True or false: Amino acids are bonded together in long chains by what are known as peptide bonds

1.True or false: Amino acids are bonded together in long chains by what are known as peptide bonds.

2.True or false: The sequence of amino acids for a protein is found on code of the DNA.

3.How many different kinds of amino acids are used by ribosomes to make proteins?

4.What is a proteome?

Biology Journal 9/16/2014

2.4 Homework Quiz!

2.4 Proteins: Proteins have a very wide range of functions in living organisms.

Nature of science: Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids.

Understandings:• Amino acids are linked together by condensation to form

polypeptides.• There are 20 different amino acids in polypeptides synthesized on

ribosomes.• Amino acids can be linked together in any sequence giving a huge

range of possible polypeptides. Most organisms use the same 20 amino acids in the same genetic code although there are some exceptions. Specific examples could be used for illustration.

• The amino acid sequence of polypeptides is coded for by genes.• A protein may consist of a single polypeptide or more than one

polypeptide linked.• The amino acid sequence determines the 3-D conformation of a

protein.• Living organisms synthesize many different proteins with a wide

range of functions.• Every individual has a unique proteome.

Applications and skills:Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.Application: Denaturation of proteins by heat or by deviation of pH from the optimum. Egg white or albumin solutions can be used in denaturation experiments.Application: Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food, pharmaceutical and other industries.Skill: Drawing molecular diagrams to show the formation of a peptide bond.

Aims: Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an international endeavour with many ethical issues.

Topic 2: Molecular biology (21 hours)

a. What kind of molecule is this? b. What are its parts called?

It’s an amino acid! (this one is called asparagine)

R group (in this case CH2CONH2)

Carboxyl(COOH)

Amine(NH2)

Alpha carbon(the middle C where the R group is attached)

Review!

•Proteins do everything! Protein makes skin stretchy, bones tough, gives your body parts their color, lets you digest different foods, makes up hormones, creates your immune system …

Protein and Amino Acids

• Proteins are 1 chain of amino acids (sometimes multiple), that fold up into specific shapes based on the chemical properties of the amino acids.

Generalized Amino Acid

How many amino acids make up this polypeptide?

There are 20 kinds of amino acids used in the human body.

What do ribosomes do?

Ribosomes: part of the cell that makes proteins from an RNA copy of the DNA code. They join amino acids together with peptide bonds.

There are infinite possibilities of proteins! They can be any length, and any combination of amino acids.

Turns garbage into bacon

Your welcome.

• We can break down proteins we eat to get energy / amino acids.

• Proteins can irreversibly lose their specific shape through a process called denaturing. Causes:1. Changes in temperature2. Changes in pH

Denaturing

A fever can kill you! Why?

Proteome: The set of all of the proteins an organism makes.

DNA in 23 chromosomes

Genome

Transcribed into mRNA

Translated into an amino acid sequence

by ribosomes

PolypeptideFolds into proteins

Proteome

Every individual has its own unique genome which leads to its own unique proteome

Motor Proteins: They move, allowing cells to change shape. Muscle cells are packed with these.

Proteins do everything! Such as…

Transport Proteins: These are proteins stuck in the cell membrane that let specific substances in or out of your cells.


Receptor Proteins: These are proteins stuck in the cell membrane that are used for cells to communicate with eachother.


• Your immune system tells the difference between “self” and “non-self” by these receptors.


• The blood types are: A, B, AB and O

• Doctors killed a lot of dogs before they figured this one out…

• Blood types are an example of receptor proteins .

Why is meat high in protein?

Muscles are made of protein. Meat is high in protein because meat is animal

muscle.

DNA HelicaseSimplified model

There are many ways of representing proteins

DNA HelicaseSpace-filling model


DNA HelicaseModel showing -helixes and -sheets.


20 amino acids bonded together in different orders can form all proteins.

What do proteins do?Everything!The function of the protein is defined by its shape.

http://www.johnkyrk.com/aminoacid.swf

FibrousLong, insoluble proteinsParallel polypeptide chains Cross-linked


Spider Silk

GlobularFolded, compact polypeptide chainsAlmost spherical shapes


Insulin

Rhodopsin

Rubisco

Immunoglobulin

Denaturation

A process that destroys the complex structure of a protein.1. Heat2. Strong acids3. Strong alkalisNew structure = new functionDenaturation of an egg protein

http://www.boredpanda.com/useless-object-design-the-unusable-katerina-kamprani/

http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html

Proteomics

DNA in 23 chromosomes

Genome

Transcribed into mRNA

Translated into an amino acid sequence

by ribosomes

PolypeptideFolds into proteins

Proteome

Every individual has its own unique genome which leads to its own unique proteome

A chemical reaction is shown below. 1. Name each reactant and product.2. What kind of reaction is this?3. Where should water be present in the reaction? How many molecules of water?

