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Advanced Higher Cells and Proteins Advanced Higher Cells and Proteins

Advanced Higher Cells and Proteins - PowerPoint Presentation

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Advanced Higher Cells and Proteins - PPT Presentation

Dna Proteins and Binding to ligands Think What proteins are associated with DNA How are proteins involved in transcription How is protein production controlled Why is it important that protein production is controlled ID: 909706

protein enzyme binding proteins enzyme protein proteins binding dna oxygen substrate active enzymes shape site change transcription conformation reactions

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Slide1

Advanced Higher Cells and Proteins

Dna

, Proteins and Binding to ligands

Slide2

Think

What proteins are associated with DNA?

How are proteins involved in transcription?

How is protein production controlled?

Why is it important that protein production is controlled?

Why is protein structure important in relation to its function?

Slide3

DNA and proteins

This lesson will cover

DNA and its associated proteins

Other proteins involved with transcription

Slide4

DNA and protein association

Slide5

DNA and protein association

DNA binds to a number of proteins.

Positively charged histone proteins bind to the

negatively charged sugar-phosphate backbone of

DNA in eukaryotes.

DNA is wrapped around histones to form nucleosomes

packing the DNA in chromosomes.

Slide6

DNA and protein association

Animation

Slide7

Histone proteins and nucleosome

Slide8

Other DNA proteins and ligand binding

Other proteins have binding sites that are specific to

particular sequences of double stranded DNA.

When this happens they can stimulate or inhibit the

initiation of transcription.

Animation

Slide9

Dna

and protein complex in transcription

Slide10

Transcription Factors

Transcription factors (TFs) are molecules involved in

regulating gene expression.

They

are usually proteins,

(they

can

be short

, non-coding

RNA).

TFs

are also usually found working in groups or

complexes

, forming

multiple

interactions

that allow for varying degrees

of control

over rates of

transcription.

Slide11

Transcription Factors

In people (and other eukaryotes), genes are usually in a

default "

off

" state, so TFs serve mainly to turn gene expression "

on

".

TFs work by recognizing certain nucleotide sequences (

motifs) before

or after the gene on the

chromosome.

The TFs bind, attract other TFs and create a complex

that eventually

facilitates

binding

by RNA polymerase, thus

beginning the

process of transcription.

Slide12

Binding changes the conformation of a protein

Proteins including enzymes are three-dimensional and have a specific shape or conformation.

As a ligand binds to a protein binding site, or a substrate binds to an enzyme’s active site, the conformation of the protein changes.

This change in conformation causes a functional change in the protein and may activate or deactivate it.

Slide13

Binding to ligands

A ligand is a substance that can bind to a protein.

R groups not involved in protein folding can allow binding to these other molecules.

Binding sites will have complementary shape and chemistry to the ligand.

The ligand can either be a substrate or a molecule that affects the activity of the protein.

Slide14

All chemical reactions require energy to enable them, this is the

activation energy

.

Enzymes lower the activation energy.

2 types of reaction are:

Anabolic (synthesis) a dehydration synthesis reaction.

Catabolic (degradation) a hydrolysis reaction

.

Enzymes

Slide15

Anabolic Reactions

Uses energy to SYNTHESISE large molecules from smaller ones e.g.

Amino Acids Proteins

Also known as endothermic reactions

ENDOTHERMIC REACTION

Slide16

Catabolic Reactions

These release energy through the BREAKDOWN of large molecules into smaller units e.g.

Cellular Respiration:

ATP ADP + Pi

Also known as exothermic reactions

EXOTHERMIC REACTION

Slide17

Enzyme types

Proteases

- break down proteins into amino acids by breaking peptide bonds (hydrolysis).

Nucleases

- break down nucleic acids into nucleotides (hydrolysis).

ATPases

- hydrolysis of ATP

.

Kinases

- add phosphate groups to molecule

.

Phosphatases

– remove phosphate groups

Slide18

Control of Enzyme activity

Control of enzyme activity occurs in these ways

number of enzyme molecules present

compartmentalisation

change of enzyme shape by

competitive inhibitors, non-competitive inhibitors,

enzyme modulators, covalent modification

end product inhibition

Slide19

How do enzymes work?

Slide20

Induced fit and enzymes

Enzymes are not necessarily a perfect sit to substrate

The enzyme changes shape in response to close association with the substrate.

This the Induced fit theory

Slide21

A molecule close to shape of substrate

competes

directly

for active site so reducing the concentration of available enzyme.

This can be reversed by increasing the concentration of the correct substrate unless the binding of competitor is irreversible.

Competitive inhibition

Slide22

Succinate dehydrogenase

catalyses

the oxidation of succinate to fumarate (respiration)

Malonate is the competitive inhibitor

Malonate example

Slide23

Slide24

An inhibitor binds to the enzyme molecule at a

different area

and

changes the shape

of the enzyme including the active site.

