MCB Exam 2

Peptide Bond

A covalent bond formed between two amino acids during protein synthesis, linking the carboxyl group of one amino acid to the amino group of another.

Polypeptide

A chain of amino acids linked by peptide bonds, forming the primary structure of proteins. Cannot interact with water

This makes backbone / protein stronger

Primary Structure

The unique sequence of amino acids in a polypeptide chain, determining the protein's characteristics and function, such as how the protein fold into 3D shapes.

True

true or false: A change of one amino acid can make up an entirely new protein

An actual amino acid monomer

Each bead is a what?

Primary Structure→ Secondary Structure→ Tertiary Structure → Quarternary Structure →

What are the steps of structure folding?

Secondary Structure

A step in structure in where amino acids interact with nearby amino acids.They are formed by hydrogen bonding along the polypeptide backbone

Polypeptide backbones and Hydrogen Bonding

What are the 2 things that fold together to stabilize secondary structure?

Tertiary Structure

Where amino acids turn into 3d polypeptide. It could be a final step to a structuring a polypeptide.

The interaction between R groups and the backbone of amino acids contributes to the overall three-dimensional shape of a protein. Additionally, these components can also form bonds with water.\

How do folding in tertiary structure work?

Quarternary Structure

Results from the interaction of other poly subunits (2 or more tertiary polypeptides)

Hydrogen Bonding

What Stabilizes Protein?

Ionic Bonding

Due to folding, R-groups with positive and negative charge can interact with each other

Folding produces charge on the outside, which creates certain functional regions for other molecules to interact with it.

How do proteins function and work?

Folding allow hydrophobic regions

What creates Phospholipids?

Peptide Chain

Polypeptide is stilla baby protein because it’s still in a primary structure. When it matures, we have this.

Phosphodiester Bonds and Hydrogen Bonding between base pairs.

What helps stabilize the structure of DNAs double stranded helix.

Primary structure determines R groups in polypeptite determine tertiary structure determine final shape determines functions

the order of determination of the function

H-bonds and Interactions between R groups can be affected by temperature, UV, pH, or exposure to chemicals.

What are the factors that can denature protein?

Denatured Proteins

These proteins are non-functional, but if the conditions are returned, protein can refold and regains its function

1- Storing genetic information

2- Copying itself

What are the 2 main function in all organisms?

Its determine by turning on a gene or gene expression.

When or whether proteins are made?

Gene

This is where DNA stors genetci instructions for how and when to make all proteins

Translation

Translates from genetic code→amino acids done by ribosomes and cytoplasm

Nucleic Acids

Monomers of nucleic acid

1- Sugar ring with 5 carbons

2- 5’ phosphate group

3- base

3 chemical group of Nucleotides

base

gives the nucleotide its identity, like what R group is to an amino acid

2 Families of Nucleotide Bases

1- Pyrimidines (cytocine, Thymine, Uracil)
2- Purines (Guanine, Adenine)

Single Ringed Structure

Pyrimidines

Double Ringed Structure

Purines

Phosphodiester Bonds

From between the OH group attached to the ( 3’) carbon of 1 nucleotide and the phosphate group (5’). Link nucleotide monomers together to form a strand of DNA

Nucleotides are connected together to form nucleic acids via…

Phosphate → Sugar → Phosphate → sugar group
—>(are phosphodiester)

The order and results in alternating pattern

With the support pof sugar phosphate backbone and base pair of H-bonding, therefore turn into a helix structures with 2 strands running anti-parallel to each other.

How do DNA Forms a regular stable shapes?

DNA And RNA Difference

DNA- Good for storing info, stable, regular in structure

RNA- less stable, more flexible in its 3d structure and thus can take on more functions. It is enconded and transcribed to make proteins.

mRNA

- carries instructions to make proteins

Non-coding RNA

Functions without making protein

The central dogma

it describes the process by which cells use information in the genes to make protein

-Leave nucleus

-Be modified/edited to fine tune details of information in the transcript

What can a disposable do?

Gene of Interest

a DNA sequence that codes for a protein or RNA molecule that a researcher wants to study or produce.

Promoter

Where do transcription begins?

Promoter

where RNA polymerize and transcription bind to start transcription process

-Neaby the gene

Transcription Factor

A protein involved in transcription

Enhancers

located very far away from the gene

1-DNA loops to bring enhancers transcription factors which are far closer to the promoter

2- The mediator complex acts as a bridge connecting enhancer transcription factors with promoter transcription factor.