+ →H2O

• Hydrolysis (water is split)• It “fills in” each monomer

Dipeptide Monopeptide(amino acid)

Monopeptide(amino acid)

Catabolic Hydrolysis Reaction

Review!


→


+ →H2O

• Hydrolysis (water is split)• It “fills in” each monomer

Dipeptide Monopeptide(amino acid)

Monopeptide(amino acid)

Catabolic Hydrolysis Reaction

Transcription and Translation

DNA has the “recipe” to make proteins.

“Hmmm… how many teaspoons of cytosine was I supposed to add?”

A gene is a segment of DNA that has the instructions to make a particular protein.

The base pairs on DNA determine the amino acids, and thus the specific shape, that the protein will have.

For example… we all have genes for hair color. The base pairs on this DNA determines what proteins are in our hair, and thus, what our hair looks like.

Of course, you can always change it later…

What does it mean to be a translator?

What does it mean to transcribe something?

What’s the difference between DNA and RNA?

DNA Structure RNA Structure•Deoxyribonucleic acid•Double stranded•Uses thymine (T)•Sugar used is deoxyribose (C5H10O4)

•Ribonucleic acid•Single stranded•Uses uracil (U)•Sugar used is ribose (C5H10O5)

DNA and RNA comparison

When does your body need to make different kinds of

proteins?

Transcription and translation is done every time a cell makes a protein.

Above: the structural protein collagen. This poor guy will be making lots of it soon to repair his body.

So, almost every cell in your body is doing this all the time!

Ancient Egypt was well known for its scribes that made copies of

documents.

Nowadays we don’t really

need them, we have copy machines…

Transcription is making a copy of the DNA onto mRNA (messenger RNA). The enzyme that makes it is called RNA polymerase.

Some people transcribe

their homework all

the time.

mRNA is a temporary, disposable copy of DNA. It’s sent from the nucleus to the ribosome.

DNA is permanent. You don’t want to change or mess with it.

RNA is a disposable copy.

If this was a chain of DNA, what would the mRNA strand

be?

C T G A C T T A G A T AG A C U G A A U C U A U

What does DNA have the “recipe” to make?

DNA is the recipe to make protein!

What do ribosomes do?

Ribosomes make proteins!

What are proteins made out of? Why do they have the shape that they

have?

Proteins are made out of amino acids. The different chemical properties of the amino acids cause the chain to fold up in specific ways.

Translation: mRNA goes to the ribosome, and it is translated into an amino acid sequence.

tRNA (transfer RNA) brings the correct amino acid for every 3 base pairs.

•Ribosomes have 2 “subunits” or pieces.

Large Subunit

Small Subunit

The 3 bases on mRNA is called a codon.

The 3 bases on tRNA is called an anti-codon.

How many different kinds of amino acids are used in the

human body?

Every 3 base pairs corresponds to a different

amino acid.

What amino acids does this mRNA code for?

AUG UUA GAC CUC UGA

A translator puts information from one language into another.

Translation puts the genetic code (AGTC’s) into the code of amino acids.

What amino acids does this mRNA code for?

GUA AAA CUU CUA UAG

What do we call this step?


Transcription Translation

DNA mRNAProtein

The scribe(RNA polymerase)

The translator(ribosome and tRNA)

Convert the DNA to mRNAThen, Convert the mRNA to amino

acids.

AUA AGU GAU GACIsoleucine Serine Aspartic Acid Aspartic Acid



Transcription

Translation

TAT TCA CTA CTGGCCCGG Argenine

Making a Protein

Making a Protein

This is called the central dogma of biology. (That just means that it is a really important idea)

•At the start of every gene is a TATA box. It tells the mRNA polymerase where to start copying.

TCCACGACTATACCGACTACTCTACGGGAATATGGGCUGAUGAGAUGCCCUUAUAC

DNA strand:

mRNA strand:

TATA boxActual gene being transcribed

•mRNA gets a 5’GTP and a poly-A tail to mark the beginning and end. This helps identify it and “protect” it.

PPPG AAAAAAAAA

5’ GTP Poly-A tail

Label each molecule (the pictures).Label the process that makes each molecule (the purple arrows).List the name of the enzymes / molecules that carry out each process.Identify the location where each of these molecules / processes are.

DNA

mRNA ProteinReplication

Transcription Translation

DNA helicaseDNA polymerase

RNA polymerase RibosometRNA

Happens in the nucleus Happens in the cytoplasm / at the ribosomes

Biology Journal 10/18/2013

This is called the central dogma of biology. (That just means that it is a really important idea)

Documents

True or false: Amino acids are bonded together in long chains by what are known as peptide bonds