This may be a permanent alteration or may not.

Non-competitive inhibition

Slide25

Slide26

Inhibition can either be reversible or non-reversible

Some inhibitors bind irreversibly with the enzyme molecules.

The enzymatic reactions will stop sooner or later and are not affected by an increase in substrate concentration.

Irreversible inhibitors include heavy metal ions such as silver, mercury and lead ions.

Slide27

Some enzymes

change their shape

in response to a

regulating molecule

.

These are called allosteric enzymes

Positive modulators (activators)

stabilise enzyme in the active form.

Negative modulators (inhibitors)

stabilise enzyme in the inactive form.

Enzyme modulators

Slide28

Allosteric Enzymes

Slide29

Involves the addition, modification or removal of a variety of chemical groups to or from an enzyme

(

often phosphate.)

These result in a change in the shape of the enzyme and so its activity.

These include phosphorylation by kinases and

dephosphorylation

by phosphatases.

Conversion of inactive forms to active forms e.g. trypsinogen and trypsin

Covalent modifications

Slide30

An example of activation is trypsinogen to trypsin

trypsinogen activated by

enterokinase

in duodenum

Slide31

Trypsin is synthesised in the pancreas, but not in its active form as it would digest the pancreatic tissue

Therefore it is synthesised as a slightly longer protein called TRYPSINOGEN

Activation occurs when trypsinogen is cleaved by a protease in the duodenum

Once active, trypsin can activate more trypsinogen

molecules

Slide32

Often seen in pathways that involve a series of enzyme controlled reactions.

The end product once produced has an inhibiting affect on an enzyme in the reaction.

Example:

Bacterial production of amino acid isoleucine from threonine.

5 stages enzyme controlled

Threonine Isoleucine

End product Inhibition

Slide33

To summarise

As a ligand binds to a protein or a substrate binds to

a

n enzyme’s active site, the conformation of the

protein changes,

This change in conformation causes a functional

change in the protein

.

Slide34

To summarise

In enzymes, specificity between the active site and substrate is

related to induced fit.

When the correct substrate starts to bind, a temporary change in

shape of the active site occurs increasing the binding and interaction with the substrate.

The chemical environment produced lowers the activation energy

required for the reaction.

Once catalysis takes place, the original enzyme conformation is

resumed and products are released from the active site.

Slide35

To summarise

In allosteric enzymes, modulators bind at secondary binding sites.

The conformation of the enzyme changes and this alters the

a

ffinity of the active site for the substrate.

Positive modulators increase the enzyme affinity whereas

n

egative modulators reduce the enzymes affinity for the substrate.

Slide36

Haemoglobin and Oxygen

Slide37

Cooperativity in hemoglobin

Deoxyhaemoglobin

has a relatively low affinity for oxygen.

As one molecule of oxygen binds to one of the four

haem

groups in a hemoglobin molecule it increases the affinity of

the remaining three

haem

groups to bind oxygen.

Conversely,

oxyhaemoglobin

increases its ability to loose

oxygen as oxygen is released by each successive

haem

group.

This creates the classic sigmoid shape of the oxygen

dissociation curve.

Slide38

Dissociation curve of

haemoglobin

Slide39

Deoxyhaemoglobin

Oxyhaemoglobin

Disassociation releasing oxygen to tissues

Association binding oxygen in lungs

Slide40

Effects of temperature and pH

Low pH = low affinity.

High temperature = low affinity.

Exercise increases body temperature and produces more

CO

2

, acidifying the blood.

This has a corresponding effect on the

oxyhaemoglobin

dissociation curve.

Slide41

Slide42

Sickle Cell Anaemia

Low oxygen levels cause

change in haemoglobin

structure.

Strands cause cells to take

o

n bent sickle shape

b

locking capillaries.

Slide43

High Altitude and Oxygen

The

concentration of oxygen (O2) in sea-level air is 20.9%, so the

partial

pressure of O2 (pO2) is 21.136

kPa

.

Atmospheric pressure decreases exponentially with

altitude

while the O2 fraction remains constant to

about

100

km, so pO2 decreases exponentially with altitude as

well

.

It

is about half of its sea-level value at 5,000 m

(

16,000

ft

), the

altitude

of the Everest Base Camp, and only

a

third at 8,848 m

(

29,029

ft

), the summit of Mount

Everest. When

pO2 drops, the

body

responds with

altitude

acclimatization

.BBC Horizon How to kill a Human Being

Slide44

To summarise

Some proteins with quaternary structure show cooperativity

i

n which changes in binding alter the affinity of the remaining

subunits.

Cooperativity exists in the binding and release of oxygen in

Haemoglobin.

Temperature and pH

influence oxygen association.