3- these protein then result in polymerization (the enzyme that make RNA)

How do the process of enhancers and promoter act in a gene?

Elongation

RNA polymerase reads the DNA template in the 3’ to 5’ direction

Steps of Elongation

1- facilitate local unwinding of the DNA

2- has channel funnel in free RNA ucleotides towards transcription site

3- Moves along DNA template 3’ → 5’. if the incoming rNTPS correctly matches the DNA template, RNA polymerase attaches it

4- RNA is synthesize in the 5’→3’ direction

5- Stabilizes pairing of DNA- RNA at active transcription site to enable base pairing

6- Restores original DNA Double helix as it passes.

Termination

Where transcription ends

1- RNA polymerase recognizes this signal

2-When it reaches signal, RNA transcript is cut, forming its 3’ end

3- RNA polymerase detaches from the DNA template, transcription ends

4- If the cell needs more RNA, then it can rebind to the promoter and restart the process.

Nucleus. Cytoplasm

Eukaryotes transcript in? Prokaryotes transcript in?

Enhancers

It is an activator protein and can be everywhere

DNA looping

Promoter acts like a binder, then some transcription will set a scene to a promoter

Eukaryotes→ mRNAs must first be process and transported to the cytolasm before they are translated

which Cell would be mRNA process only occurs?

True for Prokaryotes, false for eukaryotes

True or False: Transcription and translation occur simultaneously

RNA Processing Steps

s1→ A nucleotide “cap” will attach to the 5’ end. → A poly (a) “tail” is added to the 3’ end → introns are spliced out

5’ Cap Roles:

-gives mRNA stability

-provides a recognition site for ribosomes to bind

-it modified 5’ end

3’ Poly A tail

• gives mRNA stability

• provides recognition site for exporter proteins to bind

• export mRNA from nucleus to cytoplasm

Adds a poly (a) tail to the 3’ end

What does polyadenylation do?

introns excised from the RNA strand, and exons are spliced together.

Introns do what? and Exons do what?

Exons; Introns

contained the cofe the expressed in protein ; Introns are in between or in the trash

Alternative Splicing

allows single gene in DNA to code for many different proteins simply by editing the mRNA copy

Directionality of

1. Reading Codons

2. Ribosomes reading mRNA

3. synthesizing RNA

4. reading and DNA template

1. 5’→ 3’

2. 5’ → 3’

3. 5→3’

4. 3’→5’

Aminoacyl tRNA Synthetase

RNA and Protein

What are Ribosomes made up of?

has amino attached

what does it mean it when tRNA molecule is charged?

Initiatian process and their function

R- Groups

What makes Amino Acid unique?

Phosphate Group, 5 Carbon sugar, a Base

Nucleotides are the monomers of nucleic acids.  Which of the following chemical groups are they composed of?

Amino Group, Carboxyl group, The polypeptide backbone

all of the following that are involved in the formation of a protein’s SECONDARY structure

Hydrophobic Interactions

What interaction plays the biggest role in forming the tertiary structure?

Hydrogen Bonding

Complementary bases are attached to each other to form double stranded DNA via…

-Enhancers, promoters, mediator complex, transcription factors, RNA polymerase

What are the transcription initiation complex participators?

-tRNA Met , 5’ cap, initiation factors, small ribosomal unit,

What are the Translation initiation complex participators?

Mediator Complex

DNA-binding transcription factors (TFs) directly to RNA polymerase II (Pol II)

A charged tRNA would be the one that has amino acid attached to it

What is the difference between charged and uncharged tRA?

A charged tRNA enters the A site and catalyze the Amino acid, then P site is where the amino acids form peptide bonds. At E site, it is where uncharged tTRNA exit

What goes in the A Site of translation

Mediator Complex

This is what acts as a bridge between the enhancer and RNA polymerase binded to the promoter

-found after the coding region which is further downstream in Eukaryotes
-It is part of the template strand so RNA polymerase know where to stop trasncribing

-generally contains Poly A tail to signal mRNA processing

- In prokaryotes, it is found immediately after the gene of interest

General Placement of Teminator Sequence

1. 5’ Capping- provides stability

2. Polyadenilation - the act of adding poly A tails- provides stability as well as knowing when to exit from nucleus to cytoplasm

3. RNA splicing- removal of introns

What are the three steps of mRNA processing? Describe the role of each.