secreted proteins

Metal binding

Protein stability method where coordinated binding of a metal ion to several amino acid side chains in a single protein forms an internal metal chelate.

Binding of effector molecules

Protein stability method where adding certain molecules can improve stability. The most important one is the addition of carbohydrates to amino acids, AKA glycosylation.

Modifications can affect conformation AND function of the protein

What types of effector molecules are reversible?

1. phosphorylation - add phosphate group

2. acetylation - add acetyl group

What types of effector molecules are irreversible?

1. ubiquitination - adds uniquitin

2. methylation - adds methyl group

Motifs and domains are located between ________ and ________ structure and are NOT full tertiary structures

secondary and tertiary

List 2 types of protein motifs that improve protein stability when they are vulnerable outside the cell

1. sequence motif

2. functional motif

Protein motif

Generally consist of a few structural elements relating primary structure to tertiary structure

sequence motif

type of protein motif. Has the Zinc Finger motif that allows motif to interact with DNA and stabilizes the structure. Without it, the protein would lose stability and cease to function.

What two elements are required in the Zinc finger motif?

two cystines and two histonines

functional motif aka structural motif

Uses a Rossman fold to stabilize the protein. Protein could not function without it.

Protein domain

Protein stability method where a compact region of protein structure is capable of stable folding independent of a large protein and having a specific function. Protein would cease to function without it. Can be taken off one protein and moved to another to make another protein functional.

What are the 4 things that make up protein function?

Binding, catalysis, switching, and structural

Regulation of ___ is the primary method of controlling gene expression in prokaryotes

Transcription

Eukaryotic layers of regulation

Chromatin, transcription, RNA processing, translation, and post-translation

What two major protein classes regulate chromatin remodeling?

ATP dependent chromatin remodeling complexes, and histone modifying complexes

What are ATP dependent chromatin remodeling complexes?

Protein complexes that regulate expression by moving, ejecting, or restructuring nucleosomes using the energy of ATP.

How do ATP dependent chromatin remodeling complexes affect chromatin structure?

They loosen the chromatin structure, allowing movement of the histone core.

What is the role of ATP in chromatin remodeling complexes?

ATP provides the energy needed for the complexes to move, eject, or restructure nucleosomes.

Histone/DNA modifiying complexes

Protein complexes that enzymatically modify N-terminus histone tails

Methylation

Silencing

De-methylation

Expression

Acetylation

Expression

De-acetylation

Silencing

What are the 5 parts of transcriptional regulation?

Initiating signla, signaling pathway cascade, activation of transcription factor, recruits other members of transcription complex/trasncriptional complex recrutis RNA Polymerase II, and transcription is initiated by promoter site

Hormones

Molecule that is produced in one cellular location but whos effects are seen in another

Hormones require the target cell to have ___ specific for that hormone

Receptor

What two types of proteins does estrogen help control expression for?

Cell cycle proteins and heat shock proteins

Transcription factors

Control the rate of gene transcription either by helping/hindering RNA Polymerase binding to DNA

A single gene may have ____ binding sites for distinct transcription factors

Multiple

Transcription factors interact with other proteins to build a ____ that may increase transcription 100 fold

transcription complex

Transcription factors contain _____ in their tertiary structure that attach to specific DNA sequences

DNA binding domains

Insulators prevent transcription of what?

Non-target genes

Transcription factors are a prime target for what?

Potential drug discovery

Transcription factors bind to DNA sites/regions to affect?

Transcriotional rates of specific genes

cis-activating factors

DNA itself

trans-activating factors

Things that act on the DNA

miRNA regulation process

Transcription to processing, exported from nucelus by Exportin-5, Passenger RNA strand discarded, dicer removes the hairpin loop region leaving dsRNA, and miRNA-protein complex

miRNA-protein complex

- blocks translation by the ribosome

- speeds up deadenylation (breakdown of Poly-A Tail)

TATA box

DNA sequence found in promoter region that transcription factor complex protein binds

Promoter region

Region of DNA located upstream but near the transcription start site of a aprticular gene where transcription factors binds to initiate transcription

Enhancer region

Region of DNA where activator proteins bind to activate the transcription process

Silencer region

Region of DNA where repressor proteins bind to prevent binding of RNA Pol II to the promoter

Insulator region

Region of DNA where insulator proteins bind that blocks the interaction of enhancers with promoters

Promoter

Site of TATA binding protein and basal factor binding; responsible for basal level of expression; binding by general transcription factors

Promoter-proximal elements

Site of additional activator protein binding; responsible for induced/represed level of expression; binding by tissue specific transcription factors

What is the first thing that must happen in transcription for gene regulation?

TBP must bind

How do enhancers of promotor-proximal elements work?

Brings transcription factors and trans-activating factors together; leads to higher efficiency transcription

What are the 5 types of RNA processing?

5' capping, 3' tail poly-adenylation, RNA splicing, RNA transport, and miRNA